Menu
▾
▴
dl-learner-svn
|
From: <jen...@us...> - 2008-03-03 12:46:25
|
Revision: 675
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=675&view=rev
Author: jenslehmann
Date: 2008-03-03 04:46:23 -0800 (Mon, 03 Mar 2008)
Log Message:
-----------
continued refinement operator implementation
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/Reasoner.java
trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/refinementoperators/MathOperations.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
Modified: trunk/src/dl-learner/org/dllearner/core/Reasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/Reasoner.java 2008-03-03 07:45:57 UTC (rev 674)
+++ trunk/src/dl-learner/org/dllearner/core/Reasoner.java 2008-03-03 12:46:23 UTC (rev 675)
@@ -112,13 +112,13 @@
// currently, we do not require that datatype properties can be returned;
// the main reason is that DIG does not distinguish between datatype and
// object properties (of course one could implement it but it is not easy)
- public Set<DatatypeProperty> getDatatypeProperties() throws ReasoningMethodUnsupportedException;
+ public SortedSet<DatatypeProperty> getDatatypeProperties() throws ReasoningMethodUnsupportedException;
- public Set<DatatypeProperty> getBooleanDatatypeProperties() throws ReasoningMethodUnsupportedException;
+ public SortedSet<DatatypeProperty> getBooleanDatatypeProperties() throws ReasoningMethodUnsupportedException;
- public Set<DatatypeProperty> getDoubleDatatypeProperties() throws ReasoningMethodUnsupportedException;
+ public SortedSet<DatatypeProperty> getDoubleDatatypeProperties() throws ReasoningMethodUnsupportedException;
- public Set<DatatypeProperty> getIntDatatypeProperties() throws ReasoningMethodUnsupportedException;
+ public SortedSet<DatatypeProperty> getIntDatatypeProperties() throws ReasoningMethodUnsupportedException;
public SortedSet<Individual> getIndividuals();
Modified: trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-03-03 07:45:57 UTC (rev 674)
+++ trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-03-03 12:46:23 UTC (rev 675)
@@ -219,19 +219,19 @@
throw new ReasoningMethodUnsupportedException();
}
- public Set<DatatypeProperty> getDatatypeProperties() throws ReasoningMethodUnsupportedException {
+ public SortedSet<DatatypeProperty> getDatatypeProperties() throws ReasoningMethodUnsupportedException {
throw new ReasoningMethodUnsupportedException();
}
- public Set<DatatypeProperty> getBooleanDatatypeProperties() throws ReasoningMethodUnsupportedException {
+ public SortedSet<DatatypeProperty> getBooleanDatatypeProperties() throws ReasoningMethodUnsupportedException {
throw new ReasoningMethodUnsupportedException();
}
- public Set<DatatypeProperty> getDoubleDatatypeProperties() throws ReasoningMethodUnsupportedException {
+ public SortedSet<DatatypeProperty> getDoubleDatatypeProperties() throws ReasoningMethodUnsupportedException {
throw new ReasoningMethodUnsupportedException();
}
- public Set<DatatypeProperty> getIntDatatypeProperties() throws ReasoningMethodUnsupportedException {
+ public SortedSet<DatatypeProperty> getIntDatatypeProperties() throws ReasoningMethodUnsupportedException {
throw new ReasoningMethodUnsupportedException();
}
Modified: trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-03-03 07:45:57 UTC (rev 674)
+++ trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-03-03 12:46:23 UTC (rev 675)
@@ -467,7 +467,7 @@
return reasoner.getAtomicRoles();
}
- public Set<DatatypeProperty> getDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getDatatypeProperties() {
try {
return reasoner.getDatatypeProperties();
} catch (ReasoningMethodUnsupportedException e) {
@@ -476,7 +476,7 @@
}
}
- public Set<DatatypeProperty> getBooleanDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getBooleanDatatypeProperties() {
try {
return reasoner.getBooleanDatatypeProperties();
} catch (ReasoningMethodUnsupportedException e) {
@@ -485,7 +485,7 @@
}
}
- public Set<DatatypeProperty> getIntDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getIntDatatypeProperties() {
try {
return reasoner.getIntDatatypeProperties();
} catch (ReasoningMethodUnsupportedException e) {
@@ -494,7 +494,7 @@
}
}
- public Set<DatatypeProperty> getDoubleDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getDoubleDatatypeProperties() {
try {
return reasoner.getDoubleDatatypeProperties();
} catch (ReasoningMethodUnsupportedException e) {
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-03 07:45:57 UTC (rev 674)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-03 12:46:23 UTC (rev 675)
@@ -78,10 +78,10 @@
private Set<NamedClass> atomicConcepts;
private Set<ObjectProperty> atomicRoles;
- private Set<DatatypeProperty> datatypeProperties;
- private Set<DatatypeProperty> booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
- private Set<DatatypeProperty> doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
- private Set<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
+ private SortedSet<DatatypeProperty> datatypeProperties;
+ private SortedSet<DatatypeProperty> booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
+ private SortedSet<DatatypeProperty> doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
+ private SortedSet<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
private SortedSet<Individual> individuals;
private ReasoningService rs;
@@ -298,22 +298,22 @@
}
@Override
- public Set<DatatypeProperty> getDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getDatatypeProperties() {
return datatypeProperties;
}
@Override
- public Set<DatatypeProperty> getBooleanDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getBooleanDatatypeProperties() {
return booleanDatatypeProperties;
}
@Override
- public Set<DatatypeProperty> getDoubleDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getDoubleDatatypeProperties() {
return doubleDatatypeProperties;
}
@Override
- public Set<DatatypeProperty> getIntDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getIntDatatypeProperties() {
return intDatatypeProperties;
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-03 07:45:57 UTC (rev 674)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-03 12:46:23 UTC (rev 675)
@@ -136,10 +136,10 @@
// primitives
Set<NamedClass> atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
Set<ObjectProperty> atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
- Set<DatatypeProperty> datatypeProperties = new TreeSet<DatatypeProperty>();
- Set<DatatypeProperty> booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
- Set<DatatypeProperty> doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
- Set<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> datatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
SortedSet<Individual> individuals = new TreeSet<Individual>();
// namespaces
@@ -334,7 +334,7 @@
}
@Override
- public Set<DatatypeProperty> getDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getDatatypeProperties() {
return datatypeProperties;
}
@@ -960,7 +960,7 @@
* @return the booleanDatatypeProperties
*/
@Override
- public Set<DatatypeProperty> getBooleanDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getBooleanDatatypeProperties() {
return booleanDatatypeProperties;
}
@@ -968,7 +968,7 @@
* @return the doubleDatatypeProperties
*/
@Override
- public Set<DatatypeProperty> getDoubleDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getDoubleDatatypeProperties() {
return doubleDatatypeProperties;
}
@@ -976,7 +976,7 @@
* @return the intDatatypeProperties
*/
@Override
- public Set<DatatypeProperty> getIntDatatypeProperties() {
+ public SortedSet<DatatypeProperty> getIntDatatypeProperties() {
return intDatatypeProperties;
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/MathOperations.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/MathOperations.java 2008-03-03 07:45:57 UTC (rev 674)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/MathOperations.java 2008-03-03 12:46:23 UTC (rev 675)
@@ -23,9 +23,13 @@
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.ObjectSomeRestriction;
import org.dllearner.core.owl.Union;
+import org.dllearner.utilities.ConceptComparator;
/**
* Math operations related to refinement operators.
@@ -114,20 +118,44 @@
return combosTmp;
}
+ /**
+ * @see #getCombos(int)
+ * @param length Length of construct.
+ * @param maxValue Maximum value which can occur in sum.
+ * @return
+ */
+ public static List<List<Integer>> getCombos(int length, int maxValue) {
+ LinkedList<List<Integer>> combosTmp = new LinkedList<List<Integer>>();
+ decompose(length, maxValue, new LinkedList<Integer>(), combosTmp);
+ return combosTmp;
+ }
+
@SuppressWarnings("unchecked")
private static LinkedList<Integer> cloneList(LinkedList<Integer> list) {
return (LinkedList<Integer>) list.clone();
- }
-
- public static void main(String args[]) {
- System.out.println(getCombos(7));
}
- // neue Implementierung, die nicht mehr zur incompleteness führen soll,
- // da die Konzepte in einer MultiDisjunction als Liste gespeichert werden
- public static Set<Union> incCrossProduct(Set<Union> baseSet, Set<Description> newSet) {
- Set<Union> retSet = new HashSet<Union>();
-
+ /**
+ * Implements a cross product in the sense that each union description in the
+ * base set is extended by each description in the new set.
+ *
+ * Example:
+ * baseSet = {A1 OR A2, A1 or A3}
+ * newSet = {A1, EXISTS r.A3}
+ *
+ * Returns:
+ * {A1 OR A2 OR A1, A1 OR A2 OR EXISTS r.A3, A1 OR A3 OR A1, A1 OR A3 OR EXISTS r.A3}
+ *
+ * If the base set is empty, then the return value are union class descriptions
+ * for each value in newSet (a union with only one concept).
+ *
+ * @param baseSet A set of union class descriptions.
+ * @param newSet The descriptions to add to each union class descriptions.
+ * @return The "cross product" of baseSet and newSet.
+ */
+ public static SortedSet<Union> incCrossProduct(Set<Union> baseSet, Set<Description> newSet) {
+ SortedSet<Union> retSet = new TreeSet<Union>(new ConceptComparator());
+
if(baseSet.isEmpty()) {
for(Description c : newSet) {
Union md = new Union();
@@ -148,4 +176,26 @@
return retSet;
}
+ /**
+ * Returns true if the same property is used twice in an object some
+ * restriction, e.g. (EXISTS r.A1 AND A2 AND EXISTS r.A3) returns true,
+ * while (A1 OR A2) and (EXISTS r.A1 AND A2 AND EXISTS s.A3) return false.
+ * Note that the method does not work recursively, e.g. it return false
+ * for EXISTS r.(EXISTS r.A1 AND A2 AND EXISTS r.A3).
+ *
+ * @param d Description to test.
+ * @return See description.
+ */
+ public static boolean containsDoubleObjectSomeRestriction(Description d) {
+ Set<String> roles = new TreeSet<String>();
+ for(Description c : d.getChildren()) {
+ if(c instanceof ObjectSomeRestriction) {
+ String role = ((ObjectSomeRestriction)c).getRole().getName();
+ boolean roleExists = !roles.add(role);
+ if(roleExists)
+ return true;
+ }
+ }
+ return false;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-03 07:45:57 UTC (rev 674)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-03 12:46:23 UTC (rev 675)
@@ -25,6 +25,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
@@ -45,6 +46,7 @@
import org.dllearner.core.owl.Union;
import org.dllearner.utilities.ConceptComparator;
import org.dllearner.utilities.ConceptTransformation;
+import org.dllearner.utilities.Helper;
/**
* A downward refinement operator, which makes use of domains
@@ -81,17 +83,19 @@
// for refinements of \rho_\top(\top), the second one for \rho_A(\top)
private int topRefinementsLength = 0;
private Map<NamedClass, Integer> topARefinementsLength = new TreeMap<NamedClass, Integer>();
+ // M is finite and this value is the maximum length of any value in M
+ private static int mMaxLength = 3;
// the sets M_\top and M_A
- private Map<Integer,Set<Description>> m = new TreeMap<Integer,Set<Description>>();
- private Map<NamedClass,Map<Integer,Set<Description>>> mA = new TreeMap<NamedClass,Map<Integer,Set<Description>>>();
+ private Map<Integer,SortedSet<Description>> m = new TreeMap<Integer,SortedSet<Description>>();
+ private Map<NamedClass,Map<Integer,SortedSet<Description>>> mA = new TreeMap<NamedClass,Map<Integer,SortedSet<Description>>>();
// @see MathOperations.getCombos
private Map<Integer, List<List<Integer>>> combos = new HashMap<Integer, List<List<Integer>>>();
// refinements of the top concept ordered by length
- private Map<Integer, TreeSet<Description>> topRefinements = new TreeMap<Integer, TreeSet<Description>>();
- private Map<NamedClass,Map<Integer, TreeSet<Description>>> topARefinements = new TreeMap<NamedClass,Map<Integer, TreeSet<Description>>>();
+ private Map<Integer, SortedSet<? extends Description>> topRefinements = new TreeMap<Integer, SortedSet<? extends Description>>();
+ private Map<NamedClass,Map<Integer, SortedSet<? extends Description>>> topARefinements = new TreeMap<NamedClass,Map<Integer, SortedSet<? extends Description>>>();
// cumulated refinements of top (all from length one to the specified length)
private Map<Integer, TreeSet<Description>> topRefinementsCumulative = new HashMap<Integer, TreeSet<Description>>();
@@ -105,6 +109,8 @@
// most general applicable properties
private Map<NamedClass,Set<ObjectProperty>> mgr = new TreeMap<NamedClass,Set<ObjectProperty>>();
+ private Map<NamedClass,Set<DatatypeProperty>> mgbd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
+ private Map<NamedClass,Set<DatatypeProperty>> mgdd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
// comparator für Konzepte
private ConceptComparator conceptComparator = new ConceptComparator();
@@ -154,7 +160,7 @@
*/
public Set<Description> refine(Description description, int maxLength,
List<Description> knownRefinements) {
- return refine(description, maxLength, knownRefinements, new Thing());
+ return refine(description, maxLength, knownRefinements, startClass);
}
@SuppressWarnings({"unchecked"})
@@ -198,89 +204,84 @@
private void computeTopRefinements(int maxLength, NamedClass domain) {
long topComputationTimeStartNs = System.nanoTime();
- // M erweiteren
- computeM(maxLength);
+ if(domain == null && m.size() == 0)
+ computeM();
- // berechnen aller möglichen Kombinationen für Disjunktion,
- for(int i = topRefinementsLength+1; i <= maxLength; i++) {
- combos.put(i,MathOperations.getCombos(i));
- topRefinements.put(i, new TreeSet<Description>(conceptComparator));
- // topRefinements.put(i, new HashSet<Concept>());
+ if(domain != null && !mA.containsKey(domain))
+ computeM(domain);
+
+ // compute all possible combinations of the disjunction
+ int refinementsLength = (domain == null) ? topRefinementsLength : topARefinementsLength.get(domain);
+ for(int i = refinementsLength+1; i <= maxLength; i++) {
+ combos.put(i,MathOperations.getCombos(i, mMaxLength));
+// topRefinements.put(i, new TreeSet<Description>(conceptComparator));
for(List<Integer> combo : combos.get(i)) {
- // Kombination besteht aus nur einer Zahl => einfach M benutzen
- // if(combo.getNumbers().size()==1) {
+ // combination is a single number => try to use M
if(combo.size()==1) {
- topRefinements.get(i).addAll(m.get(i));
- // Kombination besteht aus mehreren Zahlen => Disjunktion erzeugen
+ if(domain == null)
+ topRefinements.put(i,m.get(i));
+ else
+ topARefinements.get(domain).put(i,mA.get(domain).get(i));
+ // combinations has several numbers => generate disjunct
} else {
- Set<Union> baseSet = new HashSet<Union>();
- for(Integer j : combo) { // combo.getNumbers()) {
+ SortedSet<Union> baseSet = new TreeSet<Union>(conceptComparator);
+ for(Integer j : combo) {
baseSet = MathOperations.incCrossProduct(baseSet, m.get(j));
}
- // Umwandlung aller Konzepte in Negationsnormalform
+ // convert all concepts in ordered negation normal form
for(Description concept : baseSet) {
ConceptTransformation.transformToOrderedNegationNormalForm(concept, conceptComparator);
}
+ // apply the exists filter (throwing out all refinements with
+ // double \exists r for any r)
+ // TODO: similar filtering can be done for boolean datatype
+ // properties
if(applyExistsFilter) {
- Iterator<Union> it = baseSet.iterator();
- while(it.hasNext()) {
- Union md = it.next();
- boolean remove = false;
- // falls Exists r für gleiche Rolle zweimal vorkommt,
- // dann rausschmeißen
- // Map<AtomicRole,Boolean> roleOccured = new HashMap<AtomicRole,Boolean>();
- Set<String> roles = new TreeSet<String>();
- for(Description c : md.getChildren()) {
- if(c instanceof ObjectSomeRestriction) {
- String role = ((ObjectSomeRestriction)c).getRole().getName();
- boolean roleExists = !roles.add(role);
- // falls Rolle schon vorkommt, dann kann ganzes
- // Refinement ignoriert werden (man könnte dann auch
- // gleich abbrechen, aber das hat nur minimalste
- // Auswirkungen auf Effizienz)
- if(roleExists)
- remove = true;
- }
+ Iterator<Union> it = baseSet.iterator();
+ while(it.hasNext()) {
+ if(MathOperations.containsDoubleObjectSomeRestriction(it.next()))
+ it.remove();
}
- if(remove)
- it.remove();
+ }
- }
- }
-
- topRefinements.get(i).addAll(baseSet);
+ // add computed refinements
+ if(domain == null)
+ topRefinements.put(new Integer(i), baseSet);
+ else
+ topARefinements.get(domain).put(new Integer(i), baseSet);
}
}
- // neu berechnete Refinements kumulieren, damit sie schneller abgefragt werden können
- // computeCumulativeTopRefinements(i);
+ // create cumulative versions of refinements such that they can
+ // be accessed easily
TreeSet<Description> cumulativeRefinements = new TreeSet<Description>(conceptComparator);
- // Set<Concept> cumulativeRefinements = new HashSet<Concept>();
for(int j=1; j<=i; j++) {
- cumulativeRefinements.addAll(topRefinements.get(j));
+ if(domain == null)
+ cumulativeRefinements.addAll(topRefinements.get(j));
+ else
+ cumulativeRefinements.addAll(topARefinements.get(domain).get(j));
}
- topRefinementsCumulative.put(i, cumulativeRefinements);
+ if(domain == null)
+ topRefinementsCumulative.put(i, cumulativeRefinements);
+ else
+ topARefinementsCumulative.get(domain).put(i, cumulativeRefinements);
}
- // neue Maximallänge eintragen
- topRefinementsLength = maxLength;
+ // register new top refinements length
+ if(domain == null)
+ topRefinementsLength = maxLength;
+ else
+ topARefinementsLength.put(domain,maxLength);
topComputationTimeNs += System.nanoTime() - topComputationTimeStartNs;
}
// compute M_\top
- private void computeM(int maxLength) {
- computeM(maxLength, null);
- }
-
- // computation of the set M_A
- // a major difference compared to the ILP 2007 \rho operator is that
- // M is finite and contains elements of length (currently) at most 3
- private void computeM(int maxLength, NamedClass domain) {
+ private void computeM() {
long mComputationTimeStartNs = System.nanoTime();
// initialise all possible lengths (1 to 3)
@@ -288,19 +289,19 @@
m.put(i, new TreeSet<Description>(conceptComparator));
}
- Set<Description> m1 = rs.getMoreSpecialConcepts(new Thing());
+ SortedSet<Description> m1 = rs.getMoreSpecialConcepts(new Thing());
m.put(1,m1);
if(useNegation) {
Set<Description> m2tmp = rs.getMoreGeneralConcepts(new Nothing());
- Set<Description> m2 = new TreeSet<Description>(conceptComparator);
+ SortedSet<Description> m2 = new TreeSet<Description>(conceptComparator);
for(Description c : m2tmp) {
m2.add(new Negation(c));
}
m.put(2,m2);
}
- Set<Description> m3 = new TreeSet<Description>(conceptComparator);
+ SortedSet<Description> m3 = new TreeSet<Description>(conceptComparator);
if(useExistsConstructor) {
// only uses most general roles
for(ObjectProperty r : rs.getMostGeneralRoles()) {
@@ -330,13 +331,89 @@
mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
}
+
+ // computation of the set M_A
+ // a major difference compared to the ILP 2007 \rho operator is that
+ // M is finite and contains elements of length (currently) at most 3
+ private void computeM(NamedClass nc) {
+ long mComputationTimeStartNs = System.nanoTime();
+
+ mA.put(nc, new TreeMap<Integer,SortedSet<Description>>());
+ // initialise all possible lengths (1 to 3)
+ for(int i=1; i<=3; i++) {
+ mA.get(nc).put(i, new TreeSet<Description>(conceptComparator));
+ }
- private void computeMgr(NamedClass domain) {
+ SortedSet<Description> m1 = rs.getMoreSpecialConcepts(nc);
+ m.put(1,m1);
+
+ if(useNegation) {
+ // the definition in the paper is more complex, but acutally
+ // we only have to insert the most specific concepts satisfying
+ // the mentioned restrictions; there is no need to implement a
+ // recursive method because for A subClassOf A' we have not A'
+ // subClassOf A and thus: if A and B are disjoint then also A'
+ // and B; if not A AND B = B then also not A' AND B = B
+ SortedSet<Description> m2tmp = rs.getMoreGeneralConcepts(new Nothing());
+ SortedSet<Description> m2 = new TreeSet<Description>(conceptComparator);
+ for(Description c : m2tmp) {
+ if(c instanceof Thing)
+ m2.add(c);
+ else {
+ NamedClass a = (NamedClass) c;
+ if(!isNotADisjoint(a, nc) && !isNotAMeaningFul(a, nc))
+ m2.add(new Negation(a));
+ }
+ }
+ m.put(2,m2);
+ }
+
+ // compute applicable properties
+ computeMg(nc);
+
+ SortedSet<Description> m3 = new TreeSet<Description>(conceptComparator);
+ if(useExistsConstructor) {
+ for(ObjectProperty r : mgr.get(nc)) {
+ m3.add(new ObjectSomeRestriction(r, new Thing()));
+ }
+ }
+
+ if(useAllConstructor) {
+ // we allow \forall r.\top here because otherwise the operator
+ // becomes too difficult to manage due to dependencies between
+ // M_A and M_A' where A'=ran(r)
+ for(ObjectProperty r : mgr.get(nc)) {
+ m3.add(new ObjectAllRestriction(r, new Thing()));
+ }
+ }
+
+ // boolean datatypes, e.g. testPositive = true
+ if(useBooleanDatatypes) {
+ Set<DatatypeProperty> booleanDPs = mgbd.get(nc);
+ for(DatatypeProperty dp : booleanDPs) {
+ m3.add(new BooleanValueRestriction(dp,true));
+ m3.add(new BooleanValueRestriction(dp,false));
+ }
+ }
+
+ m.put(3,m3);
+
+ mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
+ }
+
+ private void computeMg(NamedClass domain) {
// compute the applicable properties if this has not been done yet
if(appOP.get(domain) == null)
- computeApp(domain);
- Set<ObjectProperty> mostGeneral = rs.getMostGeneralRoles();
+ computeApp(domain);
+ SortedSet<ObjectProperty> mostGeneral = rs.getMostGeneralRoles();
computeMgrRecursive(domain, mostGeneral, mgr.get(domain));
+ SortedSet<DatatypeProperty> mostGeneralDP = rs.getMostGeneralDatatypeProperties();
+ // we make the (reasonable) assumption here that all sub and super
+ // datatype properties have the same type (e.g. boolean, integer, double)
+ Set<DatatypeProperty> mostGeneralBDP = Helper.intersection(mostGeneralDP, rs.getBooleanDatatypeProperties());
+ Set<DatatypeProperty> mostGeneralDDP = Helper.intersection(mostGeneralDP, rs.getDoubleDatatypeProperties());
+ computeMgbdRecursive(domain, mostGeneralBDP, mgbd.get(domain));
+ computeMgddRecursive(domain, mostGeneralDDP, mgdd.get(domain));
}
private void computeMgrRecursive(NamedClass domain, Set<ObjectProperty> currProperties, Set<ObjectProperty> mgrTmp) {
@@ -348,9 +425,27 @@
}
}
+ private void computeMgbdRecursive(NamedClass domain, Set<DatatypeProperty> currProperties, Set<DatatypeProperty> mgbdTmp) {
+ for(DatatypeProperty prop : currProperties) {
+ if(appBD.get(domain).contains(prop))
+ mgbdTmp.add(prop);
+ else
+ computeMgbdRecursive(domain, rs.getMoreSpecialDatatypeProperties(prop), mgbdTmp);
+ }
+ }
+
+ private void computeMgddRecursive(NamedClass domain, Set<DatatypeProperty> currProperties, Set<DatatypeProperty> mgddTmp) {
+ for(DatatypeProperty prop : currProperties) {
+ if(appDD.get(domain).contains(prop))
+ mgddTmp.add(prop);
+ else
+ computeMgddRecursive(domain, rs.getMoreSpecialDatatypeProperties(prop), mgddTmp);
+ }
+ }
+
// computes the set of applicable properties for a given class
private void computeApp(NamedClass domain) {
- // TODO: also implement this for boolean/double datatype properties
+ // object properties
Set<ObjectProperty> mostGeneral = rs.getAtomicRoles();
Set<ObjectProperty> applicableRoles = new TreeSet<ObjectProperty>();
for(ObjectProperty role : mostGeneral) {
@@ -361,14 +456,52 @@
applicableRoles.add(role);
}
appOP.put(domain, applicableRoles);
+
+ // boolean datatype properties
+ Set<DatatypeProperty> mostGeneralBDPs = rs.getBooleanDatatypeProperties();
+ Set<DatatypeProperty> applicableBDPs = new TreeSet<DatatypeProperty>();
+ for(DatatypeProperty role : mostGeneralBDPs) {
+ NamedClass nc = (NamedClass) rs.getDomain(role);
+ if(!isDisjoint(domain,nc))
+ applicableBDPs.add(role);
+ }
+ appBD.put(domain, applicableBDPs);
+
+ // double datatype properties
+ Set<DatatypeProperty> mostGeneralDDPs = rs.getBooleanDatatypeProperties();
+ Set<DatatypeProperty> applicableDDPs = new TreeSet<DatatypeProperty>();
+ for(DatatypeProperty role : mostGeneralDDPs) {
+ NamedClass nc = (NamedClass) rs.getDomain(role);
+ if(!isDisjoint(domain,nc))
+ applicableDDPs.add(role);
+ }
+ appDD.put(domain, applicableDDPs);
}
// computes whether two classes are disjoint; this should be computed
// by the reasoner only ones and otherwise taken from a matrix
- private boolean isDisjoint(NamedClass class1, NamedClass class2) {
+ // => this has low importance in the long run, because M is cached anyway,
+ // but avoids many duplicate queries when computing M
+ private boolean isDisjoint(NamedClass a, NamedClass b) {
// we need to test whether A AND B is equivalent to BOTTOM
- Description d = new Intersection(class1, class2);
+ Description d = new Intersection(a, b);
return rs.subsumes(new Nothing(), d);
}
+ // we need to test whether NOT A AND B is equivalent to BOTTOM
+ private boolean isNotADisjoint(NamedClass a, NamedClass b) {
+ Description notA = new Negation(a);
+ Description d = new Intersection(notA, b);
+ return rs.subsumes(new Nothing(), d);
+ }
+
+ // we need to test whether NOT A AND B = B
+ // (if not then NOT A is not meaningful in the sense that it does
+ // not semantically add anything to B)
+ private boolean isNotAMeaningFul(NamedClass a, NamedClass b) {
+ Description notA = new Negation(a);
+ Description d = new Intersection(notA, b);
+ return !rs.subsumes(b, d);
+ }
+
}
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-04 08:17:55
|
Revision: 681
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=681&view=rev
Author: jenslehmann
Date: 2008-03-04 00:17:44 -0800 (Tue, 04 Mar 2008)
Log Message:
-----------
TreeModel for search tree GUI
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/gui/EBNodeTreeModel.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-03-04 03:54:48 UTC (rev 680)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-03-04 08:17:44 UTC (rev 681)
@@ -344,4 +344,8 @@
algorithm.stop();
}
+ public ExampleBasedNode getStartNode() {
+ return algorithm.getStartNode();
+ }
+
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-04 03:54:48 UTC (rev 680)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-04 08:17:44 UTC (rev 681)
@@ -103,6 +103,9 @@
// setting to true gracefully stops the algorithm
private boolean stop = false;
+ // node from which algorithm has started
+ private ExampleBasedNode startNode;
+
// solution protocol
private boolean solutionFound = false;
private List<Description> solutions = new LinkedList<Description>();
@@ -220,7 +223,6 @@
allowedMisclassifications = (int) Math.round(noise * nrOfExamples);
// start search with start class
- ExampleBasedNode startNode;
if(startDescription == null) {
Thing top = new Thing();
startNode = new ExampleBasedNode(top);
@@ -748,6 +750,8 @@
return learningProblem.computeScore(getBestSolution());
}
-
+ public ExampleBasedNode getStartNode() {
+ return startNode;
+ }
}
Added: trunk/src/dl-learner/org/dllearner/gui/EBNodeTreeModel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/gui/EBNodeTreeModel.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/gui/EBNodeTreeModel.java 2008-03-04 08:17:44 UTC (rev 681)
@@ -0,0 +1,116 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.gui;
+
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import javax.swing.event.TreeModelEvent;
+import javax.swing.event.TreeModelListener;
+import javax.swing.tree.TreeModel;
+import javax.swing.tree.TreePath;
+
+import org.dllearner.algorithms.refexamples.ExampleBasedNode;
+import org.dllearner.algorithms.refexamples.NodeComparatorStable;
+
+/**
+ * A tree model used for displaying example based nodes. A search tree
+ * can become very large, so lazy loading should be used, i.e. never
+ * load the full search tree but only the nodes selected by the user.
+ * Note that the search tree changes over time.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class EBNodeTreeModel implements TreeModel {
+
+ // root of the search tree
+ private ExampleBasedNode rootNode;
+
+ // a mapping from nodes to their children;
+ // the main problem is that example based nodes use sets instead
+ // of lists, so we need to convert these sets to lists and store
+ // them here
+ private Map<ExampleBasedNode,List<ExampleBasedNode>> childrenMap = new TreeMap<ExampleBasedNode,List<ExampleBasedNode>>(new NodeComparatorStable());
+
+ // listeners for this model
+ private List<TreeModelListener> treeModelListeners =
+ new LinkedList<TreeModelListener>();
+
+ public EBNodeTreeModel(ExampleBasedNode rootNode) {
+ this.rootNode = rootNode;
+ }
+
+ public void addTreeModelListener(TreeModelListener l) {
+ treeModelListeners.add(l);
+ }
+
+ public Object getChild(Object parent, int index) {
+ return getChildren((ExampleBasedNode)parent).get(index);
+ }
+
+ public int getChildCount(Object parent) {
+ return ((ExampleBasedNode)parent).getChildren().size();
+ }
+
+ public int getIndexOfChild(Object parent, Object child) {
+ return getChildren((ExampleBasedNode)parent).indexOf(child);
+ }
+
+ public Object getRoot() {
+ return rootNode;
+ }
+
+ public boolean isLeaf(Object node) {
+ return (getChildCount(node)==0);
+ }
+
+ public void removeTreeModelListener(TreeModelListener l) {
+ treeModelListeners.remove(l);
+ }
+
+ public void valueForPathChanged(TreePath path, Object newValue) {
+
+ }
+
+ private void fireTreeStructureChanged(ExampleBasedNode node) {
+ TreeModelEvent e = new TreeModelEvent(this,
+ new Object[] {node});
+ for (TreeModelListener tml : treeModelListeners) {
+ tml.treeStructureChanged(e);
+ }
+ }
+
+ // convert the set of children to a list and store it in this model
+ private List<ExampleBasedNode> getChildren(ExampleBasedNode node) {
+ List<ExampleBasedNode> children = childrenMap.get(node);
+ // if the children have not been cached or the list is outdated
+ // (node has more children now) we do an update
+ if(children == null || children.size() != node.getChildren().size()) {
+ children = new LinkedList<ExampleBasedNode>(node.getChildren());
+ childrenMap.put(node, children);
+ fireTreeStructureChanged(node);
+ }
+ return children;
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-05 12:07:36
|
Revision: 688
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=688&view=rev
Author: jenslehmann
Date: 2008-03-05 04:07:28 -0800 (Wed, 05 Mar 2008)
Log Message:
-----------
implemented a new heuristic
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java
trunk/src/dl-learner/org/dllearner/core/owl/Thing.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java 2008-03-04 19:10:55 UTC (rev 687)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java 2008-03-05 12:07:28 UTC (rev 688)
@@ -39,16 +39,15 @@
*/
public class ExampleBasedNode {
- // example based variables here
+ // example based variables
private Set<Individual> coveredPositives;
private Set<Individual> coveredNegatives;
- // TOP ist einfach das TOP-Konzept, also das einzige welches nicht evaluiert wird
+ // the method by which quality was evaluated in this node
public enum QualityEvaluationMethod { TOP, REASONER, TOO_WEAK_LIST, OVERLY_GENERAL_LIST };
-
private QualityEvaluationMethod qualityEvaluationMethod = QualityEvaluationMethod.TOP;
- // alle Eigenschaften eines Knotens im Suchbaum
+ // all properties of a node in the search tree
private Description concept;
private int horizontalExpansion;
private int coveredNegativeExamples;
@@ -59,28 +58,17 @@
private static ConceptComparator conceptComparator = new ConceptComparator();
private static NodeComparatorStable nodeComparator = new NodeComparatorStable();
- // Einbettung in Suchbaum
+ // link to parent in search tree
private ExampleBasedNode parent = null;
- // private Set<Node> children = new HashSet<Node>();
private Set<ExampleBasedNode> children = new TreeSet<ExampleBasedNode>(nodeComparator);
- // es wird auch eine Liste von Kindern gehalten
+ // apart from the child nodes, we also keep child concepts
private Set<Description> childConcepts = new TreeSet<Description>(conceptComparator);
- // verwendeter Operator für Expansion des Knotens
- // private RefinementOperator operator;
-
public ExampleBasedNode(Description concept) {
this.concept = concept;
horizontalExpansion = 0;
isQualityEvaluated = false;
}
-
- public void setCoveredNegativeExamples(int coveredNegativeExamples) {
- if(isQualityEvaluated)
- throw new RuntimeException("Cannot set quality of a node more than once.");
- this.coveredNegativeExamples = coveredNegativeExamples;
- isQualityEvaluated = true;
- }
public void setHorizontalExpansion(int horizontalExpansion) {
this.horizontalExpansion = horizontalExpansion;
@@ -104,25 +92,16 @@
return children.add(child);
}
- public Description getConcept() {
- return concept;
+ public void setQualityEvaluationMethod(QualityEvaluationMethod qualityEvaluationMethod) {
+ this.qualityEvaluationMethod = qualityEvaluationMethod;
}
- public int getCoveredNegativeExamples() {
- return coveredNegativeExamples;
+
+ public void setCoveredExamples(Set<Individual> coveredPositives, Set<Individual> coveredNegatives) {
+ this.coveredPositives = coveredPositives;
+ this.coveredNegatives = coveredNegatives;
+ isQualityEvaluated = true;
}
- public int getHorizontalExpansion() {
- return horizontalExpansion;
- }
- public boolean isQualityEvaluated() {
- return isQualityEvaluated;
- }
- public boolean isRedundant() {
- return isRedundant;
- }
- public boolean isTooWeak() {
- return isTooWeak;
- }
-
+
@Override
public String toString() {
String ret = concept.toString() + " [q:";
@@ -134,7 +113,7 @@
return ret;
}
- // gibt die Refinement-Chain zurück, die zu dem Knoten geführt hat
+ // returns the refinement chain leading to this node as string
public String getRefinementChainString() {
if(parent!=null) {
String ret = parent.getRefinementChainString();
@@ -143,8 +122,8 @@
} else {
return concept.toString();
}
- }
-
+ }
+
public String getTreeString() {
return getTreeString(0).toString();
}
@@ -173,6 +152,14 @@
ret += " ("+qualityEvaluationMethod+"), he:" + horizontalExpansion + "]";
return ret;
+ }
+
+ public Set<Individual> getCoveredPositives() {
+ return coveredPositives;
+ }
+
+ public Set<Individual> getCoveredNegatives() {
+ return coveredNegatives;
}
public Set<ExampleBasedNode> getChildren() {
@@ -183,28 +170,35 @@
return childConcepts;
}
+ public Description getConcept() {
+ return concept;
+ }
+
public QualityEvaluationMethod getQualityEvaluationMethod() {
return qualityEvaluationMethod;
+ }
+
+ public int getCoveredNegativeExamples() {
+ return coveredNegativeExamples;
}
-
- public void setQualityEvaluationMethod(QualityEvaluationMethod qualityEvaluationMethod) {
- this.qualityEvaluationMethod = qualityEvaluationMethod;
+ public int getHorizontalExpansion() {
+ return horizontalExpansion;
}
-
- public Set<Individual> getCoveredPositives() {
- return coveredPositives;
+ public boolean isQualityEvaluated() {
+ return isQualityEvaluated;
}
-
- public void setCoveredPositives(Set<Individual> coveredPositives) {
- this.coveredPositives = coveredPositives;
+ public boolean isRedundant() {
+ return isRedundant;
}
-
- public Set<Individual> getCoveredNegatives() {
- return coveredNegatives;
+ public boolean isTooWeak() {
+ return isTooWeak;
}
- public void setCoveredNegatives(Set<Individual> coveredNegatives) {
- this.coveredNegatives = coveredNegatives;
- }
-
-}
+ /**
+ * @return the parent
+ */
+ public ExampleBasedNode getParent() {
+ return parent;
+ }
+
+}
\ No newline at end of file
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-04 19:10:55 UTC (rev 687)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-05 12:07:28 UTC (rev 688)
@@ -217,37 +217,25 @@
}
public void start() {
-
-
// calculate quality threshold required for a solution
allowedMisclassifications = (int) Math.round(noise * nrOfExamples);
// start search with start class
if(startDescription == null) {
- Thing top = new Thing();
- startNode = new ExampleBasedNode(top);
- // top covers all negatives
- int coveredNegativeExamples = getNumberOfNegatives();
- startNode.setCoveredNegativeExamples(coveredNegativeExamples);
- startNode.setCoveredPositives(learningProblem.getPositiveExamples());
- startNode.setCoveredNegatives(learningProblem.getNegativeExamples());
+ startNode = new ExampleBasedNode(Thing.instance);
+ startNode.setCoveredExamples(learningProblem.getPositiveExamples(), learningProblem.getNegativeExamples());
} else {
startNode = new ExampleBasedNode(startDescription);
Set<Individual> coveredNegatives = rs.instanceCheck(startDescription, learningProblem.getNegativeExamples());
- startNode.setCoveredPositives(rs.instanceCheck(startDescription, learningProblem.getPositiveExamples()));
- startNode.setCoveredNegatives(coveredNegatives);
- startNode.setCoveredNegativeExamples(coveredNegatives.size());
+ Set<Individual> coveredPositives = rs.instanceCheck(startDescription, learningProblem.getPositiveExamples());
+ startNode.setCoveredExamples(coveredPositives, coveredNegatives);
}
candidates.add(startNode);
candidatesStable.add(startNode);
- // note that TOP may already be a solution
+
ExampleBasedNode bestNode = startNode;
-// solutionFound = (coveredNegativeExamples == 0);
-// solutions = new LinkedList<Concept>();
-// if(solutionFound)
-// solutions.add(top);
-
+
int loop = 0;
algorithmStartTime = System.nanoTime();
@@ -571,8 +559,7 @@
// quality is the number of misclassifications (if it is not too weak)
quality = (nrOfPositiveExamples - newlyCoveredPositives.size())
+ newlyCoveredNegatives.size();
- newNode.setCoveredNegatives(newlyCoveredNegatives);
- newNode.setCoveredPositives(newlyCoveredPositives);
+ newNode.setCoveredExamples(newlyCoveredPositives, newlyCoveredNegatives);
}
}
@@ -588,7 +575,7 @@
solutions.add(refinement);
}
- newNode.setCoveredNegativeExamples(quality);
+// newNode.setCoveredNegativeExamples(quality);
newCandidates.add(newNode);
// candidates.add(newNode);
// candidatesStable.add(newNode);
Added: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-05 12:07:28 UTC (rev 688)
@@ -0,0 +1,114 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.algorithms.refexamples;
+
+import org.dllearner.utilities.ConceptComparator;
+
+/**
+ * This heuristic combines the following criteria to assign a
+ * double score value to a node:
+ * <ul>
+ * <li>quality/accuracy of a concept (based on the full training set, not
+ * the negative example coverage as the flexible heuristic)</li>
+ * <li>horizontal expansion</li>
+ * <li>accuracy gain: The heuristic takes into account the accuracy
+ * difference between a node and its parent. If there is no gain (even
+ * though we know that the refinement is proper) it is unlikely (although
+ * not excluded) that the refinement is a necessary path to take towards a
+ * solution.</li>
+ * </ul>
+ *
+ * The heuristic has two parameters:
+ * <ul>
+ * <li>expansion penalty factor: describes how much accuracy gain is worth
+ * an increase of horizontal expansion by one (typical value: 0.01)</li>
+ * <li>gain bonus factor: describes how accuracy gain should be weighted
+ * versus accuracy itself (typical value: 1.00)</li>
+ * </ul>
+ *
+ * The value of a node is calculated as follows:
+ *
+ * <p><code>value = accuracy + gain bonus factor * accuracy gain - expansion penalty
+ * factor * horizontal expansion</code></p>
+ *
+ * <p><code>accuracy = (TP + TN)/(P + N)</code></p>
+ *
+ * <p><code>
+ * TP = number of true positives (= covered positives)<br />
+ * TN = number of true negatives (= nr of negatives examples - covered negatives)<br />
+ * P = number of positive examples<br />
+ * N = number of negative examples<br />
+ * </code></p>
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class MultiHeuristic implements ExampleBasedHeuristic {
+
+ private ConceptComparator conceptComparator = new ConceptComparator();
+
+ // heuristic parameters
+ private double expansionPenaltyFactor = 0.01;
+ private double gainBonusFactor = 1.00;
+
+ // examples
+ private int nrOfNegativeExamples;
+ private int nrOfExamples;
+
+ public MultiHeuristic(int nrOfPositiveExamples, int nrOfNegativeExamples, double expansionPenaltyFactor, double gainBonusFactor) {
+ this.nrOfNegativeExamples = nrOfNegativeExamples;
+ nrOfExamples = nrOfPositiveExamples + nrOfNegativeExamples;
+ this.expansionPenaltyFactor = expansionPenaltyFactor;
+ this.gainBonusFactor = gainBonusFactor;
+ }
+
+ /* (non-Javadoc)
+ * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
+ */
+ public int compare(ExampleBasedNode node1, ExampleBasedNode node2) {
+ double score1 = getNodeScore(node1);
+ double score2 = getNodeScore(node2);
+ double diff = score1 - score2;
+ if(diff>0)
+ return 1;
+ else if(diff<0)
+ return -1;
+ else
+ // TODO: would it be OK to simply return 0 here (?)
+ // could improve performance a bit
+ return conceptComparator.compare(node1.getConcept(), node2.getConcept());
+ }
+
+ public double getNodeScore(ExampleBasedNode node) {
+ double accuracy = getAccuracy(node.getCoveredPositives().size(),node.getCoveredNegatives().size());
+ ExampleBasedNode parent = node.getParent();
+ double gain = 0;
+ if(parent != null) {
+ double parentAccuracy = getAccuracy(parent.getCoveredPositives().size(),parent.getCoveredNegatives().size());
+ gain = accuracy - parentAccuracy;
+ }
+ return accuracy + gainBonusFactor * gain - expansionPenaltyFactor * node.getHorizontalExpansion();
+ }
+
+ private double getAccuracy(int coveredPositives, int coveredNegatives) {
+ return (coveredPositives + nrOfNegativeExamples - coveredNegatives)/(double)nrOfExamples;
+
+ }
+}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java 2008-03-04 19:10:55 UTC (rev 687)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java 2008-03-05 12:07:28 UTC (rev 688)
@@ -1,3 +1,22 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
package org.dllearner.core.owl;
import java.util.Map;
@@ -2,13 +21,11 @@
-
-
+/**
+ * Implementation of owl:nothing/BOTTOM.
+ *
+ * @author Jens Lehmann
+ *
+ */
public class Nothing extends Description {
- /*
- @Override
- protected void calculateSets(FlatABox abox, SortedSet<String> adcPosSet, SortedSet<String> adcNegSet) {
- posSet = abox.bottom;
- negSet = abox.top;
- }
- */
+ public static final Nothing instance = new Nothing();
@@ -48,5 +65,4 @@
visitor.visit(this);
}
-
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Thing.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Thing.java 2008-03-04 19:10:55 UTC (rev 687)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Thing.java 2008-03-05 12:07:28 UTC (rev 688)
@@ -1,3 +1,22 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
package org.dllearner.core.owl;
import java.util.Map;
@@ -2,12 +21,19 @@
+/**
+ * Implementation of owl:thing/TOP.
+ *
+ * TODO: According to the OWL 1.1 spec, owl:thing is special instance of
+ * class, so it might be better to put a method there for retrieving
+ * a/the instance of owl:thing. However, some algorithms require parent
+ * links e.g. in EXISTS r.TOP we may need to know where TOP belongs
+ * (especially for genetic operators). This is instance dependant, i.e.
+ * two different instances of TOP can have different parent links.
+ *
+ * @author Jens Lehmann
+ *
+ */
public class Thing extends Description {
- /*
- @Override
- protected void calculateSets(FlatABox abox, SortedSet<String> adcPosSet, SortedSet<String> adcNegSet) {
- posSet = abox.top;
- negSet = abox.bottom;
- }
- */
-
+ public static final Thing instance = new Thing();
+
public String toString(String baseURI, Map<String,String> prefixes) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-07 08:44:26
|
Revision: 692
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=692&view=rev
Author: jenslehmann
Date: 2008-03-07 00:44:10 -0800 (Fri, 07 Mar 2008)
Log Message:
-----------
added ORE tool package
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/tools/
trunk/src/dl-learner/org/dllearner/tools/ore/
trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
Added: trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java 2008-03-07 08:44:10 UTC (rev 692)
@@ -0,0 +1,30 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.tools.ore;
+
+/**
+ * Start class for the ontology repair and enrichment tool.
+ *
+ * @author Lorenz Bühmann.
+ *
+ */
+public class ORE {
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-09 11:49:31
|
Revision: 697
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=697&view=rev
Author: jenslehmann
Date: 2008-03-09 04:49:21 -0700 (Sun, 09 Mar 2008)
Log Message:
-----------
- added disjointness test (including result cache) to further reduce refinements in new operator
- bug fix for deactivated negation
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-09 02:16:01 UTC (rev 696)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-09 11:49:21 UTC (rev 697)
@@ -260,7 +260,8 @@
bestNode = candidates.last();
// extend best node
newCandidates.clear();
- // TODO: why is the best node tempoariliy removed from the candidates set?
+ // best node is removed temporarily, because extending it can
+ // change its evaluation
candidates.remove(bestNode);
extendNodeProper(bestNode, bestNode.getHorizontalExpansion()+1);
candidates.add(bestNode);
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-09 02:16:01 UTC (rev 696)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-09 11:49:21 UTC (rev 697)
@@ -302,6 +302,11 @@
@Override
public SortedSet<Individual> retrieval(Description concept) throws ReasoningMethodUnsupportedException {
+ if(concept instanceof NamedClass)
+ return classInstancesPos.get((NamedClass)concept);
+ else if(concept instanceof Negation && concept.getChild(0) instanceof NamedClass)
+ return classInstancesNeg.get((NamedClass)concept.getChild(0));
+
// return rs.retrieval(concept);
SortedSet<Individual> inds = new TreeSet<Individual>();
for(Individual i : individuals) {
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-09 02:16:01 UTC (rev 696)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-09 11:49:21 UTC (rev 697)
@@ -35,6 +35,7 @@
import org.dllearner.core.owl.BooleanValueRestriction;
import org.dllearner.core.owl.DatatypeProperty;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Negation;
@@ -127,11 +128,14 @@
private boolean useAllConstructor = true;
private boolean useExistsConstructor = true;
private boolean useNegation = true;
- private boolean useBooleanDatatypes = true;
+ private boolean useBooleanDatatypes = true;
+ private boolean instanceBasedDisjoints = true;
// caches for reasoner queries
+ private Map<Description,Map<Description,Boolean>> cachedDisjoints = new TreeMap<Description,Map<Description,Boolean>>(conceptComparator);
+
// private Map<NamedClass,Map<NamedClass,Boolean>> abDisjoint = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
- private Map<NamedClass,Map<NamedClass,Boolean>> notABDisjoint = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
+// private Map<NamedClass,Map<NamedClass,Boolean>> notABDisjoint = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
// private Map<NamedClass,Map<NamedClass,Boolean>> notABMeaningful = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
public RhoDRDown(ReasoningService reasoningService) {
@@ -160,6 +164,18 @@
dpDomains.put(dp, rs.getDomain(dp));
}
+
+// NamedClass struc = new NamedClass("http://dl-learner.org/carcinogenesis#Structure");
+// computeTopRefinements(3,struc);
+// for(Description d : topARefinements.get(struc).get(1)) {
+ // bei 3 ist noch alles OK, bei 4 seltsamer Fehler mit Union
+// for(Description d : refine(Thing.instance,3,null,struc)) {
+// if(d instanceof Union)
+// System.out.println(d);
+// }
+// System.out.println(refine(Thing.instance,7,null,struc).size());
+// System.exit(0);
+
if(startClass != null)
this.startClass = startClass;
}
@@ -245,8 +261,7 @@
// (non-recursive variant because only depth 1 was modified)
ConceptTransformation.cleanConceptNonRecursive(mc);
ConceptTransformation.transformToOrderedNegationNormalFormNonRecursive(mc, conceptComparator);
-
- refinements.add(mc);
+
}
}
@@ -318,8 +333,9 @@
}
- // if a refinement is neither Bottom nor Top a refinement of top can be appended
- if(!(description instanceof Thing) && !(description instanceof Nothing)) {
+ // if a refinement is not Bottom, Top, ALL r.Bottom a refinement of top can be appended
+ if(!(description instanceof Thing) && !(description instanceof Nothing)
+ && !(description instanceof ObjectAllRestriction && description.getChild(0) instanceof Nothing)) {
// -1 because of the AND symbol which is appended
int topRefLength = maxLength - description.getLength() - 1;
@@ -357,6 +373,14 @@
}
}
+ // perform a disjointness check when named classes are added;
+ // this can avoid a lot of superfluous computation in the algorithm e.g.
+ // when A1 looks good, so many refinements of the form (A1 OR (A2 AND A3))
+ // are generated which are all equal to A1 due to disjointness of A2 and A3
+ if(c instanceof NamedClass && isDisjoint(description, c))
+ // refinements.add(mc);
+ skip = true;
+
if(!skip) {
Intersection mc = new Intersection();
mc.addChild(description);
@@ -365,13 +389,20 @@
// clean and transform to ordered negation normal form
ConceptTransformation.cleanConceptNonRecursive(mc);
ConceptTransformation.transformToOrderedNegationNormalFormNonRecursive(mc, conceptComparator);
-
+
refinements.add(mc);
}
}
}
}
+// for(Description refinement : refinements) {
+// if((refinement instanceof Intersection || refinement instanceof Union) && refinement.getChildren().size()<2) {
+// System.out.println(description + " " + refinement + " " + currDomain + " " + maxLength);
+// System.exit(0);
+// }
+// }
+
return refinements;
}
@@ -424,36 +455,52 @@
topARefinements.get(domain).get(i).addAll(mA.get(domain).get(i));
// combinations has several numbers => generate disjunct
} else {
- SortedSet<Union> baseSet = new TreeSet<Union>(conceptComparator);
+
+ // check whether the combination makes sense, i.e. whether
+ // all lengths mentioned in it have corresponding elements
+ // e.g. when negation is deactivated there won't be elements of
+ // length 2 in M
+ boolean validCombo = true;
for(Integer j : combo) {
- if(domain == null)
- baseSet = MathOperations.incCrossProduct(baseSet, m.get(j));
- else
- baseSet = MathOperations.incCrossProduct(baseSet, mA.get(domain).get(j));
+ if((domain == null && m.get(j).size()==0) ||
+ (domain != null && mA.get(domain).get(j).size()==0))
+ validCombo = false;
}
- // convert all concepts in ordered negation normal form
- for(Description concept : baseSet) {
- ConceptTransformation.transformToOrderedNegationNormalForm(concept, conceptComparator);
- }
-
- // apply the exists filter (throwing out all refinements with
- // double \exists r for any r)
- // TODO: similar filtering can be done for boolean datatype
- // properties
- if(applyExistsFilter) {
- Iterator<Union> it = baseSet.iterator();
- while(it.hasNext()) {
- if(MathOperations.containsDoubleObjectSomeRestriction(it.next()))
- it.remove();
+ if(validCombo) {
+
+ SortedSet<Union> baseSet = new TreeSet<Union>(conceptComparator);
+ for(Integer j : combo) {
+ if(domain == null)
+ baseSet = MathOperations.incCrossProduct(baseSet, m.get(j));
+ else
+ baseSet = MathOperations.incCrossProduct(baseSet, mA.get(domain).get(j));
}
+
+ // convert all concepts in ordered negation normal form
+ for(Description concept : baseSet) {
+ ConceptTransformation.transformToOrderedNegationNormalForm(concept, conceptComparator);
+ }
+
+ // apply the exists filter (throwing out all refinements with
+ // double \exists r for any r)
+ // TODO: similar filtering can be done for boolean datatype
+ // properties
+ if(applyExistsFilter) {
+ Iterator<Union> it = baseSet.iterator();
+ while(it.hasNext()) {
+ if(MathOperations.containsDoubleObjectSomeRestriction(it.next()))
+ it.remove();
+ }
+ }
+
+ // add computed refinements
+ if(domain == null)
+ topRefinements.get(i).addAll(baseSet);
+ else
+ topARefinements.get(domain).get(i).addAll(baseSet);
+
}
-
- // add computed refinements
- if(domain == null)
- topRefinements.get(i).addAll(baseSet);
- else
- topARefinements.get(domain).get(i).addAll(baseSet);
}
}
@@ -690,31 +737,99 @@
appDD.put(domain, applicableDDPs);
}
+ // returns true of the intersection contains elements disjoint
+ // to the given description (if true adding the description to
+ // the intersection results in a description equivalent to bottom)
+ // e.g. OldPerson AND YoungPerson; Nitrogen-34 AND Tin-113
+ // Note: currently we only check named classes in the intersection,
+ // it would be interesting to see whether it makes sense to extend this
+ // (advantage: less refinements, drawback: operator will need infinitely many
+ // reasoner queries in the long run)
+ @SuppressWarnings({"unused"})
+ private boolean containsDisjoints(Intersection intersection, Description d) {
+ List<Description> children = intersection.getChildren();
+ for(Description child : children) {
+ if(d instanceof Nothing)
+ return true;
+ else if(child instanceof NamedClass) {
+ if(isDisjoint((NamedClass)child, d))
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private boolean isDisjoint(Description d1, Description d2) {
+ // equal concepts are not disjoint (unless equivalent to bottom)
+// if(conceptComparator.compare(d1, d2)==0)
+// return false;
+
+ // check whether we have cached this query
+ Map<Description,Boolean> tmp = cachedDisjoints.get(d1);
+ Boolean tmp2 = null;
+ if(tmp != null)
+ tmp2 = tmp.get(d2);
+
+ if(tmp2==null) {
+ Boolean result;
+ if(instanceBasedDisjoints) {
+ result = isDisjointInstanceBased(d1,d2);
+ } else {
+ Description d = new Intersection(d1, d2);
+ result = rs.subsumes(new Nothing(), d);
+ }
+ // add the result to the cache (we add it twice such that
+ // the order of access does not matter)
+
+ // create new entries if necessary
+ Map<Description,Boolean> map = new TreeMap<Description,Boolean>(conceptComparator);
+ if(tmp == null)
+ cachedDisjoints.put(d1, map);
+ if(!cachedDisjoints.containsKey(d2))
+ cachedDisjoints.put(d2, map);
+
+ // add result symmetrically in the description matrix
+ cachedDisjoints.get(d1).put(d2, result);
+ cachedDisjoints.get(d2).put(d1, result);
+ return result;
+ } else
+ return tmp2;
+ }
+
+ private boolean isDisjointInstanceBased(Description d1, Description d2) {
+ Set<Individual> d1Instances = rs.retrieval(d1);
+ Set<Individual> d2Instances = rs.retrieval(d2);
+ for(Individual d1Instance : d1Instances) {
+ if(d2Instances.contains(d1Instance))
+ return false;
+ }
+ return true;
+ }
+
+ /*
// computes whether two classes are disjoint; this should be computed
// by the reasoner only ones and otherwise taken from a matrix
- // => this has low importance in the long run, because M is cached anyway,
- // but avoids many duplicate queries when computing M
private boolean isDisjoint(NamedClass a, Description d) {
// we need to test whether A AND B is equivalent to BOTTOM
Description d2 = new Intersection(a, d);
return rs.subsumes(new Nothing(), d2);
- }
+ }*/
// we need to test whether NOT A AND B is equivalent to BOTTOM
private boolean isNotADisjoint(NamedClass a, NamedClass b) {
- Map<NamedClass,Boolean> tmp = notABDisjoint.get(a);
- Boolean tmp2 = null;
- if(tmp != null)
- tmp2 = tmp.get(b);
-
- if(tmp2==null) {
+// Map<NamedClass,Boolean> tmp = notABDisjoint.get(a);
+// Boolean tmp2 = null;
+// if(tmp != null)
+// tmp2 = tmp.get(b);
+//
+// if(tmp2==null) {
Description notA = new Negation(a);
Description d = new Intersection(notA, b);
Boolean result = rs.subsumes(new Nothing(), d);
// ... add to cache ...
return result;
- } else
- return tmp2;
+// } else
+// return tmp2;
}
// we need to test whether NOT A AND B = B
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-09 19:26:51
|
Revision: 699
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=699&view=rev
Author: jenslehmann
Date: 2008-03-09 12:25:46 -0700 (Sun, 09 Mar 2008)
Log Message:
-----------
small algorithm bug fixes and reasoning improvements
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
trunk/src/dl-learner/org/dllearner/core/owl/BooleanValueRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypeValueRestriction.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java 2008-03-09 17:49:11 UTC (rev 698)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java 2008-03-09 19:25:46 UTC (rev 699)
@@ -47,8 +47,8 @@
private Set<Individual> coveredNegatives;
// the method by which quality was evaluated in this node
- public enum QualityEvaluationMethod { TOP, REASONER, TOO_WEAK_LIST, OVERLY_GENERAL_LIST };
- private QualityEvaluationMethod qualityEvaluationMethod = QualityEvaluationMethod.TOP;
+ public enum QualityEvaluationMethod { START, REASONER, TOO_WEAK_LIST, OVERLY_GENERAL_LIST };
+ private QualityEvaluationMethod qualityEvaluationMethod = QualityEvaluationMethod.START;
// all properties of a node in the search tree
private Description concept;
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-09 17:49:11 UTC (rev 698)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-09 19:25:46 UTC (rev 699)
@@ -599,6 +599,7 @@
// + nrOfNegativeExamples - bestNode.getCoveredNegatives().size())/(double)nrOfExamples);
// Refinementoperator auf Konzept anwenden
// String bestNodeString = "currently best node: " + bestNode + " accuracy: " + df.format(accuracy) + "%";
+ System.out.println("start node: " + startNode.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
String bestNodeString = "currently best node: " + bestNode.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI);
// searchTree += bestNodeString + "\n";
System.out.println(bestNodeString);
@@ -612,6 +613,7 @@
// System.out.println("max. number of children of a node: " + maxNrOfChildren);
System.out.println("subsumption time: " + Helper.prettyPrintNanoSeconds(rs.getSubsumptionReasoningTimeNs()));
System.out.println("instance check time: " + Helper.prettyPrintNanoSeconds(rs.getInstanceCheckReasoningTimeNs()));
+ System.out.println("retrieval time: " + Helper.prettyPrintNanoSeconds(rs.getRetrievalReasoningTimeNs()));
}
if(computeBenchmarkInformation) {
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-09 17:49:11 UTC (rev 698)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-09 19:25:46 UTC (rev 699)
@@ -19,6 +19,10 @@
*/
package org.dllearner.algorithms.refexamples;
+import java.util.List;
+
+import org.dllearner.core.owl.BooleanValueRestriction;
+import org.dllearner.core.owl.Description;
import org.dllearner.utilities.ConceptComparator;
/**
@@ -73,13 +77,14 @@
private double expansionPenaltyFactor;
private double gainBonusFactor;
private double nodeChildPenalty = 0.0001;
+ private double startNodeBonus = 0.8;
// examples
private int nrOfNegativeExamples;
private int nrOfExamples;
public MultiHeuristic(int nrOfPositiveExamples, int nrOfNegativeExamples) {
- this(nrOfPositiveExamples, nrOfNegativeExamples, 0.03, 0.5);
+ this(nrOfPositiveExamples, nrOfNegativeExamples, 0.02, 0.5);
}
public MultiHeuristic(int nrOfPositiveExamples, int nrOfNegativeExamples, double expansionPenaltyFactor, double gainBonusFactor) {
@@ -113,8 +118,11 @@
if(parent != null) {
double parentAccuracy = getAccuracy(parent.getCoveredPositives().size(),parent.getCoveredNegatives().size());
gain = accuracy - parentAccuracy;
+ } else {
+ accuracy += startNodeBonus;
}
- return accuracy + gainBonusFactor * gain - expansionPenaltyFactor * node.getHorizontalExpansion() - nodeChildPenalty * node.getChildren().size();
+ int he = node.getHorizontalExpansion() - getHeuristicLengthBonus(node.getConcept());
+ return accuracy + gainBonusFactor * gain - expansionPenaltyFactor * he - nodeChildPenalty * node.getChildren().size();
}
private double getAccuracy(int coveredPositives, int coveredNegatives) {
@@ -127,4 +135,18 @@
return multi.getNodeScore(node);
}
+ // this function can be used to give some constructs a length bonus
+ // compared to their syntactic length
+ private static int getHeuristicLengthBonus(Description description) {
+ int bonus = 0;
+
+ if(description instanceof BooleanValueRestriction)
+ bonus = 1;
+
+ List<Description> children = description.getChildren();
+ for(Description child : children) {
+ bonus += getHeuristicLengthBonus(child);
+ }
+ return bonus;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/BooleanValueRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/BooleanValueRestriction.java 2008-03-09 17:49:11 UTC (rev 698)
+++ trunk/src/dl-learner/org/dllearner/core/owl/BooleanValueRestriction.java 2008-03-09 19:25:46 UTC (rev 699)
@@ -50,5 +50,12 @@
public boolean getBooleanValue() {
return booleanValue;
}
-
+
+ /**
+ * Boolean value restrictions have length 2, because they encode two
+ * pieces of information: the property and the boolean value.
+ */
+ public int getLength() {
+ return 2;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypeValueRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypeValueRestriction.java 2008-03-09 17:49:11 UTC (rev 698)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypeValueRestriction.java 2008-03-09 19:25:46 UTC (rev 699)
@@ -29,7 +29,7 @@
* @author Jens Lehmann
*
*/
-public class DatatypeValueRestriction extends ValueRestriction {
+public abstract class DatatypeValueRestriction extends ValueRestriction {
public DatatypeValueRestriction(DatatypeProperty restrictedPropertyExpression, Constant value) {
super(restrictedPropertyExpression, value);
@@ -55,9 +55,12 @@
/* (non-Javadoc)
* @see org.dllearner.core.owl.KBElement#getLength()
*/
- public int getLength() {
- return 1 + restrictedPropertyExpression.getLength() + value.getLength();
- }
+ // we do not add the + 1 here because e.g. for boolean values we
+ // probably do not want to add it while for double value we may
+ // add it (because "<=" ">=" are possible while boolean has only "=")
+// public int getLength() {
+// return 1 + restrictedPropertyExpression.getLength() + value.getLength();
+// }
/* (non-Javadoc)
* @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-09 17:49:11 UTC (rev 698)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-09 19:25:46 UTC (rev 699)
@@ -659,6 +659,31 @@
return map;
}
+ public Map<Individual, SortedSet<Double>> getDoubleValues(DatatypeProperty datatypeProperty) {
+ OWLDataProperty prop = getOWLAPIDescription(datatypeProperty);
+ Map<Individual, SortedSet<Double>> map = new TreeMap<Individual, SortedSet<Double>>();
+ for(Individual i : individuals) {
+ OWLIndividual ind = factory.getOWLIndividual(URI.create(i.getName()));
+
+ // get all related individuals via OWL API
+ Set<OWLConstant> inds = null;
+ try {
+ inds = reasoner.getRelatedValues(ind, prop);
+ } catch (OWLReasonerException e) {
+ e.printStackTrace();
+ }
+
+ // convert data back to DL-Learner structures
+ SortedSet<Double> is = new TreeSet<Double>();
+ for(OWLConstant oi : inds) {
+ Double d = Double.parseDouble(oi.getLiteral());
+ is.add(d);
+ }
+ map.put(i, is);
+ }
+ return map;
+ }
+
@Override
public Map<Individual, SortedSet<Constant>> getDatatypeMembers(DatatypeProperty datatypeProperty) {
OWLDataProperty prop = getOWLAPIDescription(datatypeProperty);
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-09 17:49:11 UTC (rev 698)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-09 19:25:46 UTC (rev 699)
@@ -129,6 +129,7 @@
private boolean useExistsConstructor = true;
private boolean useNegation = true;
private boolean useBooleanDatatypes = true;
+ private boolean disjointChecks = true;
private boolean instanceBasedDisjoints = true;
// caches for reasoner queries
@@ -164,18 +165,38 @@
dpDomains.put(dp, rs.getDomain(dp));
}
-
-// NamedClass struc = new NamedClass("http://dl-learner.org/carcinogenesis#Structure");
+ /*
+ NamedClass struc = new NamedClass("http://dl-learner.org/carcinogenesis#Compound");
+ ObjectProperty op = new ObjectProperty("http://dl-learner.org/carcinogenesis#hasAtom");
+ ObjectAllRestriction oar = new ObjectAllRestriction(op,struc);
+ String str = "((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS FALSE) OR ALL \"http://dl-learner.org/carcinogenesis#hasAtom\".TOP)";
+ Description desc = null;
+ try {
+ desc = KBParser.parseConcept(str);
+ } catch (ParseException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+// System.out.println(oar.getLength());
// computeTopRefinements(3,struc);
// for(Description d : topARefinements.get(struc).get(1)) {
// bei 3 ist noch alles OK, bei 4 seltsamer Fehler mit Union
-// for(Description d : refine(Thing.instance,3,null,struc)) {
+ Set<Description> ds = refine(struc,10,null,struc);
+ Set<Description> improper = new HashSet<Description>();
+ for(Description d : ds) {
// if(d instanceof Union)
-// System.out.println(d);
-// }
+ if(rs.subsumes(d, struc)) {
+ improper.add(d);
+ System.out.println(d);
+ }
+ }
// System.out.println(refine(Thing.instance,7,null,struc).size());
-// System.exit(0);
+ System.out.println(ds.size());
+ System.out.println(improper.size());
+ System.exit(0);
+ */
+
if(startClass != null)
this.startClass = startClass;
}
@@ -199,15 +220,16 @@
public Set<Description> refine(Description description, int maxLength,
List<Description> knownRefinements, Description currDomain) {
-// System.out.println(description + " " + currDomain);
+// System.out.println(description + " " + currDomain + " " + maxLength);
// actions needing to be performed if this is the first time the
// current domain is used
if(!(currDomain instanceof Thing) && !topARefinementsLength.containsKey(currDomain))
topARefinementsLength.put((NamedClass)currDomain, 0);
- // TODO: check whether using list or set makes more sense
+ // check whether using list or set makes more sense
// here; and whether HashSet or TreeSet should be used
+ // => TreeSet because duplicates are possible
Set<Description> refinements = new TreeSet<Description>(conceptComparator);
// used as temporary variable
@@ -261,7 +283,8 @@
// (non-recursive variant because only depth 1 was modified)
ConceptTransformation.cleanConceptNonRecursive(mc);
ConceptTransformation.transformToOrderedNegationNormalFormNonRecursive(mc, conceptComparator);
-
+
+ refinements.add(mc);
}
}
@@ -270,6 +293,8 @@
// refine one of the elements
for(Description child : description.getChildren()) {
+// System.out.println("union child: " + child + " " + maxLength + " " + description.getLength() + " " + child.getLength());
+
// refine child
tmp = refine(child, maxLength - description.getLength()+child.getLength(),null,currDomain);
@@ -377,9 +402,10 @@
// this can avoid a lot of superfluous computation in the algorithm e.g.
// when A1 looks good, so many refinements of the form (A1 OR (A2 AND A3))
// are generated which are all equal to A1 due to disjointness of A2 and A3
- if(c instanceof NamedClass && isDisjoint(description, c))
- // refinements.add(mc);
+ if(disjointChecks && c instanceof NamedClass && description instanceof NamedClass && isDisjoint(description, c)) {
skip = true;
+// System.out.println(c + " ignored when refining " + description);
+ }
if(!skip) {
Intersection mc = new Intersection();
@@ -545,14 +571,23 @@
SortedSet<Description> m1 = rs.getMoreSpecialConcepts(new Thing());
m.put(1,m1);
+ SortedSet<Description> m2 = new TreeSet<Description>(conceptComparator);
if(useNegation) {
Set<Description> m2tmp = rs.getMoreGeneralConcepts(new Nothing());
- SortedSet<Description> m2 = new TreeSet<Description>(conceptComparator);
for(Description c : m2tmp) {
m2.add(new Negation(c));
}
- m.put(2,m2);
}
+
+ // boolean datatypes, e.g. testPositive = true
+ if(useBooleanDatatypes) {
+ Set<DatatypeProperty> booleanDPs = rs.getBooleanDatatypeProperties();
+ for(DatatypeProperty dp : booleanDPs) {
+ m2.add(new BooleanValueRestriction(dp,true));
+ m2.add(new BooleanValueRestriction(dp,false));
+ }
+ }
+ m.put(2,m2);
SortedSet<Description> m3 = new TreeSet<Description>(conceptComparator);
if(useExistsConstructor) {
@@ -571,15 +606,6 @@
}
}
- // boolean datatypes, e.g. testPositive = true
- if(useBooleanDatatypes) {
- Set<DatatypeProperty> booleanDPs = rs.getBooleanDatatypeProperties();
- for(DatatypeProperty dp : booleanDPs) {
- m3.add(new BooleanValueRestriction(dp,true));
- m3.add(new BooleanValueRestriction(dp,false));
- }
- }
-
m.put(3,m3);
mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
@@ -600,6 +626,7 @@
SortedSet<Description> m1 = rs.getMoreSpecialConcepts(nc);
mA.get(nc).put(1,m1);
+ SortedSet<Description> m2 = new TreeSet<Description>(conceptComparator);
if(useNegation) {
// the definition in the paper is more complex, but acutally
// we only have to insert the most specific concepts satisfying
@@ -608,7 +635,7 @@
// subClassOf A and thus: if A and B are disjoint then also A'
// and B; if not A AND B = B then also not A' AND B = B
SortedSet<Description> m2tmp = rs.getMoreGeneralConcepts(new Nothing());
- SortedSet<Description> m2 = new TreeSet<Description>(conceptComparator);
+
for(Description c : m2tmp) {
if(c instanceof Thing)
m2.add(c);
@@ -617,13 +644,23 @@
if(!isNotADisjoint(a, nc) && isNotAMeaningful(a, nc))
m2.add(new Negation(a));
}
+ }
+ }
+
+ // compute applicable properties
+ computeMg(nc);
+
+ // boolean datatypes, e.g. testPositive = true
+ if(useBooleanDatatypes) {
+ Set<DatatypeProperty> booleanDPs = mgbd.get(nc);
+ for(DatatypeProperty dp : booleanDPs) {
+ m2.add(new BooleanValueRestriction(dp,true));
+ m2.add(new BooleanValueRestriction(dp,false));
}
- mA.get(nc).put(2,m2);
}
+
+ mA.get(nc).put(2,m2);
- // compute applicable properties
- computeMg(nc);
-
SortedSet<Description> m3 = new TreeSet<Description>(conceptComparator);
if(useExistsConstructor) {
for(ObjectProperty r : mgr.get(nc)) {
@@ -640,15 +677,6 @@
}
}
- // boolean datatypes, e.g. testPositive = true
- if(useBooleanDatatypes) {
- Set<DatatypeProperty> booleanDPs = mgbd.get(nc);
- for(DatatypeProperty dp : booleanDPs) {
- m3.add(new BooleanValueRestriction(dp,true));
- m3.add(new BooleanValueRestriction(dp,false));
- }
- }
-
mA.get(nc).put(3,m3);
mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-10 17:54:15
|
Revision: 700
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=700&view=rev
Author: jenslehmann
Date: 2008-03-10 10:53:52 -0700 (Mon, 10 Mar 2008)
Log Message:
-----------
double datatype learning support
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
trunk/src/dl-learner/org/dllearner/core/Reasoner.java
trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypeSomeRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/DoubleMaxValue.java
trunk/src/dl-learner/org/dllearner/core/owl/DoubleMinValue.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
trunk/src/dl-learner/org/dllearner/utilities/ConceptComparator.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/core/owl/SimpleDoubleDataRange.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -100,6 +100,12 @@
private boolean useOverlyGeneralList = true;
private boolean useShortConceptConstruction = true;
+ // if set to false we do not test properness; this may seem wrong
+ // but the disadvantage of properness testing are additional reasoner
+ // queries and a search bias towards ALL r.something because
+ // ALL r.TOP is improper and automatically expanded further
+ private boolean testProperness = false;
+
// setting to true gracefully stops the algorithm
private boolean stop = false;
@@ -431,11 +437,13 @@
Set<Description> improperConcepts = null;
if(toEvaluateConcepts.size()>0) {
// Test aller Konzepte auf properness (mit DIG in nur einer Anfrage)
- long propCalcReasoningStart = System.nanoTime();
- improperConcepts = rs.subsumes(toEvaluateConcepts, concept);
- propernessTestsReasoner+=toEvaluateConcepts.size();
- // boolean isProper = !learningProblem.getReasoningService().subsumes(refinement, concept);
- propernessCalcReasoningTimeNs += System.nanoTime() - propCalcReasoningStart;
+ if(testProperness) {
+ long propCalcReasoningStart = System.nanoTime();
+ improperConcepts = rs.subsumes(toEvaluateConcepts, concept);
+ propernessTestsReasoner+=toEvaluateConcepts.size();
+ // boolean isProper = !learningProblem.getReasoningService().subsumes(refinement, concept);
+ propernessCalcReasoningTimeNs += System.nanoTime() - propCalcReasoningStart;
+ }
}
long improperConceptsRemovalTimeNsStart = System.nanoTime();
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -77,7 +77,7 @@
private double expansionPenaltyFactor;
private double gainBonusFactor;
private double nodeChildPenalty = 0.0001;
- private double startNodeBonus = 0.8;
+ private double startNodeBonus = 0.1;
// examples
private int nrOfNegativeExamples;
Modified: trunk/src/dl-learner/org/dllearner/core/Reasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/Reasoner.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/core/Reasoner.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -79,6 +79,12 @@
public Map<Individual, SortedSet<Constant>> getDatatypeMembers(DatatypeProperty datatypeProperty) throws ReasoningMethodUnsupportedException;
+ // some convenience methods
+ public Map<Individual, SortedSet<Double>> getDoubleDatatypeMembers(DatatypeProperty datatypeProperty) throws ReasoningMethodUnsupportedException;
+ public Map<Individual, SortedSet<Boolean>> getBooleanDatatypeMembers(DatatypeProperty datatypeProperty) throws ReasoningMethodUnsupportedException;
+ public SortedSet<Individual> getTrueDatatypeMembers(DatatypeProperty datatypeProperty) throws ReasoningMethodUnsupportedException;
+ public SortedSet<Individual> getFalseDatatypeMembers(DatatypeProperty datatypeProperty) throws ReasoningMethodUnsupportedException;
+
public boolean instanceCheck(Description concept, Individual individual) throws ReasoningMethodUnsupportedException;
// mehrere instance checks für ein Konzept - spart bei DIG Anfragen
Modified: trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -459,6 +459,42 @@
return result;
}
+ public Map<Individual, SortedSet<Double>> getDoubleDatatypeMembers(DatatypeProperty datatypeProperty) {
+ try {
+ return reasoner.getDoubleDatatypeMembers(datatypeProperty);
+ } catch (ReasoningMethodUnsupportedException e) {
+ handleExceptions(e);
+ return null;
+ }
+ }
+
+ public Map<Individual, SortedSet<Double>> getIntDatatypeMembers(DatatypeProperty datatypeProperty) {
+ try {
+ return reasoner.getDoubleDatatypeMembers(datatypeProperty);
+ } catch (ReasoningMethodUnsupportedException e) {
+ handleExceptions(e);
+ return null;
+ }
+ }
+
+ public Map<Individual, SortedSet<Double>> getTrueDatatypeMembers(DatatypeProperty datatypeProperty) {
+ try {
+ return reasoner.getDoubleDatatypeMembers(datatypeProperty);
+ } catch (ReasoningMethodUnsupportedException e) {
+ handleExceptions(e);
+ return null;
+ }
+ }
+
+ public Map<Individual, SortedSet<Double>> getFalseDatatypeMembers(DatatypeProperty datatypeProperty) {
+ try {
+ return reasoner.getDoubleDatatypeMembers(datatypeProperty);
+ } catch (ReasoningMethodUnsupportedException e) {
+ handleExceptions(e);
+ return null;
+ }
+ }
+
public Set<NamedClass> getAtomicConcepts() {
return reasoner.getAtomicConcepts();
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypeSomeRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypeSomeRestriction.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypeSomeRestriction.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -32,11 +32,14 @@
*/
public class DatatypeSomeRestriction extends DatatypeQuantorRestriction {
+ DataRange dataRange;
+
/**
* @param datatypeProperty
*/
- public DatatypeSomeRestriction(DatatypeProperty datatypeProperty) {
+ public DatatypeSomeRestriction(DatatypeProperty datatypeProperty, DataRange dataRange) {
super(datatypeProperty);
+ this.dataRange = dataRange;
}
/* (non-Javadoc)
@@ -44,7 +47,6 @@
*/
@Override
public int getArity() {
- // TODO Auto-generated method stub
return 0;
}
@@ -52,16 +54,14 @@
* @see org.dllearner.core.owl.KBElement#getLength()
*/
public int getLength() {
- // TODO Auto-generated method stub
- return 0;
+ return 1 + dataRange.getLength();
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
*/
public String toString(String baseURI, Map<String, String> prefixes) {
- // TODO Auto-generated method stub
- return null;
+ return restrictedPropertyExpression.toString(baseURI, prefixes) + dataRange.toString(baseURI, prefixes);
}
/* (non-Javadoc)
@@ -83,5 +83,12 @@
public String toManchesterSyntaxString(String baseURI, Map<String,String> prefixes) {
// TODO Auto-generated method stub
return null;
+ }
+
+ /**
+ * @return the dataRange
+ */
+ public DataRange getDataRange() {
+ return dataRange;
}
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DoubleMaxValue.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DoubleMaxValue.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DoubleMaxValue.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -28,7 +28,7 @@
* @author Jens Lehmann
*
*/
-public class DoubleMaxValue implements DoubleDataRange {
+public class DoubleMaxValue implements SimpleDoubleDataRange {
private double value;
@@ -54,8 +54,7 @@
* @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
*/
public String toString(String baseURI, Map<String, String> prefixes) {
- // TODO Auto-generated method stub
- return null;
+ return " <= " + value;
}
public void accept(KBElementVisitor visitor) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DoubleMinValue.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DoubleMinValue.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DoubleMinValue.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -22,13 +22,13 @@
import java.util.Map;
/**
- * Double data range restricted by a maximum value, e.g.
+ * Double data range restricted by a minimum value, e.g.
* hasAge >= 18.
*
* @author Jens Lehmann
*
*/
-public class DoubleMinValue implements DoubleDataRange {
+public class DoubleMinValue implements SimpleDoubleDataRange {
private double value;
@@ -54,8 +54,7 @@
* @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
*/
public String toString(String baseURI, Map<String, String> prefixes) {
- // TODO Auto-generated method stub
- return null;
+ return " >= " + value;
}
public void accept(KBElementVisitor visitor) {
Added: trunk/src/dl-learner/org/dllearner/core/owl/SimpleDoubleDataRange.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/SimpleDoubleDataRange.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/core/owl/SimpleDoubleDataRange.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -0,0 +1,33 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.core.owl;
+
+/**
+ * A double data range with a single value used for restrictions,
+ * e.g. hasAge >= 18 (but not 65 >= hasAge >= 18).
+ *
+ * @author Jens Lehmann
+ *
+ */
+public interface SimpleDoubleDataRange extends DoubleDataRange {
+
+ public double getValue();
+
+}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -37,9 +37,13 @@
import org.dllearner.core.config.ConfigEntry;
import org.dllearner.core.config.InvalidConfigOptionValueException;
import org.dllearner.core.owl.BooleanValueRestriction;
+import org.dllearner.core.owl.DataRange;
import org.dllearner.core.owl.DatatypeProperty;
import org.dllearner.core.owl.DatatypePropertyHierarchy;
+import org.dllearner.core.owl.DatatypeSomeRestriction;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.DoubleMaxValue;
+import org.dllearner.core.owl.DoubleMinValue;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.NamedClass;
@@ -206,6 +210,9 @@
@Override
public boolean instanceCheck(Description description, Individual individual)
throws ReasoningMethodUnsupportedException {
+
+// System.out.println(description + " " + individual);
+
if (description instanceof NamedClass) {
return classInstancesPos.get((NamedClass) description).contains(individual);
} else if (description instanceof Negation) {
@@ -294,6 +301,28 @@
} else {
return bdNeg.get(dp).contains(individual);
}
+ } else if (description instanceof DatatypeSomeRestriction) {
+ DatatypeSomeRestriction dsr = (DatatypeSomeRestriction) description;
+ DatatypeProperty dp = (DatatypeProperty) dsr.getRestrictedPropertyExpression();
+ DataRange dr = dsr.getDataRange();
+ SortedSet<Double> values = dd.get(dp).get(individual);
+
+ // if there is no filler for this individual and property we
+ // need to return false
+ if(values == null)
+ return false;
+
+ if(dr instanceof DoubleMaxValue) {
+ if(values.first() <= ((DoubleMaxValue)dr).getValue())
+ return true;
+ else
+ return false;
+ } else if(dr instanceof DoubleMinValue) {
+ if(values.last() >= ((DoubleMinValue)dr).getValue())
+ return true;
+ else
+ return false;
+ }
}
throw new ReasoningMethodUnsupportedException("Instance check for description "
@@ -325,6 +354,11 @@
return atomicConcepts;
}
+ @Override
+ public Map<Individual, SortedSet<Double>> getDoubleDatatypeMembers(DatatypeProperty datatypeProperty) throws ReasoningMethodUnsupportedException {
+ return rc.getDoubleDatatypeMembers(datatypeProperty);
+ }
+
/*
* (non-Javadoc)
*
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIDescriptionConvertVisitor.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIDescriptionConvertVisitor.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -35,6 +35,7 @@
import org.dllearner.core.owl.DatatypeValueRestriction;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.DescriptionVisitor;
+import org.dllearner.core.owl.DoubleMinValue;
import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Negation;
@@ -45,6 +46,7 @@
import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
import org.dllearner.core.owl.ObjectSomeRestriction;
import org.dllearner.core.owl.ObjectValueRestriction;
+import org.dllearner.core.owl.SimpleDoubleDataRange;
import org.dllearner.core.owl.Thing;
import org.dllearner.core.owl.TypedConstant;
import org.dllearner.core.owl.Union;
@@ -55,9 +57,13 @@
import org.semanticweb.owl.model.OWLConstant;
import org.semanticweb.owl.model.OWLDataFactory;
import org.semanticweb.owl.model.OWLDataProperty;
+import org.semanticweb.owl.model.OWLDataRange;
import org.semanticweb.owl.model.OWLDataType;
import org.semanticweb.owl.model.OWLDescription;
import org.semanticweb.owl.model.OWLObjectProperty;
+import org.semanticweb.owl.model.OWLTypedConstant;
+import org.semanticweb.owl.vocab.OWLRestrictedDataRangeFacetVocabulary;
+import org.semanticweb.owl.vocab.XSDVocabulary;
/**
* Converter from DL-Learner descriptions to OWL API descriptions based
@@ -212,7 +218,8 @@
public void visit(DatatypeValueRestriction description) {
// convert OWL constant to OWL API constant
Constant c = description.getValue();
- OWLConstant constant;
+ OWLConstant constant = convertConstant(c);
+ /*
if(c instanceof TypedConstant) {
Datatype dt = ((TypedConstant)c).getDatatype();
OWLDataType odt = convertDatatype(dt);
@@ -225,6 +232,7 @@
constant = factory.getOWLUntypedConstant(uc.getLiteral());
}
}
+ */
// get datatype property
DatatypeProperty dtp = description.getRestrictedPropertyExpresssion();
@@ -276,8 +284,28 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeSomeRestriction)
*/
public void visit(DatatypeSomeRestriction description) {
- // TODO Auto-generated method stub
- throw new Error("OWLAPIDescriptionConverter: not implemented");
+
+ // TODO: currently works only for double min/max
+
+ DatatypeProperty dp = (DatatypeProperty) description.getRestrictedPropertyExpression();
+ // currently only double restrictions implemented
+ SimpleDoubleDataRange dr = (SimpleDoubleDataRange) description.getDataRange();
+ Double value = dr.getValue();
+
+ OWLDataType doubleDataType = factory.getOWLDataType(XSDVocabulary.DOUBLE.getURI());
+ OWLTypedConstant constant = factory.getOWLTypedConstant(value.toString(), doubleDataType);
+
+ OWLRestrictedDataRangeFacetVocabulary facet;
+ if(dr instanceof DoubleMinValue)
+ facet = OWLRestrictedDataRangeFacetVocabulary.MIN_INCLUSIVE;
+ else
+ facet = OWLRestrictedDataRangeFacetVocabulary.MAX_INCLUSIVE;
+
+ OWLDataRange owlDataRange = factory.getOWLDataRangeRestriction(doubleDataType, facet, constant);
+ OWLDataProperty odp = factory.getOWLDataProperty(URI.create(dp.getName()));
+ OWLDescription d = factory.getOWLDataSomeRestriction(odp, owlDataRange);
+
+ stack.push(d);
}
public OWLDataType convertDatatype(Datatype datatype) {
@@ -291,4 +319,20 @@
throw new Error("OWLAPIDescriptionConverter: datatype not implemented");
}
+ private OWLConstant convertConstant(Constant constant) {
+ OWLConstant owlConstant;
+ if(constant instanceof TypedConstant) {
+ Datatype dt = ((TypedConstant)constant).getDatatype();
+ OWLDataType odt = convertDatatype(dt);
+ owlConstant = factory.getOWLTypedConstant(constant.getLiteral(), odt);
+ } else {
+ UntypedConstant uc = (UntypedConstant) constant;
+ if(uc.hasLang()) {
+ owlConstant = factory.getOWLUntypedConstant(uc.getLiteral(), uc.getLang());
+ } else {
+ owlConstant = factory.getOWLUntypedConstant(uc.getLiteral());
+ }
+ }
+ return owlConstant;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -19,6 +19,7 @@
*/
package org.dllearner.refinementoperators;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
@@ -29,12 +30,17 @@
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
+import java.util.Map.Entry;
import org.dllearner.algorithms.refinement.RefinementOperator;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.BooleanValueRestriction;
+import org.dllearner.core.owl.DataRange;
import org.dllearner.core.owl.DatatypeProperty;
+import org.dllearner.core.owl.DatatypeSomeRestriction;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.DoubleMaxValue;
+import org.dllearner.core.owl.DoubleMinValue;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.NamedClass;
@@ -119,7 +125,11 @@
// concept comparator
private ConceptComparator conceptComparator = new ConceptComparator();
- // Statistik
+ // splits for double datatype properties in ascening order
+ private Map<DatatypeProperty,List<Double>> splits = new TreeMap<DatatypeProperty,List<Double>>();
+ private int maxNrOfSplits = 20;
+
+ // staistics
public long mComputationTimeNs = 0;
public long topComputationTimeNs = 0;
@@ -129,6 +139,7 @@
private boolean useExistsConstructor = true;
private boolean useNegation = true;
private boolean useBooleanDatatypes = true;
+ private boolean useDoubleDatatypes = true;
private boolean disjointChecks = true;
private boolean instanceBasedDisjoints = true;
@@ -165,38 +176,29 @@
dpDomains.put(dp, rs.getDomain(dp));
}
+ // compute splits for double datatype properties
+ for(DatatypeProperty dp : rs.getDoubleDatatypeProperties()) {
+ computeSplits(dp);
+ }
+
/*
- NamedClass struc = new NamedClass("http://dl-learner.org/carcinogenesis#Compound");
+ NamedClass struc = new NamedClass("http://dl-learner.org/carcinogenesis#Atom");
ObjectProperty op = new ObjectProperty("http://dl-learner.org/carcinogenesis#hasAtom");
- ObjectAllRestriction oar = new ObjectAllRestriction(op,struc);
- String str = "((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS FALSE) OR ALL \"http://dl-learner.org/carcinogenesis#hasAtom\".TOP)";
- Description desc = null;
- try {
- desc = KBParser.parseConcept(str);
- } catch (ParseException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-// System.out.println(oar.getLength());
-// computeTopRefinements(3,struc);
-// for(Description d : topARefinements.get(struc).get(1)) {
- // bei 3 ist noch alles OK, bei 4 seltsamer Fehler mit Union
- Set<Description> ds = refine(struc,10,null,struc);
- Set<Description> improper = new HashSet<Description>();
+ ObjectSomeRestriction oar = new ObjectSomeRestriction(op,Thing.instance);
+
+ Set<Description> ds = refine(Thing.instance,3,null,struc);
+// Set<Description> improper = new HashSet<Description>();
for(Description d : ds) {
-// if(d instanceof Union)
- if(rs.subsumes(d, struc)) {
- improper.add(d);
+// if(rs.subsumes(d, struc)) {
+// improper.add(d);
System.out.println(d);
- }
+// }
}
-// System.out.println(refine(Thing.instance,7,null,struc).size());
System.out.println(ds.size());
- System.out.println(improper.size());
+// System.out.println(improper.size());
System.exit(0);
*/
-
-
+
if(startClass != null)
this.startClass = startClass;
}
@@ -356,6 +358,36 @@
refinements.add(new ObjectAllRestriction(moreSpecialRole, description.getChild(0)));
}
+ } else if (description instanceof DatatypeSomeRestriction) {
+ DatatypeSomeRestriction dsr = (DatatypeSomeRestriction) description;
+ DatatypeProperty dp = (DatatypeProperty) dsr.getRestrictedPropertyExpression();
+ DataRange dr = dsr.getDataRange();
+ if(dr instanceof DoubleMaxValue) {
+ double value = ((DoubleMaxValue)dr).getValue();
+ // find out which split value was used
+ int splitIndex = splits.get(dp).lastIndexOf(value);
+ if(splitIndex == -1)
+ throw new Error("split error");
+ int newSplitIndex = splitIndex - 1;
+ if(newSplitIndex >= 0) {
+ DoubleMaxValue max = new DoubleMaxValue(splits.get(dp).get(newSplitIndex));
+ DatatypeSomeRestriction newDSR = new DatatypeSomeRestriction(dp,max);
+ refinements.add(newDSR);
+// System.out.println(description + " => " + newDSR);
+ }
+ } else if(dr instanceof DoubleMinValue) {
+ double value = ((DoubleMinValue)dr).getValue();
+ // find out which split value was used
+ int splitIndex = splits.get(dp).lastIndexOf(value);
+ if(splitIndex == -1)
+ throw new Error("split error");
+ int newSplitIndex = splitIndex + 1;
+ if(newSplitIndex < splits.get(dp).size()) {
+ DoubleMinValue min = new DoubleMinValue(splits.get(dp).get(newSplitIndex));
+ DatatypeSomeRestriction newDSR = new DatatypeSomeRestriction(dp,min);
+ refinements.add(newDSR);
+ }
+ }
}
// if a refinement is not Bottom, Top, ALL r.Bottom a refinement of top can be appended
@@ -606,6 +638,16 @@
}
}
+ if(useDoubleDatatypes) {
+ Set<DatatypeProperty> doubleDPs = rs.getDoubleDatatypeProperties();
+ for(DatatypeProperty dp : doubleDPs) {
+ DoubleMaxValue max = new DoubleMaxValue(splits.get(dp).get(splits.get(dp).size()-1));
+ DoubleMinValue min = new DoubleMinValue(splits.get(dp).get(0));
+ m3.add(new DatatypeSomeRestriction(dp,max));
+ m3.add(new DatatypeSomeRestriction(dp,min));
+ }
+ }
+
m.put(3,m3);
mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
@@ -677,6 +719,24 @@
}
}
+ if(useDoubleDatatypes) {
+ Set<DatatypeProperty> doubleDPs = mgdd.get(nc);
+// System.out.println("cached disjoints " + cachedDisjoints);
+// System.out.println("appOP " + appOP);
+// System.out.println("appBD " + appBD);
+// System.out.println("appDD " + appDD);
+// System.out.println("mgr " + mgr);
+// System.out.println("mgbd " + mgbd);
+// System.out.println("mgdd " + mgdd);
+
+ for(DatatypeProperty dp : doubleDPs) {
+ DoubleMaxValue max = new DoubleMaxValue(splits.get(dp).get(splits.get(dp).size()-1));
+ DoubleMinValue min = new DoubleMinValue(splits.get(dp).get(0));
+ m3.add(new DatatypeSomeRestriction(dp,max));
+ m3.add(new DatatypeSomeRestriction(dp,min));
+ }
+ }
+
mA.get(nc).put(3,m3);
mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
@@ -755,10 +815,11 @@
appBD.put(domain, applicableBDPs);
// double datatype properties
- Set<DatatypeProperty> mostGeneralDDPs = rs.getBooleanDatatypeProperties();
+ Set<DatatypeProperty> mostGeneralDDPs = rs.getDoubleDatatypeProperties();
Set<DatatypeProperty> applicableDDPs = new TreeSet<DatatypeProperty>();
for(DatatypeProperty role : mostGeneralDDPs) {
Description d = (NamedClass) rs.getDomain(role);
+// System.out.println("domain: " + d);
if(!isDisjoint(domain,d))
applicableDDPs.add(role);
}
@@ -788,16 +849,18 @@
}
private boolean isDisjoint(Description d1, Description d2) {
- // equal concepts are not disjoint (unless equivalent to bottom)
-// if(conceptComparator.compare(d1, d2)==0)
-// return false;
+// System.out.println("| " + d1 + " " + d2);
+// System.out.println("| " + cachedDisjoints);
+
// check whether we have cached this query
Map<Description,Boolean> tmp = cachedDisjoints.get(d1);
Boolean tmp2 = null;
if(tmp != null)
tmp2 = tmp.get(d2);
+// System.out.println("| " + tmp + " " + tmp2);
+
if(tmp2==null) {
Boolean result;
if(instanceBasedDisjoints) {
@@ -809,24 +872,33 @@
// add the result to the cache (we add it twice such that
// the order of access does not matter)
+// System.out.println("| result: " + result);
+
// create new entries if necessary
- Map<Description,Boolean> map = new TreeMap<Description,Boolean>(conceptComparator);
+ Map<Description,Boolean> map1 = new TreeMap<Description,Boolean>(conceptComparator);
+ Map<Description,Boolean> map2 = new TreeMap<Description,Boolean>(conceptComparator);
if(tmp == null)
- cachedDisjoints.put(d1, map);
+ cachedDisjoints.put(d1, map1);
if(!cachedDisjoints.containsKey(d2))
- cachedDisjoints.put(d2, map);
+ cachedDisjoints.put(d2, map2);
// add result symmetrically in the description matrix
cachedDisjoints.get(d1).put(d2, result);
cachedDisjoints.get(d2).put(d1, result);
+// System.out.println("---");
return result;
- } else
+ } else {
+// System.out.println("===");
return tmp2;
+ }
}
private boolean isDisjointInstanceBased(Description d1, Description d2) {
- Set<Individual> d1Instances = rs.retrieval(d1);
- Set<Individual> d2Instances = rs.retrieval(d2);
+ SortedSet<Individual> d1Instances = rs.retrieval(d1);
+ SortedSet<Individual> d2Instances = rs.retrieval(d2);
+// System.out.println(d1 + " " + d2);
+// System.out.println(d1 + " " + d1Instances);
+// System.out.println(d2 + " " + d2Instances);
for(Individual d1Instance : d1Instances) {
if(d2Instances.contains(d1Instance))
return false;
@@ -870,4 +942,34 @@
return !rs.subsumes(d, b);
}
+ private void computeSplits(DatatypeProperty dp) {
+ Set<Double> valuesSet = new TreeSet<Double>();
+// Set<Individual> individuals = rs.getIndividuals();
+ Map<Individual,SortedSet<Double>> valueMap = rs.getDoubleDatatypeMembers(dp);
+ // add all values to the set (duplicates will be remove automatically)
+ for(Entry<Individual,SortedSet<Double>> e : valueMap.entrySet())
+ valuesSet.addAll(e.getValue());
+ // convert set to a list where values are sorted
+ List<Double> values = new LinkedList<Double>(valuesSet);
+ Collections.sort(values);
+
+ int nrOfValues = values.size();
+ // create split set
+ List<Double> splitsDP = new LinkedList<Double>();
+ for(int splitNr=0; splitNr < maxNrOfSplits; splitNr++) {
+ int index;
+ if(nrOfValues<=maxNrOfSplits)
+ index = splitNr;
+ else
+ index = (int) Math.floor(splitNr * (double)nrOfValues/(maxNrOfSplits+1));
+
+ double value = 0.5*(values.get(index)+values.get(index+1));
+ splitsDP.add(value);
+ }
+ splits.put(dp, splitsDP);
+
+// System.out.println(values);
+// System.out.println(splits);
+// System.exit(0);
+ }
}
\ No newline at end of file
Modified: trunk/src/dl-learner/org/dllearner/utilities/ConceptComparator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/ConceptComparator.java 2008-03-09 19:25:46 UTC (rev 699)
+++ trunk/src/dl-learner/org/dllearner/utilities/ConceptComparator.java 2008-03-10 17:53:52 UTC (rev 700)
@@ -4,12 +4,17 @@
import java.util.Set;
import org.dllearner.core.owl.BooleanValueRestriction;
+import org.dllearner.core.owl.DatatypeProperty;
+import org.dllearner.core.owl.DatatypeSomeRestriction;
+import org.dllearner.core.owl.DoubleMaxValue;
+import org.dllearner.core.owl.DoubleMinValue;
import org.dllearner.core.owl.ObjectAllRestriction;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Nothing;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.ObjectSomeRestriction;
import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.SimpleDoubleDataRange;
import org.dllearner.core.owl.Union;
import org.dllearner.core.owl.Negation;
import org.dllearner.core.owl.ObjectQuantorRestriction;
@@ -94,8 +99,44 @@
return cmp;
} else
return -1;
+ } else if(concept1 instanceof DatatypeSomeRestriction) {
+ if(concept2 instanceof Nothing || concept2 instanceof NamedClass || concept2 instanceof BooleanValueRestriction) {
+ return 1;
+ } else if(concept2 instanceof DatatypeSomeRestriction) {
+ DatatypeSomeRestriction dsr = (DatatypeSomeRestriction) concept1;
+ DatatypeProperty dp = (DatatypeProperty) dsr.getRestrictedPropertyExpression();
+ DatatypeSomeRestriction dsr2 = (DatatypeSomeRestriction) concept2;
+ DatatypeProperty dp2 = (DatatypeProperty) dsr2.getRestrictedPropertyExpression();
+
+ // first criterion: name of the properties
+ int cmp = rc.compare(dp, dp2);
+
+ if(cmp == 0) {
+ SimpleDoubleDataRange dr = (SimpleDoubleDataRange) dsr.getDataRange();
+ SimpleDoubleDataRange dr2 = (SimpleDoubleDataRange) dsr2.getDataRange();
+
+ // equal classes
+ if((dr instanceof DoubleMaxValue && dr2 instanceof DoubleMaxValue)
+ || (dr instanceof DoubleMinValue && dr2 instanceof DoubleMinValue)) {
+ double val1 = dr.getValue();
+ double val2 = dr2.getValue();
+ if(val1 > val2)
+ return 1;
+ else if(val1 == val2)
+ return 0;
+ else
+ return -1;
+
+ } else if(dr instanceof DoubleMaxValue)
+ return 1;
+ else
+ return -1;
+ } else
+ return cmp;
+ } else
+ return -1;
} else if(concept1 instanceof Thing) {
- if(concept2 instanceof Nothing || concept2 instanceof NamedClass || concept2 instanceof BooleanValueRestriction)
+ if(concept2 instanceof Nothing || concept2 instanceof NamedClass || concept2 instanceof BooleanValueRestriction || concept2 instanceof DatatypeSomeRestriction)
return 1;
else if(concept2 instanceof Thing)
return 0;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ton...@us...> - 2008-03-12 01:48:15
|
Revision: 702
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=702&view=rev
Author: tonytacker
Date: 2008-03-11 18:48:07 -0700 (Tue, 11 Mar 2008)
Log Message:
-----------
We can now start to show a search tree. It was not possible, without some changes.
- add abstract class getStartNode() to LearningAlgorithm.java
- implement this method in all classes which are using it
ATTENTION: I had to change getStartNode() in ROLearner.java, hope it will not produce errors.
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java
trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/gui/TreeWindow.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java 2008-03-11 17:55:22 UTC (rev 701)
+++ trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java 2008-03-12 01:48:07 UTC (rev 702)
@@ -26,6 +26,7 @@
import java.util.List;
import java.util.Map;
+import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -286,4 +287,8 @@
stop = true;
}
+ @Override
+ public ExampleBasedNode getStartNode() {
+ return null;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java 2008-03-11 17:55:22 UTC (rev 701)
+++ trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java 2008-03-12 01:48:07 UTC (rev 702)
@@ -25,6 +25,7 @@
import org.apache.log4j.Logger;
import org.dllearner.algorithms.gp.Program;
import org.dllearner.algorithms.gp.GPUtilities;
+import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -127,5 +128,9 @@
}
+ @Override
+ public ExampleBasedNode getStartNode() {
+ return null;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-03-11 17:55:22 UTC (rev 701)
+++ trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-03-12 01:48:07 UTC (rev 702)
@@ -30,6 +30,7 @@
import java.util.Map.Entry;
import org.dllearner.algorithms.hybridgp.Psi;
+import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -1003,4 +1004,9 @@
//public void setAlgorithmType(AlgorithmType algorithmType) {
// this.algorithmType = algorithmType;
//}
+
+ @Override
+ public ExampleBasedNode getStartNode() {
+ return null;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-03-11 17:55:22 UTC (rev 701)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-03-12 01:48:07 UTC (rev 702)
@@ -349,6 +349,7 @@
algorithm.stop();
}
+ @Override
public ExampleBasedNode getStartNode() {
return algorithm.getStartNode();
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-03-11 17:55:22 UTC (rev 701)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-03-12 01:48:07 UTC (rev 702)
@@ -12,6 +12,7 @@
import java.util.TreeSet;
import org.apache.log4j.Logger;
+import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -1003,8 +1004,12 @@
/**
* @return the startNode
*/
- public Node getStartNode() {
+ public Node getStartNode_original() {
return startNode;
}
+ @Override
+ public ExampleBasedNode getStartNode() {
+ return null;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-03-11 17:55:22 UTC (rev 701)
+++ trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-03-12 01:48:07 UTC (rev 702)
@@ -23,6 +23,7 @@
import java.util.LinkedList;
import java.util.List;
+import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.owl.Description;
/**
@@ -70,4 +71,9 @@
return new LinkedList<Class<? extends LearningProblem>>();
}
+ /**
+ * Root for search tree.
+ * @return
+ */
+ public abstract ExampleBasedNode getStartNode();
}
Modified: trunk/src/dl-learner/org/dllearner/gui/TreeWindow.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/gui/TreeWindow.java 2008-03-11 17:55:22 UTC (rev 701)
+++ trunk/src/dl-learner/org/dllearner/gui/TreeWindow.java 2008-03-12 01:48:07 UTC (rev 702)
@@ -22,6 +22,7 @@
import javax.swing.*;
import javax.swing.tree.*;
+import org.dllearner.algorithms.refexamples.*;
/**
* TreeWindow
@@ -45,21 +46,29 @@
// set icon
setIconImage(java.awt.Toolkit.getDefaultToolkit().getImage(
this.getClass().getResource("icon.gif")));
-
+
// tree
- DefaultMutableTreeNode root = new DefaultMutableTreeNode( "root" );
- for ( int knot = 0; knot < 4; knot++ )
- {
- DefaultMutableTreeNode node = new DefaultMutableTreeNode( "knot " + knot );
- root.add( node );
- for ( int leaf = 1; leaf < 4; leaf++ )
- node.add( new DefaultMutableTreeNode("leaf " + (knot*3+leaf )) );
- }
- JTree tree = new JTree( root );
- this.add( new JScrollPane( tree ) );
+ DefaultMutableTreeNode exampleRoot = new DefaultMutableTreeNode("root");
+ for (int knot = 0; knot < 4; knot++) {
+ DefaultMutableTreeNode node = new DefaultMutableTreeNode("knot " + knot);
+ exampleRoot.add(node);
+ for (int leaf = 1; leaf < 4; leaf++)
+ node.add(new DefaultMutableTreeNode("leaf " + (knot * 3 + leaf)));
+ }
+ ExampleBasedNode rootNode = config.getLearningAlgorithm().getStartNode();
+ EBNodeTreeModel root = new EBNodeTreeModel(rootNode);
+
+ // show tree
+ if (root != null) {
+ JTree tree = new JTree(root);
+ this.add(new JScrollPane(tree));
+ }
+ else {
+ JTree tree = new JTree(exampleRoot);
+ this.add(new JScrollPane(tree));
+ }
this.setVisible(true);
}
-
-
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ton...@us...> - 2008-03-12 16:22:27
|
Revision: 704
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=704&view=rev
Author: tonytacker
Date: 2008-03-12 09:22:24 -0700 (Wed, 12 Mar 2008)
Log Message:
-----------
removed changes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java
trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/gui/TreeWindow.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java 2008-03-12 02:45:28 UTC (rev 703)
+++ trunk/src/dl-learner/org/dllearner/algorithms/BruteForceLearner.java 2008-03-12 16:22:24 UTC (rev 704)
@@ -26,7 +26,6 @@
import java.util.List;
import java.util.Map;
-import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -287,8 +286,4 @@
stop = true;
}
- @Override
- public ExampleBasedNode getStartNode() {
- return null;
- }
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java 2008-03-12 02:45:28 UTC (rev 703)
+++ trunk/src/dl-learner/org/dllearner/algorithms/RandomGuesser.java 2008-03-12 16:22:24 UTC (rev 704)
@@ -25,7 +25,6 @@
import org.apache.log4j.Logger;
import org.dllearner.algorithms.gp.Program;
import org.dllearner.algorithms.gp.GPUtilities;
-import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -128,9 +127,4 @@
}
- @Override
- public ExampleBasedNode getStartNode() {
- return null;
- }
-
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-03-12 02:45:28 UTC (rev 703)
+++ trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-03-12 16:22:24 UTC (rev 704)
@@ -30,7 +30,6 @@
import java.util.Map.Entry;
import org.dllearner.algorithms.hybridgp.Psi;
-import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -1005,8 +1004,4 @@
// this.algorithmType = algorithmType;
//}
- @Override
- public ExampleBasedNode getStartNode() {
- return null;
- }
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-03-12 02:45:28 UTC (rev 703)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-03-12 16:22:24 UTC (rev 704)
@@ -349,7 +349,6 @@
algorithm.stop();
}
- @Override
public ExampleBasedNode getStartNode() {
return algorithm.getStartNode();
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-03-12 02:45:28 UTC (rev 703)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-03-12 16:22:24 UTC (rev 704)
@@ -12,7 +12,6 @@
import java.util.TreeSet;
import org.apache.log4j.Logger;
-import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -1004,12 +1003,8 @@
/**
* @return the startNode
*/
- public Node getStartNode_original() {
+ public Node getStartNode() {
return startNode;
}
- @Override
- public ExampleBasedNode getStartNode() {
- return null;
- }
}
Modified: trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-03-12 02:45:28 UTC (rev 703)
+++ trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java 2008-03-12 16:22:24 UTC (rev 704)
@@ -23,7 +23,6 @@
import java.util.LinkedList;
import java.util.List;
-import org.dllearner.algorithms.refexamples.ExampleBasedNode;
import org.dllearner.core.owl.Description;
/**
@@ -70,10 +69,5 @@
public static Collection<Class<? extends LearningProblem>> supportedLearningProblems() {
return new LinkedList<Class<? extends LearningProblem>>();
}
-
- /**
- * Root for search tree.
- * @return
- */
- public abstract ExampleBasedNode getStartNode();
+
}
Modified: trunk/src/dl-learner/org/dllearner/gui/TreeWindow.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/gui/TreeWindow.java 2008-03-12 02:45:28 UTC (rev 703)
+++ trunk/src/dl-learner/org/dllearner/gui/TreeWindow.java 2008-03-12 16:22:24 UTC (rev 704)
@@ -22,7 +22,6 @@
import javax.swing.*;
import javax.swing.tree.*;
-import org.dllearner.algorithms.refexamples.*;
/**
* TreeWindow
@@ -59,14 +58,14 @@
// tree model
EBNodeTreeModel root = null;
if (config.getLearningAlgorithm() != null) {
- ExampleBasedNode rootNode = config.getLearningAlgorithm().getStartNode();
- root = new EBNodeTreeModel(rootNode);
+ //ExampleBasedNode rootNode = config.getLearningAlgorithm().getStartNode();
+ //root = new EBNodeTreeModel(rootNode);
}
// show tree
if (root != null) {
- JTree tree = new JTree(root);
- this.add(new JScrollPane(tree));
+ //JTree tree = new JTree(root);
+ //this.add(new JScrollPane(tree));
}
else {
JTree tree = new JTree(exampleRoot);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-13 06:55:17
|
Revision: 707
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=707&view=rev
Author: jenslehmann
Date: 2008-03-12 23:55:13 -0700 (Wed, 12 Mar 2008)
Log Message:
-----------
- wrote script for training on one and testing on another conf file
- small algorithm improvements
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
trunk/src/dl-learner/org/dllearner/learningproblems/ScoreTwoValued.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/TestValidation.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-12 23:15:31 UTC (rev 706)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-13 06:55:13 UTC (rev 707)
@@ -267,7 +267,7 @@
long lastReductionTime = System.nanoTime();
// try a traversal after 100 seconds
long traversalInterval = 1000l * 1000000000l;
- long reductionInterval = 100l * 1000000000l;
+ long reductionInterval = 300l * 1000000000l;
long currentTime;
while(!solutionFound && !stop) {
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-12 23:15:31 UTC (rev 706)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-13 06:55:13 UTC (rev 707)
@@ -21,7 +21,8 @@
import java.util.List;
-import org.dllearner.core.owl.DatatypeValueRestriction;
+import org.dllearner.core.owl.BooleanValueRestriction;
+import org.dllearner.core.owl.DatatypeSomeRestriction;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Thing;
import org.dllearner.utilities.ConceptComparator;
@@ -78,7 +79,7 @@
private double expansionPenaltyFactor;
private double gainBonusFactor;
private double nodeChildPenalty = 0.0001;
- private double startNodeBonus = 0.8;
+ private double startNodeBonus = 1.0;
// examples
private int nrOfNegativeExamples;
@@ -144,11 +145,16 @@
// do not count TOP symbols (in particular in ALL r.TOP and EXISTS r.TOP)
// as they provide no extra information
if(description instanceof Thing)
- bonus = 1;
+ bonus = 2;
+ if(description instanceof BooleanValueRestriction)
+ bonus = -1;
+
// some bonus for doubles because they are already penalised by length 3
- if(description instanceof DatatypeValueRestriction)
- bonus = 1;
+ if(description instanceof DatatypeSomeRestriction) {
+// System.out.println(description);
+ bonus = 3;
+ }
List<Description> children = description.getChildren();
for(Description child : children) {
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-03-12 23:15:31 UTC (rev 706)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-03-13 06:55:13 UTC (rev 707)
@@ -112,6 +112,16 @@
// list of all "hasProperty" test
private static Set<String> tests = new TreeSet<String>();
+ // we ignore the ames test since its distribution in PTE-2 is so
+ // different from the training substances that a different testing
+ // strategy was probably in use
+ private static boolean ignoreAmes = false;
+ private static boolean ignoreSalmonella = false;;
+ private static boolean ignoreCytogenCa = false;
+ // if true we learn carcinogenic, if false we learn non-carcinogenic
+ private static boolean learnCarcinogenic = true;
+ private static boolean useNewGroups = true;
+
/**
* @param args
* No arguments supported.
@@ -168,8 +178,10 @@
// define properties including domain and range
String kbString = "DPDOMAIN(" + getURI2("charge") + ") = " + getURI2("Atom") + ".\n";
kbString += "DPRANGE(" + getURI2("charge") + ") = DOUBLE.\n";
- kbString += "DPDOMAIN(" + getURI2("amesTestPositive") + ") = " + getURI2("Compound") + ".\n";
- kbString += "DPRANGE(" + getURI2("amesTestPositive") + ") = BOOLEAN.\n";
+ if(!ignoreAmes) {
+ kbString += "DPDOMAIN(" + getURI2("amesTestPositive") + ") = " + getURI2("Compound") + ".\n";
+ kbString += "DPRANGE(" + getURI2("amesTestPositive") + ") = BOOLEAN.\n";
+ }
kbString += "OPDOMAIN(" + getURI2("hasAtom") + ") = " + getURI2("Compound") + ".\n";
kbString += "OPRANGE(" + getURI2("hasAtom") + ") = " + getURI2("Atom") + ".\n";
kbString += "OPDOMAIN(" + getURI2("hasBond") + ") = " + getURI2("Compound") + ".\n";
@@ -177,7 +189,10 @@
kbString += "OPDOMAIN(" + getURI2("inBond") + ") = " + getURI2("Bond") + ".\n";
kbString += "OPRANGE(" + getURI2("inBond") + ") = " + getURI2("Atom") + ".\n";
kbString += "OPDOMAIN(" + getURI2("hasStructure") + ") = " + getURI2("Compound") + ".\n";
- kbString += "OPRANGE(" + getURI2("hasStructure") + ") = " + getURI2("Structure") + ".\n";
+ kbString += "OPRANGE(" + getURI2("hasStructure") + ") = " + getURI2("Structure") + ".\n";
+ kbString += getURI2("Di") + " SUB " + getURI2("Structure") + ".\n";
+ kbString += getURI2("Halide") + " SUB " + getURI2("Structure") + ".\n";
+ kbString += getURI2("Ring") + " SUB " + getURI2("Structure") + ".\n";
KB kb2 = KBParser.parseKBFile(kbString);
kb.addKB(kb2);
@@ -195,7 +210,7 @@
// are in ames.pl [the rest is negative in Prolog by CWA], so
// we add negative test results here)
for(String compound : compounds) {
- if(!compoundsAmes.contains(compound)) {
+ if(!ignoreAmes && !compoundsAmes.contains(compound)) {
BooleanDatatypePropertyAssertion ames = getBooleanDatatypePropertyAssertion(compound, "amesTestPositive", false);
kb.addAxiom(ames);
}
@@ -255,15 +270,19 @@
// generating test examples for PTE-1
// => put all in one file, because they were used as training for PTE-2
- // File confPTE1File = new File("examples/carcinogenesis/testpte1.conf");
- // Files.clearFile(confPTE1File);
+ File confPTE1File = new File("examples/carcinogenesis/testpte1.conf");
+ Files.clearFile(confPTE1File);
File testPTE1Positives = new File(prologDirectory + "pte1.f");
File testPTE1Negatives = new File(prologDirectory + "pte1.n");
List<Individual> posPTE1Examples = getExamples(testPTE1Positives);
List<Individual> negPTE1Examples = getExamples(testPTE1Negatives);
appendPosExamples(confTrainFile, posPTE1Examples);
- appendNegExamples(confTrainFile, negPTE1Examples);
+ appendNegExamples(confTrainFile, negPTE1Examples);
+ Files.clearFile(confPTE1File);
+ Files.appendFile(confPTE1File, "import(\"pte.owl\");\nreasoner=fastInstanceChecker;\n\n");
+ appendPosExamples(confPTE1File, posPTE1Examples);
+ appendNegExamples(confPTE1File, negPTE1Examples);
// create a PTE-2 test file
File confPTE2File = new File("examples/carcinogenesis/testpte2.conf");
@@ -288,10 +307,12 @@
// remaining stuff or use closed world assumption in the
// TBox dematerialisation later on
if(headName.equals("ames")) {
+ if(!ignoreAmes) {
String compoundName = head.getArgument(0).toPLString();
BooleanDatatypePropertyAssertion ames = getBooleanDatatypePropertyAssertion(compoundName, "amesTestPositive", true);
axioms.add(ames);
compoundsAmes.add(compoundName);
+ }
} else if (headName.equals("atm")) {
String compoundName = head.getArgument(0).toPLString();
String atomName = head.getArgument(1).toPLString();
@@ -350,48 +371,67 @@
} else if (headName.equals("has_property")) {
String compoundName = head.getArgument(0).toPLString();
String testName = head.getArgument(1).toPLString();
- String resultStr = head.getArgument(2).toPLString();
- boolean testResult = (resultStr.equals("p")) ? true : false;
-
- // create a new datatype property if it does not exist already
- if(!tests.contains(testName)) {
- String axiom1 = "DPDOMAIN(" + getURI2(testName) + ") = " + getURI2("Compound") + ".\n";
- String axiom2 = "DPRANGE(" + getURI2(testName) + ") = BOOLEAN.\n";
- KB kb = KBParser.parseKBFile(axiom1 + axiom2);
- axioms.addAll(kb.getAxioms());
+ if(!(ignoreSalmonella && testName.equals("salmonella"))
+ && !(ignoreCytogenCa && testName.equals("cytogen_ca"))) {
+ String resultStr = head.getArgument(2).toPLString();
+ boolean testResult = (resultStr.equals("p")) ? true : false;
+
+ // create a new datatype property if it does not exist already
+ if(!tests.contains(testName)) {
+ String axiom1 = "DPDOMAIN(" + getURI2(testName) + ") = " + getURI2("Compound") + ".\n";
+ String axiom2 = "DPRANGE(" + getURI2(testName) + ") = BOOLEAN.\n";
+ KB kb = KBParser.parseKBFile(axiom1 + axiom2);
+ axioms.addAll(kb.getAxioms());
+ }
+ // create an axiom with the test result
+ DatatypePropertyAssertion dpa = getBooleanDatatypePropertyAssertion(compoundName, testName,
+ testResult);
+ axioms.add(dpa);
}
- // create an axiom with the test result
- DatatypePropertyAssertion dpa = getBooleanDatatypePropertyAssertion(compoundName, testName,
- testResult);
- axioms.add(dpa);
// either parse this or ashby_alert - not both - ashby_alert contains
// all information in ind already
} else if (headName.equals("ind") || headName.equals("ring_no")) {
+ // parse this only if the new groups are not parsed
+// if(!useNewGroups) {
String compoundName = head.getArgument(0).toPLString();
String structureName = head.getArgument(1).toPLString();
- int count = Integer.parseInt(head.getArgument(2).toPLString());
+// int count = Integer.parseInt(head.getArgument(2).toPLString());
// upper case first letter
String structureClass = structureName.substring(0,1).toUpperCase() + structureName.substring(1);;
String structureInstance = structureName + "-" + structureNr;
- if (!bondTypes.contains(structureClass)) {
- NamedClass subClass = getAtomicConcept(structureClass);
- SubClassAxiom sc = new SubClassAxiom(subClass, getAtomicConcept("Structure"));
- axioms.add(sc);
- structureTypes.add(structureClass);
- }
+ addStructureSubclass(axioms, structureClass);
- for(int i=0; i<count; i++) {
+// for(int i=0; i<count; i++) {
ObjectPropertyAssertion op = getRoleAssertion("hasStructure", compoundName, structureInstance);
axioms.add(op);
// make e.g. halide10-382 instance of Bond-3
ClassAssertionAxiom ca = getConceptAssertion(structureClass, structureInstance);
axioms.add(ca);
structureNr++;
- }
+// }
+// }
} else if (headName.equals("ashby_alert")) {
// ... currently ignored ...
} else if (newGroups.contains(headName)) {
+ if(useNewGroups) {
+ String compoundName = head.getArgument(0).toPLString();
+ String structureName = headName;
+// int count = Integer.parseInt(head.getArgument(2).toPLString());
+ // upper case first letter
+ String structureClass = structureName.substring(0,1).toUpperCase() + structureName.substring(1);;
+ String structureInstance = structureName + "-" + structureNr;
+
+ addStructureSubclass(axioms, structureClass);
+
+// for(int i=0; i<count; i++) {
+ ObjectPropertyAssertion op = getRoleAssertion("hasStructure", compoundName, structureInstance);
+ axioms.add(op);
+ ClassAssertionAxiom ca = getConceptAssertion(structureClass, structureInstance);
+ axioms.add(ca);
+ structureNr++;
+// }
+ }
} else {
// print clauses which are not supported yet
System.out.println("unsupported clause");
@@ -402,6 +442,23 @@
return axioms;
}
+ private static void addStructureSubclass(List<Axiom> axioms, String structureClass) {
+ // build in more fine-grained subclasses e.g. Di+number is subclass of Di
+ if (!structureTypes.contains(structureClass)) {
+ NamedClass nc = getAtomicConcept("Structure");
+ if(structureClass.contains("Di"))
+ nc = getAtomicConcept("Di");
+ else if(structureClass.contains("ring") || structureClass.contains("Ring"))
+ nc = getAtomicConcept("Ring");
+ else if(structureClass.contains("halide") || structureClass.contains("Halide"))
+ nc = getAtomicConcept("Halide");
+ NamedClass subClass = getAtomicConcept(structureClass);
+ SubClassAxiom sc = new SubClassAxiom(subClass, nc);
+ axioms.add(sc);
+ structureTypes.add(structureClass);
+ }
+ }
+
// takes a *.f or *.n file as input and returns the
// contained examples
private static List<Individual> getExamples(File file) throws FileNotFoundException, IOException, ParseException {
@@ -419,7 +476,10 @@
private static void appendPosExamples(File file, List<Individual> examples) {
StringBuffer content = new StringBuffer();
for(Individual example : examples) {
- content.append("+\""+example.toString()+"\"\n");
+ if(learnCarcinogenic)
+ content.append("+\""+example.toString()+"\"\n");
+ else
+ content.append("-\""+example.toString()+"\"\n");
}
Files.appendFile(file, content.toString());
}
@@ -427,7 +487,10 @@
private static void appendNegExamples(File file, List<Individual> examples) {
StringBuffer content = new StringBuffer();
for(Individual example : examples) {
- content.append("-\""+example.toString()+"\"\n");
+ if(learnCarcinogenic)
+ content.append("-\""+example.toString()+"\"\n");
+ else
+ content.append("+\""+example.toString()+"\"\n");
}
Files.appendFile(file, content.toString());
}
@@ -582,6 +645,7 @@
* <p>Positives (19): <br />
* <ul>
* <li>t3 (SE+3NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCACAFD4-123F-7908-7B521E4F665EFBD9</li>
+ * <li>t4 (3CE+NE) - contradicts IJCAI-97 paper and should probably be case 75-52-5 instead of 75-52-8: http://ntp.niehs.nih.gov/index.cfm?objectid=BCE49084-123F-7908-7BE127F7AF1FFBB5</li>
* <li>t5: paper</li>
* <li>t7: paper</li>
* <li>t8: paper</li>
@@ -607,7 +671,7 @@
* <ul>
* <li>t1 (4NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BD9FF53C-123F-7908-7B123DAE0A25B122 </li>
* <li>t2 (4NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BCF8651E-123F-7908-7B21DD5ED83CD0FF </li>
- * <li>t4: paper</li>
+ * <li><strike>t4: paper</strike></li>
* <li>t6: paper</li>
* <li>t11: paper</li>
* <li>t13 (4NE): http://ntp.niehs.nih.gov/index.cfm?objectid=BD136ED6-123F-7908-7B619EE79F2FD062</li>
@@ -623,21 +687,47 @@
* <li>t29: probably a negative (see http://ntp.niehs.nih.gov/index.cfm?objectid=BD855EA1-123F-7908-7B573FC3C08188DC) but
* no tests directly for this substance</li>
* </ul>
+ *
+ * <p>The following examples are probably not part of the IJCAI PTE-2 challenge
+ * (reports younger than 1998):
+ * <ul>
+ * <li>pos: t21 (5/99), t25 (9/04), t30(10/01)</li>
+ * <li>neg: t26 (5/99), t27 (05/01), t28 (05/00), t29 (09/02)</li>
+ * </ul>
* </p>
+ * </p>
* @return A string for all examples as used in the conf file.
*/
public static String getPTE2Examples() {
- String[] pos = new String[] {"t3","t5","t7","t8","t9","t10","t12",
- "t14","t15","t16","t18","t19","t20","t21","t22","t23","t24",
- "t25","t30"};
- String[] neg = new String[] {"t1", "t2", "t4", "t6", "t11", "t13",
- "t17","t26","t27","t28"};
+ String[] pos = new String[] {"t3","t4","t5","t7","t8",
+ "t9",
+ "t10","t12",
+ "t14","t15","t16","t18","t19","t20",
+ "t21",
+ "t22",
+ "t23",
+ "t24",
+ "t25",
+ "t30"};
+ String[] neg = new String[] {"t1", "t2",
+ "t6", "t11", "t13",
+ "t17","t26","t27",
+ "t28","t29"
+ };
String ret = "";
- for(String posEx : pos)
- ret += "+" + getURI2(posEx) + "\n";
- for(String negEx : neg)
- ret += "-" + getURI2(negEx) + "\n";
+ for(String posEx : pos) {
+ if(learnCarcinogenic)
+ ret += "+" + getURI2(posEx) + "\n";
+ else
+ ret += "-" + getURI2(posEx) + "\n";
+ }
+ for(String negEx : neg) {
+ if(learnCarcinogenic)
+ ret += "-" + getURI2(negEx) + "\n";
+ else
+ ret += "+" + getURI2(negEx) + "\n";
+ }
return ret;
}
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/ScoreTwoValued.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/ScoreTwoValued.java 2008-03-12 23:15:31 UTC (rev 706)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/ScoreTwoValued.java 2008-03-13 06:55:13 UTC (rev 707)
@@ -54,9 +54,9 @@
String str = "";
str += "score: " + score + "\n";
str += "accuracy: " + (1 + classificationScore) + "\n";
- str += "posAsPos: " + posAsPos + "\n";
- str += "positive examples classified as negative: " + posAsNeg + "\n";
- str += "negative examples classified as positive: " + negAsPos + "\n";
+ str += "posAsPos (" + posAsPos.size() + "): " + posAsPos + "\n";
+ str += "positive examples classified as negative (" + posAsNeg.size() + "): " + posAsNeg + "\n";
+ str += "negative examples classified as positive (" + negAsPos.size() + "): " + negAsPos + "\n";
return str;
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-12 23:15:31 UTC (rev 706)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-13 06:55:13 UTC (rev 707)
@@ -286,7 +286,9 @@
ConceptTransformation.cleanConceptNonRecursive(mc);
ConceptTransformation.transformToOrderedNegationNormalFormNonRecursive(mc, conceptComparator);
- refinements.add(mc);
+ // check whether the intersection is OK (sanity checks), then add it
+ if(checkIntersection(mc))
+ refinements.add(mc);
}
}
@@ -431,6 +433,17 @@
}
}
+ // check for double datatype properties
+ if(c instanceof DatatypeSomeRestriction &&
+ description instanceof DatatypeSomeRestriction) {
+ DataRange dr = ((DatatypeSomeRestriction)c).getDataRange();
+ DataRange dr2 = ((DatatypeSomeRestriction)description).getDataRange();
+ // it does not make sense to have statements like height >= 1.8 AND height >= 1.7
+ if((dr instanceof DoubleMaxValue && dr2 instanceof DoubleMaxValue)
+ ||(dr instanceof DoubleMinValue && dr2 instanceof DoubleMinValue))
+ skip = true;
+ }
+
// perform a disjointness check when named classes are added;
// this can avoid a lot of superfluous computation in the algorithm e.g.
// when A1 looks good, so many refinements of the form (A1 OR (A2 AND A3))
@@ -465,6 +478,33 @@
return refinements;
}
+ // when a child of an intersection is refined and reintegrated into the
+ // intersection, we can perform some sanity checks;
+ // method returns true if everything is OK and false otherwise
+ private boolean checkIntersection(Intersection intersection) {
+ // rule 1: max. restrictions at most once
+ boolean maxDoubleOccurence = false;
+ // rule 2: min restrictions at most once
+ boolean minDoubleOccurence = false;
+ for(Description child : intersection.getChildren()) {
+ if(child instanceof DatatypeSomeRestriction) {
+ DataRange dr = ((DatatypeSomeRestriction)child).getDataRange();
+ if(dr instanceof DoubleMaxValue) {
+ if(maxDoubleOccurence)
+ return false;
+ else
+ maxDoubleOccurence = true;
+ } else if(dr instanceof DoubleMinValue) {
+ if(minDoubleOccurence)
+ return false;
+ else
+ minDoubleOccurence = true;
+ }
+ }
+ }
+ return true;
+ }
+
private void computeTopRefinements(int maxLength) {
computeTopRefinements(maxLength, null);
}
Added: trunk/src/dl-learner/org/dllearner/utilities/TestValidation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/TestValidation.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/TestValidation.java 2008-03-13 06:55:13 UTC (rev 707)
@@ -0,0 +1,75 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.utilities;
+
+import java.io.File;
+import java.util.Set;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.cli.Start;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.LearningProblem;
+import org.dllearner.core.ReasoningService;
+import org.dllearner.core.Score;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+
+/**
+ * @author Jens Lehmann
+ *
+ */
+public class TestValidation {
+
+ private static Logger logger = Logger.getRootLogger();
+
+ public static void main(String args[]) throws ComponentInitException {
+
+ // create logger (a simple logger which outputs
+ // its messages to the console)
+ SimpleLayout layout = new SimpleLayout();
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ logger.removeAllAppenders();
+ logger.addAppender(consoleAppender);
+ logger.setLevel(Level.DEBUG);
+
+ String filenameTrain = args[0];
+ String filenameTest = args[1];
+
+ Start start = new Start(new File(filenameTrain));
+ start.start(false);
+ Description solution = start.getLearningAlgorithm().getBestSolution();
+
+ logger.setLevel(Level.WARN);
+
+ Start startTest = new Start(new File(filenameTest));
+ ReasoningService rs = startTest.getReasoningService();
+ LearningProblem lp = startTest.getLearningProblem();
+
+ Set<Individual> result = rs.retrieval(solution);
+ System.out.println("retrieval result: " + result);
+
+ Score score = lp.computeScore(solution);
+ System.out.println(score);
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-16 19:03:58
|
Revision: 713
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=713&view=rev
Author: jenslehmann
Date: 2008-03-16 12:03:46 -0700 (Sun, 16 Mar 2008)
Log Message:
-----------
partial cardinality restriction learning support
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/Info.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
trunk/src/dl-learner/org/dllearner/core/ComponentPool.java
trunk/src/dl-learner/org/dllearner/core/Reasoner.java
trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
trunk/src/dl-learner/org/dllearner/utilities/ConceptComparator.java
trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java
Modified: trunk/src/dl-learner/org/dllearner/Info.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/Info.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/Info.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -3,6 +3,6 @@
package org.dllearner;
public class Info {
- public static final String build = "2008-02-18";
+ public static final String build = "2008-03-16";
}
\ No newline at end of file
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -30,7 +30,6 @@
import java.util.SortedSet;
import java.util.TreeSet;
-import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.dllearner.algorithms.refinement.RefinementOperator;
import org.dllearner.core.LearningProblem;
@@ -39,8 +38,8 @@
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.Thing;
import org.dllearner.core.owl.Union;
-import org.dllearner.core.owl.Thing;
import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.learningproblems.PosOnlyDefinitionLP;
import org.dllearner.refinementoperators.RhoDRDown;
@@ -116,7 +115,7 @@
// the divide&conquer approach in many ILP programs using a
// clause by clause search; after a period of time the candidate
// set is reduced to focus CPU time on the most promising concepts
- private boolean useCandidateReduction = true;
+ private boolean useCandidateReduction = false;
private int candidatePostReductionSize = 30;
// setting to true gracefully stops the algorithm
@@ -214,6 +213,11 @@
posOnly = false;
nrOfPositiveExamples = lp.getPositiveExamples().size();
nrOfNegativeExamples = lp.getNegativeExamples().size();
+
+// System.out.println(nrOfPositiveExamples);
+// System.out.println(nrOfNegativeExamples);
+// System.exit(0);
+
} else if(learningProblem instanceof PosOnlyDefinitionLP) {
PosOnlyDefinitionLP lp = (PosOnlyDefinitionLP) learningProblem;
this.posOnlyLearningProblem = lp;
@@ -236,10 +240,40 @@
this.useShortConceptConstruction = useShortConceptConstruction;
baseURI = rs.getBaseURI();
- logger.setLevel(Level.DEBUG);
+// logger.setLevel(Level.DEBUG);
}
public void start() {
+ /*
+// String conceptStr = "(\"http://dl-learner.org/carcinogenesis#Compound\" AND (>= 2 \"http://dl-learner.org/carcinogenesis#hasStructure\".\"http://dl-learner.org/carcinogenesis#Ar_halide\" OR ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) AND >= 5 \"http://dl-learner.org/carcinogenesis#hasBond\". TOP)))";
+ String conceptStr = "(\"http://dl-learner.org/carcinogenesis#Compound\" AND ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) AND (\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE)))";
+ try {
+ NamedClass struc = new NamedClass("http://dl-learner.org/carcinogenesis#Compound");
+ Description d = KBParser.parseConcept(conceptStr);
+// SortedSet<Description> ds = (SortedSet<Description>) operator.refine(d,15,null,struc);
+// System.out.println(ds);
+
+ System.out.println(RhoDRDown.checkIntersection((Intersection)d));
+
+
+ Set<Individual> coveredNegatives = rs.instanceCheck(d, learningProblem.getNegativeExamples());
+ Set<Individual> coveredPositives = rs.instanceCheck(d, learningProblem.getPositiveExamples());
+ ExampleBasedNode ebn = new ExampleBasedNode(d);
+ ebn.setCoveredExamples(coveredPositives, coveredNegatives);
+ extendNodeProper(ebn,15);
+
+ // Individual i = new Individual("http://dl-learner.org/carcinogenesis#d101");
+// for(Individual i : learningProblem.getPositiveExamples())
+// rs.instanceCheck(ds.last(), i);
+
+ System.out.println("finished");
+ } catch (ParseException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ System.exit(0);
+ */
+
// calculate quality threshold required for a solution
allowedMisclassifications = (int) Math.round(noise * nrOfExamples);
@@ -290,8 +324,10 @@
if(useCandidateReduction && (currentTime - lastReductionTime > reductionInterval)) {
reduceCandidates();
lastReductionTime = System.nanoTime();
+// Logger.getRootLogger().setLevel(Level.TRACE);
}
+ System.out.println("next expanded: " + candidates.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
// chose best node according to heuristics
bestNode = candidates.last();
// extend best node
@@ -304,7 +340,8 @@
// newCandidates has been filled during node expansion
candidates.addAll(newCandidates);
candidatesStable.addAll(newCandidates);
-
+// System.out.println("done");
+
if(writeSearchTree) {
// String treeString = "";
String treeString = "best node: " + bestNode+ "\n";
@@ -338,13 +375,13 @@
logger.info(" " + c + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
}
}
- System.out.println("size of candidate set: " + candidates.size());
+ logger.debug("size of candidate set: " + candidates.size());
printStatistics(true);
if(stop)
- System.out.println("Algorithm stopped.");
+ logger.info("Algorithm stopped.");
else
- System.out.println("Algorithm terminated succesfully.");
+ logger.info("Algorithm terminated succesfully.");
}
// we apply the operator recursively until all proper refinements up
@@ -397,14 +434,18 @@
childConceptsDeletionTimeNs += System.nanoTime() - childConceptsDeletionTimeNsStart;
+// if(refinements.size()<30)
+// System.out.println("refinements: " + refinements);
+
long evaluateSetCreationTimeNsStart = System.nanoTime();
// alle Konzepte, die länger als horizontal expansion sind, müssen ausgewertet
// werden
- Set<Description> toEvaluateConcepts = new TreeSet<Description>(conceptComparator);
+ TreeSet<Description> toEvaluateConcepts = new TreeSet<Description>(conceptComparator);
Iterator<Description> it = refinements.iterator();
// for(Concept refinement : refinements) {
- while(it.hasNext()) {
+ while(it.hasNext()) {
+
Description refinement = it.next();
if(refinement.getLength()>node.getHorizontalExpansion()) {
// sagt aus, ob festgestellt wurde, ob refinement proper ist
@@ -413,7 +454,6 @@
// 1. short concept construction
if(useShortConceptConstruction) {
-
// kurzes Konzept konstruieren
Description shortConcept = ConceptTransformation.getShortConcept(refinement, conceptComparator);
int n = conceptComparator.compare(shortConcept, concept);
@@ -422,11 +462,14 @@
if(n==0) {
propernessTestsAvoidedByShortConceptConstruction++;
propernessDetected = true;
+
+ System.out.println("refinement " + refinement + " can be shortened");
+// System.exit(0);
}
}
// 2. too weak test
- if(!propernessDetected && useTooWeakList) {
+ if(!propernessDetected && useTooWeakList) {
if(refinement instanceof Intersection) {
boolean tooWeakElement = containsTooWeakElement((Intersection)refinement);
if(tooWeakElement) {
@@ -454,14 +497,28 @@
}
// properness konnte nicht vorher ermittelt werden
- if(!propernessDetected)
+ if(!propernessDetected) {
toEvaluateConcepts.add(refinement);
+// if(!res) {
+// System.out.println("already in: " + refinement);
+// Comparator comp = toEvaluateConcepts.comparator();
+// for(Description d : toEvaluateConcepts) {
+// if(comp.compare(d,refinement)==0)
+// System.out.println("see: " + d);
+// }
+// }
+ }
}
+
+// System.out.println("handled " + refinement + " length: " + refinement.getLength() + " (new size: " + toEvaluateConcepts.size() + ")");
+
}
evaluateSetCreationTimeNs += System.nanoTime() - evaluateSetCreationTimeNsStart;
+// System.out.println("intermediate 1");
+
// System.out.println(toEvaluateConcepts.size());
Set<Description> improperConcepts = null;
@@ -476,6 +533,11 @@
}
}
+// if(toEvaluateConcepts.size()<10)
+// System.out.println("to evaluate: " + toEvaluateConcepts);
+// else
+// System.out.println("to evaluate: more than 10");
+
long improperConceptsRemovalTimeNsStart = System.nanoTime();
// die improper Konzepte werden von den auszuwertenden gelöscht, d.h.
// alle proper concepts bleiben übrig (einfache Umbenennung)
@@ -486,6 +548,13 @@
refinements.removeAll(properConcepts);
improperConceptsRemovalTimeNs += System.nanoTime() - improperConceptsRemovalTimeNsStart;
+// if(refinements.size()<10)
+// System.out.println("refinements: " + refinements);
+// else
+// System.out.println("refinements: more than 10");
+//
+// System.out.println("improper concepts: " + improperConcepts);
+
for(Description refinement : properConcepts) {
long redundancyCheckTimeNsStart = System.nanoTime();
boolean nonRedundant = properRefinements.add(refinement);
@@ -603,18 +672,18 @@
}
}
-
// es sind jetzt noch alle Konzepte übrig, die improper refinements sind
// auf jedem dieser Konzepte wird die Funktion erneut aufgerufen, da sich
// proper refinements ergeben könnten
for(Description refinement : refinements) {
// for(int i=0; i<=recDepth; i++)
// System.out.print(" ");
- // System.out.println("call: " + refinement + " [maxLength " + maxLength + "]");
+// System.out.println("call: " + refinement + " [maxLength " + maxLength + "]");
extendNodeProper(node, refinement, maxLength, recDepth+1);
// for(int i=0; i<=recDepth; i++)
// System.out.print(" ");
- // System.out.println("finished: " + refinement + " [maxLength " + maxLength + "]");
+ // System.out.println("finished: " + refinement + " [maxLength " + maxLength + "]");
+// System.exit(0);
}
}
@@ -637,26 +706,25 @@
// + nrOfNegativeExamples - bestNode.getCoveredNegatives().size())/(double)nrOfExamples);
// Refinementoperator auf Konzept anwenden
// String bestNodeString = "currently best node: " + bestNode + " accuracy: " + df.format(accuracy) + "%";
- System.out.println("start node: " + startNode.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
+ logger.debug("start node: " + startNode.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
String bestNodeString = "currently best node: " + bestNode.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI);
// searchTree += bestNodeString + "\n";
- System.out.println(bestNodeString);
+ logger.debug(bestNodeString);
String expandedNodeString = "next expanded node: " + candidates.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI);
// searchTree += expandedNodeString + "\n";
- System.out.println(expandedNodeString);
- System.out.println("algorithm runtime " + Helper.prettyPrintNanoSeconds(algorithmRuntime));
- System.out.println("size of candidate set: " + candidates.size());
+ logger.debug(expandedNodeString);
+ logger.debug("algorithm runtime " + Helper.prettyPrintNanoSeconds(algorithmRuntime));
+ logger.debug("size of candidate set: " + candidates.size());
// System.out.println("properness max recursion depth: " + maxRecDepth);
// System.out.println("max. number of one-step refinements: " + maxNrOfRefinements);
// System.out.println("max. number of children of a node: " + maxNrOfChildren);
- System.out.println("subsumption time: " + Helper.prettyPrintNanoSeconds(rs.getSubsumptionReasoningTimeNs()));
- System.out.println("instance check time: " + Helper.prettyPrintNanoSeconds(rs.getInstanceCheckReasoningTimeNs()));
- System.out.println("retrieval time: " + Helper.prettyPrintNanoSeconds(rs.getRetrievalReasoningTimeNs()));
+ logger.debug("subsumption time: " + Helper.prettyPrintNanoSeconds(rs.getSubsumptionReasoningTimeNs()));
+ logger.debug("instance check time: " + Helper.prettyPrintNanoSeconds(rs.getInstanceCheckReasoningTimeNs()));
+ logger.debug("retrieval time: " + Helper.prettyPrintNanoSeconds(rs.getRetrievalReasoningTimeNs()));
}
if(computeBenchmarkInformation) {
-
long reasoningTime = rs.getOverallReasoningTimeNs();
double reasoningPercentage = 100 * reasoningTime/(double)algorithmRuntime;
long propWithoutReasoning = propernessCalcTimeNs-propernessCalcReasoningTimeNs;
@@ -674,24 +742,24 @@
double onnfTimePercentage = 100 * ConceptTransformation.onnfTimeNs/(double)algorithmRuntime;
double shorteningTimePercentage = 100 * ConceptTransformation.shorteningTimeNs/(double)algorithmRuntime;
- System.out.println("reasoning percentage: " + df.format(reasoningPercentage) + "%");
- System.out.println(" subsumption check time: " + df.format(subPercentage) + "%");
- System.out.println("proper calculation percentage (wo. reasoning): " + df.format(propPercentage) + "%");
- System.out.println(" deletion time percentage: " + df.format(deletionPercentage) + "%");
- System.out.println(" refinement calculation percentage: " + df.format(refinementPercentage) + "%");
- System.out.println(" m calculation percentage: " + df.format(mComputationTimePercentage) + "%");
- System.out.println(" top calculation percentage: " + df.format(topComputationTimePercentage) + "%");
- System.out.println(" redundancy check percentage: " + df.format(redundancyCheckPercentage) + "%");
- System.out.println(" evaluate set creation time percentage: " + df.format(evaluateSetCreationTimePercentage) + "%");
- System.out.println(" improper concepts removal time percentage: " + df.format(improperConceptsRemovalTimePercentage) + "%");
- System.out.println("clean time percentage: " + df.format(cleanTimePercentage) + "%");
- System.out.println("onnf time percentage: " + df.format(onnfTimePercentage) + "%");
- System.out.println("shortening time percentage: " + df.format(shorteningTimePercentage) + "%");
+ logger.debug("reasoning percentage: " + df.format(reasoningPercentage) + "%");
+ logger.debug(" subsumption check time: " + df.format(subPercentage) + "%");
+ logger.debug("proper calculation percentage (wo. reasoning): " + df.format(propPercentage) + "%");
+ logger.debug(" deletion time percentage: " + df.format(deletionPercentage) + "%");
+ logger.debug(" refinement calculation percentage: " + df.format(refinementPercentage) + "%");
+ logger.debug(" m calculation percentage: " + df.format(mComputationTimePercentage) + "%");
+ logger.debug(" top calculation percentage: " + df.format(topComputationTimePercentage) + "%");
+ logger.debug(" redundancy check percentage: " + df.format(redundancyCheckPercentage) + "%");
+ logger.debug(" evaluate set creation time percentage: " + df.format(evaluateSetCreationTimePercentage) + "%");
+ logger.debug(" improper concepts removal time percentage: " + df.format(improperConceptsRemovalTimePercentage) + "%");
+ logger.debug("clean time percentage: " + df.format(cleanTimePercentage) + "%");
+ logger.debug("onnf time percentage: " + df.format(onnfTimePercentage) + "%");
+ logger.debug("shortening time percentage: " + df.format(shorteningTimePercentage) + "%");
}
- System.out.println("properness tests (reasoner/short concept/too weak list): " + propernessTestsReasoner + "/" + propernessTestsAvoidedByShortConceptConstruction
+ logger.debug("properness tests (reasoner/short concept/too weak list): " + propernessTestsReasoner + "/" + propernessTestsAvoidedByShortConceptConstruction
+ "/" + propernessTestsAvoidedByTooWeakList);
- System.out.println("concept tests (reasoner/too weak list/overly general list/redundant concepts): " + conceptTestsReasoner + "/"
+ logger.debug("concept tests (reasoner/too weak list/overly general list/redundant concepts): " + conceptTestsReasoner + "/"
+ conceptTestsTooWeakList + "/" + conceptTestsOverlyGeneralList + "/" + redundantConcepts);
}
@@ -737,8 +805,8 @@
Set<Individual> currentCoveredNeg = startNode.getCoveredNegatives();
double currentAccuracy = startNode.getAccuracy(nrOfPositiveExamples, nrOfNegativeExamples);
int currentMisclassifications = nrOfPositiveExamples - currentCoveredPos.size() + currentCoveredNeg.size();
- System.out.println("tree traversal start node " + startNode.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
- System.out.println("tree traversal start accuracy: " + currentAccuracy);
+ logger.debug("tree traversal start node " + startNode.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
+ logger.debug("tree traversal start accuracy: " + currentAccuracy);
int i=0;
// start from the most promising nodes
NavigableSet<ExampleBasedNode> reverseView = candidatesStable.descendingSet();
@@ -775,9 +843,9 @@
ConceptTransformation.transformToOrderedNegationNormalFormNonRecursive(mc, conceptComparator);
// System.out.println("extended concept to: " + mc);
- System.out.println("misclassifications: " + misclassifications);
- System.out.println("misclassified positives: " + misclassifiedPositives);
- System.out.println("accuracy: " + accuracy);
+ logger.debug("misclassifications: " + misclassifications);
+ logger.debug("misclassified positives: " + misclassifiedPositives);
+ logger.debug("accuracy: " + accuracy);
// update variables
currentDescription = mc;
@@ -787,8 +855,8 @@
currentAccuracy = accuracy;
if(accuracy > 1 - noise) {
- System.out.println("traversal found " + mc);
- System.out.println("accuracy: " + accuracy);
+ logger.info("traversal found " + mc);
+ logger.info("accuracy: " + accuracy);
System.exit(0);
}
}
@@ -844,9 +912,9 @@
i++;
}
candidates.retainAll(promisingNodes);
- System.out.println("searched " + i + " nodes and picked the following promising descriptions:");
+ logger.debug("searched " + i + " nodes and picked the following promising descriptions:");
for(ExampleBasedNode node : promisingNodes)
- System.out.println(node.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
+ logger.debug(node.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
}
/*
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -21,7 +21,6 @@
import java.util.List;
-import org.dllearner.core.owl.BooleanValueRestriction;
import org.dllearner.core.owl.DatatypeSomeRestriction;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Thing;
@@ -145,10 +144,10 @@
// do not count TOP symbols (in particular in ALL r.TOP and EXISTS r.TOP)
// as they provide no extra information
if(description instanceof Thing)
- bonus = 2;
+ bonus = 1;
- if(description instanceof BooleanValueRestriction)
- bonus = -1;
+// if(description instanceof BooleanValueRestriction)
+// bonus = -1;
// some bonus for doubles because they are already penalised by length 3
if(description instanceof DatatypeSomeRestriction) {
Modified: trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -355,6 +355,10 @@
pool.unregisterComponent(component);
}
+ public void freeAllComponents() {
+ pool.clearComponents();
+ }
+
public <T> T getConfigOptionValue(Component component, ConfigOption<T> option) {
T object = pool.getLastValidConfigValue(component, option);
if(object==null)
Modified: trunk/src/dl-learner/org/dllearner/core/ComponentPool.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ComponentPool.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/core/ComponentPool.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -70,4 +70,11 @@
lastValidConfigValue.get(component).put(entry.getOption(), entry.getValue());
}
+ // unregisters all components
+ public void clearComponents() {
+ components = new LinkedList<Component>();
+ lastValidConfigValue = new HashMap<Component,Map<ConfigOption<?>,Object>>();
+ configEntryHistory = new HashMap<Component,List<ConfigEntry<?>>>();
+ }
+
}
Modified: trunk/src/dl-learner/org/dllearner/core/Reasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/Reasoner.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/core/Reasoner.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -128,4 +128,5 @@
public SortedSet<Individual> getIndividuals();
+ public void releaseKB();
}
Modified: trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -251,4 +251,6 @@
throw new ReasoningMethodUnsupportedException();
}
+ public abstract void releaseKB();
+
}
Modified: trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -603,6 +603,10 @@
return reasoner.getPrefixes();
}
+ public void releaseKB() {
+ reasoner.releaseKB();
+ }
+
public long getInstanceCheckReasoningTimeNs() {
return instanceCheckReasoningTimeNs;
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectCardinalityRestriction.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectCardinalityRestriction.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -13,7 +13,7 @@
}
public int getLength() {
- return 1 + role.getLength() + getChild(0).getLength();
+ return 2 + role.getLength() + getChild(0).getLength();
}
public int getNumber() {
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -118,6 +118,7 @@
private static boolean ignoreAmes = false;
private static boolean ignoreSalmonella = false;;
private static boolean ignoreCytogenCa = false;
+ private static boolean includeMutagenesis = true;
// if true we learn carcinogenic, if false we learn non-carcinogenic
private static boolean learnCarcinogenic = true;
private static boolean useNewGroups = true;
@@ -134,10 +135,11 @@
// TODO: newgroups are not mapped currently
String[] files = new String[] { "newgroups.pl", "ames.pl", "atoms.pl", "bonds.pl", "gentoxprops.pl",
- "ind_nos.pl", "ind_pos.pl", "pte2/canc_nos.pl", "pte2/pte2ames.pl", "pte2/pte2atoms.pl",
- "pte2/pte2bonds.pl", "pte2/pte2gentox.pl", "pte2/pte2ind_nos.pl", "pte2/pte2newgroups.pl"
+ "ind_nos.pl", "ind_pos.pl"};
+ // "pte2/canc_nos.pl", "pte2/pte2ames.pl", "pte2/pte2atoms.pl",
+ // "pte2/pte2bonds.pl", "pte2/pte2gentox.pl", "pte2/pte2ind_nos.pl", "pte2/pte2newgroups.pl"
// "train.b" => not a pure Prolog file but Progol/Aleph specific
- };
+ // };
File owlFile = new File("examples/carcinogenesis/pte.owl");
Program program = null;
@@ -182,6 +184,10 @@
kbString += "DPDOMAIN(" + getURI2("amesTestPositive") + ") = " + getURI2("Compound") + ".\n";
kbString += "DPRANGE(" + getURI2("amesTestPositive") + ") = BOOLEAN.\n";
}
+ if(includeMutagenesis) {
+ kbString += "DPDOMAIN(" + getURI2("isMutagenic") + ") = " + getURI2("Compound") + ".\n";
+ kbString += "DPRANGE(" + getURI2("isMutagenic") + ") = BOOLEAN.\n";
+ }
kbString += "OPDOMAIN(" + getURI2("hasAtom") + ") = " + getURI2("Compound") + ".\n";
kbString += "OPRANGE(" + getURI2("hasAtom") + ") = " + getURI2("Atom") + ".\n";
kbString += "OPDOMAIN(" + getURI2("hasBond") + ") = " + getURI2("Compound") + ".\n";
@@ -205,6 +211,10 @@
for (Axiom axiom : axioms)
kb.addAxiom(axiom);
}
+
+ if(includeMutagenesis)
+ addMutagenesis(kb);
+
// special handling for ames test (we assume the ames test
// was performed on all compounds but only the positive ones
// are in ames.pl [the rest is negative in Prolog by CWA], so
@@ -395,42 +405,39 @@
// if(!useNewGroups) {
String compoundName = head.getArgument(0).toPLString();
String structureName = head.getArgument(1).toPLString();
-// int count = Integer.parseInt(head.getArgument(2).toPLString());
+ int count = Integer.parseInt(head.getArgument(2).toPLString());
// upper case first letter
String structureClass = structureName.substring(0,1).toUpperCase() + structureName.substring(1);;
String structureInstance = structureName + "-" + structureNr;
addStructureSubclass(axioms, structureClass);
-// for(int i=0; i<count; i++) {
+ for(int i=0; i<count; i++) {
ObjectPropertyAssertion op = getRoleAssertion("hasStructure", compoundName, structureInstance);
axioms.add(op);
// make e.g. halide10-382 instance of Bond-3
ClassAssertionAxiom ca = getConceptAssertion(structureClass, structureInstance);
axioms.add(ca);
structureNr++;
+ }
// }
-// }
} else if (headName.equals("ashby_alert")) {
// ... currently ignored ...
} else if (newGroups.contains(headName)) {
if(useNewGroups) {
String compoundName = head.getArgument(0).toPLString();
String structureName = headName;
-// int count = Integer.parseInt(head.getArgument(2).toPLString());
// upper case first letter
String structureClass = structureName.substring(0,1).toUpperCase() + structureName.substring(1);;
String structureInstance = structureName + "-" + structureNr;
addStructureSubclass(axioms, structureClass);
-// for(int i=0; i<count; i++) {
ObjectPropertyAssertion op = getRoleAssertion("hasStructure", compoundName, structureInstance);
axioms.add(op);
ClassAssertionAxiom ca = getConceptAssertion(structureClass, structureInstance);
axioms.add(ca);
structureNr++;
-// }
}
} else {
// print clauses which are not supported yet
@@ -732,4 +739,36 @@
return ret;
}
+ private static void addMutagenesis(KB kb) {
+ String[] mutagenicCompounds = new String[] {
+ "d101", "d104", "d106", "d107", "d112", "d113", "d117",
+ "d121", "d123", "d126", "d128", "d13", "d135", "d137",
+ "d139", "d140", "d143", "d144", "d145", "d146", "d147",
+ "d152", "d153", "d154", "d155", "d156", "d159", "d160",
+ "d161", "d163", "d164", "d166", "d168", "d171", "d173",
+ "d174", "d177", "d179", "d18", "d180", "d182", "d183",
+ "d185", "d186", "d187", "d188", "d189", "d19", "d191",
+ "d192", "d193", "d195", "d197", "d2", "d201", "d202",
+ "d205", "d206", "d207", "d211", "d214", "d215", "d216",
+ "d224", "d225", "d227", "d228", "d229", "d231", "d235",
+ "d237", "d239", "d242", "d245", "d246", "d249", "d251",
+ "d254", "d257", "d258", "d261", "d264", "d266", "d269",
+ "d27", "d270", "d271", "d28", "d288", "d292", "d297",
+ "d300", "d308", "d309", "d311", "d313", "d314", "d322",
+ "d323", "d324", "d329", "d330", "d332", "d334", "d35",
+ "d36", "d37", "d38", "d41", "d42", "d48", "d50", "d51",
+ "d54", "d58", "d61", "d62", "d63", "d66", "d69", "d72",
+ "d76", "d77", "d78", "d84", "d86", "d89", "d92", "d96"};
+ TreeSet<String> mutagenic = new TreeSet<String>(Arrays.asList(mutagenicCompounds));
+
+ for(String compound : compounds) {
+ if(mutagenic.contains(compound)) {
+ BooleanDatatypePropertyAssertion muta = getBooleanDatatypePropertyAssertion(compound, "isMutagenic", true);
+ kb.addAxiom(muta);
+ } else {
+ BooleanDatatypePropertyAssertion muta = getBooleanDatatypePropertyAssertion(compound, "isMutagenic", false);
+ kb.addAxiom(muta);
+ }
+ }
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -760,6 +760,7 @@
return identifier;
}
+ @Override
public void releaseKB() {
connector.releaseKB(kbURI);
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -50,6 +50,9 @@
import org.dllearner.core.owl.Negation;
import org.dllearner.core.owl.Nothing;
import org.dllearner.core.owl.ObjectAllRestriction;
+import org.dllearner.core.owl.ObjectCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMaxCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.ObjectPropertyExpression;
import org.dllearner.core.owl.ObjectPropertyHierarchy;
@@ -290,6 +293,82 @@
return false;
}
return true;
+ } else if (description instanceof ObjectMinCardinalityRestriction) {
+ ObjectPropertyExpression ope = ((ObjectCardinalityRestriction) description).getRole();
+ if (!(ope instanceof ObjectProperty))
+ throw new ReasoningMethodUnsupportedException("Instance check for description "
+ + description + " unsupported. Inverse object properties not supported.");
+ ObjectProperty op = (ObjectProperty) ope;
+ Description child = description.getChild(0);
+ Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
+
+ if (mapping == null) {
+ logger.warn("Instance check of a description with an undefinied property (" + op
+ + ").");
+ return true;
+ }
+
+ int number = ((ObjectCardinalityRestriction) description).getNumber();
+ int nrOfFillers = 0;
+
+ SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+ // return false if there are none or not enough role fillers
+ if (roleFillers == null || roleFillers.size() < number)
+ return false;
+
+ int index = 0;
+ for (Individual roleFiller : roleFillers) {
+ index++;
+ if (instanceCheck(child, roleFiller)) {
+ nrOfFillers++;
+ if(nrOfFillers == number)
+ return true;
+ // earyl abort: e.g. >= 10 hasStructure.Methyl;
+ // if there are 11 fillers and 2 are not Methyl, the result is false
+ } /* else {
+ if(roleFillers.size() - index < number)
+ return false;
+ }*/
+ }
+ return false;
+ } else if (description instanceof ObjectMaxCardinalityRestriction) {
+ ObjectPropertyExpression ope = ((ObjectCardinalityRestriction) description).getRole();
+ if (!(ope instanceof ObjectProperty))
+ throw new ReasoningMethodUnsupportedException("Instance check for description "
+ + description + " unsupported. Inverse object properties not supported.");
+ ObjectProperty op = (ObjectProperty) ope;
+ Description child = description.getChild(0);
+ Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
+
+ if (mapping == null) {
+ logger.warn("Instance check of a description with an undefinied property (" + op
+ + ").");
+ return true;
+ }
+
+ int number = ((ObjectCardinalityRestriction) description).getNumber();
+ int nrOfFillers = 0;
+
+ SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+ // return false if there are none or not enough role fillers
+ if (roleFillers == null || roleFillers.size() > number)
+ return true;
+
+ int index = 0;
+ for (Individual roleFiller : roleFillers) {
+ index++;
+ if (instanceCheck(child, roleFiller)) {
+ nrOfFillers++;
+ if(nrOfFillers == number)
+ return false;
+ // earyl abort: e.g. <= 5 hasStructure.Methyl;
+ // if there are 6 fillers and 2 are not Methyl, the result is true
+ } /* else {
+ if(roleFillers.size() - index <= number)
+ return true;
+ } */
+ }
+ return true;
} else if (description instanceof BooleanValueRestriction) {
DatatypeProperty dp = ((BooleanValueRestriction)description).getRestrictedPropertyExpresssion();
boolean value = ((BooleanValueRestriction)description).getBooleanValue();
@@ -503,6 +582,19 @@
@Override
public Description getRange(ObjectProperty objectProperty) {
return rc.getRange(objectProperty);
+ }
+
+ @Override
+ public Map<Individual, SortedSet<Individual>> getRoleMembers(ObjectProperty atomicRole) {
+ return opPos.get(atomicRole);
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.ReasonerComponent#releaseKB()
+ */
+ @Override
+ public void releaseKB() {
+ rc.releaseKB();
}
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -182,5 +182,13 @@
*/
public Map<String, String> getPrefixes() {
return rc.getPrefixes();
- }
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.ReasonerComponent#releaseKB()
+ */
+ @Override
+ public void releaseKB() {
+ rc.releaseKB();
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -1021,4 +1021,18 @@
return prefixes;
}
+ /* (non-Javadoc)
+ * @see org.dllearner.core.ReasonerComponent#releaseKB()
+ */
+ @Override
+ public void releaseKB() {
+ try {
+ reasoner.clearOntologies();
+ reasoner.dispose();
+ } catch (OWLReasonerException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -32,6 +32,7 @@
import java.util.TreeSet;
import java.util.Map.Entry;
+import org.apache.log4j.Logger;
import org.dllearner.algorithms.refinement.RefinementOperator;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.BooleanValueRestriction;
@@ -47,6 +48,9 @@
import org.dllearner.core.owl.Negation;
import org.dllearner.core.owl.Nothing;
import org.dllearner.core.owl.ObjectAllRestriction;
+import org.dllearner.core.owl.ObjectCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMaxCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.ObjectPropertyExpression;
import org.dllearner.core.owl.ObjectQuantorRestriction;
@@ -72,6 +76,10 @@
*/
public class RhoDRDown implements RefinementOperator {
+ @SuppressWarnings({"unused"})
+ private static Logger logger = Logger
+ .getLogger(RhoDRDown.class);
+
private ReasoningService rs;
// hierarchies
@@ -82,6 +90,9 @@
private Map<DatatypeProperty,Description> dpDomains = new TreeMap<DatatypeProperty,Description>();
private Map<ObjectProperty,Description> opRanges = new TreeMap<ObjectProperty,Description>();
+ // maximum number of fillers for eeach role
+ private Map<ObjectProperty,Integer> maxNrOfFillers = new TreeMap<ObjectProperty,Integer>();
+
// start concept (can be used to start from an arbitrary concept, needs
// to be Thing or NamedClass), note that when you use e.g. Compound as
// start class, then the algorithm should start the search with class
@@ -137,6 +148,7 @@
private boolean applyExistsFilter = true;
private boolean useAllConstructor = true;
private boolean useExistsConstructor = true;
+ private boolean useCardinalityRestrictions = true;
private boolean useNegation = true;
private boolean useBooleanDatatypes = true;
private boolean useDoubleDatatypes = true;
@@ -181,7 +193,36 @@
computeSplits(dp);
}
+ // determine the maximum number of fillers for each role
+ for(ObjectProperty op : rs.getAtomicRoles()) {
+ int maxFillers = 0;
+ Map<Individual,SortedSet<Individual>> opMembers = rs.getRoleMembers(op);
+ for(SortedSet<Individual> inds : opMembers.values()) {
+ if(inds.size()>maxFillers)
+ maxFillers = inds.size();
+ }
+ maxNrOfFillers.put(op, maxFillers);
+ }
+
/*
+ String conceptStr = "(\"http://dl-learner.org/carcinogenesis#Compound\" AND (>= 2 \"http://dl-learner.org/carcinogenesis#hasStructure\".\"http://dl-learner.org/carcinogenesis#Ar_halide\" OR ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) AND >= 5 \"http://dl-learner.org/carcinogenesis#hasBond\". TOP)))";
+ try {
+ NamedClass struc = new NamedClass("http://dl-learner.org/carcinogenesis#Compound");
+ Description d = KBParser.parseConcept(conceptStr);
+ SortedSet<Description> ds = (SortedSet<Description>) refine(d,15,null,struc);
+ System.out.println(ds);
+
+ Individual i = new Individual("http://dl-learner.org/carcinogenesis#d101");
+ rs.instanceCheck(ds.first(), i);
+
+ } catch (ParseException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ System.exit(0);
+ */
+
+ /*
NamedClass struc = new NamedClass("http://dl-learner.org/carcinogenesis#Atom");
ObjectProperty op = new ObjectProperty("http://dl-learner.org/carcinogenesis#hasAtom");
ObjectSomeRestriction oar = new ObjectSomeRestriction(op,Thing.instance);
@@ -222,7 +263,7 @@
public Set<Description> refine(Description description, int maxLength,
List<Description> knownRefinements, Description currDomain) {
-// System.out.println(description + " " + currDomain + " " + maxLength);
+// logger.trace(description + " " + currDomain + " " + maxLength);
// actions needing to be performed if this is the first time the
// current domain is used
@@ -336,6 +377,15 @@
for(ObjectProperty moreSpecialRole : moreSpecialRoles)
refinements.add(new ObjectSomeRestriction(moreSpecialRole, description.getChild(0)));
+ // rule 3: EXISTS r.D => >= 2 r.D
+ // (length increases by 1 so we have to check whether max length is sufficient)
+ if(useCardinalityRestrictions) {
+ if(maxLength > description.getLength() && maxNrOfFillers.get(ar)>1) {
+ ObjectMinCardinalityRestriction min = new ObjectMinCardinalityRestriction(2,role,description.getChild(0));
+ refinements.add(min);
+ }
+ }
+
} else if (description instanceof ObjectAllRestriction) {
ObjectPropertyExpression role = ((ObjectQuantorRestriction)description).getRole();
Description range = opRanges.get(role);
@@ -360,6 +410,28 @@
refinements.add(new ObjectAllRestriction(moreSpecialRole, description.getChild(0)));
}
+ // rule 4: ALL r.D => <= (maxFillers-1) r.D
+ // (length increases by 1 so we have to check whether max length is sufficient)
+ if(useCardinalityRestrictions) {
+ if(maxLength > description.getLength() && maxNrOfFillers.get(ar)>1) {
+ ObjectMaxCardinalityRestriction max = new ObjectMaxCardinalityRestriction(maxNrOfFillers.get(ar)-1,role,description.getChild(0));
+ refinements.add(max);
+ }
+ }
+ } else if (description instanceof ObjectCardinalityRestriction) {
+ if(description instanceof ObjectMaxCardinalityRestriction) {
+ // <= x r.C => <= (x-1) r.C
+ ObjectMaxCardinalityRestriction max = (ObjectMaxCardinalityRestriction) description;
+ int number = max.getNumber();
+ if(number > 0)
+ refinements.add(new ObjectMaxCardinalityRestriction(number-1,max.getRole(),max.getChild(0)));
+ } else if(description instanceof ObjectMinCardinalityRestriction) {
+ // >= x r.C => >= (x+1) r.C
+ ObjectMinCardinalityRestriction min = (ObjectMinCardinalityRestriction) description;
+ int number = min.getNumber();
+ if(number < maxNrOfFillers.get(min.getRole()))
+ refinements.add(new ObjectMinCardinalityRestriction(number+1,min.getRole(),min.getChild(0)));
+ }
} else if (description instanceof DatatypeSomeRestriction) {
DatatypeSomeRestriction dsr = (DatatypeSomeRestriction) description;
@@ -434,6 +506,7 @@
}
// check for double datatype properties
+ /*
if(c instanceof DatatypeSomeRestriction &&
description instanceof DatatypeSomeRestriction) {
DataRange dr = ((DatatypeSomeRestriction)c).getDataRange();
@@ -442,7 +515,7 @@
if((dr instanceof DoubleMaxValue && dr2 instanceof DoubleMaxValue)
||(dr instanceof DoubleMinValue && dr2 instanceof DoubleMinValue))
skip = true;
- }
+ }*/
// perform a disjointness check when named classes are added;
// this can avoid a lot of superfluous computation in the algorithm e.g.
@@ -462,7 +535,9 @@
ConceptTransformation.cleanConceptNonRecursive(mc);
ConceptTransformation.transformToOrderedNegationNormalFormNonRecursive(mc, conceptComparator);
- refinements.add(mc);
+ // last check before intersection is added
+ if(checkIntersection(mc))
+ refinements.add(mc);
}
}
}
@@ -481,11 +556,15 @@
// when a child of an intersection is refined and reintegrated into the
// intersection, we can perform some sanity checks;
// method returns true if everything is OK and false otherwise
- private boolean checkIntersection(Intersection intersection) {
+ // TODO: can be implemented more efficiently if the newly added child
+ // is given as parameter
+ public static boolean checkIntersection(Intersection intersection) {
// rule 1: max. restrictions at most once
boolean maxDoubleOccurence = false;
// rule 2: min restrictions at most once
boolean minDoubleOccurence = false;
+ // rule 3: no double boolean datatypes
+ TreeSet<DatatypeProperty> occuredDP = new TreeSet<DatatypeProperty>();
for(Description child : intersection.getChildren()) {
if(child instanceof DatatypeSomeRestriction) {
DataRange dr = ((DatatypeSomeRestriction)child).getDataRange();
@@ -500,7 +579,14 @@
else
minDoubleOccurence = true;
}
+ } else if(child instanceof BooleanValueRestriction) {
+ DatatypeProperty dp = (DatatypeProperty) ((BooleanValueRestriction)child).getRestrictedPropertyExpression();
+// System.out.println("dp: " + dp);
+ // return false if the boolean property exists already
+ if(!occuredDP.add(dp))
+ return false;
}
+// System.out.println(child.getClass());
}
return true;
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/ConceptComparator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/ConceptComparator.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/utilities/ConceptComparator.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -12,6 +12,9 @@
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Nothing;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.ObjectCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMaxCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
import org.dllearner.core.owl.ObjectSomeRestriction;
import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.SimpleDoubleDataRange;
@@ -172,6 +175,46 @@
return roleCompare;
} else
return -1;
+ } else if(concept1 instanceof ObjectMinCardinalityRestriction) {
+ if(concept2.getChildren().size()<1 || concept2 instanceof Negation || concept2 instanceof ObjectQuantorRestriction)
+ return 1;
+ // first criterion: object property
+ // second criterion: number
+ // third criterion: children
+ else if(concept2 instanceof ObjectMinCardinalityRestriction) {
+ int roleCompare = rc.compare(((ObjectCardinalityRestriction)concept1).getRole(), ((ObjectCardinalityRestriction)concept2).getRole());
+ if(roleCompare == 0) {
+ Integer number1 = ((ObjectCardinalityRestriction)concept1).getNumber();
+ Integer number2 = ((ObjectCardinalityRestriction)concept2).getNumber();
+ int numberCompare = number1.compareTo(number2);
+ if(numberCompare == 0)
+ return compare(concept1.getChild(0), concept2.getChild(0));
+ else
+ return numberCompare;
+ } else
+ return roleCompare;
+ } else
+ return -1;
+ } else if(concept1 instanceof ObjectMaxCardinalityRestriction) {
+ if(concept2.getChildren().size()<1 || concept2 instanceof Negation || concept2 instanceof ObjectQuantorRestriction || concept2 instanceof ObjectMinCardinalityRestriction)
+ return 1;
+ // first criterion: object property
+ // second criterion: number
+ // third criterion: children
+ else if(concept2 instanceof ObjectMaxCardinalityRestriction) {
+ int roleCompare = rc.compare(((ObjectCardinalityRestriction)concept1).getRole(), ((ObjectCardinalityRestriction)concept2).getRole());
+ if(roleCompare == 0) {
+ Integer number1 = ((ObjectCardinalityRestriction)concept1).getNumber();
+ Integer number2 = ((ObjectCardinalityRestriction)concept2).getNumber();
+ int numberCompare = number1.compareTo(number2);
+ if(numberCompare == 0)
+ return compare(concept1.getChild(0), concept2.getChild(0));
+ else
+ return numberCompare;
+ } else
+ return roleCompare;
+ } else
+ return -1;
} else if(concept1 instanceof Intersection) {
if(concept2.getChildren().size()<2)
return 1;
Modified: trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java 2008-03-14 22:58:35 UTC (rev 712)
+++ trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java 2008-03-16 19:03:46 UTC (rev 713)
@@ -21,9 +21,11 @@
import java.io.File;
import java.text.DecimalFormat;
+import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
+import java.util.Random;
import java.util.Set;
import org.apache.log4j.ConsoleAppender;
@@ -65,20 +67,27 @@
else
leaveOneOut = true;
+ if(folds < 2) {
+ System.out.println("At least 2 fold needed.");
+ System.exit(0);
+ }
+
// create logger (a simple logger which outputs
// its messages to the console)
SimpleLayout layout = new SimpleLayout();
ConsoleAppender consoleAppender = new ConsoleAppender(layout);
logger.removeAllAppenders();
logger.addAppender(consoleAppender);
- logger.setLevel(Level.WARN);
+ logger.setLevel(Level.WARN);
+ // disable OWL API info output
+ java.util.logging.Logger.getLogger("").setLevel(java.util.logging.Level.WARNING);
new CrossValidation(file, folds, leaveOneOut);
}
public CrossValidation(File file, int folds, boolean leaveOneOut) {
-
+
DecimalFormat df = new DecimalFormat();
ComponentManager cm = ComponentManager.getInstance();
@@ -104,10 +113,13 @@
if(lp instanceof PosNegLP) {
+ // get examples and shuffle them to
Set<Individual> posExamples = ((PosNegLP)lp).getPositiveExamples();
List<Individual> posExamplesList = new LinkedList<Individual>(posExamples);
+ Collections.shuffle(posExamplesList, new Random(1));
Set<Individual> negExamples = ((PosNegLP)lp).getNegativeExamples();
List<Individual> negExamplesList = new LinkedList<Individual>(negExamples);
+ Collections.shuffle(negExamplesList, new Random(2));
// sanity check whether nr. of folds makes sense for this benchmark
if(!leaveOneOut && (posExamples.size()<folds && negExamples.size()<folds)) {
@@ -138,6 +150,9 @@
int[] splitsPos = calculateSplits(posExamples.size(),folds);
int[] splitsNeg = calculateSplits(negExamples.size(),folds);
+// System.out.println(splitsPos[0]);
+// System.out.println(splitsNeg[0]);
+
// calculating training and test sets
for(int i=0; i<folds; i++) {
Set<Individual> testPos = getTestingSet(posExamplesList, splitsPos, i);
@@ -180,16 +195,45 @@
Set<String> neg = Datastructures.individualSetToStringSet(trainingSetsNeg.get(currFold));
cm.applyConfigEntry(lp, "positiveExamples", pos);
cm.applyConfigEntry(lp, "negativeExamples", neg);
+// System.out.println("pos: " + pos.size());
+// System.out.println("neg: " + neg.size());
+// System.exit(0);
+ // es fehlt init zwischendurch
+
LearningAlgorithm la = start.getLearningAlgorithm();
+ // init again, because examples have changed
+ try {
+ la.init();
+ } catch (ComponentInitException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
long algorithmStartTime = System.nanoTime();
la.start();
long algorithmDuration = System.nanoTime() - algorithmStartTime;
runtime.addNumber(algorithmDuration/(double)1000000000);
Description concept = la.getBestSolution();
- int correctExamples = getCorrectPosClassified(rs, concept, testSetsPos.get(currFold))
- + getCorrectNegClassified(rs, concept, testSetsNeg.get(currFold));
+
+ Set<Individual> tmp = rs.instanceCheck(concept, testSetsPos.get(currFold));
+ Set<Individual> tmp2 = Helper.difference(testSetsPos.get(currFold), tmp);
+ Set<Individual> tmp3 = rs.instanceCheck(concept, testSetsNeg.get(currFold));
+
+ System.out.println("test set errors pos: " + tmp2);
+ System.out.println("test set errors neg: " + tmp3);
+
+ // calculate training accuracies
+ int trainingCorrectPosClassified = getCorrectPosClassified(rs, concept, trainingSetsPos.get(currFold));
+ int trainingCorrectNegClassified = getCorrectNegClassified(rs, concept, trainingSetsNeg.get(currFold));
+ int trainingCorrectExamples = trainingCorrectPosClassified + trainingCorrectNegClassified;
+ double trainingAccuracy = 100*((double)trainingCorrectExamples/(trainingSetsPos.get(currFold).size()+
+ trainingSetsNeg.get(currFold).size()));
+
+ // calculate test accuracies
+ int correctPosClassified = getCorrectPosClassified(rs, concept, testSetsPos.get(currFold));
+ int correctNegClassified = getCorrectNegClassified(rs, concept, testSetsNeg.get(currFold));
+ int correctExamples = correctPosClassified + correctNegClassified;
double currAccuracy = 100*((double)correctExamples/(testSetsPos.get(currFold).size()+
testSetsNeg.get(currFold).size()));
accuracy.addNumber(currAccuracy);
@@ -197,10 +241,17 @@
length.addNumber(concept.getLength());
System.out.println("fold " + currFold + " (" + file + "):");
+ System.out.println(" training: " + pos.size() + " positive and " + neg.size() + " negative examples");
+ System.out.println(" testing: " + correctPosClassified + "/" + testSetsPos.get(currFold).size() + " correct positives, "
+ + correctNegClassified + "/" + testSetsNeg.get(currFold).size() + " correct negatives");
System.out.println(" concept: " + concept);
- System.out.println(" accuracy: " + df.format(currAccuracy) + "%");
+ System.out.println(" accuracy: " + df.format(currAccuracy) + "% (" + df.format(trainingAccuracy) + "% on training set)");
System.out.println(" length: " + df.format(concept.getLength()));
System.out.println(" runtime: " + df.format(algorithmDuration/(double)1000000000) + "s");
+
+ // free all resources
+ start.getReasoningService().releaseKB();
+ cm.freeAllComponents();
}
System.out.println();
@@ -211,12 +262,12 @@
}
- private int getCorrectPosClassified(ReasoningService rs, Description concept, Set<Individual> posClassified) {
- return rs.instanceCheck(concept, posClassified).size();
+ private int getCorrectPosClassified(ReasoningService rs, Description concept, Set<Individual> testSetPos) {
+ return rs.instanceCheck(concept, testSetPos).size();
}
- private int getCorrectNegClassified(ReasoningService rs, Description concept, Set<Individual> negClassified) {
- return negClassified.size() - rs.instanceCheck(concept, negClassified).size();
+ private int getCorrectNegClassified(ReasoningService rs, Description concept, Set<Individual> testSetNeg) {
+ return testSetNeg.size() - rs.instanceCheck(concept, testSetNeg).size();
}
private Set<Individual> getTestingSet(List<Individual> examples, int[] splits, int fold) {
@@ -229,6 +280,8 @@
// the split corresponds to the ends of the folds
int toIndex = splits[fold];
+// System.out.println("from " + fromIndex + " to " + toIndex);
+
Set<Individual> testingSet = new HashSet<Individual>();
// +1 because 2nd element is exclusive in subList method
testingSet.addAll(examples.subList(fromIndex, toIndex));
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-19 08:11:25
|
Revision: 715
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=715&view=rev
Author: jenslehmann
Date: 2008-03-19 01:11:19 -0700 (Wed, 19 Mar 2008)
Log Message:
-----------
redundancy check bug fixes
changes in heuristic
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-17 10:21:51 UTC (rev 714)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-03-19 08:11:19 UTC (rev 715)
@@ -115,7 +115,7 @@
// the divide&conquer approach in many ILP programs using a
// clause by clause search; after a period of time the candidate
// set is reduced to focus CPU time on the most promising concepts
- private boolean useCandidateReduction = false;
+ private boolean useCandidateReduction = true;
private int candidatePostReductionSize = 30;
// setting to true gracefully stops the algorithm
@@ -244,24 +244,36 @@
}
public void start() {
+
+ // TODO: write a JUnit test for this problem (long-lasting or infinite loops because
+ // redundant children of a node are called recursively after when the node is extended
+ // twice)
/*
// String conceptStr = "(\"http://dl-learner.org/carcinogenesis#Compound\" AND (>= 2 \"http://dl-learner.org/carcinogenesis#hasStructure\".\"http://dl-learner.org/carcinogenesis#Ar_halide\" OR ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) AND >= 5 \"http://dl-learner.org/carcinogenesis#hasBond\". TOP)))";
- String conceptStr = "(\"http://dl-learner.org/carcinogenesis#Compound\" AND ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) AND (\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE)))";
+// String conceptStr = "(\"http://dl-learner.org/carcinogenesis#Compound\" AND ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) AND (\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE)))";
+ String conceptStr = "(\"http://dl-learner.org/carcinogenesis#Compound\" AND (>= 3 \"http://dl-learner.org/carcinogenesis#hasStructure\".\"http://dl-learner.org/carcinogenesis#Halide\" OR ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) AND ALL \"http://dl-learner.org/carcinogenesis#hasAtom\".TOP)))";
+ String conceptStr2 = "(\"http://dl-learner.org/carcinogenesis#Compound\" AND (>= 4 \"http://dl-learner.org/carcinogenesis#hasStructure\".\"http://dl-learner.org/carcinogenesis#Halide\" OR ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) AND ALL \"http://dl-learner.org/carcinogenesis#hasAtom\".TOP)))";
try {
NamedClass struc = new NamedClass("http://dl-learner.org/carcinogenesis#Compound");
Description d = KBParser.parseConcept(conceptStr);
+ Description d2 = KBParser.parseConcept(conceptStr2);
// SortedSet<Description> ds = (SortedSet<Description>) operator.refine(d,15,null,struc);
// System.out.println(ds);
- System.out.println(RhoDRDown.checkIntersection((Intersection)d));
+// System.out.println(RhoDRDown.checkIntersection((Intersection)d));
Set<Individual> coveredNegatives = rs.instanceCheck(d, learningProblem.getNegativeExamples());
Set<Individual> coveredPositives = rs.instanceCheck(d, learningProblem.getPositiveExamples());
ExampleBasedNode ebn = new ExampleBasedNode(d);
ebn.setCoveredExamples(coveredPositives, coveredNegatives);
- extendNodeProper(ebn,15);
+ properRefinements.add(d2);
+ extendNodeProper(ebn,13);
+ extendNodeProper(ebn,14);
+ for(Description refinement: ebn.getChildConcepts())
+ System.out.println("refinement: " + refinement);
+
// Individual i = new Individual("http://dl-learner.org/carcinogenesis#d101");
// for(Individual i : learningProblem.getPositiveExamples())
// rs.instanceCheck(ds.last(), i);
@@ -308,7 +320,7 @@
// print statistics at most once a second
currentTime = System.nanoTime();
- if(currentTime - lastPrintTime > 1000000000) {
+ if(currentTime - lastPrintTime > 3000000000l) {
printStatistics(false);
lastPrintTime = currentTime;
logger.debug("--- loop " + loop + " started ---");
@@ -327,7 +339,7 @@
// Logger.getRootLogger().setLevel(Level.TRACE);
}
- System.out.println("next expanded: " + candidates.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
+// System.out.println("next expanded: " + candidates.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
// chose best node according to heuristics
bestNode = candidates.last();
// extend best node
@@ -434,8 +446,11 @@
childConceptsDeletionTimeNs += System.nanoTime() - childConceptsDeletionTimeNsStart;
-// if(refinements.size()<30)
-// System.out.println("refinements: " + refinements);
+// if(refinements.size()<30) {
+//// System.out.println("refinements: " + refinements);
+// for(Description refinement: refinements)
+// System.out.println("refinement: " + refinement);
+// }
long evaluateSetCreationTimeNsStart = System.nanoTime();
@@ -463,7 +478,7 @@
propernessTestsAvoidedByShortConceptConstruction++;
propernessDetected = true;
- System.out.println("refinement " + refinement + " can be shortened");
+// System.out.println("refinement " + refinement + " can be shortened");
// System.exit(0);
}
}
@@ -517,7 +532,7 @@
}
evaluateSetCreationTimeNs += System.nanoTime() - evaluateSetCreationTimeNsStart;
-// System.out.println("intermediate 1");
+// System.out.println("intermediate 1 " + node.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
// System.out.println(toEvaluateConcepts.size());
@@ -678,8 +693,17 @@
for(Description refinement : refinements) {
// for(int i=0; i<=recDepth; i++)
// System.out.print(" ");
-// System.out.println("call: " + refinement + " [maxLength " + maxLength + "]");
- extendNodeProper(node, refinement, maxLength, recDepth+1);
+// System.out.println("call: " + refinement + " [maxLength " + maxLength + ", rec depth " + recDepth + "]");
+
+ // check for redundancy (otherwise we may run into very time-intensive loops,
+ // see planned JUnit test case $x)
+
+ long redundancyCheckTimeNsStart = System.nanoTime();
+ boolean redundant = properRefinements.contains(refinement);
+ redundancyCheckTimeNs += System.nanoTime() - redundancyCheckTimeNsStart;
+
+ if(!redundant)
+ extendNodeProper(node, refinement, maxLength, recDepth+1);
// for(int i=0; i<=recDepth; i++)
// System.out.print(" ");
// System.out.println("finished: " + refinement + " [maxLength " + maxLength + "]");
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-17 10:21:51 UTC (rev 714)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-03-19 08:11:19 UTC (rev 715)
@@ -79,6 +79,9 @@
private double gainBonusFactor;
private double nodeChildPenalty = 0.0001;
private double startNodeBonus = 1.0;
+ // penalise errors on positive examples harder than on negative examples
+ // (positive weight = 1)
+ private double negativeWeight = 0.8;
// examples
private int nrOfNegativeExamples;
@@ -113,11 +116,11 @@
}
public double getNodeScore(ExampleBasedNode node) {
- double accuracy = getAccuracy(node.getCoveredPositives().size(),node.getCoveredNegatives().size());
+ double accuracy = getWeightedAccuracy(node.getCoveredPositives().size(),node.getCoveredNegatives().size());
ExampleBasedNode parent = node.getParent();
double gain = 0;
if(parent != null) {
- double parentAccuracy = getAccuracy(parent.getCoveredPositives().size(),parent.getCoveredNegatives().size());
+ double parentAccuracy = getWeightedAccuracy(parent.getCoveredPositives().size(),parent.getCoveredNegatives().size());
gain = accuracy - parentAccuracy;
} else {
accuracy += startNodeBonus;
@@ -126,9 +129,8 @@
return accuracy + gainBonusFactor * gain - expansionPenaltyFactor * he - nodeChildPenalty * node.getChildren().size();
}
- private double getAccuracy(int coveredPositives, int coveredNegatives) {
- return (coveredPositives + nrOfNegativeExamples - coveredNegatives)/(double)nrOfExamples;
-
+ private double getWeightedAccuracy(int coveredPositives, int coveredNegatives) {
+ return (coveredPositives + negativeWeight * (nrOfNegativeExamples - coveredNegatives))/(double)nrOfExamples;
}
public static double getNodeScore(ExampleBasedNode node, int nrOfPositiveExamples, int nrOfNegativeExamples) {
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-03-17 10:21:51 UTC (rev 714)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-03-19 08:11:19 UTC (rev 715)
@@ -123,6 +123,9 @@
private static boolean learnCarcinogenic = true;
private static boolean useNewGroups = true;
+ private static boolean createPTE1Conf = false;
+ private static boolean createPTE2Conf = false;
+
/**
* @param args
* No arguments supported.
@@ -133,14 +136,13 @@
public static void main(String[] args) throws FileNotFoundException, IOException,
ParseException {
- // TODO: newgroups are not mapped currently
String[] files = new String[] { "newgroups.pl", "ames.pl", "atoms.pl", "bonds.pl", "gentoxprops.pl",
"ind_nos.pl", "ind_pos.pl"};
// "pte2/canc_nos.pl", "pte2/pte2ames.pl", "pte2/pte2atoms.pl",
// "pte2/pte2bonds.pl", "pte2/pte2gentox.pl", "pte2/pte2ind_nos.pl", "pte2/pte2newgroups.pl"
// "train.b" => not a pure Prolog file but Progol/Aleph specific
// };
- File owlFile = new File("examples/carcinogenesis/pte.owl");
+ File owlFile = new File("examples/carcinogenesis/carcinogenesis.owl");
Program program = null;
long startTime, duration;
@@ -281,7 +283,6 @@
// generating test examples for PTE-1
// => put all in one file, because they were used as training for PTE-2
File confPTE1File = new File("examples/carcinogenesis/testpte1.conf");
- Files.clearFile(confPTE1File);
File testPTE1Positives = new File(prologDirectory + "pte1.f");
File testPTE1Negatives = new File(prologDirectory + "pte1.n");
@@ -289,16 +290,20 @@
List<Individual> negPTE1Examples = getExamples(testPTE1Negatives);
appendPosExamples(confTrainFile, posPTE1Examples);
appendNegExamples(confTrainFile, negPTE1Examples);
- Files.clearFile(confPTE1File);
- Files.appendFile(confPTE1File, "import(\"pte.owl\");\nreasoner=fastInstanceChecker;\n\n");
- appendPosExamples(confPTE1File, posPTE1Examples);
- appendNegExamples(confPTE1File, negPTE1Examples);
+ if(createPTE1Conf) {
+ Files.clearFile(confPTE1File);
+ Files.appendFile(confPTE1File, "import(\"pte.owl\");\nreasoner=fastInstanceChecker;\n\n");
+ appendPosExamples(confPTE1File, posPTE1Examples);
+ appendNegExamples(confPTE1File, negPTE1Examples);
+ }
// create a PTE-2 test file
- File confPTE2File = new File("examples/carcinogenesis/testpte2.conf");
- Files.clearFile(confPTE2File);
- Files.appendFile(confPTE2File, "import(\"pte.owl\");\nreasoner=fastInstanceChecker;\n\n");
- Files.appendFile(confPTE2File, getPTE2Examples());
+ if(createPTE2Conf) {
+ File confPTE2File = new File("examples/carcinogenesis/testpte2.conf");
+ Files.clearFile(confPTE2File);
+ Files.appendFile(confPTE2File, "import(\"pte.owl\");\nreasoner=fastInstanceChecker;\n\n");
+ Files.appendFile(confPTE2File, getPTE2Examples());
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-17 10:21:51 UTC (rev 714)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-19 08:11:19 UTC (rev 715)
@@ -325,10 +325,10 @@
return true;
// earyl abort: e.g. >= 10 hasStructure.Methyl;
// if there are 11 fillers and 2 are not Methyl, the result is false
- } /* else {
+ } else {
if(roleFillers.size() - index < number)
return false;
- }*/
+ }
}
return false;
} else if (description instanceof ObjectMaxCardinalityRestriction) {
@@ -363,10 +363,10 @@
return false;
// earyl abort: e.g. <= 5 hasStructure.Methyl;
// if there are 6 fillers and 2 are not Methyl, the result is true
- } /* else {
+ } else {
if(roleFillers.size() - index <= number)
return true;
- } */
+ }
}
return true;
} else if (description instanceof BooleanValueRestriction) {
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-17 10:21:51 UTC (rev 714)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-19 08:11:19 UTC (rev 715)
@@ -92,6 +92,10 @@
// maximum number of fillers for eeach role
private Map<ObjectProperty,Integer> maxNrOfFillers = new TreeMap<ObjectProperty,Integer>();
+ // limit for cardinality restrictions (this makes sense if we e.g. have compounds with up to
+ // more than 200 atoms but we are only interested in atoms with certain characteristics and do
+ // not want something like e.g. >= 204 hasAtom.NOT Carbon-87; which blows up the search space
+ private int cardinalityLimit = 5;
// start concept (can be used to start from an arbitrary concept, needs
// to be Thing or NamedClass), note that when you use e.g. Compound as
@@ -105,7 +109,7 @@
private int topRefinementsLength = 0;
private Map<NamedClass, Integer> topARefinementsLength = new TreeMap<NamedClass, Integer>();
// M is finite and this value is the maximum length of any value in M
- private static int mMaxLength = 3;
+ private static int mMaxLength = 4;
// the sets M_\top and M_A
private Map<Integer,SortedSet<Description>> m = new TreeMap<Integer,SortedSet<Description>>();
@@ -194,15 +198,22 @@
}
// determine the maximum number of fillers for each role
+ // (up to a specified cardinality maximum)
+ if(useCardinalityRestrictions) {
for(ObjectProperty op : rs.getAtomicRoles()) {
int maxFillers = 0;
Map<Individual,SortedSet<Individual>> opMembers = rs.getRoleMembers(op);
for(SortedSet<Individual> inds : opMembers.values()) {
if(inds.size()>maxFillers)
maxFillers = inds.size();
+ if(maxFillers >= cardinalityLimit) {
+ maxFillers = cardinalityLimit;
+ break;
+ }
}
maxNrOfFillers.put(op, maxFillers);
}
+ }
/*
String conceptStr = "(\"http://dl-learner.org/carcinogenesis#Compound\" AND (>= 2 \"http://dl-learner.org/carcinogenesis#hasStructure\".\"http://dl-learner.org/carcinogenesis#Ar_halide\" OR ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) AND >= 5 \"http://dl-learner.org/carcinogenesis#hasBond\". TOP)))";
@@ -412,23 +423,41 @@
// rule 4: ALL r.D => <= (maxFillers-1) r.D
// (length increases by 1 so we have to check whether max length is sufficient)
- if(useCardinalityRestrictions) {
- if(maxLength > description.getLength() && maxNrOfFillers.get(ar)>1) {
- ObjectMaxCardinalityRestriction max = new ObjectMaxCardinalityRestriction(maxNrOfFillers.get(ar)-1,role,description.getChild(0));
- refinements.add(max);
- }
- }
+ // => commented out because this is acutally not a downward refinement
+// if(useCardinalityRestrictions) {
+// if(maxLength > description.getLength() && maxNrOfFillers.get(ar)>1) {
+// ObjectMaxCardinalityRestriction max = new ObjectMaxCardinalityRestriction(maxNrOfFillers.get(ar)-1,role,description.getChild(0));
+// refinements.add(max);
+// }
+// }
} else if (description instanceof ObjectCardinalityRestriction) {
+ ObjectPropertyExpression role = ((ObjectCardinalityRestriction)description).getRole();
+ Description range = opRanges.get(role);
+ int number = ((ObjectCardinalityRestriction)description).getCardinality();
if(description instanceof ObjectMaxCardinalityRestriction) {
- // <= x r.C => <= (x-1) r.C
+ // rule 1: <= x r.C => <= x r.D
+ tmp = refine(description.getChild(0), maxLength-3, null, range);
+
+ for(Description d : tmp) {
+ refinements.add(new ObjectMaxCardinalityRestriction(number,role,d));
+ }
+
+ // rule 2: <= x r.C => <= (x-1) r.C
ObjectMaxCardinalityRestriction max = (ObjectMaxCardinalityRestriction) description;
- int number = max.getNumber();
- if(number > 0)
+// int number = max.getNumber();
+ if(number > 1)
refinements.add(new ObjectMaxCardinalityRestriction(number-1,max.getRole(),max.getChild(0)));
+
} else if(description instanceof ObjectMinCardinalityRestriction) {
+ tmp = refine(description.getChild(0), maxLength-3, null, range);
+
+ for(Description d : tmp) {
+ refinements.add(new ObjectMinCardinalityRestriction(number,role,d));
+ }
+
// >= x r.C => >= (x+1) r.C
ObjectMinCardinalityRestriction min = (ObjectMinCardinalityRestriction) description;
- int number = min.getNumber();
+// int number = min.getNumber();
if(number < maxNrOfFillers.get(min.getRole()))
refinements.add(new ObjectMinCardinalityRestriction(number+1,min.getRole(),min.getChild(0)));
}
@@ -723,7 +752,7 @@
long mComputationTimeStartNs = System.nanoTime();
// initialise all possible lengths (1 to 3)
- for(int i=1; i<=3; i++) {
+ for(int i=1; i<=mMaxLength; i++) {
m.put(i, new TreeSet<Description>(conceptComparator));
}
@@ -777,6 +806,15 @@
m.put(3,m3);
+ SortedSet<Description> m4 = new TreeSet<Description>(conceptComparator);
+ if(useCardinalityRestrictions) {
+ for(ObjectProperty r : rs.getMostGeneralRoles()) {
+ int maxFillers = maxNrOfFillers.get(r);
+ m4.add(new ObjectMaxCardinalityRestriction(maxFillers-1, r, new Thing()));
+ }
+ }
+ m.put(4,m4);
+
mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
}
@@ -866,6 +904,15 @@
mA.get(nc).put(3,m3);
+ SortedSet<Description> m4 = new TreeSet<Description>(conceptComparator);
+ if(useCardinalityRestrictions) {
+ for(ObjectProperty r : mgr.get(nc)) {
+ int maxFillers = maxNrOfFillers.get(r);
+ m4.add(new ObjectMaxCardinalityRestriction(maxFillers-1, r, new Thing()));
+ }
+ }
+ mA.get(nc).put(4,m4);
+
mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-19 16:15:56
|
Revision: 717
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=717&view=rev
Author: jenslehmann
Date: 2008-03-19 09:15:18 -0700 (Wed, 19 Mar 2008)
Log Message:
-----------
added template for DBpedia navigation link suggestor
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java
Added: trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/algorithms/DBpediaNavigationSuggestor.java 2008-03-19 16:15:18 UTC (rev 717)
@@ -0,0 +1,85 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.algorithms;
+
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.LearningAlgorithm;
+import org.dllearner.core.ReasoningService;
+import org.dllearner.core.Score;
+import org.dllearner.core.config.ConfigEntry;
+import org.dllearner.core.config.InvalidConfigOptionValueException;
+import org.dllearner.core.owl.Description;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.learningproblems.PosOnlyDefinitionLP;
+
+/**
+ * The DBpedia Navigation suggestor takes a knowledge fragment extracted
+ * from DBpedia, performs some preprocessing steps, invokes a learning
+ * algorithm, and then performs postprocessing steps. It does not
+ * implement a completely new learning algorithm itself, but uses the
+ * example based refinement operator learning algorithm.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class DBpediaNavigationSuggestor extends LearningAlgorithm {
+
+ public DBpediaNavigationSuggestor(PosNegLP learningProblem, ReasoningService rs) {
+
+ }
+
+ public DBpediaNavigationSuggestor(PosOnlyDefinitionLP learningProblem, ReasoningService rs) {
+
+ }
+
+ @Override
+ public <T> void applyConfigEntry(ConfigEntry<T> entry) throws InvalidConfigOptionValueException {
+ // TODO Auto-generated method stub
+ }
+
+ @Override
+ public void init() throws ComponentInitException {
+ // TODO Auto-generated method stub
+ }
+
+ @Override
+ public void start() {
+ // TODO Auto-generated method stub
+ }
+
+ @Override
+ public void stop() {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public Description getBestSolution() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public Score getSolutionScore() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java 2008-03-19 14:29:21 UTC (rev 716)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java 2008-03-19 16:15:18 UTC (rev 717)
@@ -519,6 +519,7 @@
Thread laThread = new Thread()
{
+ @Override
public void run(){
la.start();
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sk...@us...> - 2008-03-26 13:41:27
|
Revision: 726
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=726&view=rev
Author: sknappe
Date: 2008-03-26 06:41:24 -0700 (Wed, 26 Mar 2008)
Log Message:
-----------
a sparql query is created, that gets all individuals to a given concept
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/owl/Description.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Description.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Description.java 2008-03-25 19:11:32 UTC (rev 725)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Description.java 2008-03-26 13:41:24 UTC (rev 726)
@@ -33,6 +33,7 @@
protected Description parent = null;
protected List<Description> children = new LinkedList<Description>();
+ protected String sparqlVar = "subject";
public abstract int getArity();
@@ -200,4 +201,12 @@
public abstract String toManchesterSyntaxString(String baseURI, Map<String,String> prefixes);
public abstract void accept(DescriptionVisitor visitor);
+
+ public String getSparqlVar() {
+ return sparqlVar;
+ }
+
+ public void setSparqlVar(String sparqlVar) {
+ this.sparqlVar = sparqlVar;
+ }
}
Added: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-03-26 13:41:24 UTC (rev 726)
@@ -0,0 +1,213 @@
+package org.dllearner.kb.sparql;
+
+
+import org.dllearner.algorithms.gp.ADC;
+import org.dllearner.core.owl.DatatypeExactCardinalityRestriction;
+import org.dllearner.core.owl.DatatypeMaxCardinalityRestriction;
+import org.dllearner.core.owl.DatatypeMinCardinalityRestriction;
+import org.dllearner.core.owl.DatatypeSomeRestriction;
+import org.dllearner.core.owl.DatatypeValueRestriction;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.DescriptionVisitor;
+import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.Negation;
+import org.dllearner.core.owl.Nothing;
+import org.dllearner.core.owl.ObjectAllRestriction;
+import org.dllearner.core.owl.ObjectExactCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMaxCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
+import org.dllearner.core.owl.ObjectSomeRestriction;
+import org.dllearner.core.owl.ObjectValueRestriction;
+import org.dllearner.core.owl.Thing;
+import org.dllearner.core.owl.Union;
+import org.dllearner.parser.KBParser;
+import org.dllearner.parser.ParseException;
+
+/**
+ * Converter from DL-Learner descriptions to a corresponding SPARQL query
+ * to get all instances that are described by this description.
+ * @author Sebastian Knappe
+ *
+ */
+public class SparqlQueryDescriptionConvertVisitor implements DescriptionVisitor{
+
+ private String query="";
+
+ private int currentObject=0;
+
+ public String getSparqlQuery()
+ {
+ query="SELECT ?subject\nWHERE {"+query;
+ query+="}\n";
+ query+="LIMIT 5";
+ return query;
+ }
+
+ public static String getSparqlQuery(Description description)
+ {
+ SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
+ description.accept(visitor);
+ return visitor.getSparqlQuery();
+ }
+
+ /**
+ * Used for testing the Sparql Query converter.
+ *
+ * @param args
+ */
+ public static void main(String[] args) {
+ try {
+ Description d = KBParser.parseConcept("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
+ String query = SparqlQueryDescriptionConvertVisitor.getSparqlQuery(d);
+ System.out.println(d);
+ System.out.println(query);
+ } catch (ParseException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Negation)
+ */
+ public void visit(Negation description) {
+ System.out.println("Negation");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectAllRestriction)
+ */
+ public void visit(ObjectAllRestriction description) {
+ System.out.println("ObjectAllRestriction");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectSomeRestriction)
+ */
+ public void visit(ObjectSomeRestriction description) {
+ System.out.println("ObjectSomeRestriction");
+ query+="?"+description.getSparqlVar()+" <"+description.getRole()+"> ?object"+currentObject+".";
+ description.getChild(0).setSparqlVar("object"+currentObject);
+ currentObject++;
+ description.getChild(0).accept(this);
+ System.out.println(description.getRole());
+ System.out.println(description.getChild(0));
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Nothing)
+ */
+ public void visit(Nothing description) {
+ System.out.println("Nothing");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Thing)
+ */
+ public void visit(Thing description) {
+ System.out.println("Thing");
+
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Intersection)
+ */
+ public void visit(Intersection description) {
+ System.out.println("Intersection");
+ description.getChild(0).accept(this);
+ query+=".";
+ description.getChild(1).accept(this);
+ query+=".";
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Union)
+ */
+ public void visit(Union description) {
+ System.out.println("Union");
+ query+="{";
+ description.getChild(0).accept(this);
+ query+="} UNION {";
+ description.getChild(1).accept(this);
+ query+="}";
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectMinCardinalityRestriction)
+ */
+ public void visit(ObjectMinCardinalityRestriction description) {
+ System.out.println("ObjectMinCardinalityRestriction");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectExactCardinalityRestriction)
+ */
+ public void visit(ObjectExactCardinalityRestriction description) {
+ System.out.println("ObjectExactCardinalityRestriction");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectMaxCardinalityRestriction)
+ */
+ public void visit(ObjectMaxCardinalityRestriction description) {
+ System.out.println("ObjectMaxCardinalityRestriction");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectValueRestriction)
+ */
+ public void visit(ObjectValueRestriction description) {
+ System.out.println("ObjectValueRestriction");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeValueRestriction)
+ */
+ public void visit(DatatypeValueRestriction description) {
+ System.out.println("DatatypeValueRestriction");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.NamedClass)
+ */
+ public void visit(NamedClass description) {
+ System.out.println("NamedClass");
+ query+="?"+description.getSparqlVar()+" a <"+description.getName()+">";
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.algorithms.gp.ADC)
+ */
+ public void visit(ADC description) {
+ System.out.println("ADC");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeMinCardinalityRestriction)
+ */
+ public void visit(DatatypeMinCardinalityRestriction description) {
+ System.out.println("DatatypeMinCardinalityRestriction");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeExactCardinalityRestriction)
+ */
+ public void visit(DatatypeExactCardinalityRestriction description) {
+ System.out.println("DatatypeExactCardinalityRestriction");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeMaxCardinalityRestriction)
+ */
+ public void visit(DatatypeMaxCardinalityRestriction description) {
+ System.out.println("DatatypeMaxCardinalityRestriction");
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeSomeRestriction)
+ */
+ public void visit(DatatypeSomeRestriction description) {
+ System.out.println("DatatypeSomeRestriction");
+ }
+}
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-03-25 19:11:32 UTC (rev 725)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-03-26 13:41:24 UTC (rev 726)
@@ -56,6 +56,7 @@
import org.dllearner.kb.OWLFile;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.kb.sparql.SparqlQueryException;
import org.dllearner.kb.sparql.SparqlQueryThreaded;
import org.dllearner.learningproblems.PosNegDefinitionLP;
@@ -590,6 +591,13 @@
}
@WebMethod
+ public String getSparqlForConcept(int id) throws ClientNotKnownException {
+ ClientState state = getState(id);
+ Description solution=state.getLearningAlgorithm().getBestSolution();
+ return SparqlQueryDescriptionConvertVisitor.getSparqlQuery(solution);
+ }
+
+ @WebMethod
public void debug(String deb)
{
System.out.println(deb);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sk...@us...> - 2008-03-27 13:26:17
|
Revision: 732
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=732&view=rev
Author: sknappe
Date: 2008-03-27 06:26:15 -0700 (Thu, 27 Mar 2008)
Log Message:
-----------
deleted variable in Description
a web service method now exists to get instances to a certain concept
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/owl/Description.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Description.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Description.java 2008-03-27 08:26:58 UTC (rev 731)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Description.java 2008-03-27 13:26:15 UTC (rev 732)
@@ -33,8 +33,7 @@
protected Description parent = null;
protected List<Description> children = new LinkedList<Description>();
- protected String sparqlVar = "subject";
-
+
public abstract int getArity();
/**
@@ -202,11 +201,4 @@
public abstract void accept(DescriptionVisitor visitor);
- public String getSparqlVar() {
- return sparqlVar;
- }
-
- public void setSparqlVar(String sparqlVar) {
- this.sparqlVar = sparqlVar;
- }
}
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-03-27 08:26:58 UTC (rev 731)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-03-27 13:26:15 UTC (rev 732)
@@ -1,6 +1,8 @@
package org.dllearner.kb.sparql;
+import java.util.Stack;
+
import org.dllearner.algorithms.gp.ADC;
import org.dllearner.core.owl.DatatypeExactCardinalityRestriction;
import org.dllearner.core.owl.DatatypeMaxCardinalityRestriction;
@@ -32,10 +34,17 @@
*/
public class SparqlQueryDescriptionConvertVisitor implements DescriptionVisitor{
+ private Stack<String> stack = new Stack<String>();
+
private String query="";
private int currentObject=0;
+ public SparqlQueryDescriptionConvertVisitor()
+ {
+ stack.push("subject");
+ }
+
public String getSparqlQuery()
{
query="SELECT ?subject\nWHERE {"+query;
@@ -44,6 +53,14 @@
return query;
}
+ public static String getSparqlQuery(String description) throws ParseException
+ {
+ Description d = KBParser.parseConcept(description);
+ SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
+ d.accept(visitor);
+ return visitor.getSparqlQuery();
+ }
+
public static String getSparqlQuery(Description description)
{
SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
@@ -58,7 +75,7 @@
*/
public static void main(String[] args) {
try {
- Description d = KBParser.parseConcept("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
+ String d = "EXISTS \"http://dbpedia.org/property/disambiguates\".TOP";
String query = SparqlQueryDescriptionConvertVisitor.getSparqlQuery(d);
System.out.println(d);
System.out.println(query);
@@ -87,10 +104,11 @@
*/
public void visit(ObjectSomeRestriction description) {
System.out.println("ObjectSomeRestriction");
- query+="?"+description.getSparqlVar()+" <"+description.getRole()+"> ?object"+currentObject+".";
- description.getChild(0).setSparqlVar("object"+currentObject);
+ query+="?"+stack.peek()+" <"+description.getRole()+"> ?object"+currentObject+".";
+ stack.push("object"+currentObject);
currentObject++;
description.getChild(0).accept(this);
+ stack.pop();
System.out.println(description.getRole());
System.out.println(description.getChild(0));
}
@@ -173,7 +191,7 @@
*/
public void visit(NamedClass description) {
System.out.println("NamedClass");
- query+="?"+description.getSparqlVar()+" a <"+description.getName()+">";
+ query+="?"+stack.peek()+" a <"+description.getName()+">";
}
/* (non-Javadoc)
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-03-27 08:26:58 UTC (rev 731)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-03-27 13:26:15 UTC (rev 732)
@@ -522,10 +522,10 @@
}
@WebMethod
- public int sparqlQueryThreaded(int sessionID, int componentID, final String query) throws ClientNotKnownException
+ public int sparqlQueryThreaded(int sessionID, int componentID, String query) throws ClientNotKnownException
{
final ClientState state = getState(sessionID);
- final Component component = state.getComponent(componentID);
+ Component component = state.getComponent(componentID);
final int id=state.addQuery(((SparqlKnowledgeSource)component).sparqlQueryThreaded(query));
Thread sparqlThread = new Thread() {
@Override
@@ -591,10 +591,11 @@
}
@WebMethod
- public String getSparqlForConcept(int id) throws ClientNotKnownException {
+ public void SparqlRetrievalThreaded(int id, int componentID, String conceptString) throws ClientNotKnownException, ParseException {
ClientState state = getState(id);
- Description solution=state.getLearningAlgorithm().getBestSolution();
- return SparqlQueryDescriptionConvertVisitor.getSparqlQuery(solution);
+ // call parser to parse concept
+ String sparqlQuery = SparqlQueryDescriptionConvertVisitor.getSparqlQuery(conceptString);
+ sparqlQueryThreaded(id, componentID,sparqlQuery);
}
@WebMethod
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-03-31 14:36:15
|
Revision: 744
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=744&view=rev
Author: jenslehmann
Date: 2008-03-31 07:36:13 -0700 (Mon, 31 Mar 2008)
Log Message:
-----------
fix for #1928052
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
Modified: trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-03-31 14:30:50 UTC (rev 743)
+++ trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-03-31 14:36:13 UTC (rev 744)
@@ -71,7 +71,7 @@
// you can either use the components.ini file or directly specify the classes to use
private static String componentsFile = "lib/components.ini";
private static String[] componentClasses = new String[]{};
- private static ComponentManager cm = new ComponentManager();
+ private static ComponentManager cm = null;
// list of all configuration options of all components
private static Map<Class<? extends Component>, String> componentNames;
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-31 14:30:50 UTC (rev 743)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-31 14:36:13 UTC (rev 744)
@@ -27,6 +27,7 @@
import java.util.Comparator;
import java.util.HashSet;
import java.util.LinkedList;
+import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
@@ -146,6 +147,9 @@
private Map<String, String> prefixes = new TreeMap<String,String>();
private String baseURI;
+ // references to OWL API ontologies
+ private List<OWLOntology> owlAPIOntologies = new LinkedList<OWLOntology>();
+
public OWLAPIReasoner(Set<KnowledgeSource> sources) {
this.sources = sources;
}
@@ -201,6 +205,7 @@
try {
OWLOntology ontology = manager.loadOntologyFromPhysicalURI(url.toURI());
+ owlAPIOntologies.add(ontology);
allImports.addAll(manager.getImportsClosure(ontology));
classes.addAll(ontology.getReferencedClasses());
owlObjectProperties.addAll(ontology.getReferencedObjectProperties());
@@ -234,6 +239,7 @@
e.printStackTrace();
}
OWLAPIAxiomConvertVisitor.fillOWLOntology(manager, ontology, kb);
+ owlAPIOntologies.add(ontology);
allImports.add(ontology);
atomicConcepts.addAll(kb.findAllAtomicConcepts());
atomicRoles.addAll(kb.findAllAtomicRoles());
@@ -1035,4 +1041,8 @@
}
}
+ public List<OWLOntology> getOWLAPIOntologies() {
+ return owlAPIOntologies;
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-01 10:23:37
|
Revision: 745
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=745&view=rev
Author: kurzum
Date: 2008-04-01 03:23:30 -0700 (Tue, 01 Apr 2008)
Log Message:
-----------
added function getUsage() to components for writing a better doc file.
implemented it in some component, where I was sure.
added some output to ConfigOptionScriptGenerator, respectively to ComponentManager
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
trunk/src/dl-learner/org/dllearner/kb/KBFile.java
trunk/src/dl-learner/org/dllearner/kb/OWLFile.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosOnlyDefinitionLP.java
trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -324,6 +324,10 @@
return "example driven refinement operator based learning algorithm";
}
+ public static String getUsage() {
+ return "algorithm = refexamples;";
+ }
+
@Override
public void start() {
algorithm.start();
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -327,6 +327,10 @@
return "refinement operator based learning algorithm";
}
+ public static String getUsage() {
+ return "algorithm = refinement;";
+ }
+
private int coveredNegativesOrTooWeak(Description concept) {
if(posOnly)
return posOnlyLearningProblem.coveredPseudoNegativeExamplesOrTooWeak(concept);
Modified: trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -421,10 +421,24 @@
private String getComponentConfigString(Class<? extends Component> component) {
String componentDescription = "component: " + invokeStaticMethod(component,"getName") + " (" + component.getName() + ")";
String str = componentDescription + "\n";
+ String usage ="";
+
+ usage = invokeStaticMethod(component,"getUsage")+"";
+
+
+ if(usage.equals("null")) {
+ System.out.println("Component "+component.getName()+" needs Usage definition");
+ }
+ else {
+ System.out.println(usage +" |in| "+ component.getName());
+ }
+
for(int i=0; i<componentDescription.length(); i++)
str += "=";
str += "\n\n";
+ str += "Usage:\n"+usage+"\n\n";
+
for(ConfigOption<?> option : componentOptions.get(component)) {
str += option.toString() + "\n";
}
Modified: trunk/src/dl-learner/org/dllearner/kb/KBFile.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -82,6 +82,10 @@
public static String getName() {
return "KB file";
}
+
+ public static String getUsage() {
+ return "import(\"kbFileName.kb\");";
+ }
public static Collection<ConfigOption<?>> createConfigOptions() {
Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
Modified: trunk/src/dl-learner/org/dllearner/kb/OWLFile.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/OWLFile.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/kb/OWLFile.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -47,6 +47,11 @@
public static String getName() {
return "OWL file";
}
+
+ public static String getUsage() {
+ return "import(\"owlFileName.owl\");";
+ }
+
public static Collection<ConfigOption<?>> createConfigOptions() {
Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -104,6 +104,9 @@
public static String getName() {
return "SPARQL Endpoint";
}
+ public static String getUsage() {
+ return "Example: import(\"http://dbpedia.openlinksw.com:8890/sparql\",\"SPARQL\");";
+ }
private static Logger logger = Logger
.getLogger(SparqlKnowledgeSource.class);
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -64,6 +64,10 @@
public static String getName() {
return "two valued definition learning problem";
}
+
+ public static String getUsage() {
+ return "problem = XXX DEFAULT";
+ }
public static Collection<ConfigOption<?>> createConfigOptions() {
return PosNegLP.createConfigOptions();
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -76,6 +76,11 @@
return "inclusion learning problem";
}
+ public static String getUsage() {
+ return "problem = posNegInclusion;";
+ }
+
+
/*
* (non-Javadoc)
*
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosOnlyDefinitionLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosOnlyDefinitionLP.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosOnlyDefinitionLP.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -46,6 +46,10 @@
public static String getName() {
return "positive only definition learning problem";
}
+
+ public static String getUsage() {
+ return "problem = posOnlyDefinition;";
+ }
/* (non-Javadoc)
* @see org.dllearner.core.Component#init()
Modified: trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -173,6 +173,10 @@
public static String getName() {
return "DIG reasoner";
}
+
+ public static String getUsage() {
+ return "reasoner = dig;";
+ }
public static Collection<ConfigOption<?>> createConfigOptions() {
Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -133,6 +133,10 @@
return "fast instance checker";
}
+ public static String getUsage() {
+ return "reasoner = fastInstanceChecker;";
+ }
+
/*
* (non-Javadoc)
*
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -150,8 +150,12 @@
public static String getName() {
return "fast retrieval reasoner";
- }
+ }
+ public static String getUsage() {
+ return "reasoner = XXX;";
+ }
+
/* (non-Javadoc)
* @see org.dllearner.core.Component#applyConfigEntry(org.dllearner.core.ConfigEntry)
*/
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-31 14:36:13 UTC (rev 744)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-04-01 10:23:30 UTC (rev 745)
@@ -158,6 +158,10 @@
return "OWL API reasoner";
}
+ public static String getUsage() {
+ return "reasoner = owlAPI;";
+ }
+
public static Collection<ConfigOption<?>> createConfigOptions() {
Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
StringConfigOption type = new StringConfigOption("reasonerType", "FaCT++ or Pellet", "pellet");
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-01 10:46:17
|
Revision: 747
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=747&view=rev
Author: kurzum
Date: 2008-04-01 03:46:11 -0700 (Tue, 01 Apr 2008)
Log Message:
-----------
rollback
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
trunk/src/dl-learner/org/dllearner/kb/KBFile.java
trunk/src/dl-learner/org/dllearner/kb/OWLFile.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosOnlyDefinitionLP.java
trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
Modified: trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -423,21 +423,22 @@
String str = componentDescription + "\n";
String usage ="";
- usage = invokeStaticMethod(component,"getUsage")+"";
+ //usage = invokeStaticMethod(component,"getUsage")+"";
- if(usage.equals("null")) {
+ /*if(usage.equals("null")) {
System.out.println("Component "+component.getName()+" needs Usage definition");
}
else {
System.out.println(usage +" |in| "+ component.getName());
}
+ */
for(int i=0; i<componentDescription.length(); i++)
str += "=";
str += "\n\n";
- str += "Usage:\n"+usage+"\n\n";
+ //str += "Usage:\n"+usage+"\n\n";
for(ConfigOption<?> option : componentOptions.get(component)) {
str += option.toString() + "\n";
Modified: trunk/src/dl-learner/org/dllearner/kb/KBFile.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -83,9 +83,6 @@
return "KB file";
}
- public static String getUsage() {
- return "import(\"kbFileName.kb\");";
- }
public static Collection<ConfigOption<?>> createConfigOptions() {
Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
Modified: trunk/src/dl-learner/org/dllearner/kb/OWLFile.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/OWLFile.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/kb/OWLFile.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -48,9 +48,6 @@
return "OWL file";
}
- public static String getUsage() {
- return "import(\"owlFileName.owl\");";
- }
public static Collection<ConfigOption<?>> createConfigOptions() {
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -104,9 +104,7 @@
public static String getName() {
return "SPARQL Endpoint";
}
- public static String getUsage() {
- return "Example: import(\"http://dbpedia.openlinksw.com:8890/sparql\",\"SPARQL\");";
- }
+
private static Logger logger = Logger
.getLogger(SparqlKnowledgeSource.class);
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosNegDefinitionLP.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -65,9 +65,6 @@
return "two valued definition learning problem";
}
- public static String getUsage() {
- return "problem = XXX DEFAULT";
- }
public static Collection<ConfigOption<?>> createConfigOptions() {
return PosNegLP.createConfigOptions();
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosNegInclusionLP.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -76,11 +76,7 @@
return "inclusion learning problem";
}
- public static String getUsage() {
- return "problem = posNegInclusion;";
- }
-
-
+
/*
* (non-Javadoc)
*
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosOnlyDefinitionLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosOnlyDefinitionLP.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosOnlyDefinitionLP.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -46,10 +46,7 @@
public static String getName() {
return "positive only definition learning problem";
}
-
- public static String getUsage() {
- return "problem = posOnlyDefinition;";
- }
+
/* (non-Javadoc)
* @see org.dllearner.core.Component#init()
Modified: trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/reasoning/DIGReasoner.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -174,9 +174,6 @@
return "DIG reasoner";
}
- public static String getUsage() {
- return "reasoner = dig;";
- }
public static Collection<ConfigOption<?>> createConfigOptions() {
Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -133,10 +133,7 @@
return "fast instance checker";
}
- public static String getUsage() {
- return "reasoner = fastInstanceChecker;";
- }
-
+
/*
* (non-Javadoc)
*
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -152,10 +152,8 @@
return "fast retrieval reasoner";
}
- public static String getUsage() {
- return "reasoner = XXX;";
- }
+
/* (non-Javadoc)
* @see org.dllearner.core.Component#applyConfigEntry(org.dllearner.core.ConfigEntry)
*/
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-04-01 10:24:36 UTC (rev 746)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-04-01 10:46:11 UTC (rev 747)
@@ -158,9 +158,6 @@
return "OWL API reasoner";
}
- public static String getUsage() {
- return "reasoner = owlAPI;";
- }
public static Collection<ConfigOption<?>> createConfigOptions() {
Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-02 10:31:33
|
Revision: 750
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=750&view=rev
Author: kurzum
Date: 2008-04-02 03:31:31 -0700 (Wed, 02 Apr 2008)
Log Message:
-----------
some more changes to the option doc generator, still not perfect
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
trunk/src/dl-learner/org/dllearner/core/config/ConfigOption.java
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-04-01 11:48:39 UTC (rev 749)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-04-02 10:31:31 UTC (rev 750)
@@ -224,9 +224,12 @@
componentPrefixMapping.put(SparqlKnowledgeSource.class, "sparql");
// reasoners
componentPrefixMapping.put(DIGReasoner.class, "digReasoner");
+ componentPrefixMapping.put(FastInstanceChecker.class, "fastInstanceChecker");
componentPrefixMapping.put(OWLAPIReasoner.class, "owlAPIReasoner");
// learning problems - configured via + and - flags for examples
componentPrefixMapping.put(PosNegDefinitionLP.class, "posNegDefinitionLP");
+ componentPrefixMapping.put(PosNegInclusionLP.class, "posNegInclusionLP");
+ componentPrefixMapping.put(PosOnlyDefinitionLP.class, "posOnlyDefinitionLP");
// learning algorithms
componentPrefixMapping.put(ROLearner.class, "refinement");
componentPrefixMapping.put(ExampleBasedROLComponent.class, "refexamples");
Modified: trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-04-01 11:48:39 UTC (rev 749)
+++ trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-04-02 10:31:31 UTC (rev 750)
@@ -40,6 +40,7 @@
import java.util.TreeMap;
import java.util.TreeSet;
+import org.dllearner.cli.Start;
import org.dllearner.core.config.ConfigEntry;
import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.config.InvalidConfigOptionValueException;
@@ -421,31 +422,43 @@
private String getComponentConfigString(Class<? extends Component> component) {
String componentDescription = "component: " + invokeStaticMethod(component,"getName") + " (" + component.getName() + ")";
String str = componentDescription + "\n";
+ String CLI = getCLIMapping(component.getSuperclass().getSimpleName()+"");
String usage ="";
- //usage = invokeStaticMethod(component,"getUsage")+"";
-
-
- /*if(usage.equals("null")) {
- System.out.println("Component "+component.getName()+" needs Usage definition");
+ Map<Class<? extends Component>, String> m=Start.createComponentPrefixMapping();
+ for (Class<? extends Component> c : m.keySet()) {
+ if(c.getCanonicalName().equals(component.getCanonicalName()))
+ { usage=m.get(c);
+ }
}
- else {
- System.out.println(usage +" |in| "+ component.getName());
+
+ for(int i=0; i<componentDescription.length(); i++) {
+ str += "=";
}
- */
-
- for(int i=0; i<componentDescription.length(); i++)
- str += "=";
str += "\n\n";
+ str += "CLI usage: "+CLI+" = "+usage+";\n\n";
- //str += "Usage:\n"+usage+"\n\n";
for(ConfigOption<?> option : componentOptions.get(component)) {
- str += option.toString() + "\n";
+ str += option.toString() +
+ "CLI usage: "+usage+"."+
+ option.getName()+" = "+option.getDefaultValue()+
+ ";\n\n";
}
- return str;
+ return str+"\n";
}
+ public static String getCLIMapping(String componentSuperClass){
+ HashMap<String, String> m = new HashMap<String, String>();
+ m.put("KnowledgeSource", "import");
+ m.put("ReasonerComponent", "reasoner");
+ m.put("PosNegLP", "problem");
+ m.put("PosOnlyLP", "problem");
+ m.put("LearningAlgorithm", "algorithm");
+ return m.get(componentSuperClass);
+ }
+
+
private Object invokeStaticMethod(Class<?> clazz, String methodName, Object... args) {
// unfortunately Java does not seem to offer a way to call
// a static method given a class object directly, so we have
Modified: trunk/src/dl-learner/org/dllearner/core/config/ConfigOption.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/config/ConfigOption.java 2008-04-01 11:48:39 UTC (rev 749)
+++ trunk/src/dl-learner/org/dllearner/core/config/ConfigOption.java 2008-04-02 10:31:31 UTC (rev 750)
@@ -77,10 +77,12 @@
public abstract boolean isValidValue(T value);
+ //TODO maybe change the function getClass in the options to get simpleName
public String getAllowedValuesDescription() {
return getClass().toString();
}
+
@Override
public String toString() {
return "option name: " + name + "\ndescription: " + description + "\nvalues: "
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-03 14:03:33
|
Revision: 764
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=764&view=rev
Author: kurzum
Date: 2008-04-03 07:03:19 -0700 (Thu, 03 Apr 2008)
Log Message:
-----------
some minor changes, verification works now with kb parse, but still yields strange results
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/Info.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java
trunk/src/dl-learner/org/dllearner/core/owl/Thing.java
trunk/src/dl-learner/org/dllearner/examples/KRK.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/OntologyCloser.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/examples/OntologyCloser.java
Modified: trunk/src/dl-learner/org/dllearner/Info.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/Info.java 2008-04-03 11:57:35 UTC (rev 763)
+++ trunk/src/dl-learner/org/dllearner/Info.java 2008-04-03 14:03:19 UTC (rev 764)
@@ -3,6 +3,6 @@
package org.dllearner;
public class Info {
- public static final String build = "2008-03-16";
+ public static final String build = "2008-03-31";
}
\ No newline at end of file
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-03 11:57:35 UTC (rev 763)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-03 14:03:19 UTC (rev 764)
@@ -386,8 +386,11 @@
logger.info("\nsolutions:");
for(Description c : solutions) {
logger.info(" " + c + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
- //TODO remove this line
- logger.info(" MANCHESTER: " + c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()) );
+ //TODO remove this line maybe
+ // watch for String.replace Quick hack
+ logger.info(" MANCHESTER: " +
+ c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()).
+ replace("\"", ""));
}
}
logger.debug("size of candidate set: " + candidates.size());
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-03 11:57:35 UTC (rev 763)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-03 14:03:19 UTC (rev 764)
@@ -513,7 +513,11 @@
logger.info("\nsolutions:");
for(Description c : solutions) {
logger.info(" " + c + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
- logger.info(" MANCHESTER: " + c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()) );
+ //TODO remove this line maybe
+ // watch for String.replace Quick hack
+ logger.info(" MANCHESTER: " +
+ c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()).
+ replace("\"", ""));
}
}
logger.info(" horizontal expansion: " + minimumHorizontalExpansion + " to " + maximumHorizontalExpansion);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java 2008-04-03 11:57:35 UTC (rev 763)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java 2008-04-03 14:03:19 UTC (rev 764)
@@ -40,8 +40,10 @@
*/
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
- // TODO: check whether this is correct
- return "owl:Nothing";
+ // in Protege 3.3 owl:Nothing
+ // in Protege 4.0 only Nothing
+ //return "owl:Nothing";
+ return "Nothing";
}
public int getLength() {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Thing.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Thing.java 2008-04-03 11:57:35 UTC (rev 763)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Thing.java 2008-04-03 14:03:19 UTC (rev 764)
@@ -44,7 +44,11 @@
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
- return "owl:Thing";
+ // in Protege 3.3 owl:Thing
+ // in Protege 4.0 only Thing
+ //return "owl:Thing";
+ return "Thing";
+
}
public int getLength() {
Modified: trunk/src/dl-learner/org/dllearner/examples/KRK.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-03 11:57:35 UTC (rev 763)
+++ trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-03 14:03:19 UTC (rev 764)
@@ -30,6 +30,7 @@
import org.dllearner.core.owl.SymmetricObjectPropertyAxiom;
import org.dllearner.core.owl.TransitiveObjectPropertyAxiom;
import org.dllearner.reasoning.OWLAPIReasoner;
+import org.dllearner.utilities.OntologyCloser;
/*
* Structure
@@ -223,14 +224,37 @@
writeOWLFile("test.owl");
}
if(writeClosedOWL) {
+ OntologyCloser oc = new OntologyCloser(kb);
+ oc.applyNumberRestrictions();
+
+
String conceptStr = "ALL \"http://www.test.de/test#hasPiece\".(EXISTS \"http://www.test.de/test#fileDistanceLessThan6\".((NOT \"http://www.test.de/test#WKing\") AND ALL \"http://www.test.de/test#rankDistance1\".(\"http://www.test.de/test#WKing\" AND ALL \"http://www.test.de/test#fileDistanceLessThan2\".\"http://www.test.de/test#BKing\" AND ALL \"http://www.test.de/test#hasLowerFileThan\".\"http://www.test.de/test#WKing\")) AND ALL \"http://www.test.de/test#fileDistance1\".\"http://www.test.de/test#WRook\")";
//conceptStr = "ALL http://www.test.de/test#hasPiece.(EXISTS http://www.test.de/test#fileDistanceLessThan6.((NOT http://www.test.de/test#WKing) AND ALL http://www.test.de/test#rankDistance1.(http://www.test.de/test#WKing AND ALL http://www.test.de/test#fileDistanceLessThan2.http://www.test.de/test#WKing AND ALL http://www.test.de/test#hasLowerFileThan.http://www.test.de/test#WKing)) AND ALL http://www.test.de/test#fileDistance1.http://www.test.de/test#WRook)";
//conceptStr = "ALL hasPiece.(EXISTS fileDistanceLessThan6.((NOT WKing) AND ALL rankDistance1.(WKing AND ALL fileDistanceLessThan2.WKing AND ALL hasLowerFileThan.WKing)) AND ALL fileDistance1.WRook)";
- conceptStr = "ALL \"http://www.test.de/test#hasPiece\".\"http://www.test.de/test#WKing\"";
- OntologyCloser oc = new OntologyCloser(kb);
- oc.applyNumberRestrictions();
+ //conceptStr = "ALL \"http://www.test.de/test#hasPiece\".\"http://www.test.de/test#WKing\"";
+ //conceptStr = "EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#hasLowerRankThan\".(\"http://www.test.de/test#WRook\" AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\")";
+
+
+ conceptStr = "\"http://www.test.de/test#WRook\"";
+
oc.verifyConcept(conceptStr);
- writeOWLFile("test_Closed.owl");
+ conceptStr = "ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
+ "\"http://www.test.de/test#WKing\" ";
+
+ oc.verifyConcept(conceptStr);
+ conceptStr = "(\"http://www.test.de/test#WRook\" "+
+ " AND " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
+ "\"http://www.test.de/test#WKing\") ";
+
+ oc.verifyConcept(conceptStr);
+ conceptStr = "EXISTS \"http://www.test.de/test#hasLowerRankThan\"."+
+ "(\"http://www.test.de/test#WRook\""+
+ "AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\") ";
+
+
+ oc.verifyConcept(conceptStr);
+ //writeOWLFile("test_Closed.owl");
}
} catch (Exception e) {
Deleted: trunk/src/dl-learner/org/dllearner/examples/OntologyCloser.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/OntologyCloser.java 2008-04-03 11:57:35 UTC (rev 763)
+++ trunk/src/dl-learner/org/dllearner/examples/OntologyCloser.java 2008-04-03 14:03:19 UTC (rev 764)
@@ -1,102 +0,0 @@
-package org.dllearner.examples;
-
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-import java.util.SortedSet;
-
-import org.dllearner.core.KnowledgeSource;
-import org.dllearner.core.ReasoningService;
-import org.dllearner.core.owl.ClassAssertionAxiom;
-import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.Individual;
-import org.dllearner.core.owl.KB;
-import org.dllearner.core.owl.ObjectExactCardinalityRestriction;
-import org.dllearner.core.owl.ObjectProperty;
-import org.dllearner.core.owl.PropertyAxiom;
-import org.dllearner.core.owl.Thing;
-import org.dllearner.kb.KBFile;
-import org.dllearner.parser.KBParser;
-import org.dllearner.reasoning.OWLAPIReasoner;
-
-public class OntologyCloser {
- KB kb;
- KBFile kbFile;
- Set<KnowledgeSource> ks;
- ReasoningService rs;
-
- public OntologyCloser(KB kb) {
- super();
- this.kb = kb;
- this.kbFile = new KBFile(this.kb);
- this.ks = new HashSet<KnowledgeSource>();
- this.ks.add(this.kbFile);
- OWLAPIReasoner owlapi = new OWLAPIReasoner(ks);
- owlapi.init();
-
- this.rs = new ReasoningService(owlapi);
-
- }
-
- /**
- * counts the number of roles used by each individual and assigns
- * ExactCardinalityRestriction
- */
- public void applyNumberRestrictions() {
- Set<ObjectProperty> allRoles = this.rs.getAtomicRoles();
- // Set<Individual> allind = this.rs.getIndividuals();
- Set<PropertyAxiom> ax = kb.getRbox();
- for (PropertyAxiom propertyAxiom : ax) {
- if (propertyAxiom.getClass().getSimpleName().equals(
- "TransitiveObjectPropertyAxiom")) {
-
- System.out
- .println("WARNING transitive object property can't be used in cardinality restriction\n"
- + propertyAxiom.toString());
- }
- }
-
- for (ObjectProperty oneRole : allRoles) {
-
- // System.out.println(oneRole.getClass());
- Map<Individual, SortedSet<Individual>> allRoleMembers = this.rs
- .getRoleMembers(oneRole);
- for (Individual oneInd : allRoleMembers.keySet()) {
- SortedSet<Individual> fillers = allRoleMembers.get(oneInd);
- if (fillers.size() > 0) {
- ObjectExactCardinalityRestriction oecr = new ObjectExactCardinalityRestriction(
- fillers.size(), oneRole, new Thing());
- kb.addABoxAxiom(new ClassAssertionAxiom(oecr, oneInd));
- }
- }
-
- }
- // System.out.println("good ontology? " + rs.isSatisfiable());
-
- }
-
- public static void closeKB(KB kb) {
- new OntologyCloser(kb).applyNumberRestrictions();
- }
-
- public void verifyConcept(String conceptStr) {
- Description d;
- StringBuffer sb = new StringBuffer();
- sb.append(conceptStr);
- conceptStr = sb.toString();
- try {
- d = KBParser.parseConcept(conceptStr);
- System.out.println("Starting retrieval");
- SortedSet<Individual> ind = this.rs.retrieval(d);
- System.out.println("retrieved: " + ind.size() + " instances");
-
- for (Individual individual : ind) {
- System.out.println(individual + "");
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
-}
Copied: trunk/src/dl-learner/org/dllearner/utilities/OntologyCloser.java (from rev 760, trunk/src/dl-learner/org/dllearner/examples/OntologyCloser.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/OntologyCloser.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/OntologyCloser.java 2008-04-03 14:03:19 UTC (rev 764)
@@ -0,0 +1,105 @@
+package org.dllearner.utilities;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.SortedSet;
+
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.ReasoningService;
+import org.dllearner.core.owl.ClassAssertionAxiom;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.KB;
+import org.dllearner.core.owl.ObjectExactCardinalityRestriction;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.PropertyAxiom;
+import org.dllearner.core.owl.Thing;
+import org.dllearner.kb.KBFile;
+import org.dllearner.parser.KBParser;
+import org.dllearner.reasoning.OWLAPIReasoner;
+
+public class OntologyCloser {
+ KB kb;
+ KBFile kbFile;
+ Set<KnowledgeSource> ks;
+ ReasoningService rs;
+
+ public OntologyCloser(KB kb) {
+ super();
+ this.kb = kb;
+ this.kbFile = new KBFile(this.kb);
+ this.ks = new HashSet<KnowledgeSource>();
+ this.ks.add(this.kbFile);
+ OWLAPIReasoner owlapi = new OWLAPIReasoner(ks);
+ owlapi.init();
+
+ this.rs = new ReasoningService(owlapi);
+
+ }
+
+ /**
+ * counts the number of roles used by each individual and assigns
+ * ExactCardinalityRestriction
+ */
+ public void applyNumberRestrictions() {
+ Set<ObjectProperty> allRoles = this.rs.getAtomicRoles();
+ // Set<Individual> allind = this.rs.getIndividuals();
+ Set<PropertyAxiom> ax = kb.getRbox();
+ for (PropertyAxiom propertyAxiom : ax) {
+ if (propertyAxiom.getClass().getSimpleName().equals(
+ "TransitiveObjectPropertyAxiom")) {
+
+ System.out
+ .println("WARNING transitive object property can't be used in cardinality restriction\n"
+ + propertyAxiom.toString());
+ }
+ }
+
+ for (ObjectProperty oneRole : allRoles) {
+
+ // System.out.println(oneRole.getClass());
+ Map<Individual, SortedSet<Individual>> allRoleMembers = this.rs
+ .getRoleMembers(oneRole);
+ for (Individual oneInd : allRoleMembers.keySet()) {
+ SortedSet<Individual> fillers = allRoleMembers.get(oneInd);
+ if (fillers.size() > 0) {
+ ObjectExactCardinalityRestriction oecr = new ObjectExactCardinalityRestriction(
+ fillers.size(), oneRole, new Thing());
+ kb.addABoxAxiom(new ClassAssertionAxiom(oecr, oneInd));
+ }
+ }
+
+ }
+ // System.out.println("good ontology? " + rs.isSatisfiable());
+
+ }
+
+ public static void closeKB(KB kb) {
+ new OntologyCloser(kb).applyNumberRestrictions();
+ }
+
+ public void verifyConcept(String conceptStr) {
+ Description d;
+ StringBuffer sb = new StringBuffer();
+ sb.append(conceptStr);
+ conceptStr = sb.toString();
+ try {
+ d = KBParser.parseConcept(conceptStr);
+ System.out.println(d.toManchesterSyntaxString("", new HashMap<String,String>()));
+ System.out.println(d.toString());
+ System.out.println("Starting retrieval");
+ SortedSet<Individual> ind = this.rs.retrieval(d);
+ System.out.println("retrieved: " + ind.size() + " instances");
+
+ //for (Individual individual : ind) {
+ //System.out.println(individual + "");
+ //}
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-07 07:48:13
|
Revision: 769
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=769&view=rev
Author: kurzum
Date: 2008-04-07 00:48:07 -0700 (Mon, 07 Apr 2008)
Log Message:
-----------
script and classes for closing ontologies
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/examples/KRK.java
trunk/src/dl-learner/org/dllearner/utilities/OntologyCloser.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/CloseOntology.java
trunk/src/dl-learner/org/dllearner/utilities/OntologyCloserOWLAPI.java
trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java
Modified: trunk/src/dl-learner/org/dllearner/examples/KRK.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-07 07:46:21 UTC (rev 768)
+++ trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-07 07:48:07 UTC (rev 769)
@@ -7,6 +7,7 @@
import java.io.FileReader;
import java.io.IOException;
import java.net.URI;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.SortedSet;
@@ -50,9 +51,16 @@
//
// turn off to not write the owl, needs about 30 seconds or more
static boolean writeOWL = true;
- static boolean writeClosedOWL = true ;
static boolean useTransitivity = false;
+ static boolean writeExampleSets = true;
+ static boolean writeConciseOWLAllDifferent = false;
+
+ static boolean closeKB=true;
+ static boolean closeConcise= true && closeKB;
+ static boolean writeClosedOWL = true && closeKB;
+ static boolean verifySomeConcepts = false && closeKB;
+
static boolean useInverse = false;
// dependent, love and marriage, horse and carriage
@@ -216,53 +224,116 @@
finishBackgroundForRoles();
System.out.println("Finished Background");
// WRITE
- writeExampleSets();
- writeConciseOWLAllDifferent();
+ if(writeExampleSets)writeExampleSets();
+ if(writeConciseOWLAllDifferent)writeConciseOWLAllDifferent();
+ if (writeOWL)writeOWLFile("test.owl");
-
- if (writeOWL) {
- writeOWLFile("test.owl");
+ OntologyCloser oc = new OntologyCloser(kb);
+ String kbaddition= "_Closed";
+ if(closeKB) {
+
+ if(closeConcise) {
+ oc.applyNumberRestrictionsNamed();
+ kbaddition = "_CloseConcise";
+ }
+ else oc.applyNumberRestrictions();
}
- if(writeClosedOWL) {
- OntologyCloser oc = new OntologyCloser(kb);
- oc.applyNumberRestrictions();
-
- String conceptStr = "ALL \"http://www.test.de/test#hasPiece\".(EXISTS \"http://www.test.de/test#fileDistanceLessThan6\".((NOT \"http://www.test.de/test#WKing\") AND ALL \"http://www.test.de/test#rankDistance1\".(\"http://www.test.de/test#WKing\" AND ALL \"http://www.test.de/test#fileDistanceLessThan2\".\"http://www.test.de/test#BKing\" AND ALL \"http://www.test.de/test#hasLowerFileThan\".\"http://www.test.de/test#WKing\")) AND ALL \"http://www.test.de/test#fileDistance1\".\"http://www.test.de/test#WRook\")";
- //conceptStr = "ALL http://www.test.de/test#hasPiece.(EXISTS http://www.test.de/test#fileDistanceLessThan6.((NOT http://www.test.de/test#WKing) AND ALL http://www.test.de/test#rankDistance1.(http://www.test.de/test#WKing AND ALL http://www.test.de/test#fileDistanceLessThan2.http://www.test.de/test#WKing AND ALL http://www.test.de/test#hasLowerFileThan.http://www.test.de/test#WKing)) AND ALL http://www.test.de/test#fileDistance1.http://www.test.de/test#WRook)";
- //conceptStr = "ALL hasPiece.(EXISTS fileDistanceLessThan6.((NOT WKing) AND ALL rankDistance1.(WKing AND ALL fileDistanceLessThan2.WKing AND ALL hasLowerFileThan.WKing)) AND ALL fileDistance1.WRook)";
- //conceptStr = "ALL \"http://www.test.de/test#hasPiece\".\"http://www.test.de/test#WKing\"";
- //conceptStr = "EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#hasLowerRankThan\".(\"http://www.test.de/test#WRook\" AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\")";
-
- conceptStr = "\"http://www.test.de/test#WRook\"";
+ if (verifySomeConcepts) verifySomeConcepts(oc);
+ if (writeClosedOWL) writeOWLFile("test"+kbaddition+".owl");
- oc.verifyConcept(conceptStr);
- conceptStr = "ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
- "\"http://www.test.de/test#WKing\" ";
-
- oc.verifyConcept(conceptStr);
- conceptStr = "(\"http://www.test.de/test#WRook\" "+
- " AND " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
- "\"http://www.test.de/test#WKing\") ";
-
- oc.verifyConcept(conceptStr);
- conceptStr = "EXISTS \"http://www.test.de/test#hasLowerRankThan\"."+
- "(\"http://www.test.de/test#WRook\""+
- "AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\") ";
-
-
- oc.verifyConcept(conceptStr);
- //writeOWLFile("test_Closed.owl");
- }
-
} catch (Exception e) {
e.printStackTrace();
}
System.out.println("Done");
}// end main
+
+ protected static void verifySomeConcepts(OntologyCloser oc) {
+
+ ArrayList<String> test=new ArrayList<String>();
+
+ //String conceptStr = "ALL \"http://www.test.de/test#hasPiece\".(EXISTS \"http://www.test.de/test#fileDistanceLessThan6\".((NOT \"http://www.test.de/test#WKing\") AND ALL \"http://www.test.de/test#rankDistance1\".(\"http://www.test.de/test#WKing\" AND ALL \"http://www.test.de/test#fileDistanceLessThan2\".\"http://www.test.de/test#BKing\" AND ALL \"http://www.test.de/test#hasLowerFileThan\".\"http://www.test.de/test#WKing\")) AND ALL \"http://www.test.de/test#fileDistance1\".\"http://www.test.de/test#WRook\")";
+ //conceptStr = "ALL http://www.test.de/test#hasPiece.(EXISTS http://www.test.de/test#fileDistanceLessThan6.((NOT http://www.test.de/test#WKing) AND ALL http://www.test.de/test#rankDistance1.(http://www.test.de/test#WKing AND ALL http://www.test.de/test#fileDistanceLessThan2.http://www.test.de/test#WKing AND ALL http://www.test.de/test#hasLowerFileThan.http://www.test.de/test#WKing)) AND ALL http://www.test.de/test#fileDistance1.http://www.test.de/test#WRook)";
+ //conceptStr = "ALL hasPiece.(EXISTS fileDistanceLessThan6.((NOT WKing) AND ALL rankDistance1.(WKing AND ALL fileDistanceLessThan2.WKing AND ALL hasLowerFileThan.WKing)) AND ALL fileDistance1.WRook)";
+ //conceptStr = "ALL \"http://www.test.de/test#hasPiece\".\"http://www.test.de/test#WKing\"";
+ //conceptStr = "EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#hasLowerRankThan\".(\"http://www.test.de/test#WRook\" AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\")";
+
+
+ test.add("\"http://www.test.de/test#WRook\"");
+ /*test.add("ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
+ "\"http://www.test.de/test#WKing\"");
+ /*test.add("(\"http://www.test.de/test#WRook\" "+
+ " AND " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
+ "\"http://www.test.de/test#WKing\") ");*/
+ /*test.add("(\"http://www.test.de/test#Piece\" "+
+ " AND " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan8\"." +
+ "\"http://www.test.de/test#Piece\") ");
+ test.add("(\"http://www.test.de/test#Piece\" "+
+ " AND ( " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan8\"." +
+ "\"http://www.test.de/test#Piece\" " +
+ " AND " +
+ " EXISTS \"http://www.test.de/test#fileDistanceLessThan8\"." +
+ "\"http://www.test.de/test#Piece\"))") ;
+ test.add("(\"http://www.test.de/test#Piece\" "+
+ " AND ( " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan7\"." +
+ "\"http://www.test.de/test#Piece\" " +
+ " AND " +
+ " EXISTS \"http://www.test.de/test#fileDistanceLessThan7\"." +
+ "\"http://www.test.de/test#Piece\"))") ;
+ test.add("(\"http://www.test.de/test#Piece\" "+
+ " AND ( " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan5\"." +
+ "\"http://www.test.de/test#Piece\" " +
+ " AND " +
+ " EXISTS \"http://www.test.de/test#fileDistanceLessThan5\"." +
+ "\"http://www.test.de/test#Piece\"))") ;*/
+ test.add("(\"http://www.test.de/test#Piece\" "+
+ " AND ( " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan3\"." +
+ "\"http://www.test.de/test#Piece\" " +
+ " AND " +
+ " EXISTS \"http://www.test.de/test#fileDistanceLessThan3\"." +
+ "\"http://www.test.de/test#Piece\"))") ;
+ test.add("(\"http://www.test.de/test#BKing\" "+
+ " AND ( " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan3\"." +
+ "\"http://www.test.de/test#Piece\" " +
+ " AND " +
+ " EXISTS \"http://www.test.de/test#fileDistanceLessThan3\"." +
+ "\"http://www.test.de/test#Piece\"))") ;
+ test.add("(\"http://www.test.de/test#BKing\" "+
+ " AND ( " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan2\"." +
+ "\"http://www.test.de/test#Piece\" " +
+ " AND " +
+ " EXISTS \"http://www.test.de/test#fileDistanceLessThan2\"." +
+ "\"http://www.test.de/test#Piece\"))") ;
+
+ /*test.add("(\"http://www.test.de/test#Piece\" "+
+ " AND " +
+ " ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
+ "\"http://www.test.de/test#WKing\") ");*/
+
+ for (int i = 0; i < test.size(); i++) {
+ String conceptStr = test.get(i);
+ oc.verifyConcept(conceptStr);
+ }
+
+
+ /*conceptStr = "EXISTS \"http://www.test.de/test#hasLowerRankThan\"."+
+ "(\"http://www.test.de/test#WRook\""+
+ "AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\") ";
+
+ */
+ System.out.println();
+ }
+
static void makeDistanceRoles(KRKPiece A, KRKPiece B) {
int Fdist = A.getFileDistance(B);
int Rdist = A.getRankDistance(B);
Added: trunk/src/dl-learner/org/dllearner/utilities/CloseOntology.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/CloseOntology.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/CloseOntology.java 2008-04-07 07:48:07 UTC (rev 769)
@@ -0,0 +1,69 @@
+package org.dllearner.utilities;
+
+import java.io.File;
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.kb.OWLFile;
+import org.dllearner.reasoning.OWLAPIReasoner;
+
+public class CloseOntology {
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ String ontopath="examples/krkworking/test.owl";
+ ontopath = args[0];
+ File file = new File(ontopath);
+
+ //System.out.println(file.getAbsolutePath());
+ System.out.println(file.toURI());
+
+
+ try{
+ URI inputURI = file.toURI();
+ URI outputURI;
+ OWLFile owlFile=new OWLFile();
+ owlFile.setURL(inputURI.toURL());
+
+ Set<KnowledgeSource> ks = new HashSet<KnowledgeSource>();
+ ks.add(owlFile);
+ OWLAPIReasoner owlapireasoner = new OWLAPIReasoner(ks);
+ owlapireasoner.init();
+ OntologyCloserOWLAPI oc= new OntologyCloserOWLAPI(owlapireasoner);
+ oc.testForTransitiveProperties(true);
+ String ending = ontopath.substring(ontopath.lastIndexOf(".") + 1);
+ /*ontopath=ontopath.replace("."+ending, "_test."+ending);
+ file=new File(ontopath);
+ URI outputURI = file.toURI();
+ oc.writeOWLFile(outputURI);*/
+ System.out.println("Attempting to close");
+ oc.applyNumberRestrictionsConcise();
+ System.out.println("Finished, preparing output");
+ //String ending = ontopath.substring(ontopath.lastIndexOf(".") + 1);
+ ontopath=ontopath.replace("."+ending, "_closedConcise."+ending);
+ file=new File(ontopath);
+ outputURI = file.toURI();
+ oc.writeOWLFile(outputURI);
+
+ //ontopath=ontopath.replace("_closed."+ending, "_ClosedConcise."+ending);
+ //file=new File(ontopath);
+ //outputURI = file.toURI();
+ //oc.writeOWLFile(outputURI);
+
+
+ //System.out.println(ontopath);
+
+ /*manager.saveOntology(ontology, new OWLXMLOntologyFormat(),
+ physicalURI2);
+
+ manager.removeOntology(ontology.getURI());
+ */
+
+ }catch (Exception e) {e.printStackTrace();}
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/utilities/OntologyCloser.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/OntologyCloser.java 2008-04-07 07:46:21 UTC (rev 768)
+++ trunk/src/dl-learner/org/dllearner/utilities/OntologyCloser.java 2008-04-07 07:48:07 UTC (rev 769)
@@ -2,16 +2,21 @@
import java.util.HashMap;
import java.util.HashSet;
+import java.util.LinkedList;
import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
+import java.util.TreeSet;
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.ClassAssertionAxiom;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.EquivalentClassesAxiom;
import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.KB;
+import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectExactCardinalityRestriction;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.PropertyAxiom;
@@ -19,22 +24,31 @@
import org.dllearner.kb.KBFile;
import org.dllearner.parser.KBParser;
import org.dllearner.reasoning.OWLAPIReasoner;
+import org.semanticweb.owl.model.OWLOntology;
public class OntologyCloser {
KB kb;
KBFile kbFile;
- Set<KnowledgeSource> ks;
+ OWLOntology onto;
+ OWLAPIReasoner reasoner;
+ boolean isKB = true;
+
+ // Set<KnowledgeSource> ks;
ReasoningService rs;
+ HashMap<Individual, Set<ObjectExactCardinalityRestriction>> indToRestr;
+ HashMap<Individual, Set<Description>> indToNamedClass;
+ HashSet<Description> classes;
public OntologyCloser(KB kb) {
super();
this.kb = kb;
this.kbFile = new KBFile(this.kb);
- this.ks = new HashSet<KnowledgeSource>();
- this.ks.add(this.kbFile);
+ Set<KnowledgeSource> ks = new HashSet<KnowledgeSource>();
+ ks.add(this.kbFile);
OWLAPIReasoner owlapi = new OWLAPIReasoner(ks);
owlapi.init();
-
+ this.indToRestr = new HashMap<Individual, Set<ObjectExactCardinalityRestriction>>();
+ this.classes = new HashSet<Description>();
this.rs = new ReasoningService(owlapi);
}
@@ -46,17 +60,38 @@
public void applyNumberRestrictions() {
Set<ObjectProperty> allRoles = this.rs.getAtomicRoles();
// Set<Individual> allind = this.rs.getIndividuals();
- Set<PropertyAxiom> ax = kb.getRbox();
- for (PropertyAxiom propertyAxiom : ax) {
- if (propertyAxiom.getClass().getSimpleName().equals(
- "TransitiveObjectPropertyAxiom")) {
+ testForTransitiveProperties(true);
- System.out
- .println("WARNING transitive object property can't be used in cardinality restriction\n"
- + propertyAxiom.toString());
+ for (ObjectProperty oneRole : allRoles) {
+
+ // System.out.println(oneRole.getClass());
+ Map<Individual, SortedSet<Individual>> allRoleMembers = this.rs
+ .getRoleMembers(oneRole);
+ for (Individual oneInd : allRoleMembers.keySet()) {
+ SortedSet<Individual> fillers = allRoleMembers.get(oneInd);
+ if (fillers.size() > 0) {
+ ObjectExactCardinalityRestriction oecr = new ObjectExactCardinalityRestriction(
+ fillers.size(), oneRole, new Thing());
+ kb.addABoxAxiom(new ClassAssertionAxiom(oecr, oneInd));
+ }
}
+
}
+ // System.out.println("good ontology? " + rs.isSatisfiable());
+ }
+
+
+
+ /**
+ * counts the number of roles used by each individual and assigns
+ * ExactCardinalityRestriction
+ */
+ public void applyNumberRestrictionsConcise() {
+ Set<ObjectProperty> allRoles = this.rs.getAtomicRoles();
+ // Set<Individual> allind = this.rs.getIndividuals();
+ testForTransitiveProperties(true);
+
for (ObjectProperty oneRole : allRoles) {
// System.out.println(oneRole.getClass());
@@ -67,39 +102,165 @@
if (fillers.size() > 0) {
ObjectExactCardinalityRestriction oecr = new ObjectExactCardinalityRestriction(
fillers.size(), oneRole, new Thing());
- kb.addABoxAxiom(new ClassAssertionAxiom(oecr, oneInd));
+ // indToRestr.put(oneInd,)
+ collectExObjRestrForInd(oneInd, oecr);
}
}
+ //
+
+ }// end for
+
+ // Intersection intersection = null;
+ LinkedList<Description> ll = new LinkedList<Description>();
+ Set<ObjectExactCardinalityRestriction> s = null;
+
+ for (Individual oneInd : indToRestr.keySet()) {
+ s = indToRestr.get(oneInd);
+ for (ObjectExactCardinalityRestriction oecr : s) {
+ ll.add(oecr);
+ }
+ kb.addABoxAxiom(new ClassAssertionAxiom(new Intersection(ll),
+ oneInd));
+ s = null;
+ ll = new LinkedList<Description>();
}
+
+ //
+
// System.out.println("good ontology? " + rs.isSatisfiable());
}
+
+
+ /**
+ * counts the number of roles used by each individual and assigns
+ * ExactCardinalityRestriction
+ */
+ public void applyNumberRestrictionsNamed() {
+ Set<ObjectProperty> allRoles = this.rs.getAtomicRoles();
+ // Set<Individual> allind = this.rs.getIndividuals();
+ testForTransitiveProperties(true);
+
+ for (ObjectProperty oneRole : allRoles) {
+
+ // System.out.println(oneRole.getClass());
+ Map<Individual, SortedSet<Individual>> allRoleMembers = this.rs
+ .getRoleMembers(oneRole);
+ for (Individual oneInd : allRoleMembers.keySet()) {
+ SortedSet<Individual> fillers = allRoleMembers.get(oneInd);
+ //if (fillers.size() > 0) {
+ ObjectExactCardinalityRestriction oecr = new ObjectExactCardinalityRestriction(
+ fillers.size(), oneRole, new Thing());
+ // indToRestr.put(oneInd,)
+ //make Description
+ Description d = new NamedClass(oneRole+"Exact"+fillers.size()+"gen");
+ d.addChild(oecr);
+ kb.addTBoxAxiom(new EquivalentClassesAxiom(d,oecr));
+ //System.out.println(d.toManchesterSyntaxString("", new HashMap<String, String>()));
+ kb.addABoxAxiom(new ClassAssertionAxiom(d,oneInd));
+ //collectExObjRestrForInd(oneInd, oecr);
+
+ }
+
+ //
+
+ }// end for
+
+ // Intersection intersection = null;
+ /*
+ LinkedList<Description> ll = new LinkedList<Description>();
+ Set<ObjectExactCardinalityRestriction> s = null;
+
+ for (Individual oneInd : indToRestr.keySet()) {
+ s = indToRestr.get(oneInd);
+ for (ObjectExactCardinalityRestriction oecr : s) {
+ ll.add(oecr);
+ }
+ kb.addABoxAxiom(new ClassAssertionAxiom(new Intersection(ll),
+ oneInd));
+ s = null;
+ ll = new LinkedList<Description>();
+ }*/
+
+ //
+
+ // System.out.println("good ontology? " + rs.isSatisfiable());
+
+ }
+
+ public boolean testForTransitiveProperties(boolean printflag) {
+ boolean retval = false;
+ Set<PropertyAxiom> ax = kb.getRbox();
+ for (PropertyAxiom propertyAxiom : ax) {
+ if (propertyAxiom.getClass().getSimpleName().equals(
+ "TransitiveObjectPropertyAxiom")) {
+ retval = true;
+ if (printflag) {
+ System.out
+ .println("WARNING transitive object property can't be used in cardinality restriction\n"
+ + propertyAxiom.toString());
+ }
+ }
+ }
+
+ return retval;
+ }
+
public static void closeKB(KB kb) {
new OntologyCloser(kb).applyNumberRestrictions();
}
- public void verifyConcept(String conceptStr) {
+ public SortedSet<Individual> verifyConcept(String conceptStr) {
Description d;
+ SimpleClock sc = new SimpleClock();
StringBuffer sb = new StringBuffer();
sb.append(conceptStr);
conceptStr = sb.toString();
+ SortedSet<Individual> ind = new TreeSet<Individual>();
try {
d = KBParser.parseConcept(conceptStr);
- System.out.println(d.toManchesterSyntaxString("", new HashMap<String,String>()));
- System.out.println(d.toString());
- System.out.println("Starting retrieval");
- SortedSet<Individual> ind = this.rs.retrieval(d);
+ System.out.println("\n*******************\nStarting retrieval");
+ System.out.println(d.toManchesterSyntaxString("",
+ new HashMap<String, String>()));
+ // System.out.println(d.toString());
+ sc.setTime();
+ this.rs.retrieval(d);
+
System.out.println("retrieved: " + ind.size() + " instances");
+ sc.printAndSet();
+ for (Individual individual : ind) {
+ System.out.print(individual + "|");
+ }
- //for (Individual individual : ind) {
- //System.out.println(individual + "");
- //}
-
} catch (Exception e) {
e.printStackTrace();
}
+ return ind;
}
+ private boolean collectExObjRestrForInd(Individual ind,
+ ObjectExactCardinalityRestriction oecr) {
+ Set<ObjectExactCardinalityRestriction> s = indToRestr.get(ind);
+ if (s == null) {
+ indToRestr.put(ind,
+ new HashSet<ObjectExactCardinalityRestriction>());
+ s = indToRestr.get(ind);
+ }
+ return s.add(oecr);
+ }
+
+ @SuppressWarnings("unused")
+ private boolean collectDescriptionForInd(Individual ind,
+ Description d) {
+ Set<Description> s = indToNamedClass.get(ind);
+ if (s == null) {
+ indToNamedClass.put(ind,
+ new HashSet<Description>());
+ s = indToNamedClass.get(ind);
+ }
+ return s.add(d);
+ }
+
}
Added: trunk/src/dl-learner/org/dllearner/utilities/OntologyCloserOWLAPI.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/OntologyCloserOWLAPI.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/OntologyCloserOWLAPI.java 2008-04-07 07:48:07 UTC (rev 769)
@@ -0,0 +1,264 @@
+package org.dllearner.utilities;
+
+import java.net.URI;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.core.ReasoningService;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.parser.KBParser;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.io.OWLXMLOntologyFormat;
+import org.semanticweb.owl.model.AddAxiom;
+import org.semanticweb.owl.model.OWLAxiom;
+import org.semanticweb.owl.model.OWLDataFactory;
+import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyManager;
+import org.semanticweb.owl.model.OWLPropertyAxiom;
+
+import uk.ac.manchester.cs.owl.OWLObjectExactCardinalityRestrictionImpl;
+import uk.ac.manchester.cs.owl.OWLObjectIntersectionOfImpl;
+
+public class OntologyCloserOWLAPI {
+
+ OWLOntology onto;
+ OWLAPIReasoner reasoner;
+ //Set<KnowledgeSource> ks;
+ ReasoningService rs;
+ HashMap<Individual,Set<OWLObjectExactCardinalityRestrictionImpl>> indToRestr;
+ OWLDataFactory factory;
+ OWLOntologyManager manager;
+ public int numberOfStatementsChanged = 0;
+
+ public OntologyCloserOWLAPI(OWLAPIReasoner reasoner) {
+ //this.onto = reasoner.getOWLAPIOntologies().get(0);
+ this.reasoner = reasoner;
+ this.indToRestr = new HashMap<Individual,Set<OWLObjectExactCardinalityRestrictionImpl>> ();
+ this.rs = new ReasoningService(reasoner);
+ this.manager = OWLManager.createOWLOntologyManager();
+ this.factory = manager.getOWLDataFactory();
+
+ this.onto = reasoner.getOWLAPIOntologies().get(0);
+ //URI ontologyURI = URI.create(reasoner.getBaseURI());
+ //URI physicalURI = URI.create(owlFile);
+ //SimpleURIMapper mapper = new SimpleURIMapper(ontologyURI, physicalURI);
+ //manager.addURIMapper(mapper);
+ /*try{
+ this.onto = manager.loadOntologyFromPhysicalURI(physicalURI);
+ }catch (Exception e) {e.printStackTrace();}
+ //manager.getOntologies().add(this.onto);
+ System.out.println(manager.getOntologies());
+ System.out.println(this.onto);*/
+ //reasoner = new org.mindswap.pellet.owlapi.Reasoner(manager);
+ //System.out.println(this.rs.getAtomicConcepts());
+
+ }
+
+
+ /**
+ * counts the number of roles used by each individual and assigns
+ * ExactCardinalityRestriction
+ */
+ public void applyNumberRestrictions() {
+ System.out.println("applyNRES");
+ Set<ObjectProperty> allRoles = this.rs.getAtomicRoles();
+ System.out.println("found: "+allRoles.size()+" roles");
+ // Set<Individual> allind = this.rs.getIndividuals();
+ //testForTransitiveProperties(true);
+
+
+
+ for (ObjectProperty oneRole : allRoles) {
+
+ // System.out.println(oneRole.getClass());
+ Map<Individual, SortedSet<Individual>> allRoleMembers = this.rs
+ .getRoleMembers(oneRole);
+ for (Individual oneInd : allRoleMembers.keySet()) {
+ SortedSet<Individual> fillers = allRoleMembers.get(oneInd);
+ if (fillers.size() > 0) {
+ OWLObjectExactCardinalityRestrictionImpl oecr =
+ new OWLObjectExactCardinalityRestrictionImpl(
+ factory,
+ factory.getOWLObjectProperty(URI.create(oneRole.getName())),
+ fillers.size(),
+ factory.getOWLThing()
+ );
+ //System.out.println(oneRole.getName()+"||"+fillers.size()+"||"+oneInd);
+ /*ObjectExactCardinalityRestriction oecr = new ObjectExactCardinalityRestriction(
+ fillers.size(), oneRole, new Thing());*/
+ //kb.addABoxAxiom(new ClassAssertionAxiom(oecr, oneInd));
+ OWLAxiom axiom = factory.getOWLClassAssertionAxiom(
+ factory.getOWLIndividual(URI.create(oneInd.getName()))
+ , oecr);
+ AddAxiom addAxiom = new AddAxiom(this.onto, axiom);
+ try{
+ manager.applyChange(addAxiom);
+ }catch (Exception e) {e.printStackTrace();}
+ }
+ }
+
+ }
+ // System.out.println("good ontology? " + rs.isSatisfiable());
+
+ }
+
+ /**
+ * counts the number of roles used by each individual and assigns
+ * ExactCardinalityRestriction
+ */
+ public void applyNumberRestrictionsConcise() {
+
+ Set<ObjectProperty> allRoles = this.rs.getAtomicRoles();
+ // Set<Individual> allind = this.rs.getIndividuals();
+ // testForTransitiveProperties(true);
+
+ for (ObjectProperty oneRole : allRoles) {
+
+ // System.out.println(oneRole.getClass());
+ Map<Individual, SortedSet<Individual>> allRoleMembers = this.rs
+ .getRoleMembers(oneRole);
+ for (Individual oneInd : allRoleMembers.keySet()) {
+ SortedSet<Individual> fillers = allRoleMembers.get(oneInd);
+ if (fillers.size() > 0) {
+ OWLObjectExactCardinalityRestrictionImpl oecr =
+ new OWLObjectExactCardinalityRestrictionImpl(
+ factory,
+ factory.getOWLObjectProperty(URI.create(oneRole.getName())),
+ fillers.size(),
+ factory.getOWLThing()
+ );
+ //indToRestr.put(oneInd,)
+
+ collectExObjRestrForInd(oneInd, oecr);
+ }
+ }
+
+ //
+
+ }//end for
+
+ //Intersection intersection = null;
+ Set<OWLDescription> target = new HashSet<OWLDescription>();
+ Set<OWLObjectExactCardinalityRestrictionImpl> s = null;
+
+ for (Individual oneInd : indToRestr.keySet()) {
+ s = indToRestr.get(oneInd);
+ for (OWLObjectExactCardinalityRestrictionImpl oecr : s) {
+ target.add(oecr);
+ }
+ OWLObjectIntersectionOfImpl intersection =
+ new OWLObjectIntersectionOfImpl(this.factory,target);
+ //kb.addABoxAxiom(new ClassAssertionAxiom(new OWLIntersection(ll), oneInd));
+
+
+ s = null;
+ target = new HashSet<OWLDescription>();
+
+ OWLAxiom axiom = factory.getOWLClassAssertionAxiom(
+ factory.getOWLIndividual(URI.create(oneInd.getName()))
+ , intersection);
+ AddAxiom addAxiom = new AddAxiom(this.onto, axiom);
+ try{
+ manager.applyChange(addAxiom);
+ numberOfStatementsChanged++;
+ }catch (Exception e) {e.printStackTrace();}
+
+ }//end for
+
+
+
+ //
+
+ // System.out.println("good ontology? " + rs.isSatisfiable());
+
+ }
+
+
+ public boolean testForTransitiveProperties(boolean printflag) {
+
+ boolean retval = false;
+
+ Set<OWLPropertyAxiom> ax = onto.getObjectPropertyAxioms();
+ for (OWLPropertyAxiom propertyAxiom : ax) {
+ //System.out.println(propertyAxiom.getClass().getSimpleName());
+ if (propertyAxiom.getClass().getSimpleName().equals(
+ "OWLTransitiveObjectPropertyAxiomImpl")) {
+ retval = true;
+ if(printflag) {
+ System.out.println(
+ "WARNING transitive object property can't be used in cardinality restriction\n"
+ + propertyAxiom.toString()+"but I'm ignoring it");
+ }
+ }
+ }
+ if(printflag) {
+ System.out.println(
+ "No transitive Properties found");
+ }
+ return retval;
+ }
+
+/*
+ public static void closeKB(KB kb) {
+ new OntologyCloserOWLAPI(kb).applyNumberRestrictions();
+ }
+*/
+
+ public SortedSet<Individual> verifyConcept(String conceptStr) {
+
+ Description d;
+ SimpleClock sc=new SimpleClock();
+ StringBuffer sb = new StringBuffer();
+ sb.append(conceptStr);
+ conceptStr = sb.toString();
+ SortedSet<Individual> ind = new TreeSet<Individual>();
+ try {
+ d = KBParser.parseConcept(conceptStr);
+ System.out.println("\n*******************\nStarting retrieval");
+ System.out.println(d.toManchesterSyntaxString("", new HashMap<String,String>()));
+ //System.out.println(d.toString());
+ sc.setTime();
+ this.rs.retrieval(d);
+
+ System.out.println("retrieved: " + ind.size() + " instances");
+ sc.printAndSet();
+ for (Individual individual : ind) {
+ System.out.print(individual + "|");
+ }
+
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ return ind;
+ }
+
+ public void writeOWLFile(URI filename){
+ try{
+ manager.saveOntology(this.onto, new OWLXMLOntologyFormat(),
+ filename);
+ }catch (Exception e) {e.printStackTrace();}
+ }
+
+
+ private boolean collectExObjRestrForInd(Individual ind, OWLObjectExactCardinalityRestrictionImpl oecr){
+ Set<OWLObjectExactCardinalityRestrictionImpl> s = indToRestr.get(ind);
+
+ if(s==null){
+
+ indToRestr.put(ind, new HashSet<OWLObjectExactCardinalityRestrictionImpl>());
+ s = indToRestr.get(ind);
+ }
+ return s.add(oecr);
+ }
+
+}
Added: trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java 2008-04-07 07:48:07 UTC (rev 769)
@@ -0,0 +1,20 @@
+package org.dllearner.utilities;
+
+public class SimpleClock {
+ private long time;
+
+ public SimpleClock() {
+ time=System.currentTimeMillis();
+ }
+
+ public void printAndSet() {
+ long now=System.currentTimeMillis();
+ System.out.println("needed "+(now-time)+" ms");
+ time=now;
+ }
+
+ public void setTime() {
+ time=System.currentTimeMillis();
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-07 15:05:57
|
Revision: 775
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=775&view=rev
Author: kurzum
Date: 2008-04-07 08:05:51 -0700 (Mon, 07 Apr 2008)
Log Message:
-----------
added toKBSyntaxString method
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/gp/ADC.java
trunk/src/dl-learner/org/dllearner/core/owl/BooleanDataRange.java
trunk/src/dl-learner/org/dllearner/core/owl/BooleanDatatypePropertyAssertion.java
trunk/src/dl-learner/org/dllearner/core/owl/BooleanValueRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/ClassAssertionAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/Datatype.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypeExactCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypeMaxCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypeMinCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypeProperty.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypePropertyDomainAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypePropertyRangeAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypeSomeRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/DatatypeValueRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/DifferentIndividualsAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/DisjointClassesAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/DoubleDatatypePropertyAssertion.java
trunk/src/dl-learner/org/dllearner/core/owl/DoubleMaxValue.java
trunk/src/dl-learner/org/dllearner/core/owl/DoubleMinValue.java
trunk/src/dl-learner/org/dllearner/core/owl/EquivalentClassesAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/FunctionalObjectPropertyAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/Individual.java
trunk/src/dl-learner/org/dllearner/core/owl/Intersection.java
trunk/src/dl-learner/org/dllearner/core/owl/InverseObjectPropertyAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/KB.java
trunk/src/dl-learner/org/dllearner/core/owl/KBElement.java
trunk/src/dl-learner/org/dllearner/core/owl/NamedClass.java
trunk/src/dl-learner/org/dllearner/core/owl/Negation.java
trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectAllRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectExactCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectMaxCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectMinCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectProperty.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyAssertion.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyDomainAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyInverse.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyRangeAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectSomeRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectValueRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/SubClassAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/SubObjectPropertyAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/SymmetricObjectPropertyAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/Thing.java
trunk/src/dl-learner/org/dllearner/core/owl/TransitiveObjectPropertyAxiom.java
trunk/src/dl-learner/org/dllearner/core/owl/TypedConstant.java
trunk/src/dl-learner/org/dllearner/core/owl/Union.java
trunk/src/dl-learner/org/dllearner/core/owl/UntypedConstant.java
trunk/src/dl-learner/org/dllearner/examples/KRK.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/gp/ADC.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/gp/ADC.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/algorithms/gp/ADC.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -37,6 +37,12 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "ADC";
}
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "ADC";
+ }
+
+
/* (non-Javadoc)
* @see org.dllearner.core.owl.Description#toManchesterSyntaxString()
Modified: trunk/src/dl-learner/org/dllearner/core/owl/BooleanDataRange.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/BooleanDataRange.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/BooleanDataRange.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -58,6 +58,13 @@
// TODO Auto-generated method stub
return null;
}
+
+
+ public String toKBSyntaxString (String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
public void accept(KBElementVisitor visitor) {
visitor.visit(this);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/BooleanDatatypePropertyAssertion.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/BooleanDatatypePropertyAssertion.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/BooleanDatatypePropertyAssertion.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -37,6 +37,11 @@
public String toString(String baseURI, Map<String, String> prefixes) {
return datatypeProperty.toString(baseURI, prefixes) + "(" + individual.toString(baseURI, prefixes) + "," + value +")";
}
+
+ @Override
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ return datatypeProperty.toKBSyntaxString(baseURI,prefixes) + "(" + individual.toKBSyntaxString( baseURI, prefixes) + "," + value +")";
+ }
public boolean getValue() {
return value;
Modified: trunk/src/dl-learner/org/dllearner/core/owl/BooleanValueRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/BooleanValueRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/BooleanValueRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -19,6 +19,7 @@
*/
package org.dllearner.core.owl;
+
/**
* Convenience class for boolean value restrictions.
*
@@ -58,4 +59,10 @@
public int getLength() {
return 2;
}
+
+ /*@Override
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ throw new Error("BooleanValueRestriction: not implemented");
+
+ }*/
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ClassAssertionAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ClassAssertionAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ClassAssertionAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -51,9 +51,18 @@
}
public String toString(String baseURI, Map<String,String> prefixes) {
- return concept.toString(baseURI, prefixes) + "(" + individual + ")";
+ return concept.toString(baseURI, prefixes) + "(" + individual.toString(baseURI, prefixes) + ")";
}
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return concept.toKBSyntaxString(baseURI, prefixes) + "(" + individual.toKBSyntaxString(baseURI, prefixes) + ")";
+ }
+
+ /*@Override
+ public String toKBSyntaxString() {
+ return concept.toKBSyntaxString() + "(" + individual + ")";
+ }*/
+
@Override
public void accept(AxiomVisitor visitor) {
visitor.visit(this);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Datatype.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Datatype.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Datatype.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -55,6 +55,10 @@
return uri.toString();
}
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ return uri.toString();
+ }
+
public void accept(KBElementVisitor visitor) {
visitor.visit(this);
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypeExactCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypeExactCardinalityRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypeExactCardinalityRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -63,6 +63,11 @@
return null;
}
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
/* (non-Javadoc)
* @see org.dllearner.core.owl.Description#toManchesterSyntaxString()
*/
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypeMaxCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypeMaxCardinalityRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypeMaxCardinalityRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -62,6 +62,11 @@
// TODO Auto-generated method stub
return null;
}
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
@Override
public void accept(DescriptionVisitor visitor) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypeMinCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypeMinCardinalityRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypeMinCardinalityRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -62,6 +62,11 @@
// TODO Auto-generated method stub
return null;
}
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
/* (non-Javadoc)
* @see org.dllearner.core.owl.Description#accept(org.dllearner.core.owl.DescriptionVisitor)
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypeProperty.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypeProperty.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypeProperty.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -52,6 +52,10 @@
}
public String toString(String baseURI, Map<String, String> prefixes) {
+ return Helper.getAbbreviatedString(name, baseURI, prefixes);
+ }
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
return "\"" + Helper.getAbbreviatedString(name, baseURI, prefixes) + "\"";
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypePropertyDomainAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypePropertyDomainAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypePropertyDomainAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -52,6 +52,15 @@
}
/* (non-Javadoc)
+ * @see org.dllearner.core.owl.KBElement#toKBSyntaxString(java.lang.String, java.util.Map)
+ */
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+
+ /* (non-Javadoc)
* @see org.dllearner.core.owl.Axiom#accept(org.dllearner.core.owl.AxiomVisitor)
*/
@Override
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypePropertyRangeAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypePropertyRangeAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypePropertyRangeAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -50,6 +50,11 @@
// TODO Auto-generated method stub
return null;
}
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
/* (non-Javadoc)
* @see org.dllearner.core.owl.Axiom#accept(org.dllearner.core.owl.AxiomVisitor)
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypeSomeRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypeSomeRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypeSomeRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -63,6 +63,13 @@
public String toString(String baseURI, Map<String, String> prefixes) {
return restrictedPropertyExpression.toString(baseURI, prefixes) + dataRange.toString(baseURI, prefixes);
}
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.KBElement#toKBSyntaxString(java.lang.String, java.util.Map)
+ */
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ return restrictedPropertyExpression.toKBSyntaxString(baseURI, prefixes) + dataRange.toKBSyntaxString(baseURI, prefixes);
+ }
/* (non-Javadoc)
* @see org.dllearner.core.owl.Description#accept(org.dllearner.core.owl.DescriptionVisitor)
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DatatypeValueRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DatatypeValueRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DatatypeValueRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -68,6 +68,10 @@
public String toString(String baseURI, Map<String, String> prefixes) {
return restrictedPropertyExpression.toString(baseURI, prefixes) + " = " + value.toString(baseURI, prefixes);
}
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ return restrictedPropertyExpression.toKBSyntaxString(baseURI, prefixes) + " = " + value.toKBSyntaxString(baseURI, prefixes);
+ }
public DatatypeProperty getRestrictedPropertyExpresssion() {
return (DatatypeProperty) restrictedPropertyExpression;
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DifferentIndividualsAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DifferentIndividualsAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DifferentIndividualsAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -48,6 +48,11 @@
// TODO Auto-generated method stub
return null;
}
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ throw new Error("DifferentIndividualsAxiom: Not implemented");
+ }
public Set<Individual> getIndividuals() {
return individuals;
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DisjointClassesAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DisjointClassesAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DisjointClassesAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -51,6 +51,13 @@
// TODO Auto-generated method stub
return null;
}
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ throw new Error("DisjointClassesAxiom: Not implemented");
+ }
+
+
@Override
public void accept(AxiomVisitor visitor) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DoubleDatatypePropertyAssertion.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DoubleDatatypePropertyAssertion.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DoubleDatatypePropertyAssertion.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -40,6 +40,13 @@
public String toString(String baseURI, Map<String, String> prefixes) {
return datatypeProperty.toString(baseURI, prefixes) + "(" + individual.toString(baseURI, prefixes) + "," + value +")";
}
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.KBElement#toKBSyntaxString(java.lang.String, java.util.Map)
+ */
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ return datatypeProperty.toKBSyntaxString(baseURI, prefixes) + "(" + individual.toKBSyntaxString(baseURI, prefixes) + "," + value +")";
+ }
public double getValue() {
return value;
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DoubleMaxValue.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DoubleMaxValue.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DoubleMaxValue.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -57,6 +57,10 @@
return " <= " + value;
}
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ return " <= " + value;
+ }
+
public void accept(KBElementVisitor visitor) {
visitor.visit(this);
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/DoubleMinValue.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/DoubleMinValue.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/DoubleMinValue.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -57,6 +57,10 @@
return " >= " + value;
}
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ return " >= " + value;
+ }
+
public void accept(KBElementVisitor visitor) {
visitor.visit(this);
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/EquivalentClassesAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/EquivalentClassesAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/EquivalentClassesAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -27,6 +27,10 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return concept1.toString(baseURI, prefixes) + " = " + concept2.toString(baseURI, prefixes);
}
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return concept1.toKBSyntaxString(baseURI, prefixes) + " = " + concept2.toKBSyntaxString(baseURI, prefixes);
+ }
@Override
public void accept(AxiomVisitor visitor) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/FunctionalObjectPropertyAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/FunctionalObjectPropertyAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/FunctionalObjectPropertyAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -18,9 +18,19 @@
return 1 + role.getLength();
}
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
+ */
public String toString(String baseURI, Map<String,String> prefixes) {
return "Functional(" + role.toString(baseURI, prefixes) + ")";
}
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.owl.KBElement#toKBSyntaxString(java.lang.String, java.util.Map)
+ */
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "Functional(" + role.toKBSyntaxString(baseURI, prefixes) + ")";
+ }
@Override
public void accept(AxiomVisitor visitor) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Individual.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Individual.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Individual.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -60,6 +60,10 @@
}
public String toString(String baseURI, Map<String,String> prefixes) {
+ return Helper.getAbbreviatedString(name, baseURI, prefixes);
+ }
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
return "\"" + Helper.getAbbreviatedString(name, baseURI, prefixes) + "\"";
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Intersection.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Intersection.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Intersection.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -39,16 +39,28 @@
return "EMPTY_AND";
String ret = "(";
+ for(int i=0; i<children.size()-1; i++) {
+ ret += children.get(i).toString(baseURI, prefixes) + " AND ";
+ }
+ ret += children.get(children.size()-1).toString(baseURI, prefixes) + ")";
+ return ret;
+ }
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ if(children.size()==0)
+ return "EMPTY_AND";
+
+ String ret = "(";
String bracketCollect = "";
for(int i=0; i<children.size()-1; i++) {
- ret += children.get(i).toString(baseURI, prefixes) + " AND ";
+ ret += children.get(i).toKBSyntaxString(baseURI, prefixes) + " AND ";
if( i != (children.size()-2) ) {
ret += "(";
bracketCollect += ")";
}
}
- ret += children.get(children.size()-1).toString(baseURI, prefixes) + ")";
+ ret += children.get(children.size()-1).toKBSyntaxString(baseURI, prefixes) + ")";
ret += bracketCollect;
return ret;
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/InverseObjectPropertyAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/InverseObjectPropertyAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/InverseObjectPropertyAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -26,6 +26,10 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "Inverse(" + inverseRole + "," + role.toString(baseURI, prefixes) + ")";
+ }
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "Inverse(" + inverseRole.toKBSyntaxString(baseURI, prefixes) + "," + role.toKBSyntaxString(baseURI, prefixes) + ")";
}
@Override
Modified: trunk/src/dl-learner/org/dllearner/core/owl/KB.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/KB.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/KB.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -203,6 +203,19 @@
return str;
}
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ String str = "TBox["+tbox.size()+"]:\n";
+ for(Axiom a : tbox)
+ str += " " + a.toString(baseURI, prefixes)+"\n";
+ str += "RBox["+rbox.size()+"]:\n";
+ for(Axiom a : rbox)
+ str += " " + a.toString(baseURI, prefixes)+"\n";
+ str += "ABox["+abox.size()+"]:\n";
+ for(Axiom a : abox)
+ str += " " + a.toString(baseURI, prefixes)+"\n";
+ return str;
+ }
+
public Set<Individual> findRelatedIndividuals(Individual individual) {
return findRelatedIndividuals(individual, new TreeSet<Individual>());
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/KBElement.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/KBElement.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/KBElement.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -14,5 +14,7 @@
public String toString(String baseURI, Map<String,String> prefixes);
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes);
+
public void accept(KBElementVisitor visitor);
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/NamedClass.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/NamedClass.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/NamedClass.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -52,6 +52,10 @@
}
public String toString(String baseURI, Map<String,String> prefixes) {
+ return Helper.getAbbreviatedString(name, baseURI, prefixes);
+ }
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
return "\"" + Helper.getAbbreviatedString(name, baseURI, prefixes) + "\"";
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Negation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Negation.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Negation.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -21,6 +21,11 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "(NOT " +children.get(0).toString(baseURI, prefixes) + ")";
}
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ //TODO brackets removed, but they maybe have to be here
+ return "NOT " +children.get(0).toKBSyntaxString(baseURI, prefixes) + "";
+ }
public int getLength() {
return 1 + children.get(0).getLength();
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -34,6 +34,10 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "BOTTOM";
}
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "BOTTOM";
+ }
/* (non-Javadoc)
* @see org.dllearner.core.owl.Description#toManchesterSyntaxString(java.lang.String, java.util.Map)
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectAllRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectAllRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectAllRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -37,6 +37,10 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "ALL " + restrictedPropertyExpression.toString(baseURI, prefixes) + "." + children.get(0).toString(baseURI, prefixes);
}
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "ALL " + restrictedPropertyExpression.toKBSyntaxString(baseURI, prefixes) + "." + children.get(0).toKBSyntaxString(baseURI, prefixes);
+ }
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectExactCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectExactCardinalityRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectExactCardinalityRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -39,6 +39,10 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "= " + number + " " + role.toString(baseURI, prefixes) + " " + getChild(0).toString(baseURI, prefixes);
}
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "= " + number + " " + role.toKBSyntaxString(baseURI, prefixes) + " " + getChild(0).toKBSyntaxString(baseURI, prefixes);
+ }
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectMaxCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectMaxCardinalityRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectMaxCardinalityRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -15,8 +15,12 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "<= " + number + " " + role.toString(baseURI, prefixes) + " " + getChild(0).toString(baseURI, prefixes);
- }
+ }
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "<= " + number + " " + role.toKBSyntaxString(baseURI, prefixes) + " " + getChild(0).toKBSyntaxString(baseURI, prefixes);
+ }
+
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
return role.toString(baseURI, prefixes) + " max " + number + " " + getChild(0).toManchesterSyntaxString(baseURI, prefixes);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectMinCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectMinCardinalityRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectMinCardinalityRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -17,6 +17,10 @@
return ">= " + number + " " + role.toString(baseURI, prefixes) + " " + getChild(0).toString(baseURI, prefixes);
}
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return ">= " + number + " " + role.toKBSyntaxString(baseURI, prefixes) + " " + getChild(0).toKBSyntaxString(baseURI, prefixes);
+ }
+
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
return role.toString(baseURI, prefixes) + " min " + number + " " + getChild(0).toManchesterSyntaxString(baseURI, prefixes);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectProperty.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectProperty.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectProperty.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -46,8 +46,12 @@
}
public String toString(String baseURI, Map<String,String> prefixes) {
+ return Helper.getAbbreviatedString(name, baseURI, prefixes) ;
+ }
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
return "\"" + Helper.getAbbreviatedString(name, baseURI, prefixes) + "\"";
- }
+ }
public void accept(KBElementVisitor visitor) {
visitor.visit(this);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyAssertion.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyAssertion.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyAssertion.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -65,6 +65,10 @@
return role.toString(baseURI, prefixes) + "(" + individual1.toString(baseURI, prefixes) + "," + individual2.toString(baseURI, prefixes) +")";
}
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return role.toKBSyntaxString(baseURI, prefixes) + "(" + individual1.toKBSyntaxString(baseURI, prefixes) + "," + individual2.toKBSyntaxString(baseURI, prefixes) +")";
+ }
+
public void accept(KBElementVisitor visitor) {
visitor.visit(this);
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyDomainAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyDomainAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyDomainAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -52,6 +52,12 @@
// TODO Auto-generated method stub
return null;
}
+
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
@Override
public void accept(AxiomVisitor visitor) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyInverse.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyInverse.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyInverse.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -50,6 +50,10 @@
return Helper.getAbbreviatedString(name, baseURI, prefixes) + "-";
}
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return Helper.getAbbreviatedString(name, baseURI, prefixes) + "-";
+ }
+
public void accept(KBElementVisitor visitor) {
visitor.visit(this);
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyRangeAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyRangeAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyRangeAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -46,6 +46,11 @@
// TODO Auto-generated method stub
return null;
}
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
@Override
public Description getRange() {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectSomeRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectSomeRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectSomeRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -36,6 +36,10 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "EXISTS " + restrictedPropertyExpression.toString(baseURI, prefixes) + "." + children.get(0).toString(baseURI, prefixes);
}
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "EXISTS " + restrictedPropertyExpression.toKBSyntaxString(baseURI, prefixes) + "." + children.get(0).toKBSyntaxString(baseURI, prefixes);
+ }
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectValueRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectValueRestriction.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectValueRestriction.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -71,6 +71,11 @@
return null;
}
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
public Individual getIndividual() {
return (Individual) value;
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/SubClassAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/SubClassAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/SubClassAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -28,6 +28,10 @@
return subConcept.toString(baseURI, prefixes) + " SUBCONCEPTOF " + superConcept.toString(baseURI, prefixes);
}
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return subConcept.toKBSyntaxString(baseURI, prefixes) + " SUBCONCEPTOF " + superConcept.toKBSyntaxString(baseURI, prefixes);
+ }
+
@Override
public void accept(AxiomVisitor visitor) {
visitor.visit(this);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/SubObjectPropertyAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/SubObjectPropertyAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/SubObjectPropertyAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -26,8 +26,12 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "Subrole(" + subRole.toString(baseURI, prefixes) + "," + role.toString(baseURI, prefixes) + ")";
- }
+ }
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "Subrole(" + subRole.toKBSyntaxString(baseURI, prefixes) + "," + role.toKBSyntaxString(baseURI, prefixes) + ")";
+ }
+
@Override
public void accept(AxiomVisitor visitor) {
visitor.visit(this);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/SymmetricObjectPropertyAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/SymmetricObjectPropertyAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/SymmetricObjectPropertyAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -22,6 +22,10 @@
return "Symmetric(" + role.toString(baseURI, prefixes) + ")";
}
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "Symmetric(" + role.toKBSyntaxString(baseURI, prefixes) + ")";
+ }
+
@Override
public void accept(AxiomVisitor visitor) {
visitor.visit(this);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Thing.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Thing.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Thing.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -41,6 +41,10 @@
public String toString(String baseURI, Map<String,String> prefixes) {
return "TOP";
}
+
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "TOP";
+ }
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/TransitiveObjectPropertyAxiom.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/TransitiveObjectPropertyAxiom.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/TransitiveObjectPropertyAxiom.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -22,6 +22,10 @@
return "Transitive(" + role.toString(baseURI, prefixes) + ")";
}
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+ return "Transitive(" + role.toKBSyntaxString(baseURI, prefixes) + ")";
+ }
+
@Override
public void accept(AxiomVisitor visitor) {
visitor.visit(this);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/TypedConstant.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/TypedConstant.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/TypedConstant.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -50,6 +50,11 @@
return literal;
// return literal + "^^" + datatype;
}
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ return literal;
+// return literal + "^^" + datatype;
+ }
/**
* @return the datatype
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Union.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Union.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Union.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -48,6 +48,25 @@
return ret;
}
+ public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
+
+ if(children.size()==0)
+ return "EMPTY_OR";
+
+ String ret = "(";
+ String bracketCollect = "";
+ for(int i=0; i<children.size()-1; i++) {
+ ret += children.get(i).toKBSyntaxString(baseURI, prefixes) + " OR ";
+ if( i != (children.size()-2) ) {
+ ret += "(";
+ bracketCollect += ")";
+ }
+ }
+ ret += children.get(children.size()-1).toKBSyntaxString(baseURI, prefixes) + ")";
+ ret += bracketCollect;
+ return ret;
+ }
+
@Override
public String toManchesterSyntaxString(String baseURI, Map<String,String> prefixes) {
if(children.size()==0)
Modified: trunk/src/dl-learner/org/dllearner/core/owl/UntypedConstant.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/UntypedConstant.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/core/owl/UntypedConstant.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -61,6 +61,13 @@
else
return literal;
}
+
+ public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
+ if(hasLang)
+ return literal + "@" + lang;
+ else
+ return literal;
+ }
/**
* @return the lang
Modified: trunk/src/dl-learner/org/dllearner/examples/KRK.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-07 12:18:57 UTC (rev 774)
+++ trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-07 15:05:51 UTC (rev 775)
@@ -233,14 +233,17 @@
if(closeKB) {
if(closeConcise) {
- oc.applyNumberRestrictionsNamed();
+ oc.applyNumberRestrictionsConcise();
kbaddition = "_CloseConcise";
}
else oc.applyNumberRestrictions();
}
-
- if (verifySomeConcepts) verifySomeConcepts(oc);
+
+ if (verifySomeConcepts) {
+ oc.updateReasoner();
+ verifySomeConcepts(oc);
+ }
if (writeClosedOWL) writeOWLFile("test"+kbaddition+".owl");
} catch (Exception e) {
@@ -319,6 +322,9 @@
" ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
"\"http://www.test.de/test#WKing\") ");*/
+
+ test.add("EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#hasLowerRankThan\".(\"http://www.test.de/test#WRook\" AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\")") ;
+
for (int i = 0; i < test.size(); i++) {
String conceptStr = test.get(i);
oc.verifyConcept(conceptStr);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-07 15:18:05
|
Revision: 776
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=776&view=rev
Author: kurzum
Date: 2008-04-07 08:17:58 -0700 (Mon, 07 Apr 2008)
Log Message:
-----------
changed output of learning algorithms ROL and REF, now has simple, Manchester, KBSyntax output
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/core/owl/Description.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-07 15:05:51 UTC (rev 775)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-07 15:17:58 UTC (rev 776)
@@ -385,12 +385,13 @@
logger.info("best node " + candidatesStable.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
logger.info("\nsolutions:");
for(Description c : solutions) {
- logger.info(" " + c + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
+ logger.info(" " + c.toString(baseURI,null) + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
//TODO remove this line maybe
// watch for String.replace Quick hack
logger.info(" MANCHESTER: " +
c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()).
replace("\"", ""));
+ logger.info(" KBSyntax: " + c.toKBSyntaxString());
}
}
logger.debug("size of candidate set: " + candidates.size());
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-07 15:05:51 UTC (rev 775)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-07 15:17:58 UTC (rev 776)
@@ -512,12 +512,13 @@
if(solutionFound) {
logger.info("\nsolutions:");
for(Description c : solutions) {
- logger.info(" " + c + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
+ logger.info(" " + c.toString(baseURI,null) + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
//TODO remove this line maybe
// watch for String.replace Quick hack
logger.info(" MANCHESTER: " +
c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()).
replace("\"", ""));
+ logger.info(" KBSyntax: " + c.toKBSyntaxString());
}
}
logger.info(" horizontal expansion: " + minimumHorizontalExpansion + " to " + maximumHorizontalExpansion);
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-04-07 15:05:51 UTC (rev 775)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-04-07 15:17:58 UTC (rev 776)
@@ -711,7 +711,7 @@
Set<Individual> result = null;
result = rs.retrieval(concept);
- System.out.println("retrieval result: " + result);
+ System.out.println("retrieval result ("+result.size()+"): " + result);
Score score = lp.computeScore(concept);
System.out.println(score);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Description.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Description.java 2008-04-07 15:05:51 UTC (rev 775)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Description.java 2008-04-07 15:17:58 UTC (rev 776)
@@ -190,6 +190,11 @@
return toString(null, null);
}
+
+ public String toKBSyntaxString() {
+ return toKBSyntaxString(null, null);
+ }
+
/**
* Returns a manchester syntax string of this description. For a
* reference, see
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-10 13:20:23
|
Revision: 785
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=785&view=rev
Author: kurzum
Date: 2008-04-10 06:20:09 -0700 (Thu, 10 Apr 2008)
Log Message:
-----------
some kbsyntax manchester fixes, added option useCardinalityRestrictions
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectExactCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectMaxCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectMinCardinalityRestriction.java
trunk/src/dl-learner/org/dllearner/examples/KRK.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-04-10 13:01:21 UTC (rev 784)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-04-10 13:20:09 UTC (rev 785)
@@ -101,6 +101,7 @@
private boolean improveSubsumptionHierarchy = true;
private boolean useAllConstructor = true;
private boolean useExistsConstructor = true;
+ private boolean useCardinalityRestrictions = true;
private boolean useNegation = true;
private boolean useBooleanDatatypes = true;
private double noisePercentage = 0.0;
@@ -160,8 +161,10 @@
options.add(CommonConfigOptions.ignoredRoles());
options.add(CommonConfigOptions.useAllConstructor());
options.add(CommonConfigOptions.useExistsConstructor());
+ options.add(CommonConfigOptions.useCardinalityRestrictions());
options.add(CommonConfigOptions.useNegation());
options.add(CommonConfigOptions.useBooleanDatatypes());
+
DoubleConfigOption noisePercentage = new DoubleConfigOption("noisePercentage", "the (approximated) percentage of noise within the examples");
noisePercentage.setLowerLimit(0);
noisePercentage.setUpperLimit(100);
@@ -213,6 +216,8 @@
useAllConstructor = (Boolean) entry.getValue();
} else if(name.equals("useExistsConstructor")) {
useExistsConstructor = (Boolean) entry.getValue();
+ } else if(name.equals("useCardinalityRestrictions")) {
+ useCardinalityRestrictions = (Boolean) entry.getValue();
} else if(name.equals("useNegation")) {
useNegation = (Boolean) entry.getValue();
} else if(name.equals("noisePercentage")) {
@@ -292,6 +297,7 @@
applyExistsFilter,
useAllConstructor,
useExistsConstructor,
+ useCardinalityRestrictions,
useNegation,
useBooleanDatatypes,
startClass
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-10 13:01:21 UTC (rev 784)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-10 13:20:09 UTC (rev 785)
@@ -739,8 +739,11 @@
// String bestNodeString = "currently best node: " + bestNode + " accuracy: " + df.format(accuracy) + "%";
logger.debug("start node: " + startNode.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
String bestNodeString = "currently best node: " + bestNode.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI);
+ String bestNodeStringKBSyntax = "currently best node KBSyntax: " + bestNode.getConcept().toKBSyntaxString();
+
// searchTree += bestNodeString + "\n";
logger.debug(bestNodeString);
+ logger.debug(bestNodeStringKBSyntax);
String expandedNodeString = "next expanded node: " + candidates.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI);
// searchTree += expandedNodeString + "\n";
logger.debug(expandedNodeString);
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-04-10 13:01:21 UTC (rev 784)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2008-04-10 13:20:09 UTC (rev 785)
@@ -78,7 +78,7 @@
private double expansionPenaltyFactor;
private double gainBonusFactor;
private double nodeChildPenalty = 0.0001;
- private double startNodeBonus = 2.0;
+ private double startNodeBonus = 0.1; //was 2.0
// penalise errors on positive examples harder than on negative examples
// (positive weight = 1)
private double negativeWeight = 0.8;
Modified: trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java 2008-04-10 13:01:21 UTC (rev 784)
+++ trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java 2008-04-10 13:20:09 UTC (rev 785)
@@ -28,6 +28,21 @@
*
*/
public final class CommonConfigOptions {
+
+ //public static boolean applyAllFilterDefault = true;
+ //public static boolean applyExistsFilterDefault = true;
+ //public static boolean useTooWeakListDefault = true;
+ //public static boolean useOverlyGeneralListDefault = true;
+ //public static boolean useShortConceptConstructionDefault = true;
+ //public static boolean improveSubsumptionHierarchyDefault = true;
+ public static boolean useAllConstructorDefault = true;
+ public static boolean useExistsConstructorDefault = true;
+ public static boolean useCardinalityRestrictionsDefault = true;
+ public static boolean useNegationDefault = true;
+ public static boolean useBooleanDatatypesDefault = true;
+ //public static double noisePercentageDefault = 0.0;
+
+
public static StringConfigOption getVerbosityOption() {
StringConfigOption verbosityOption = new StringConfigOption("verbosity", "control verbosity of output for this component", "warning");
@@ -72,18 +87,22 @@
}
public static BooleanConfigOption useAllConstructor() {
- return new BooleanConfigOption("useAllConstructor", "specifies whether to universal concept constructor is used in the learning algorothm");
+ return new BooleanConfigOption("useAllConstructor", "specifies whether the universal concept constructor is used in the learning algorithm",useAllConstructorDefault);
}
public static BooleanConfigOption useExistsConstructor() {
- return new BooleanConfigOption("useExistsConstructor", "specifies whether to existential concept constructor is used in the learning algorothm");
+ return new BooleanConfigOption("useExistsConstructor", "specifies whether the existential concept constructor is used in the learning algorithm",useExistsConstructorDefault);
}
+ public static BooleanConfigOption useCardinalityRestrictions() {
+ return new BooleanConfigOption("useCardinalityRestrictions", "specifies whether CardinalityRestrictions is used in the learning algorithm",useCardinalityRestrictionsDefault);
+ }
+
public static BooleanConfigOption useNegation() {
- return new BooleanConfigOption("useNegation", "specifies whether negation is used in the learning algorothm");
+ return new BooleanConfigOption("useNegation", "specifies whether negation is used in the learning algorothm",useNegationDefault);
}
public static BooleanConfigOption useBooleanDatatypes() {
- return new BooleanConfigOption("useBooleanDatatypes", "specifies whether boolean datatypes are used in the learning algorothm");
+ return new BooleanConfigOption("useBooleanDatatypes", "specifies whether boolean datatypes are used in the learning algorothm",useBooleanDatatypesDefault);
}
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectExactCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectExactCardinalityRestriction.java 2008-04-10 13:01:21 UTC (rev 784)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectExactCardinalityRestriction.java 2008-04-10 13:20:09 UTC (rev 785)
@@ -37,11 +37,11 @@
}
public String toString(String baseURI, Map<String,String> prefixes) {
- return "= " + number + " " + role.toString(baseURI, prefixes) + " " + getChild(0).toString(baseURI, prefixes);
+ return "= " + number + " " + role.toString(baseURI, prefixes) + "." + getChild(0).toString(baseURI, prefixes);
}
public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
- return "= " + number + " " + role.toKBSyntaxString(baseURI, prefixes) + " " + getChild(0).toKBSyntaxString(baseURI, prefixes);
+ return "= " + number + " " + role.toKBSyntaxString(baseURI, prefixes) + "." + getChild(0).toKBSyntaxString(baseURI, prefixes);
}
@Override
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectMaxCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectMaxCardinalityRestriction.java 2008-04-10 13:01:21 UTC (rev 784)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectMaxCardinalityRestriction.java 2008-04-10 13:20:09 UTC (rev 785)
@@ -14,11 +14,11 @@
}
public String toString(String baseURI, Map<String,String> prefixes) {
- return "<= " + number + " " + role.toString(baseURI, prefixes) + " " + getChild(0).toString(baseURI, prefixes);
+ return "<= " + number + " " + role.toString(baseURI, prefixes) + "." + getChild(0).toString(baseURI, prefixes);
}
public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
- return "<= " + number + " " + role.toKBSyntaxString(baseURI, prefixes) + " " + getChild(0).toKBSyntaxString(baseURI, prefixes);
+ return "<= " + number + " " + role.toKBSyntaxString(baseURI, prefixes) + "." + getChild(0).toKBSyntaxString(baseURI, prefixes);
}
@Override
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectMinCardinalityRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectMinCardinalityRestriction.java 2008-04-10 13:01:21 UTC (rev 784)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectMinCardinalityRestriction.java 2008-04-10 13:20:09 UTC (rev 785)
@@ -14,11 +14,11 @@
}
public String toString(String baseURI, Map<String,String> prefixes) {
- return ">= " + number + " " + role.toString(baseURI, prefixes) + " " + getChild(0).toString(baseURI, prefixes);
+ return ">= " + number + " " + role.toString(baseURI, prefixes) + "." + getChild(0).toString(baseURI, prefixes);
}
public String toKBSyntaxString(String baseURI, Map<String,String> prefixes) {
- return ">= " + number + " " + role.toKBSyntaxString(baseURI, prefixes) + " " + getChild(0).toKBSyntaxString(baseURI, prefixes);
+ return ">= " + number + " " + role.toKBSyntaxString(baseURI, prefixes) + "." + getChild(0).toKBSyntaxString(baseURI, prefixes);
}
@Override
Modified: trunk/src/dl-learner/org/dllearner/examples/KRK.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-10 13:01:21 UTC (rev 784)
+++ trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-10 13:20:09 UTC (rev 785)
@@ -56,7 +56,7 @@
static boolean writeConciseOWLAllDifferent = false;
- static boolean closeKB=true;
+ static boolean closeKB=false;
static boolean closeConcise= true && closeKB;
static boolean writeClosedOWL = true && closeKB;
static boolean verifySomeConcepts = false && closeKB;
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-04-10 13:01:21 UTC (rev 784)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-04-10 13:20:09 UTC (rev 785)
@@ -167,16 +167,17 @@
// private Map<NamedClass,Map<NamedClass,Boolean>> notABMeaningful = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
public RhoDRDown(ReasoningService reasoningService) {
- this(reasoningService, true, true, true, true, true, true, null);
+ this(reasoningService, true, true, true, true, true, true, true, null);
}
public RhoDRDown(ReasoningService reasoningService, boolean applyAllFilter, boolean applyExistsFilter, boolean useAllConstructor,
- boolean useExistsConstructor, boolean useNegation, boolean useBooleanDatatypes, NamedClass startClass) {
+ boolean useExistsConstructor,boolean useCardinalityRestrictions,boolean useNegation, boolean useBooleanDatatypes, NamedClass startClass) {
this.rs = reasoningService;
this.applyAllFilter = applyAllFilter;
this.applyExistsFilter = applyExistsFilter;
this.useAllConstructor = useAllConstructor;
this.useExistsConstructor = useExistsConstructor;
+ this.useCardinalityRestrictions = useCardinalityRestrictions;
this.useNegation = useNegation;
this.useBooleanDatatypes = useBooleanDatatypes;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-15 10:20:25
|
Revision: 788
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=788&view=rev
Author: kurzum
Date: 2008-04-15 03:20:23 -0700 (Tue, 15 Apr 2008)
Log Message:
-----------
added some functions at some places nothing big
new approach to KRK
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/examples/KRK.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLP.java
trunk/src/dl-learner/org/dllearner/parser/KBParser.java
trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
trunk/src/dl-learner/org/dllearner/examples/KRKOntologyTBox.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java 2008-04-14 22:45:16 UTC (rev 787)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedNode.java 2008-04-15 10:20:23 UTC (rev 788)
@@ -174,6 +174,30 @@
return ret;
}
+ //TODO integrate this method with the one above
+ public String getStats(int nrOfPositiveExamples, int nrOfNegativeExamples) {
+ String ret = " [";
+
+ if(isTooWeak)
+ ret += "q:tw";
+ else {
+ double accuracy = 100 * (coveredPositives.size() + nrOfNegativeExamples - coveredNegatives.size())/(double)(nrOfPositiveExamples+nrOfNegativeExamples);
+ ret += "acc:" + df.format(accuracy) + "% ";
+
+ // comment this out to display the heuristic score with default parameters
+ double heuristicScore = MultiHeuristic.getNodeScore(this, nrOfPositiveExamples, nrOfNegativeExamples);
+ ret += "h:" +df.format(heuristicScore) + " ";
+
+ int wrongPositives = nrOfPositiveExamples - coveredPositives.size();
+ ret += "q:" + wrongPositives + "p-" + coveredNegatives.size() + "n";
+ }
+
+ ret += " ("+qualityEvaluationMethod+"), he:" + horizontalExpansion;
+ ret += " c:" + children.size() + "]";
+
+ return ret;
+ }
+
public double getAccuracy(int nrOfPositiveExamples, int nrOfNegativeExamples) {
return (coveredPositives.size() + nrOfNegativeExamples - coveredNegatives.size())/(double)(nrOfPositiveExamples+nrOfNegativeExamples);
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-14 22:45:16 UTC (rev 787)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-15 10:20:23 UTC (rev 788)
@@ -743,6 +743,7 @@
// searchTree += bestNodeString + "\n";
logger.debug(bestNodeString);
+ logger.debug(startNode.getStats(nrOfPositiveExamples, nrOfNegativeExamples));
logger.debug(bestNodeStringKBSyntax);
String expandedNodeString = "next expanded node: " + candidates.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI);
// searchTree += expandedNodeString + "\n";
Modified: trunk/src/dl-learner/org/dllearner/examples/KRK.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-14 22:45:16 UTC (rev 787)
+++ trunk/src/dl-learner/org/dllearner/examples/KRK.java 2008-04-15 10:20:23 UTC (rev 788)
@@ -5,6 +5,7 @@
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
+import java.io.FileWriter;
import java.io.IOException;
import java.net.URI;
import java.util.ArrayList;
@@ -17,7 +18,6 @@
import org.dllearner.core.owl.ClassAssertionAxiom;
import org.dllearner.core.owl.DatatypeProperty;
import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.DisjointClassesAxiom;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.InverseObjectPropertyAxiom;
import org.dllearner.core.owl.KB;
@@ -51,7 +51,9 @@
//
// turn off to not write the owl, needs about 30 seconds or more
static boolean writeOWL = true;
+ static boolean writeKB = false;
static boolean useTransitivity = false;
+ static boolean useHigherThan = false;
static boolean writeExampleSets = true;
static boolean writeConciseOWLAllDifferent = false;
@@ -103,6 +105,9 @@
static ObjectProperty rankLessThan = getRole("hasLowerRankThan");
static ObjectProperty fileLessThan = getRole("hasLowerFileThan");
+
+ static ObjectProperty rankHigherThan = getRole("hasHigherRankThan");
+ static ObjectProperty fileHigherThan = getRole("hasHigherFileThan");
// static ObjectProperty lessThan = getRole("strictLessThan");
@@ -142,10 +147,13 @@
+
+
try {
String line = "";
String[] ar = new String[6];
+ String currentclass="";
int x = 0;
while ((line = in.readLine()) != null) {
@@ -154,11 +162,15 @@
System.out.println("Currently at line" + x);
ar = tokenize(line);
+ currentclass = ar[6];
+
gameind = getIndividual("game" + x);
wkingind = getIndividual("wking_" + ar[0] + ar[1] + "_" + x);
wrookind = getIndividual("wrook_" + ar[2] + ar[3] + "_" + x);
bkingind = getIndividual("bking_" + ar[4] + ar[5] + "_" + x);
+
+
allInstances.add(gameind+"");
allInstances.add(wkingind+"");
allInstances.add(wrookind+"");
@@ -180,6 +192,34 @@
kb.addABoxAxiom(new ClassAssertionAxiom(WRook, wrookind));
kb.addABoxAxiom(new ClassAssertionAxiom(BKing, bkingind));
+
+ /**Files and Ranks***/
+ // FILES are letters
+ // RANKS are numbers
+
+ //WKing
+ NamedClass tmp=getAtomicConcept(ar[0].toUpperCase());
+ kb.addABoxAxiom(new ClassAssertionAxiom(tmp, wkingind));
+
+ tmp=getAtomicConcept("F"+ar[1]);
+ kb.addABoxAxiom(new ClassAssertionAxiom(tmp , wkingind));
+
+ //WRook
+ tmp=getAtomicConcept(ar[2].toUpperCase());
+ kb.addABoxAxiom(new ClassAssertionAxiom(tmp, wrookind));
+
+ tmp=getAtomicConcept("F"+ar[3]);
+ kb.addABoxAxiom(new ClassAssertionAxiom(tmp , wrookind));
+
+ //BKing
+ tmp=getAtomicConcept(ar[4].toUpperCase());
+ kb.addABoxAxiom(new ClassAssertionAxiom(tmp, bkingind));
+
+ tmp=getAtomicConcept("F"+ar[5]);
+ kb.addABoxAxiom(new ClassAssertionAxiom(tmp, bkingind));
+
+
+
// PROPERTIES
kb.addABoxAxiom(new ObjectPropertyAssertion(hasPiece, gameind,
wkingind));
@@ -227,11 +267,12 @@
if(writeExampleSets)writeExampleSets();
if(writeConciseOWLAllDifferent)writeConciseOWLAllDifferent();
if (writeOWL)writeOWLFile("test.owl");
-
- OntologyCloser oc = new OntologyCloser(kb);
+ if(writeKB)writeKBFile("test.kb");
+
+ OntologyCloser oc = null;
String kbaddition= "_Closed";
if(closeKB) {
-
+ oc= new OntologyCloser(kb);
if(closeConcise) {
oc.applyNumberRestrictionsConcise();
kbaddition = "_CloseConcise";
@@ -241,6 +282,7 @@
if (verifySomeConcepts) {
+
oc.updateReasoner();
verifySomeConcepts(oc);
}
@@ -252,79 +294,25 @@
System.out.println("Done");
}// end main
+
+
+ static void makeOntology(){
+
+
+
+ }
+
+
protected static void verifySomeConcepts(OntologyCloser oc) {
ArrayList<String> test=new ArrayList<String>();
- //String conceptStr = "ALL \"http://www.test.de/test#hasPiece\".(EXISTS \"http://www.test.de/test#fileDistanceLessThan6\".((NOT \"http://www.test.de/test#WKing\") AND ALL \"http://www.test.de/test#rankDistance1\".(\"http://www.test.de/test#WKing\" AND ALL \"http://www.test.de/test#fileDistanceLessThan2\".\"http://www.test.de/test#BKing\" AND ALL \"http://www.test.de/test#hasLowerFileThan\".\"http://www.test.de/test#WKing\")) AND ALL \"http://www.test.de/test#fileDistance1\".\"http://www.test.de/test#WRook\")";
- //conceptStr = "ALL http://www.test.de/test#hasPiece.(EXISTS http://www.test.de/test#fileDistanceLessThan6.((NOT http://www.test.de/test#WKing) AND ALL http://www.test.de/test#rankDistance1.(http://www.test.de/test#WKing AND ALL http://www.test.de/test#fileDistanceLessThan2.http://www.test.de/test#WKing AND ALL http://www.test.de/test#hasLowerFileThan.http://www.test.de/test#WKing)) AND ALL http://www.test.de/test#fileDistance1.http://www.test.de/test#WRook)";
- //conceptStr = "ALL hasPiece.(EXISTS fileDistanceLessThan6.((NOT WKing) AND ALL rankDistance1.(WKing AND ALL fileDistanceLessThan2.WKing AND ALL hasLowerFileThan.WKing)) AND ALL fileDistance1.WRook)";
- //conceptStr = "ALL \"http://www.test.de/test#hasPiece\".\"http://www.test.de/test#WKing\"";
- //conceptStr = "EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#hasLowerRankThan\".(\"http://www.test.de/test#WRook\" AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\")";
-
- test.add("\"http://www.test.de/test#WRook\"");
- /*test.add("ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
- "\"http://www.test.de/test#WKing\"");
- /*test.add("(\"http://www.test.de/test#WRook\" "+
- " AND " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
- "\"http://www.test.de/test#WKing\") ");*/
- /*test.add("(\"http://www.test.de/test#Piece\" "+
- " AND " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan8\"." +
- "\"http://www.test.de/test#Piece\") ");
- test.add("(\"http://www.test.de/test#Piece\" "+
- " AND ( " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan8\"." +
- "\"http://www.test.de/test#Piece\" " +
- " AND " +
- " EXISTS \"http://www.test.de/test#fileDistanceLessThan8\"." +
- "\"http://www.test.de/test#Piece\"))") ;
- test.add("(\"http://www.test.de/test#Piece\" "+
- " AND ( " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan7\"." +
- "\"http://www.test.de/test#Piece\" " +
- " AND " +
- " EXISTS \"http://www.test.de/test#fileDistanceLessThan7\"." +
- "\"http://www.test.de/test#Piece\"))") ;
- test.add("(\"http://www.test.de/test#Piece\" "+
- " AND ( " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan5\"." +
- "\"http://www.test.de/test#Piece\" " +
- " AND " +
- " EXISTS \"http://www.test.de/test#fileDistanceLessThan5\"." +
- "\"http://www.test.de/test#Piece\"))") ;*/
- test.add("(\"http://www.test.de/test#Piece\" "+
- " AND ( " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan3\"." +
- "\"http://www.test.de/test#Piece\" " +
- " AND " +
- " EXISTS \"http://www.test.de/test#fileDistanceLessThan3\"." +
- "\"http://www.test.de/test#Piece\"))") ;
- test.add("(\"http://www.test.de/test#BKing\" "+
- " AND ( " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan3\"." +
- "\"http://www.test.de/test#Piece\" " +
- " AND " +
- " EXISTS \"http://www.test.de/test#fileDistanceLessThan3\"." +
- "\"http://www.test.de/test#Piece\"))") ;
- test.add("(\"http://www.test.de/test#BKing\" "+
- " AND ( " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan2\"." +
- "\"http://www.test.de/test#Piece\" " +
- " AND " +
- " EXISTS \"http://www.test.de/test#fileDistanceLessThan2\"." +
- "\"http://www.test.de/test#Piece\"))") ;
+ test.add("(EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#rankDistanceLessThan2\".(\"http://www.test.de/test#BKing\" AND EXISTS \"http://www.test.de/test#fileDistanceLessThan1\".(\"http://www.test.de/test#A\" OR \"http://www.test.de/test#WKing\")) AND EXISTS \"http://www.test.de/test#hasPiece\".(\"http://www.test.de/test#WKing\" AND ((\"http://www.test.de/test#C\" AND EXISTS \"http://www.test.de/test#hasLowerRankThan\".\"http://www.test.de/test#A\") OR (\"http://www.test.de/test#F3\" AND EXISTS \"http://www.test.de/test#rankDistance2\".\"http://www.test.de/test#WRook\"))))");
- /*test.add("(\"http://www.test.de/test#Piece\" "+
- " AND " +
- " ALL \"http://www.test.de/test#fileDistanceLessThan1\"." +
- "\"http://www.test.de/test#WKing\") ");*/
+
- test.add("EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#hasLowerRankThan\".(\"http://www.test.de/test#WRook\" AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\")") ;
-
for (int i = 0; i < test.size(); i++) {
String conceptStr = test.get(i);
oc.verifyConcept(conceptStr);
@@ -352,21 +340,37 @@
kb.addABoxAxiom(new ObjectPropertyAssertion(getRole(fdistance + Fdist),
A.id, B.id));
symmetricRoleSet.add(fdistance + Fdist);
+
+
- if (A.meHasLowerFileThan(B))
+ if (A.meHasLowerFileThan(B)){
kb.addABoxAxiom(new ObjectPropertyAssertion(fileLessThan, A.id,
B.id));
+ if(useHigherThan)kb.addABoxAxiom(new ObjectPropertyAssertion(fileHigherThan, B.id,
+ A.id));
+
+ }
// 18:00
- else if (B.meHasLowerFileThan(A))
+ else if (B.meHasLowerFileThan(A)){
kb.addABoxAxiom(new ObjectPropertyAssertion(fileLessThan, B.id,
A.id));
+ if(useHigherThan)kb.addABoxAxiom(new ObjectPropertyAssertion(fileHigherThan, A.id,
+ B.id));
+ }
- if (A.meHasLowerRankThan(B))
+ if (A.meHasLowerRankThan(B)){
kb.addABoxAxiom(new ObjectPropertyAssertion(rankLessThan, A.id,
B.id));
- else if (B.meHasLowerRankThan(A))
+ if(useHigherThan)kb.addABoxAxiom(new ObjectPropertyAssertion(rankHigherThan, B.id,
+ A.id));
+ }
+ else if (B.meHasLowerRankThan(A)){
kb.addABoxAxiom(new ObjectPropertyAssertion(rankLessThan, B.id,
A.id));
+ if(useHigherThan)kb.addABoxAxiom(new ObjectPropertyAssertion(rankHigherThan, A.id,
+ B.id));
+
+ }
}
public static void init() {
@@ -384,7 +388,7 @@
// DisJointClasses1.add(Rank);
// DisJointClasses1.add(File);
DisJointClasses1.add(Game);
- kb.addTBoxAxiom(new DisjointClassesAxiom(DisJointClasses1));
+ //kb.addTBoxAxiom(new DisjointClassesAxiom(DisJointClasses1));
SortedSet<Description> DisJointClasses2 = new TreeSet<Description>();
DisJointClasses2 = new TreeSet<Description>();
@@ -395,7 +399,7 @@
// DisJointClasses2.add(File);
// DisJointClasses2.add(Game);
- kb.addTBoxAxiom(new DisjointClassesAxiom(DisJointClasses2));
+ //kb.addTBoxAxiom(new DisjointClassesAxiom(DisJointClasses2));
}
public static void initClassHierarchy() {
@@ -404,6 +408,19 @@
kb.addTBoxAxiom(new SubClassAxiom(WKing, Piece));
kb.addTBoxAxiom(new SubClassAxiom(WRook, Piece));
kb.addTBoxAxiom(new SubClassAxiom(BKing, Piece));
+
+ String[] letters=new String[]{"A","B","C","D","E","F","G","H"};
+ String[] numbers=new String[8];
+ for (int i = 0; i < numbers.length; i++) {
+ numbers[i]="F"+i;
+ }
+ //System.out.println(numbers);
+
+ for (int i = 0; i < numbers.length; i++) {
+ kb.addTBoxAxiom(new SubClassAxiom(getAtomicConcept(letters[i]),Piece));
+ kb.addTBoxAxiom(new SubClassAxiom(getAtomicConcept(letters[i]),Piece));
+ }
+
}
static void initClassesForRankAndFile() {
@@ -458,10 +475,15 @@
kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(rankLessThan, Piece));
kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(rankLessThan, Piece));
-
kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(fileLessThan, Piece));
kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(fileLessThan, Piece));
-
+
+ if(useHigherThan) {
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(rankHigherThan, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(rankHigherThan, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(fileHigherThan, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(fileHigherThan, Piece));
+ }
}
static void finishBackgroundForRoles() {
@@ -469,6 +491,11 @@
if (useTransitivity) {
kb.addRBoxAxiom(new TransitiveObjectPropertyAxiom(rankLessThan));
kb.addRBoxAxiom(new TransitiveObjectPropertyAxiom(fileLessThan));
+ if(useHigherThan) {
+ kb.addRBoxAxiom(new TransitiveObjectPropertyAxiom(rankHigherThan));
+ kb.addRBoxAxiom(new TransitiveObjectPropertyAxiom(fileHigherThan));
+ }
+
}
if (useInverse)
// INVERSE
@@ -677,7 +704,20 @@
OWLAPIReasoner.exportKBToOWL(owlfile, kb, ontologyURI);
}
+
+ protected static void writeKBFile(String filename) {
+ System.out.println("Writing kb");
+ try{
+ FileWriter fw = new FileWriter(workingDir+"/" + filename,false);
+ fw.write(kb.toKBSyntaxString(ontologyURI.toString(), null));
+ fw.flush();
+ }catch (Exception e) {e.printStackTrace();}
+ System.out.println("done writing kb");
+
+
+ }
+
protected static Individual getIndividual(String name) {
return new Individual(ontologyURI + "#" + name);
}
Added: trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRKModular.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/examples/KRKModular.java 2008-04-15 10:20:23 UTC (rev 788)
@@ -0,0 +1,775 @@
+package org.dllearner.examples;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.net.URI;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Random;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.StringTokenizer;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.refexamples.ExampleBasedROLComponent;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.LearningAlgorithm;
+import org.dllearner.core.LearningProblem;
+import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.ReasoningService;
+import org.dllearner.core.owl.ClassAssertionAxiom;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.KB;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.ObjectPropertyAssertion;
+import org.dllearner.kb.KBFile;
+import org.dllearner.learningproblems.PosNegDefinitionLP;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.parser.KBParser;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.dllearner.utilities.SimpleClock;
+
+/*
+ * Structure
+ *
+ *
+ *
+ *
+ * */
+
+public class KRKModular {
+
+ // REMEMBER
+ // FILES are letters
+ // RANKS are numbers
+
+ // FLAGS
+ //
+ // turn off to not write the owl, needs about 30 seconds or more
+ /*static boolean writeOWL = true;
+ static boolean writeKB = false;
+ static boolean useTransitivity = false;
+
+ static boolean writeExampleSets = true;
+ static boolean writeConciseOWLAllDifferent = false;
+ */
+ boolean useHigherThan = KRKOntologyTBox.useHigherThan;
+
+
+
+ //static boolean useInverse = false;
+ // dependent, love and marriage, horse and carriage
+ //static boolean useTripleSubProps = useInverse && false;
+
+
+ static String workingDir = "examples/krk/";
+ static String allData = workingDir+"krkopt_no_draw.data";
+
+ static URI ontologyURI = KRKOntologyTBox.ontologyURI;
+
+ // static SortedSet<String> fileSet = new TreeSet<String>();
+ //static SortedSet<String> allInstances = new TreeSet<String>();
+ //static SortedSet<String> classSet = new TreeSet<String>();
+ //static SortedSet<String> symmetricRoleSet = new TreeSet<String>();
+
+ static HashMap<String, SortedSet<Individual>> classToInd = new HashMap<String, SortedSet<Individual>>();
+ static HashMap<Individual, String> indToClass = new HashMap<Individual, String>();
+
+ static Set<ReasonerComponent> allReasoners = new HashSet<ReasonerComponent>();
+ static int negativeExamplesAdded = 300;
+
+ // static LinkedList<String> words;
+ public KB kb;
+ public ReasonerComponent reasoner;
+
+
+ //public FastInstanceChecker fic;
+ // static HashMap<String,SortedSet<String>> classToInd;
+
+
+ public static void init(){
+ if (!new File(workingDir).exists()) {
+ System.out.println("Created directory: " + workingDir +
+ " : " + new File(workingDir).mkdir()+ ".");
+ }
+ }
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ init();
+ initAllInstancesAndReasoners();
+ System.out.println("initializing finished");
+ String currentClass = "ZERO";
+ SortedSet<Individual> allPos = classToInd.get(currentClass);
+ //if(allPos.size()<400)negativeExamplesAdded = allPos.size();
+ //else negativeExamplesAdded = 400;
+ SortedSet<Individual> tmp = new TreeSet<Individual>();
+ for (Individual individual : indToClass.keySet()) {
+ tmp.add(individual);
+ }
+
+ SortedSet<Individual> neg = getNegativeExamples(currentClass, tmp, negativeExamplesAdded);
+ SortedSet<Integer> lines = getLines(allPos, neg);
+ KB kb = getKB(lines);
+
+
+ while (true){
+
+ /*for (String set : classToInd.keySet()) {
+ for (Individual individual : classToInd.get(set)) {
+ if(indToClass.get(individual)==null)System.out.println(indToClass.get(individual));
+ }}*/
+
+
+
+ Description d= learn(kb, allPos, neg);
+ SortedSet<Individual> result = retrieveAll(d);
+ System.out.println("still left: " + (result.size()-allPos.size()));
+ if(verify(currentClass, result)) {
+ System.out.println("Correct solution: "+ d.toKBSyntaxString(ontologyURI+"#", null));
+ break;}
+ neg.addAll(getNegativeExamples(currentClass, result, negativeExamplesAdded));
+ lines = getLines(allPos, neg);
+ kb = getKB(lines);
+
+
+ }
+ //System.out.println(allPos);
+ //System.out.println(neg);
+
+ //cm.
+
+
+ /*Map<Class<? extends Component>, String> componentPrefixMapping = Start.createComponentPrefixMapping();
+ ComponentManager cm = ComponentManager.getInstance();
+
+ Set<KnowledgeSource> sources = new HashSet<KnowledgeSource>();
+ KnowledgeSource ks = cm.knowledgeSource(KBFile.class);
+ sources.add(ks);
+ cm.applyConfigEntry(ks, "url", null);
+ ks.init();
+ */
+
+
+
+
+
+
+ //verifyConcept("EXISTS hasPiece.EXISTS fileDistance0.TOP");
+ //verifyConcept("(EXISTS \"http://dl-learner.org/krk#hasPiece\".EXISTS \"http://dl-learner.org/krk#rankDistanceLessThan2\".(\"http://dl-learner.org/krk#BKing\" AND EXISTS \"http://dl-learner.org/krk#fileDistanceLessThan1\".(\"http://dl-learner.org/krk#A\" OR \"http://dl-learner.org/krk#F3\")) AND EXISTS \"http://dl-learner.org/krk#hasPiece\".(\"http://dl-learner.org/krk#WKing\" AND ((\"http://dl-learner.org/krk#C\" AND EXISTS \"http://dl-learner.org/krk#hasLowerRankThan\".\"http://dl-learner.org/krk#A\") OR (\"http://dl-learner.org/krk#F3\" AND EXISTS \"http://dl-learner.org/krk#rankDistance2\".\"http://dl-learner.org/krk#WRook\"))))");
+ //verifyConcept("EXISTS hasPiece.TOP");
+
+ //.writeOWLFile("test.owl");
+
+ }
+
+ static Description learn(KB kb, SortedSet<Individual> pos,SortedSet<Individual> neg){
+
+ System.out.println(pos);
+ System.out.println(neg);
+
+ ComponentManager cm = ComponentManager.getInstance();
+ LearningAlgorithm la = null;
+ try {
+ Set<KnowledgeSource> sources = new HashSet<KnowledgeSource>();
+ sources.add(new KBFile(kb));
+ ReasonerComponent r = new FastInstanceChecker(sources);
+ r.init();
+ ReasoningService rs = new ReasoningService(r);
+
+ LearningProblem lp = new PosNegDefinitionLP(rs);
+ ((PosNegLP)lp).setPositiveExamples(pos);
+ ((PosNegLP)lp).setNegativeExamples(neg);
+ lp.init();
+
+ la = cm.learningAlgorithm(ExampleBasedROLComponent.class, lp, rs);
+ SortedSet<String> ignoredConcepts = getIgnoredConcepts(pos, neg);
+
+ cm.applyConfigEntry(la,"useAllConstructor",false);
+ cm.applyConfigEntry(la,"useExistsConstructor",true);
+ cm.applyConfigEntry(la,"useCardinalityRestrictions",false);
+ cm.applyConfigEntry(la,"useNegation",false);
+ //cm.applyConfigEntry(la,"quiet",false);
+ cm.applyConfigEntry(la,"ignoredConcepts",ignoredConcepts);
+
+
+ la.init();
+
+ System.out.println("start learning");
+
+ la.start();
+ //System.out.println("best"+la.getBestSolution());
+
+ }catch (Exception e) {e.printStackTrace();}
+ return la.getBestSolution();
+ }
+
+ static KB getKB(SortedSet<Integer> lines){
+ BufferedReader in = null;
+ try {
+ in = new BufferedReader(new FileReader(allData));
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+
+ KRKModular km = new KRKModular();
+ try {
+ String line = "";
+ int x = 0;
+ while ((line = in.readLine()) != null) {
+ Integer tmp = new Integer(x);
+ if(lines.contains(tmp))
+ km.addOneLineToKB(x, line);
+ x++;
+ }// endWhile
+ }catch (Exception e) {e.printStackTrace();}
+ return km.kb;
+
+ }
+
+
+ static SortedSet<Integer> getLines(SortedSet<Individual> pos,SortedSet<Individual> neg){
+ SortedSet<Integer> ret = new TreeSet<Integer>();
+
+ for (Individual individual : pos) {
+ int a = Integer.parseInt(individual.getName().substring((ontologyURI+"#g").length()));
+ ret.add(new Integer(a));
+ }
+ for (Individual individual : neg) {
+ int a = Integer.parseInt(individual.getName().substring((ontologyURI+"#g").length()));
+ ret.add(new Integer(a));
+ }
+ return ret;
+
+ }
+
+ static SortedSet<String> getIgnoredConcepts(SortedSet<Individual> pos,SortedSet<Individual> neg){
+ SortedSet<String> ret = new TreeSet<String>();
+
+ for (Individual individual : pos) {
+ String tmp = indToClass.get(individual);
+ //System.out.println("pos"+tmp+individual);
+ ret.add(ontologyURI+"#"+tmp);
+ }
+ for (Individual individual : neg) {
+ //String tmp = indToClass.get((Individual)individual);
+ //System.out.println("neg"+tmp+individual);
+ for (Individual string : indToClass.keySet()) {
+ if(string.toString().equals(individual.getName())){
+ ret.add(ontologyURI+"#"+indToClass.get(string));
+ //System.out.println("aaaaaaaa"+individual.getName());
+ }
+
+ }
+
+ }
+
+ //System.out.println(indToClass);
+ return ret;
+
+ }
+
+ public KRKModular() {
+ this.kb = makeOntologyTBox();
+ }
+
+ public KRKModular(String concept) {
+ this.kb = makeOntologyTBox(concept);
+ }
+
+ public static void initAllInstancesAndReasoners(){
+ // Datei \xF6ffnen
+ BufferedReader in = null;
+ try {
+ in = new BufferedReader(new FileReader(allData));
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ SimpleClock sc= new SimpleClock();
+ KRKModular km =null;
+ km = new KRKModular();
+ try {
+ String line = "";
+ int x = 0;
+ while ((line = in.readLine()) != null) {
+ if (x % 10000 == 0)
+ {sc.print("Currently at line " + x+" : ");}
+ km.addOneLineToKBinit(x, line);
+ if(x%1000==0 && x!=0){
+ km.initReasonerFact();
+ allReasoners.add(km.reasoner);
+ km = new KRKModular();
+ }
+ if(x==26000)break;
+ x++;
+ }// endWhile
+
+ km.initReasonerFact();
+ allReasoners.add(km.reasoner);
+ km = null;
+
+
+ sc.printAndSet("initialization finished");
+
+ //sc.printAndSet("nach Retrieval");
+ //km.writeOWLFile();
+ /*SortedSet<Individual> s = new TreeSet<Individual>();
+ for (int i = 0; i < x; i++) {
+ s.add(getIndividual("g"+i));
+ //if(km.check2(i))howmany++;
+ }*/
+ //writeExampleSet(s);
+
+
+ //sc.printAndSet("before ");
+ //km.initReasonerFact();
+ //sc.printAndSet("after initfact");
+
+ //SortedSet<Individual> ret = km.checkAllOWLAPI(concept, s);
+ //sc.print("totalfic ("+ret.size()+") for 1000: ");
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+
+
+ public static SortedSet<Individual> retrieveAll(String concept){
+ Description d = null;
+ try{
+ d = KBParser.parseConcept(concept);
+ }catch (Exception e) {e.printStackTrace();}
+ return retrieveAll(d);
+ }
+
+ public static SortedSet<Individual> retrieveAll(Description d){
+ SortedSet<Individual> ret = new TreeSet<Individual>();
+ try{
+
+ for (ReasonerComponent onereasoner : allReasoners) {
+ ret.addAll(onereasoner.retrieval(d));
+ }
+
+ }catch (Exception e) {e.printStackTrace();}
+ return ret;
+ }
+
+
+
+
+
+ public void initReasonerFact(){
+ KBFile kbFile = new KBFile(this.kb);
+ Set<KnowledgeSource> ks = new HashSet<KnowledgeSource>();
+ ks.add(kbFile);
+ reasoner = new OWLAPIReasoner(ks);
+ ((OWLAPIReasoner)reasoner).setReasonerType("fact");
+ try{
+ reasoner.init();
+ }catch (Exception e) {e.printStackTrace();}
+ }
+
+
+
+ public void initFIC(){
+ KBFile kbFile = new KBFile(this.kb);
+ Set<KnowledgeSource> ks = new HashSet<KnowledgeSource>();
+ ks.add(kbFile);
+ //System.out.println("blabla");
+ reasoner = new FastInstanceChecker(ks);
+ //fic.setReasonerType("fact");
+ try{
+ reasoner.init();
+ }catch (Exception e) {e.printStackTrace();}
+ }
+
+ public KB makeOntologyTBox(){
+
+ KRKOntologyTBox tbox = new KRKOntologyTBox();
+ return tbox.getKb();
+
+ }
+
+ public KB makeOntologyTBox(String concept){
+
+ KRKOntologyTBox tbox = new KRKOntologyTBox();
+ tbox.addConcept(concept);
+ return tbox.getKb();
+
+ }
+
+
+ public void addOneLineToKBinit(int x, String line){
+
+ String[] ar = new String[6];
+ Individual gameind = KRKOntologyTBox.getIndividual("g" + x);
+ ar = tokenize(line);
+ addToHM(ar[6], gameind);
+ addOneLineToKB( x, line);
+
+
+ }
+
+ public void addOneLineToKB(int x, String line){
+
+ Individual gameind;
+ Individual wkingind;
+ Individual wrookind;
+ Individual bkingind;
+
+ String[] ar = new String[6];
+
+ ar = tokenize(line);
+
+ //String currentclass = ar[6];
+
+ gameind = KRKOntologyTBox.getIndividual("g" + x);
+ wkingind = KRKOntologyTBox.getIndividual("wking_" + ar[0] + ar[1] + "_" + x);
+ wrookind = KRKOntologyTBox.getIndividual("wrook_" + ar[2] + ar[3] + "_" + x);
+ bkingind = KRKOntologyTBox.getIndividual("bking_" + ar[4] + ar[5] + "_" + x);
+
+
+
+ //allInstances.add(gameind+"");
+ //allInstances.add(wkingind+"");
+ //allInstances.add(wrookind+"");
+ //allInstances.add(bkingind+"");
+
+ // save it for examplegeneration
+
+ // .add(gameind.getName());
+ //classSet.add(ar[6]);
+
+ // CLASSES
+ kb.addABoxAxiom(new ClassAssertionAxiom(KRKOntologyTBox.Game, gameind));
+ kb.addABoxAxiom(new ClassAssertionAxiom(
+ getAtomicConcept(ar[6]), gameind));
+ kb.addABoxAxiom(new ClassAssertionAxiom(KRKOntologyTBox.WKing, wkingind));
+ kb.addABoxAxiom(new ClassAssertionAxiom(KRKOntologyTBox.WRook, wrookind));
+ kb.addABoxAxiom(new ClassAssertionAxiom(KRKOntologyTBox.BKing, bkingind));
+
+
+ /**Files and Ranks***/
+ // FILES are letters
+ // RANKS are numbers
+
+ //WKing
+ kb.addABoxAxiom(new ClassAssertionAxiom(getAtomicConcept(ar[0].toUpperCase()), wkingind));
+ kb.addABoxAxiom(new ClassAssertionAxiom(getAtomicConcept("F"+ar[1]) , wkingind));
+
+ //WRook
+ kb.addABoxAxiom(new ClassAssertionAxiom(getAtomicConcept(ar[2].toUpperCase()), wrookind));
+ kb.addABoxAxiom(new ClassAssertionAxiom(getAtomicConcept("F"+ar[3]) , wrookind));
+
+ //BKing
+ kb.addABoxAxiom(new ClassAssertionAxiom(getAtomicConcept(ar[4].toUpperCase()), bkingind));
+ kb.addABoxAxiom(new ClassAssertionAxiom(getAtomicConcept("F"+ar[5]), bkingind));
+
+
+
+ // PROPERTIES
+ kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.hasPiece, gameind,
+ wkingind));
+ kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.hasPiece, gameind,
+ wrookind));
+ kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.hasPiece, gameind,
+ bkingind));
+
+ // labels
+
+ KRKPiece WKingPiece = new KRKPiece(wkingind, ar[0], Integer
+ .parseInt(ar[1]));
+ KRKPiece WRookPiece = new KRKPiece(wrookind, ar[2], Integer
+ .parseInt(ar[3]));
+ KRKPiece BKingPiece = new KRKPiece(bkingind, ar[4], Integer
+ .parseInt(ar[5]));
+
+ makeDistanceRoles(WKingPiece, WRookPiece);
+ makeDistanceRoles(WKingPiece, BKingPiece);
+ makeDistanceRoles(WRookPiece, BKingPiece);
+
+ }
+
+
+ /*protected static void verifySomeConcepts(OntologyCloser oc) {
+
+ ArrayList<String> test=new ArrayList<String>();
+ test.add("(EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#rankDistanceLessThan2\".(\"http://www.test.de/test#BKing\" AND EXISTS \"http://www.test.de/test#fileDistanceLessThan1\".(\"http://www.test.de/test#A\" OR \"http://www.test.de/test#WKing\")) AND EXISTS \"http://www.test.de/test#hasPiece\".(\"http://www.test.de/test#WKing\" AND ((\"http://www.test.de/test#C\" AND EXISTS \"http://www.test.de/test#hasLowerRankThan\".\"http://www.test.de/test#A\") OR (\"http://www.test.de/test#F3\" AND EXISTS \"http://www.test.de/test#rankDistance2\".\"http://www.test.de/test#WRook\"))))");
+ for (int i = 0; i < test.size(); i++) {
+ String conceptStr = test.get(i);
+ oc.verifyConcept(conceptStr);
+ }
+ /*conceptStr = "EXISTS \"http://www.test.de/test#hasLowerRankThan\"."+
+ "(\"http://www.test.de/test#WRook\""+
+ "AND ALL \"http://www.test.de/test#fileDistanceLessThan1\".\"http://www.test.de/test#WKing\") ";
+
+ System.out.println();
+ }*/
+
+ public void makeDistanceRoles(KRKPiece A, KRKPiece B) {
+ int Fdist = A.getFileDistance(B);
+ int Rdist = A.getRankDistance(B);
+ String rdistance = "rankDistance";
+ String fdistance = "fileDistance";
+
+ kb.addABoxAxiom(new ObjectPropertyAssertion(getRole(rdistance + Rdist),
+ A.id, B.id));
+ kb.addABoxAxiom(new ObjectPropertyAssertion(getRole(fdistance + Fdist),
+ A.id, B.id));
+
+ if (A.meHasLowerFileThan(B)){
+ kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.fileLessThan, A.id,
+ B.id));
+ if(useHigherThan)kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.fileHigherThan, B.id,
+ A.id));
+ }
+ else if (B.meHasLowerFileThan(A)){
+ kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.fileLessThan, B.id,
+ A.id));
+ if(useHigherThan)kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.fileHigherThan, A.id,
+ B.id));
+ }
+
+ if (A.meHasLowerRankThan(B)){
+ kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.rankLessThan, A.id,
+ B.id));
+ if(useHigherThan)kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.rankHigherThan, B.id,
+ A.id));
+ }
+ else if (B.meHasLowerRankThan(A)){
+ kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.rankLessThan, B.id,
+ A.id));
+ if(useHigherThan)kb.addABoxAxiom(new ObjectPropertyAssertion(KRKOntologyTBox.rankHigherThan, A.id,
+ B.id));
+
+ }
+ }
+
+
+
+
+ protected static void writeExampleSet(Set<Individual> s) {
+ for (Individual individual : s) {
+ writeToFile(workingDir+"example.txt", "+\""+individual.getName()+"\"\n");
+ }
+
+ }
+
+
+
+
+
+ /*protected static void writeExampleSets() {
+ StringBuffer collect1 = new StringBuffer();
+ StringBuffer collect2 = new StringBuffer();
+ System.out.println("start writing sets");
+
+ for (String keys : classToInd.keySet()) {
+ System.out.println(keys);
+ SortedSet<String> tmpset = classToInd.get(keys);
+ for (String individuals : tmpset) {
+ collect1.append("+\"" + individuals + "\"\n");
+ collect2.append("-\"" + individuals + "\"\n");
+ }
+
+ writeToFile(workingDir+"/examples_for_" + keys + ".txt", collect1
+ + "\n\n" + collect2 + "\n");
+ collect1 = new StringBuffer();
+ collect2 = new StringBuffer();
+ }
+ // System.out.println("Sets written");
+ collect1 = new StringBuffer();
+ collect2 = new StringBuffer();
+ for (String key : classToInd.keySet()) {
+
+ SortedSet<String> tmpset = classToInd.get(key);
+
+ if (key.equals("ZERO")) {*/
+ // collect1.append("/**" + key + "**/\n");
+ /* for (String individuals : tmpset) {
+ collect1.append("+\"" + individuals + "\"\n");
+ }
+
+ continue;
+ } else { */
+ // collect2.append("/**" + key + "**/\n");
+ /* for (String individuals : tmpset) {
+ collect2.append("-\"" + individuals + "\"\n");
+ }
+ }
+
+ }
+ writeToFile(workingDir+"/examples_for_ZERO_and_Rest.txt", collect1
+ + "\n\n" + collect2 + "\n");
+ System.out.println("Example sets written");
+ }
+ */
+
+
+
+
+
+
+ /*protected void writeOWLFile(String filename) {
+
+ Iterator<String> it = classSet.iterator();
+ System.out.println("import(\"" + filename + "\");");
+ String collect = "refinement.ignoredConcepts={";
+ while (it.hasNext()) {
+ String tmp = (String) it.next();
+ collect += "\n\"" + getAtomicConcept(tmp).getName() + "\",";
+ }
+ collect = collect.substring(0, collect.length() - 1);
+ System.out.println(collect + "};");
+
+ System.out.println("Writing owl");
+ File owlfile = new File(workingDir+"/" + filename);
+ // System.out.println(kb.toString("http://www.test.de/test", new
+ // HashMap<String, String>()));
+ OWLAPIReasoner.exportKBToOWL(owlfile, kb, ontologyURI);
+
+ }*/
+
+ protected void writeOWLFile() {
+ writeOWLFile("test.owl");
+ }
+
+ protected void writeOWLFile(String filename) {
+
+ System.out.println("Writing owl");
+ File owlfile = new File(workingDir+"/" + filename);
+ OWLAPIReasoner.exportKBToOWL(owlfile, this.kb, ontologyURI);
+
+ }
+
+
+
+ protected static void writeToFile(String filename, String content) {
+ // create the file we want to use
+ File file = new File(filename);
+
+ try {
+ file.createNewFile();
+ FileOutputStream fos = new FileOutputStream(filename, true);
+ // ObjectOutputStream o = new ObjectOutputStream(fos);
+ fos.write(content.getBytes());
+ fos.flush();
+ fos.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ protected static void addToHM(String className, Individual ind) {
+ if (classToInd.get(className) == null)
+ classToInd.put(className, new TreeSet<Individual>());
+
+ classToInd.get(className).add(ind);
+ indToClass.put(ind, className);
+
+ }
+
+
+ protected static Individual getIndividual(String name) {
+ return new Individual(ontologyURI + "#" + name);
+ }
+
+ protected static ObjectProperty getRole(String name) {
+ return new ObjectProperty(ontologyURI + "#" + name);
+ }
+
+ protected static NamedClass getAtomicConcept(String name) {
+ return new NamedClass(ontologyURI + "#" + name);
+ }
+
+ public static String[] tokenize(String s) {
+ StringTokenizer st = new StringTokenizer(s, ",");
+
+ String tmp = "";
+ String[] ret = new String[7];
+ int x = 0;
+ while (st.hasMoreTokens()) {
+ tmp = st.nextToken();
+ if (x == 6)
+ tmp = tmp.toUpperCase();
+ ret[x] = tmp;
+ x++;
+ }
+ return ret;
+
+ }
+
+ static SortedSet<Individual> getNegativeExamples(String currentClass, SortedSet<Individual> allRetrieved, int howmany) {
+ SortedSet<Individual> ret = new TreeSet<Individual>();
+
+ //clean
+ SortedSet<Individual> allPos = classToInd.get(currentClass);
+ for (Individual individual : allPos) {
+ if(!allRetrieved.remove(individual))System.out.println("WARNING, not all positives covered");;
+ }
+
+ Random r = new Random();
+ double treshold = ((double)howmany)/allRetrieved.size();
+ //System.out.println("treshold"+howmany);
+ //System.out.println("treshold"+allRetrieved.size());
+ //System.out.println("treshold"+treshold);
+ int added=0;
+ for (Individual oneInd : allRetrieved) {
+ if(r.nextDouble()<treshold) {
+ ret.add(oneInd);
+ added++;
+ }
+ }
+ System.out.println(added+" new negs added");
+ return ret;
+ }
+ static boolean verify(String currentClass, SortedSet<Individual> allRetrieved) {
+ //clean
+ SortedSet<Individual> allPos = classToInd.get(currentClass);
+ boolean hasAll=true;
+ for (Individual individual : allPos) {
+ if(!allRetrieved.contains(individual))hasAll=false;
+ }
+ if(hasAll && allRetrieved.size()==allPos.size()){return true;}
+ else return false;
+
+ }
+
+ /*public SortedSet<Individual> checkAll(String concept, SortedSet<Individual> s){
+ try{
+ Description d = KBParser.parseConcept(concept,ontologyURI.toString()+"#");
+
+ return reasoner.instanceCheck(d, s);
+ }catch (Exception e) {e.printStackTrace();}
+ return null;
+}
+
+public SortedSet<Individual> checkAllOWLAPI(String concept,SortedSet<Individual> s){
+ try{
+ Description d = KBParser.parseConcept(concept,ontologyURI.toString()+"#");
+ return reasoner.instanceCheck(d, s);
+ }catch (Exception e) {e.printStackTrace();}
+ return null;
+}
+
+/*public SortedSet<Individual> retrieveAllowlAPI(String concept){
+ try{
+ Description d = KBParser.parseConcept(concept,ontologyURI.toString()+"#");
+ return reasoner.retrieval(d);
+ }catch (Exception e) {e.printStackTrace();}
+ return null;
+}*/
+
+}
Added: trunk/src/dl-learner/org/dllearner/examples/KRKOntologyTBox.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRKOntologyTBox.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/examples/KRKOntologyTBox.java 2008-04-15 10:20:23 UTC (rev 788)
@@ -0,0 +1,251 @@
+package org.dllearner.examples;
+
+import java.net.URI;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.core.owl.ClassAssertionAxiom;
+import org.dllearner.core.owl.DatatypeProperty;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.DisjointClassesAxiom;
+import org.dllearner.core.owl.EquivalentClassesAxiom;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.KB;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.ObjectPropertyAssertion;
+import org.dllearner.core.owl.ObjectPropertyDomainAxiom;
+import org.dllearner.core.owl.ObjectPropertyRangeAxiom;
+import org.dllearner.core.owl.SubClassAxiom;
+import org.dllearner.core.owl.SubObjectPropertyAxiom;
+import org.dllearner.core.owl.SymmetricObjectPropertyAxiom;
+import org.dllearner.parser.KBParser;
+
+public class KRKOntologyTBox {
+
+ private KB kb;
+ static URI ontologyURI = URI.create("http://dl-learner.org/krk");
+
+ static boolean useHigherThan=false;
+ static boolean useInverse = false;
+
+ static NamedClass Game = getAtomicConcept("Game");
+ static NamedClass WKing = getAtomicConcept("WKing");
+ static NamedClass WRook = getAtomicConcept("WRook");
+ static NamedClass BKing = getAtomicConcept("BKing");
+ // had to rename, too much similarity to java.io.File
+ static NamedClass FileData = getAtomicConcept("File");
+ static NamedClass Rank = getAtomicConcept("Rank");
+ static NamedClass Piece = getAtomicConcept("Piece");
+
+ static ObjectProperty hasPiece = getRole("hasPiece");
+ static ObjectProperty hasWKing = getRole("hasWKing");
+ static ObjectProperty hasWRook = getRole("hasWRook");
+ static ObjectProperty hasBKing = getRole("hasBKing");
+
+ static ObjectProperty hasPieceInv = getRole("hasGame");
+ static ObjectProperty hasWKingInv = getRole("hasWKingInv");
+ static ObjectProperty hasWRookInv = getRole("hasWRookInv");
+ static ObjectProperty hasBKingInv = getRole("hasBKingInv");
+
+ static ObjectProperty rankLessThan = getRole("hasLowerRankThan");
+ static ObjectProperty fileLessThan = getRole("hasLowerFileThan");
+
+ static ObjectProperty rankHigherThan = getRole("hasHigherRankThan");
+ static ObjectProperty fileHigherThan = getRole("hasHigherFileThan");
+
+
+ /*public KRKOntologyTBox(KB kbin){
+ this.kb=kbin;
+
+ }*/
+
+ public KRKOntologyTBox(){
+ this.kb=new KB();
+ initOntologyTBox();
+
+
+ }
+
+ public void addConcept(String concept){
+ try{
+ //make Description
+ Description d = KBParser.parseConcept(concept,ontologyURI.toString()+"#");
+ //d.addChild(oecr);
+ kb.addTBoxAxiom(new EquivalentClassesAxiom(getAtomicConcept("test"),d));
+
+ }catch (Exception e) {e.printStackTrace();}
+ }
+
+ public void initOntologyTBox(){
+
+ //DISJOINTCLASSES
+ SortedSet<Description> DisJointClasses1 = new TreeSet<Description>();
+ DisJointClasses1.add(Piece);
+ DisJointClasses1.add(Game);
+ kb.addTBoxAxiom(new DisjointClassesAxiom(DisJointClasses1));
+
+ SortedSet<Description> DisJointClasses2 = new TreeSet<Description>();
+ DisJointClasses2 = new TreeSet<Description>();
+ DisJointClasses2.add(WKing);
+ DisJointClasses2.add(WRook);
+ DisJointClasses2.add(BKing);
+ // DisJointClasses2.add(Rank);
+ // DisJointClasses2.add(File);
+ // DisJointClasses2.add(Game);
+ kb.addTBoxAxiom(new DisjointClassesAxiom(DisJointClasses2));
+
+ /**CLASSES***/
+ // all sub of piece
+ kb.addTBoxAxiom(new SubClassAxiom(WKing, Piece));
+ kb.addTBoxAxiom(new SubClassAxiom(WRook, Piece));
+ kb.addTBoxAxiom(new SubClassAxiom(BKing, Piece));
+
+ String[] letters=new String[]{"A","B","C","D","E","F","G","H"};
+ String[] numbers=new String[8];
+ for (int i = 0; i < numbers.length; i++) {
+ numbers[i]="F"+(i+1);
+ }
+ //System.out.println(numbers);
+
+ for (int i = 0; i < numbers.length; i++) {
+ kb.addTBoxAxiom(new SubClassAxiom(getAtomicConcept(letters[i]),Piece));
+ kb.addTBoxAxiom(new SubClassAxiom(getAtomicConcept(numbers[i]),Piece));
+ }
+
+
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(hasPiece, Game));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(hasPiece, Piece));
+
+
+ if (useInverse) {
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(hasPieceInv, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(hasPieceInv, Game));
+
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(hasWKingInv, WKing));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(hasWKingInv, Game));
+
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(hasWRookInv, WRook));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(hasWRookInv, Game));
+
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(hasBKingInv, BKing));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(hasBKingInv, Game));
+ }
+
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(rankLessThan, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(rankLessThan, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(fileLessThan, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(fileLessThan, Piece));
+
+ if(useHigherThan) {
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(rankHigherThan, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(rankHigherThan, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(fileHigherThan, Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(fileHigherThan, Piece));
+ }
+
+ finishBackgroundForRoles();
+
+ //return this.kb;
+
+ }
+
+
+ public void finishBackgroundForRoles() {
+
+ for (int i = 8; i > 0; i--) {
+
+
+ ObjectProperty rankDistance = getRole("rankDistance"+(i-1));
+ ObjectProperty fileDistance = getRole("fileDistance"+(i-1));
+ kb.addRBoxAxiom(new SymmetricObjectPropertyAxiom(rankDistance));
+ kb.addRBoxAxiom(new SymmetricObjectPropertyAxiom(fileDistance));
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(rankDistance,
+ KRKOntologyTBox.Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(rankDistance,
+ KRKOntologyTBox.Piece));
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(fileDistance,
+ KRKOntologyTBox.Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(fileDistance,
+ KRKOntologyTBox.Piece));
+
+
+
+ kb.addRBoxAxiom(new SubObjectPropertyAxiom(
+ getRole("rankDistance" + (i - 1)),
+ getRole("rankDistanceLessThan" + i)));
+ kb.addRBoxAxiom(new SubObjectPropertyAxiom(
+ getRole("fileDistance" + (i - 1)),
+ getRole("fileDistanceLessThan" + i)));
+
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(
+ getRole("rankDistanceLessThan" + i), KRKOntologyTBox.Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(
+ getRole("rankDistanceLessThan" + i), KRKOntologyTBox.Piece));
+
+ kb.addRBoxAxiom(new ObjectPropertyDomainAxiom(
+ getRole("fileDistanceLessThan" + i), KRKOntologyTBox.Piece));
+ kb.addRBoxAxiom(new ObjectPropertyRangeAxiom(
+ getRole("fileDistanceLessThan" + i), KRKOntologyTBox.Piece));
+
+
+ if(i==1) continue;
+
+ kb.addRBoxAxiom(new SubObjectPropertyAxiom(
+ getRole("rankDistanceLessThan" + (i - 1)),
+ getRole("rankDistanceLessThan" + i)));
+ kb.addRBoxAxiom(new SubObjectPropertyAxiom(
+ getRole("fileDistanceLessThan" + (i - 1)),
+ getRole("fileDistanceLessThan" + i)));
+
+
+ }
+
+
+ }
+
+
+ protected static Individual getIndividual(String name) {
+ return new Individual(ontologyURI + "#" + name);
+ }
+
+ protected static ObjectProperty getRole(String name) {
+ return new ObjectProperty(ontologyURI + "#" + name);
+ }
+
+ @SuppressWarnings("unused")
+ protected static DatatypeProperty getDatatypeProperty(String name) {
+ return new DatatypeProperty(ontologyURI + "#" + name);
+ }
+
+ protected static NamedClass getAtomicConcept(String name) {
+ return new NamedClass(ontologyURI + "#" + name);
+ }
+
+ @SuppressWarnings("unused")
+ protected static String getURI(String name) {
+ return ontologyURI + "#" + name;
+ }
+
+ @SuppressWarnings("unused")
+ protected static ClassAssertionAxiom getConceptAssertion(String concept,
+ String instance) {
+ Individual ind = getIndividual(instance);
+ NamedClass c = getAtomicConcept(concept);
+ return new ClassAssertionAxiom(c, ind);
+ }
+
+ @SuppressWarnings("unused")
+ protected static ObjectPropertyAssertion getRoleAssertion(String role,
+ String i1, String i2) {
+ Individual ind1 = getIndividual(i1);
+ Individual ind2 = getIndividual(i2);
+ ObjectProperty ar = getRole(role);
+ return new ObjectPropertyAssertion(ar, ind1, ind2);
+ }
+
+ public KB getKb() {
+ return kb;
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLP.java 2008-04-14 22:45:16 UTC (rev 787)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLP.java 2008-04-15 10:20:23 UTC (rev 788)
@@ -145,6 +145,14 @@
return positiveExamples;
}
+ public void setNegativeExamples(SortedSet<Individual> set) {
+ this.negativeExamples=set;
+ }
+
+ public void setPositiveExamples(SortedSet<Individual> set) {
+ this.positiveExamples=set;
+ }
+
public abstract int coveredNegativeExamplesOrTooWeak(Description concept);
public double getPercentPerLengthUnit() {
Modified: trunk/src/dl-learner/org/dllearner/parser/KBParser.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/parser/KBParser.java 2008-04-14 22:45:16 UTC (rev 787)
+++ trunk/src/dl-learner/org/dllearner/parser/KBParser.java 2008-04-15 10:20:23 UTC (rev 788)
@@ -18,6 +18,12 @@
return internalNamespace + name;
}
+ //TODO beware of this function it is evil
+ public static Description parseConcept(String string, String namespace) throws ParseException {
+ internalNamespace = namespace;
+ return parseConcept(string);
+ }
+
public static Description parseConcept(String string) throws ParseException {
// when just parsing the string as concept, we have no guarantee
// that the parser uses all symbols, e.g. a AND b returns just a
Modified: trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java 2008-04-14 22:45:16 UTC (rev 787)
+++ trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java 2008-04-15 10:20:23 UTC (rev 788)
@@ -11,6 +11,10 @@
time=System.currentTimeMillis();
}
+
+
+
+
/**
* prints time needed
* and resets the clock
@@ -33,6 +37,18 @@
time=now;
}
+
+ /**
+ * prints time needed
+ *
+ * @param s String for printing
+ */
+ public void print(String s) {
+ long now=System.currentTimeMillis();
+ System.out.println(s+" needed "+(now-time)+" ms");
+
+ }
+
public void setTime() {
time=System.currentTimeMillis();
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X