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[DL-Learner SVN] SF.net SVN: dl-learner: [687] trunk
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From: <jen...@us...> - 2008-03-04 19:11:41
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Revision: 687
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=687&view=rev
Author: jenslehmann
Date: 2008-03-04 11:10:55 -0800 (Tue, 04 Mar 2008)
Log Message:
-----------
reasoning bug fixes and extensions
Modified Paths:
--------------
trunk/examples/commandcollection.txt
trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
trunk/src/dl-learner/org/dllearner/core/owl/TypedConstant.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/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
Modified: trunk/examples/commandcollection.txt
===================================================================
--- trunk/examples/commandcollection.txt 2008-03-04 13:40:00 UTC (rev 686)
+++ trunk/examples/commandcollection.txt 2008-03-04 19:10:55 UTC (rev 687)
@@ -66,3 +66,4 @@
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
sparql.instances = {};
+posNegDefinition.percentPerLengthUnit = 0.10;
\ No newline at end of file
Modified: trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-03-04 13:40:00 UTC (rev 686)
+++ trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-03-04 19:10:55 UTC (rev 687)
@@ -149,6 +149,22 @@
return ret;
}
+ // convenience method returning those values which have value "false" for this
+ // datatype property
+ public SortedSet<Individual> getFalseDatatypeMembers(DatatypeProperty datatypeProperty) throws ReasoningMethodUnsupportedException {
+ Map<Individual, SortedSet<Constant>> mapping = getDatatypeMembers(datatypeProperty);
+ SortedSet<Individual> ret = new TreeSet<Individual>();
+ for(Entry<Individual, SortedSet<Constant>> e : mapping.entrySet()) {
+ SortedSet<Constant> values = e.getValue();
+ for(Constant c : values) {
+ boolean v = Boolean.parseBoolean(c.getLiteral());
+ if(v == false)
+ ret.add(e.getKey());
+ }
+ }
+ return ret;
+ }
+
public boolean instanceCheck(Description concept, Individual individual)
throws ReasoningMethodUnsupportedException {
throw new ReasoningMethodUnsupportedException();
Modified: trunk/src/dl-learner/org/dllearner/core/owl/TypedConstant.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/TypedConstant.java 2008-03-04 13:40:00 UTC (rev 686)
+++ trunk/src/dl-learner/org/dllearner/core/owl/TypedConstant.java 2008-03-04 19:10:55 UTC (rev 687)
@@ -27,7 +27,7 @@
* @author Jens Lehmann
*
*/
-public class TypedConstant extends Constant {
+public class TypedConstant extends Constant implements Comparable<TypedConstant> {
private Datatype datatype;
@@ -47,7 +47,8 @@
* @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
*/
public String toString(String baseURI, Map<String, String> prefixes) {
- return literal + "^^" + datatype;
+ return literal;
+// return literal + "^^" + datatype;
}
/**
@@ -62,6 +63,19 @@
*/
public void accept(KBElementVisitor visitor) {
visitor.visit(this);
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Comparable#compareTo(java.lang.Object)
+ */
+ public int compareTo(TypedConstant o) {
+ // the first criteria is the datatype
+ int datatypeComparision = datatype.getURI().compareTo(datatype.getURI());
+ if(datatypeComparision == 0) {
+ // the second criterion is the literal value
+ return literal.compareTo(o.literal);
+ } else
+ return datatypeComparision;
}
}
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-03-04 13:40:00 UTC (rev 686)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-03-04 19:10:55 UTC (rev 687)
@@ -204,6 +204,10 @@
// and cannot parser its own generated file
// DisjointClassesAxiom disjointAtomTypes = getDisjointClassesAxiom(atomTypes);
// kb.addAxiom(disjointAtomTypes);
+ String[] mainClasses = new String[] {"Compound", "Atom", "Bond", "Structure"};
+ Set<String> mainClassesSet = new HashSet<String>(Arrays.asList(mainClasses));
+ DisjointClassesAxiom disjointAtomTypes = getDisjointClassesAxiom(mainClassesSet);
+ kb.addAxiom(disjointAtomTypes);
// all different axiom (UNA)
// exporting differentIndividuals axioms is broken in OWL API
@@ -230,9 +234,12 @@
String confHeader = "import(\"pte.owl\");\n\n";
confHeader += "reasoner = fastInstanceChecker;\n";
confHeader += "algorithm = refexamples;\n";
-// confHeader += "refinement.writeSearchTree = true;";
-// confHeader += "refinement.searchTreeFile = \"log/carcinogenesis/searchTree.log\"";
- confHeader += "\n\n";
+ confHeader += "refexamples.noisePercentage = 35;\n";
+ confHeader += "refexamples.startClass = " + getURI2("Compound") + ";\n";
+ confHeader += "refexamples.writeSearchTree = false;\n";
+ confHeader += "refexamples.searchTreeFile = \"log/carcinogenesis/searchTree.log\";\n";
+ confHeader += "posNegDefinition.percentPerLengthUnit = 0.10;\n";
+ confHeader += "\n";
Files.appendFile(confTrainFile, confHeader);
// generating training examples
@@ -338,7 +345,9 @@
} else if (headName.equals("has_property")) {
String compoundName = head.getArgument(0).toPLString();
String testName = head.getArgument(1).toPLString();
- boolean testResult = Boolean.parseBoolean(head.getArgument(2).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";
@@ -453,7 +462,7 @@
private static DisjointClassesAxiom getDisjointClassesAxiom(Set<String> classes) {
Set<Description> descriptions = new HashSet<Description>();
for(String namedClass : classes)
- descriptions.add(new NamedClass(namedClass));
+ descriptions.add(new NamedClass(getURI(namedClass)));
return new DisjointClassesAxiom(descriptions);
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-04 13:40:00 UTC (rev 686)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-03-04 19:10:55 UTC (rev 687)
@@ -56,6 +56,7 @@
import org.dllearner.kb.OWLFile;
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
+import org.dllearner.utilities.Helper;
/**
* Reasoner for fast instance checks. It works by completely dematerialising the
@@ -76,6 +77,8 @@
private static Logger logger = Logger.getLogger(FastInstanceChecker.class);
+ private boolean defaultNegation = true;
+
private Set<NamedClass> atomicConcepts;
private Set<ObjectProperty> atomicRoles;
private SortedSet<DatatypeProperty> datatypeProperties;
@@ -96,10 +99,9 @@
// object property mappings
private Map<ObjectProperty, Map<Individual, SortedSet<Individual>>> opPos = new TreeMap<ObjectProperty, Map<Individual, SortedSet<Individual>>>();
// datatype property mappings
- // (for booleans we assume that just one mapping exists, e.g.
- // hasValue(object,true) and hasValue(object,false) will
- // lead to undefined behaviour (they are logical contradictions)
- private Map<DatatypeProperty, SortedSet<Individual>> bd = new TreeMap<DatatypeProperty, SortedSet<Individual>>();
+ // we have one mapping for true and false for efficiency reasons
+ private Map<DatatypeProperty, SortedSet<Individual>> bdPos = new TreeMap<DatatypeProperty, SortedSet<Individual>>();
+ private Map<DatatypeProperty, SortedSet<Individual>> bdNeg = new TreeMap<DatatypeProperty, SortedSet<Individual>>();
// for int and double we assume that a property can have several values,
// althoug this should be rare,
// e.g. hasValue(object,2) and hasValue(object,3)
@@ -151,20 +153,39 @@
// FastRetrievalReasoner later)
long dematStartTime = System.currentTimeMillis();
- for (NamedClass atomicConcept : rs.getAtomicConcepts()) {
- classInstancesPos.put(atomicConcept, rs.retrieval(atomicConcept));
- Negation negatedAtomicConcept = new Negation(atomicConcept);
- classInstancesNeg.put(atomicConcept, rs.retrieval(negatedAtomicConcept));
+ logger.debug("dematerialising concepts");
+
+ for (NamedClass atomicConcept : rs.getAtomicConcepts()) {
+
+ SortedSet<Individual> pos = rs.retrieval(atomicConcept);
+ classInstancesPos.put(atomicConcept, pos);
+
+ if(defaultNegation) {
+ classInstancesNeg.put(atomicConcept, Helper.difference(individuals,pos));
+ } else {
+ // Pellet needs approximately infinite time to answer negated queries
+ // on the carcinogenesis data set (and probably others), so we have to
+ // be careful here
+ Negation negatedAtomicConcept = new Negation(atomicConcept);
+ classInstancesNeg.put(atomicConcept, rs.retrieval(negatedAtomicConcept));
+ }
+
+
}
+ logger.debug("dematerialising object properties");
+
for (ObjectProperty atomicRole : atomicRoles) {
opPos.put(atomicRole, rc.getRoleMembers(atomicRole));
}
+ logger.debug("dematerialising datatype properties");
+
for (DatatypeProperty dp : booleanDatatypeProperties) {
- bd.put(dp, rc.getTrueDatatypeMembers(dp));
+ bdPos.put(dp, rc.getTrueDatatypeMembers(dp));
+ bdNeg.put(dp, rc.getFalseDatatypeMembers(dp));
}
-
+
for (DatatypeProperty dp : intDatatypeProperties) {
id.put(dp, rc.getIntDatatypeMembers(dp));
}
@@ -269,9 +290,9 @@
if(value) {
// check whether the individual is in the set of individuals mapped
// to true by this datatype property
- return bd.get(dp).contains(individual);
+ return bdPos.get(dp).contains(individual);
} else {
- return !bd.get(dp).contains(individual);
+ return bdNeg.get(dp).contains(individual);
}
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-04 13:40:00 UTC (rev 686)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-03-04 19:10:55 UTC (rev 687)
@@ -248,7 +248,8 @@
reasoner = new uk.ac.manchester.cs.factplusplus.owlapi.Reasoner(manager);
} catch (Exception e) {
e.printStackTrace();
- }
+ }
+ System.out.println("Using FaCT++.");
} else {
// instantiate Pellet reasoner
reasoner = new org.mindswap.pellet.owlapi.Reasoner(manager);
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-04 13:40:00 UTC (rev 686)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-03-04 19:10:55 UTC (rev 687)
@@ -115,7 +115,7 @@
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
+ // concept comparator
private ConceptComparator conceptComparator = new ConceptComparator();
// Statistik
@@ -129,6 +129,11 @@
private boolean useNegation = true;
private boolean useBooleanDatatypes = true;
+ // caches for reasoner queries
+// 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>> notABMeaningful = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
+
public RhoDRDown(ReasoningService reasoningService) {
this(reasoningService, true, true, true, true, true, true, null);
}
@@ -562,7 +567,7 @@
m2.add(c);
else {
NamedClass a = (NamedClass) c;
- if(!isNotADisjoint(a, nc) && isNotAMeaningFul(a, nc))
+ if(!isNotADisjoint(a, nc) && isNotAMeaningful(a, nc))
m2.add(new Negation(a));
}
}
@@ -697,19 +702,29 @@
// 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);
+ 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;
}
// 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) {
+ private boolean isNotAMeaningful(NamedClass a, NamedClass b) {
Description notA = new Negation(a);
Description d = new Intersection(notA, b);
// check b subClassOf b AND NOT A (if yes then it is not meaningful)
return !rs.subsumes(d, b);
- }
+ }
}
\ No newline at end of file
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