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[DL-Learner SVN] SF.net SVN: dl-learner:[1708] trunk
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From: <jen...@us...> - 2009-04-16 18:12:12
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Revision: 1708
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1708&view=rev
Author: jenslehmann
Date: 2009-04-16 18:12:06 +0000 (Thu, 16 Apr 2009)
Log Message:
-----------
- fixed bug occurring in KRK examples
- added corresponding unit test
Modified Paths:
--------------
trunk/examples/krk/KRK_ONE_ZERO_fastInstance.conf
trunk/src/dl-learner/org/dllearner/algorithms/refinement2/ROLComponent2.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement2/ROLearner2.java
trunk/src/dl-learner/org/dllearner/core/configurators/ROLComponent2Configurator.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
trunk/src/dl-learner/org/dllearner/scripts/ConfigJavaGenerator.java
trunk/src/dl-learner/org/dllearner/test/junit/RefinementOperatorTests.java
trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
Modified: trunk/examples/krk/KRK_ONE_ZERO_fastInstance.conf
===================================================================
--- trunk/examples/krk/KRK_ONE_ZERO_fastInstance.conf 2009-04-16 14:21:43 UTC (rev 1707)
+++ trunk/examples/krk/KRK_ONE_ZERO_fastInstance.conf 2009-04-16 18:12:06 UTC (rev 1708)
@@ -1,38 +1,23 @@
/*
-DEBUG - --- loop 5279 started ---
-INFO - best node EXISTS "hasPiece".EXISTS "hasLowerRankThan".("WRook" AND ALL "fileDistanceLessThan1"."WKing") [acc:100% h:0,853 q:0p-0n (REASONER), he:8 c:0]
-INFO -
-solutions:
-INFO - 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") (length 9, depth 5)
-INFO - MANCHESTER: hasPiece some hasLowerRankThan some (WRook and fileDistanceLessThan1 only WKing)
-DEBUG - size of candidate set: 50434
-DEBUG - properness tests (reasoner/short concept/too weak list): 0/3/56
-DEBUG - concept tests (reasoner/too weak list/overly general list/redundant concepts): 12609/56/38684/4153
-INFO - Algorithm terminated succesfully.
-number of retrievals: 12
-retrieval reasoning time: 0ms ( 0ms per retrieval)
-number of instance checks: 1232144 (0 multiple)
-instance check reasoning time: 9s 613ms ( 0ms per instance check)
-subsumption hierarchy queries: 14
-(complex) subsumption checks: 8 (0 multiple)
-subsumption reasoning time: 17ms ( 2ms per subsumption check)
-overall reasoning time: 9s 630ms (24,91% of overall runtime)
-overall algorithm runtime: 38s 662ms
+ * Chess - King and Rook vs. lone King
+ *
+ * Here, we learn the difference between mate and mate in 1.
+ *
+ * Solutions:
+ *
+ * 1: hasPiece some hasLowerRankThan some (WRook and fileDistance0 only WKing)
+ * 2: hasPiece some hasLowerRankThan some (WRook and fileDistanceLessThan1 only WKing)
+ */
-
-
-*/
-
import("KRK_ZERO_ONE.owl");
+
refexamples.ignoredConcepts={
"http://www.test.de/test#ONE",
"http://www.test.de/test#ZERO"};
-
algorithm = refexamples;
reasoner=fastInstanceChecker;
-
+"http://www.test.de/test#game100"
+"http://www.test.de/test#game101"
+"http://www.test.de/test#game102"
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement2/ROLComponent2.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement2/ROLComponent2.java 2009-04-16 14:21:43 UTC (rev 1707)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement2/ROLComponent2.java 2009-04-16 18:12:06 UTC (rev 1708)
@@ -205,8 +205,6 @@
options.add(CommonConfigOptions.maxClassDescriptionTests());
options.add(CommonConfigOptions.getLogLevel());
options.add(new BooleanConfigOption("usePropernessChecks", "specifies whether to check for equivalence (i.e. discard equivalent refinements)",usePropernessChecksDefault));
- options.add(new IntegerConfigOption("maxPosOnlyExpansion", "specifies how often a node in the search tree of a posonly learning problem needs to be expanded before it is" +
- " considered as solution candidate",maxPosOnlyExpansionDefault));
options.add(CommonConfigOptions.getNoisePercentage());
options.add(CommonConfigOptions.getTerminateOnNoiseReached());
options.add(new StringConfigOption("startClass", "the named class which should be used to start the algorithm (GUI: needs a widget for selecting a class)"));
@@ -366,6 +364,9 @@
if(improveSubsumptionHierarchy)
classHierarchy.thinOutSubsumptionHierarchy();
+// System.out.println(classHierarchy);
+// System.exit(0);
+
// reasoner.prepareRoleHierarchy(usedRoles);
// prepare datatype hierarchy only if necessary
// if(reasoner.hasDatatypeSupport())
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement2/ROLearner2.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement2/ROLearner2.java 2009-04-16 14:21:43 UTC (rev 1707)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement2/ROLearner2.java 2009-04-16 18:12:06 UTC (rev 1708)
@@ -44,8 +44,6 @@
import org.dllearner.learningproblems.EvaluatedDescriptionPosNeg;
import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.learningproblems.ScorePosNeg;
-import org.dllearner.parser.KBParser;
-import org.dllearner.parser.ParseException;
import org.dllearner.refinementoperators.RefinementOperator;
import org.dllearner.refinementoperators.RhoDRDown;
import org.dllearner.utilities.Files;
@@ -85,15 +83,6 @@
private double noise = 0.0;
private int allowedMisclassifications = 0;
- // positive only learning options:
- // if no negatives are given, then one possible strategy is to find a very
- // special concept still entailing all positive examples;
- // this is realised by changing the termination criterion: a concept is a
- // solution if it has been expanded x times (x is
- // configurable) but no more special concept is found (all are either
- // equivalent or too weak)
- private int maxPosOnlyExpansion;
-
// search tree options
private boolean writeSearchTree;
private File searchTreeFile;
@@ -266,7 +255,6 @@
this.usePropernessChecks = usePropernessChecks;
baseURI = rs.getBaseURI();
prefixes = rs.getPrefixes();
- this.maxPosOnlyExpansion = maxPosOnlyExpansion;
this.maxExecutionTimeInSeconds = maxExecutionTimeInSeconds;
this.minExecutionTimeInSeconds = minExecutionTimeInSeconds;
this.guaranteeXgoodDescriptions = guaranteeXgoodDescriptions;
@@ -467,38 +455,6 @@
Files.appendFile(searchTreeFile, treeString);
}
- // special situation for positive only learning: the expanded node
- // can become a solution (see explanations
- // for maxPosOnlyExpansion above)
-
- // DEPRECATED CODE
- if (false
- && bestNode.isPosOnlyCandidate()
- && (bestNode.getHorizontalExpansion() - bestNode.getConcept().getLength() >= maxPosOnlyExpansion)) {
-
- boolean solution = checkSubtreePosOnly(bestNode);
-
- if (solution) {
- solutions.add(bestNode);
- ExampleBasedNode bestChild = bestNode.getChildren().last();
- System.out.println("solution: " + bestNode.getConcept());
- System.out.println("maxPosOnlyExpansion: " + maxPosOnlyExpansion);
- System.out.println("best child of this node: " + bestChild);
- if(bestNode.getChildConcepts().size()<100) {
- System.out.println(bestNode.getChildConcepts());
- }
- System.out.println("TODO: needs to be integrated with other stopping criteria");
- System.out
- .println("You tried to use this algorithm for positive only learning, which is not recommended (yet).");
- // System.out.println("Exiting.");
- // System.exit(0);
- } else {
- // tag as non-candidate so we do not need to search again
- bestNode.setPosOnlyCandidate(false);
- }
-
- }
-
// Anzahl Schleifendurchläufe
loop++;
}// end while
@@ -571,6 +527,7 @@
// System.out.println("node: " + node);
// System.out.println("concept: " + concept);
+// System.out.println("max length: " + maxLength);
// do not execute methods if algorithm has been stopped (this means that
// the algorithm
@@ -896,26 +853,6 @@
// System.out.println("node " + node);
// System.out.println("refinement " + refinement);
- /*
- try {
- Description c = KBParser.parseConcept("EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#hasLowerRankThan\".\"http://www.test.de/test#WRook\"");
- if(conceptComparator.compare(c, node.getConcept()) == 0) {
- System.out.println("TEST");
- Set<Description> refs = operator.refine(c, 8, null);
- for(Description d : refs) {
- System.out.println(" " + d);
- }
- System.out.println();
- System.exit(0);
- }
- } catch (ParseException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- */
-
-
-
extendNodeProper(node, refinement, maxLength, recDepth + 1);
}
@@ -1322,45 +1259,9 @@
public ExampleBasedNode getStartNode() {
return startNode;
}
-
- // returns true if there is any meaningful node in the subtree
- private boolean checkSubtreePosOnly(ExampleBasedNode node) {
- for (ExampleBasedNode refinement : node.getChildren()) {
-
- if (!node.isTooWeak()) {
- // refinement meaningful
- if (isPosOnlyRefinementMeaningful(node, refinement))
- return true;
-
- // subtree with refinement as root contains a meaningful node
- if (checkSubtreePosOnly(refinement))
- return true;
- }
-
- }
- return false;
- }
-
- // returns whether the refinement is "meaningful", i.e. the refinement
- // actually represents a different concept
- // than its parent; this is needed to determine when a positive only
- // learning algorithm should stop (when a node
- // has been expaned x times without yielding any meaningful refinements, it
- // is considered a possible solution)
- private boolean isPosOnlyRefinementMeaningful(ExampleBasedNode node, ExampleBasedNode refinement) {
- Description d1 = node.getConcept();
- Description d2 = refinement.getConcept();
- // check whether d2 can be shortened, e.g. male AND male => male
- Description shortConcept = ConceptTransformation.getShortConcept(d2, conceptComparator);
- if (conceptComparator.compare(d1, shortConcept) != 0)
- return false;
- return true;
- }
-
-
/**
- * In this function it is calculated if the algorithm should stop.
+ * In this function it is calculated whether the algorithm should stop.
* This is not always depends whether an actual solution was found
* The algorithm stops if:
* 1. the object attribute stop is set to true (possibly by an outside source)
Modified: trunk/src/dl-learner/org/dllearner/core/configurators/ROLComponent2Configurator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/configurators/ROLComponent2Configurator.java 2009-04-16 14:21:43 UTC (rev 1707)
+++ trunk/src/dl-learner/org/dllearner/core/configurators/ROLComponent2Configurator.java 2009-04-16 18:12:06 UTC (rev 1708)
@@ -31,7 +31,7 @@
* automatically generated, do not edit manually.
* run org.dllearner.scripts.ConfigJavaGenerator to update
**/
-public class ROLComponent2Configurator implements Configurator {
+public class ROLComponent2Configurator extends RefinementOperatorConfigurator implements Configurator {
private boolean reinitNecessary = false;
@SuppressWarnings("unused")
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2009-04-16 14:21:43 UTC (rev 1707)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2009-04-16 18:12:06 UTC (rev 1708)
@@ -372,7 +372,7 @@
public Set<Description> refine(Description description, int maxLength,
List<Description> knownRefinements, Description currDomain) {
-// logger.trace(description + " " + currDomain + " " + maxLength);
+// System.out.println("|- " + description + " " + currDomain + " " + maxLength);
// actions needing to be performed if this is the first time the
// current domain is used
@@ -399,7 +399,6 @@
}
refinements = (TreeSet<Description>) topARefinementsCumulative.get(currDomain).get(maxLength).clone();
}
-
// refinements.addAll(subHierarchy.getMoreSpecialConcepts(description));
} else if(description instanceof Nothing) {
// cannot be further refined
@@ -881,7 +880,9 @@
if(useNegation) {
Set<Description> m2tmp = subHierarchy.getSuperClasses(new Nothing());
for(Description c : m2tmp) {
- m2.add(new Negation(c));
+ if(!(c instanceof Thing)) {
+ m2.add(new Negation(c));
+ }
}
}
@@ -968,9 +969,11 @@
SortedSet<Description> m2tmp = subHierarchy.getSuperClasses(new Nothing());
for(Description c : m2tmp) {
- if(c instanceof Thing)
- m2.add(c);
- else {
+// if(c instanceof Thing)
+// m2.add(c);
+// else {
+ // we obviously do not add \top (\top refines \top does not make sense)
+ if(!(c instanceof Thing)) {
NamedClass a = (NamedClass) c;
if(!isNotADisjoint(a, nc) && isNotAMeaningful(a, nc))
m2.add(new Negation(a));
Modified: trunk/src/dl-learner/org/dllearner/scripts/ConfigJavaGenerator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/ConfigJavaGenerator.java 2009-04-16 14:21:43 UTC (rev 1707)
+++ trunk/src/dl-learner/org/dllearner/scripts/ConfigJavaGenerator.java 2009-04-16 18:12:06 UTC (rev 1708)
@@ -39,6 +39,7 @@
import org.dllearner.core.LearningProblemUnsupportedException;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.configurators.CELOEConfigurator;
+import org.dllearner.core.configurators.ROLComponent2Configurator;
import org.dllearner.core.configurators.ROLearnerConfigurator;
import org.dllearner.core.configurators.RefinementOperatorConfigurator;
import org.dllearner.core.options.ConfigOption;
@@ -65,6 +66,7 @@
private static final SortedSet<String> EXTENDSREFINEMENTOPERATOR =
new TreeSet<String>(Arrays.asList(new String[]{
ROLearnerConfigurator.class.getSimpleName(),
+ ROLComponent2Configurator.class.getSimpleName(),
CELOEConfigurator.class.getSimpleName(),
}));
Modified: trunk/src/dl-learner/org/dllearner/test/junit/RefinementOperatorTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/RefinementOperatorTests.java 2009-04-16 14:21:43 UTC (rev 1707)
+++ trunk/src/dl-learner/org/dllearner/test/junit/RefinementOperatorTests.java 2009-04-16 18:12:06 UTC (rev 1708)
@@ -24,18 +24,27 @@
import java.io.File;
import java.net.MalformedURLException;
import java.util.Set;
+import java.util.TreeSet;
+import org.dllearner.algorithms.refinement2.ROLComponent2;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.ComponentManager;
import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.LearningProblem;
+import org.dllearner.core.LearningProblemUnsupportedException;
import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.owl.ClassHierarchy;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.Thing;
import org.dllearner.kb.OWLFile;
+import org.dllearner.learningproblems.PosNegLPStandard;
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.refinementoperators.RhoDRDown;
import org.dllearner.test.junit.TestOntologies.TestOntology;
+import org.dllearner.utilities.Helper;
import org.junit.Test;
/**
@@ -115,6 +124,56 @@
assertTrue(results.size()==desiredResultSize);
}
+ @Test
+ public void rhoDRDownTest3() throws ParseException, LearningProblemUnsupportedException {
+ ReasonerComponent reasoner = TestOntologies.getTestOntology(TestOntology.KRK_ZERO_ONE);
+ baseURI = reasoner.getBaseURI();
+
+ // create learning algorithm in order to test under similar conditions than
+ // within a learning algorithm
+ ComponentManager cm = ComponentManager.getInstance();
+ LearningProblem lp = cm.learningProblem(PosNegLPStandard.class, reasoner);
+ ROLComponent2 la = cm.learningAlgorithm(ROLComponent2.class, lp, reasoner);
+
+ Set<NamedClass> ignoredConcepts = new TreeSet<NamedClass>();
+ ignoredConcepts.add(new NamedClass("http://www.test.de/test#ZERO"));
+ ignoredConcepts.add(new NamedClass("http://www.test.de/test#ONE"));
+ Set<NamedClass> usedConcepts = Helper.computeConceptsUsingIgnoreList(reasoner, ignoredConcepts);
+
+ ClassHierarchy classHierarchy = reasoner.getClassHierarchy().cloneAndRestrict(usedConcepts);
+ classHierarchy.thinOutSubsumptionHierarchy();
+ RhoDRDown op = new RhoDRDown(
+ reasoner,
+ classHierarchy,
+ Thing.instance,
+ la.getConfigurator()
+ );
+
+ Description concept = KBParser.parseConcept("EXISTS \"http://www.test.de/test#hasPiece\".EXISTS \"http://www.test.de/test#hasLowerRankThan\".(\"http://www.test.de/test#WRook\" AND TOP)");
+ Set<Description> results = op.refine(concept,8);
+
+ for(Description result : results) {
+ System.out.println(result.toString("http://www.test.de/test#",null));
+ }
+
+ int desiredResultSize = 8;
+ if(results.size() != desiredResultSize) {
+ System.out.println(results.size() + " results found, but should be " + desiredResultSize + ".");
+ }
+
+ // the 8 refinements found on 2009/04/16 are as follows:
+ // EXISTS hasPiece.EXISTS hasLowerRankThan.(BKing AND WRook)
+ // EXISTS hasPiece.EXISTS hasLowerRankThan.(WKing AND WRook)
+ // EXISTS hasPiece.EXISTS hasLowerRankThan.(WRook AND WRook)
+ // EXISTS hasPiece.EXISTS hasLowerRankThan.(WRook AND (NOT BKing))
+ // EXISTS hasPiece.EXISTS hasLowerRankThan.(WRook AND (NOT WKing))
+ // EXISTS hasPiece.EXISTS hasLowerRankThan.(WRook AND (NOT WRook))
+ // EXISTS hasPiece.>= 2 hasLowerRankThan.(WRook AND TOP)
+ // >= 2 hasPiece.EXISTS hasLowerRankThan.(WRook AND TOP)
+
+ assertTrue(results.size()==desiredResultSize);
+ }
+
private String uri(String name) {
return "\""+baseURI+name+"\"";
}
Modified: trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2009-04-16 14:21:43 UTC (rev 1707)
+++ trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2009-04-16 18:12:06 UTC (rev 1708)
@@ -41,7 +41,7 @@
*/
public final class TestOntologies {
- public enum TestOntology { EMPTY, SIMPLE, SIMPLE_NO_DR, SIMPLE_NO_DISJOINT, SIMPLE_NO_DR_DISJOINT, SIMPLE2, SIMPLE3, R1SUBR2, DATA1, FIVE_ROLES, FATHER_OE, CARCINOGENESIS, EPC_OE };
+ public enum TestOntology { EMPTY, SIMPLE, SIMPLE_NO_DR, SIMPLE_NO_DISJOINT, SIMPLE_NO_DR_DISJOINT, SIMPLE2, SIMPLE3, R1SUBR2, DATA1, FIVE_ROLES, FATHER_OE, CARCINOGENESIS, EPC_OE, KRK_ZERO_ONE };
public static ReasonerComponent getTestOntology(TestOntology ont) {
String kbString = "";
@@ -115,7 +115,9 @@
owlFile = "examples/carcinogenesis/carcinogenesis.owl";
} else if(ont.equals(TestOntology.EPC_OE)) {
owlFile = "examples/epc/sap_epc_oe.owl";
- }
+ } else if(ont.equals(TestOntology.KRK_ZERO_ONE)) {
+ owlFile = "examples/krk/KRK_ZERO_ONE.owl";
+ }
try {
ComponentManager cm = ComponentManager.getInstance();
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