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[DL-Learner SVN] SF.net SVN: dl-learner:[1606] trunk
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From: <jen...@us...> - 2009-02-16 17:09:37
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Revision: 1606
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1606&view=rev
Author: jenslehmann
Date: 2009-02-16 17:09:30 +0000 (Mon, 16 Feb 2009)
Log Message:
-----------
continued ontology engineering algorithm
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/celoe/CELOE.java
trunk/src/dl-learner/org/dllearner/algorithms/celoe/OENode.java
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/core/configurators/CELOEConfigurator.java
trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java
trunk/src/dl-learner/org/dllearner/learningproblems/ClassLearningProblem.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
Added Paths:
-----------
trunk/examples/family/father_oe.conf
trunk/examples/family/father_oe.owl
Added: trunk/examples/family/father_oe.conf
===================================================================
--- trunk/examples/family/father_oe.conf (rev 0)
+++ trunk/examples/family/father_oe.conf 2009-02-16 17:09:30 UTC (rev 1606)
@@ -0,0 +1,7 @@
+
+import("father_oe.owl");
+
+problem = classLearning;
+classLearning.classToDescribe = "http://example.com/father#father";
+
+algorithm = celoe;
Added: trunk/examples/family/father_oe.owl
===================================================================
--- trunk/examples/family/father_oe.owl (rev 0)
+++ trunk/examples/family/father_oe.owl 2009-02-16 17:09:30 UTC (rev 1606)
@@ -0,0 +1,136 @@
+<?xml version="1.0"?>
+
+
+<!DOCTYPE rdf:RDF [
+ <!ENTITY father "http://example.com/father#" >
+ <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
+ <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
+ <!ENTITY owl2xml "http://www.w3.org/2006/12/owl2-xml#" >
+ <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
+ <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+]>
+
+
+<rdf:RDF xmlns="http://example.com/father#"
+ xml:base="http://example.com/father"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:father="http://example.com/father#">
+ <owl:Ontology rdf:about=""/>
+
+
+
+ <!--
+ ///////////////////////////////////////////////////////////////////////////////////////
+ //
+ // Object Properties
+ //
+ ///////////////////////////////////////////////////////////////////////////////////////
+ -->
+
+
+
+
+ <!-- http://example.com/father#hasChild -->
+
+ <owl:ObjectProperty rdf:about="#hasChild"/>
+
+
+
+ <!--
+ ///////////////////////////////////////////////////////////////////////////////////////
+ //
+ // Classes
+ //
+ ///////////////////////////////////////////////////////////////////////////////////////
+ -->
+
+
+
+
+ <!-- http://example.com/father#father -->
+
+ <owl:Class rdf:about="#father">
+ <rdfs:subClassOf rdf:resource="#male"/>
+ </owl:Class>
+
+
+
+ <!-- http://example.com/father#female -->
+
+ <owl:Class rdf:about="#female">
+ <owl:disjointWith rdf:resource="#male"/>
+ </owl:Class>
+
+
+
+ <!-- http://example.com/father#male -->
+
+ <owl:Class rdf:about="#male"/>
+
+
+
+ <!--
+ ///////////////////////////////////////////////////////////////////////////////////////
+ //
+ // Individuals
+ //
+ ///////////////////////////////////////////////////////////////////////////////////////
+ -->
+
+
+
+
+ <!-- http://example.com/father#anna -->
+
+ <female rdf:about="#anna">
+ <hasChild rdf:resource="#heinz"/>
+ </female>
+
+
+
+ <!-- http://example.com/father#heinz -->
+
+ <male rdf:about="#heinz"/>
+
+
+
+ <!-- http://example.com/father#markus -->
+
+ <male rdf:about="#markus">
+ <rdf:type rdf:resource="#father"/>
+ <hasChild rdf:resource="#anna"/>
+ </male>
+
+
+
+ <!-- http://example.com/father#martin -->
+
+ <male rdf:about="#martin">
+ <rdf:type rdf:resource="#father"/>
+ <hasChild rdf:resource="#heinz"/>
+ </male>
+
+
+
+ <!-- http://example.com/father#michelle -->
+
+ <female rdf:about="#michelle"/>
+
+
+
+ <!-- http://example.com/father#stefan -->
+
+ <father rdf:about="#stefan">
+ <rdf:type rdf:resource="#male"/>
+ <hasChild rdf:resource="#markus"/>
+ </father>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 2.2.1.974) http://owlapi.sourceforge.net -->
+
Modified: trunk/src/dl-learner/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/celoe/CELOE.java 2009-02-16 13:03:46 UTC (rev 1605)
+++ trunk/src/dl-learner/org/dllearner/algorithms/celoe/CELOE.java 2009-02-16 17:09:30 UTC (rev 1606)
@@ -19,9 +19,11 @@
*/
package org.dllearner.algorithms.celoe;
+import java.text.DecimalFormat;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
@@ -85,7 +87,13 @@
// important parameters
private double minAcc;
+ private double maxDepth;
+ // utility variables
+ private String baseURI;
+ private Map<String, String> prefixes;
+ DecimalFormat dfPercent = new DecimalFormat("0.00%");
+
@Override
public Configurator getConfigurator() {
return configurator;
@@ -93,6 +101,7 @@
public CELOE(ClassLearningProblem problem, ReasonerComponent reasoner) {
super(problem, reasoner);
+ configurator = new CELOEConfigurator(this);
classToDescribe = problem.getClassToDescribe();
isEquivalenceProblem = problem.isEquivalenceProblem();
}
@@ -114,8 +123,9 @@
options.add(CommonConfigOptions.useNegation());
options.add(CommonConfigOptions.useBooleanDatatypes());
options.add(CommonConfigOptions.useDoubleDatatypes());
- options.add(CommonConfigOptions.maxExecutionTimeInSeconds());
+ options.add(CommonConfigOptions.maxExecutionTimeInSeconds(10));
options.add(CommonConfigOptions.getNoisePercentage());
+ options.add(CommonConfigOptions.getMaxDepth(4));
return options;
}
@@ -135,6 +145,7 @@
// we put important parameters in class variables
minAcc = configurator.getNoisePercentage()/100d;
+ maxDepth = configurator.getMaxDepth();
}
@Override
@@ -164,6 +175,10 @@
reset();
nanoStartTime = System.nanoTime();
+ // highest accuracy so far
+ double highestAccuracy = 0.0;
+ OENode bestNode;
+
// start class: intersection of super classes for definitions (since it needs to
// capture all instances), but owl:Thing for learning subclasses (since it is
// superfluous to add super classes in this case)
@@ -176,16 +191,67 @@
}
addNode(startClass, null);
+ int loop = 0;
+ while (!terminationCriteriaSatisfied()) {
+
+ if(bestEvaluatedDescriptions.getBest().getAccuracy() > highestAccuracy) {
+ highestAccuracy = bestEvaluatedDescriptions.getBest().getAccuracy();
+ logger.info("more accurate (" + dfPercent.format(100*highestAccuracy) + ") class expression found: " + descriptionToString(bestEvaluatedDescriptions.getBest().getDescription()));
+ }
+
+ // chose best node according to heuristics
+ bestNode = nodes.last();
+ int horizExp = bestNode.getHorizontalExpansion();
+
+ // apply operator
+ TreeSet<Description> refinements = refineNode(bestNode);
+
+ while(refinements.size() != 0) {
+ // pick element from set
+ Description refinement = refinements.pollFirst();
+ int length = refinement.getLength();
+
+ // we ignore all refinements with lower length and too high depth
+ if(length >= horizExp && refinement.getDepth() <= maxDepth) {
+ boolean added = addNode(refinement, bestNode);
+
+ // if refinements have the same length, we apply the operator again
+ // (descending the subsumption hierarchy)
+ if(added && length == horizExp) {
+ // ... refine node (first check whether we need this as there will
+ // the penalty for longer descriptions will be quite hard anyway)
+ }
+
+ }
+
+ }
+
+ // Anzahl Schleifendurchläufe
+ loop++;
+ }
+
+ if (stop) {
+ logger.info("Algorithm stopped.\n");
+ } else {
+ logger.info("Algorithm terminated succesfully.\n");
+ }
+
// print solution(s)
- logger.info("solution : " + bestEvaluatedDescriptions.getBest());
+ logger.info("solution : " + bestDescriptionToString());
isRunning = false;
}
// expand node horizontically
- private void expandNode(OENode node) {
-
+ private TreeSet<Description> refineNode(OENode node) {
+ // we have to remove and add the node since its heuristic evaluation changes through the expansion
+ nodes.remove(node);
+ int horizExp = node.getHorizontalExpansion();
+ TreeSet<Description> refinements = (TreeSet<Description>) operator.refine(node.getDescription(), horizExp+1);
+ node.incHorizontalExpansion();
+ nodes.add(node);
+ return refinements;
}
// add node to search tree if it is not too weak
@@ -212,9 +278,13 @@
} else {
parentNode.addChild(node);
}
+
+ nodes.add(node);
// maybe add to best descriptions (method keeps set size fixed)
- bestEvaluatedDescriptions.add(description, accuracy, learningProblem);
+ if(checkNode(node)) {
+ bestEvaluatedDescriptions.add(description, accuracy, learningProblem);
+ }
return true;
}
@@ -222,11 +292,16 @@
// check whether the node is a potential solution candidate
// (sufficient accuracy; minimal; rewriting steps?)
private boolean checkNode(OENode node) {
+
+ // what to do if super class occurs? either return false, but then it
+ // does not make sense to expand it further; or rewrite but then we have to
+ // take care of double occurrences
+
return true;
}
private boolean terminationCriteriaSatisfied() {
- return !stop && (System.nanoTime() - nanoStartTime >= (configurator.getMaxExecutionTimeInSeconds()/1000000));
+ return stop || (System.nanoTime() - nanoStartTime >= (configurator.getMaxExecutionTimeInSeconds()*1000000));
}
private void reset() {
@@ -248,4 +323,17 @@
stop = true;
}
+ public OENode getSearchTreeRoot() {
+ return startNode;
+ }
+
+ // central function for printing description
+ private String descriptionToString(Description description) {
+ return description.toManchesterSyntaxString(baseURI, prefixes);
+ }
+
+ private String bestDescriptionToString() {
+ EvaluatedDescription best = bestEvaluatedDescriptions.getBest();
+ return best.getDescription().toManchesterSyntaxString(baseURI, prefixes) + " (accuracy: " + dfPercent.format(best.getAccuracy()*100) + ")";
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/celoe/OENode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/celoe/OENode.java 2009-02-16 13:03:46 UTC (rev 1605)
+++ trunk/src/dl-learner/org/dllearner/algorithms/celoe/OENode.java 2009-02-16 17:09:30 UTC (rev 1606)
@@ -44,6 +44,8 @@
private double accuracy;
+ private int horizontalExpansion;
+
private OENode parent;
private List<OENode> children;
@@ -51,12 +53,17 @@
this.parent = parentNode;
this.description = description;
this.accuracy = accuracy;
+ horizontalExpansion = 0;
}
public void addChild(OENode node) {
children.add(node);
}
+ public void incHorizontalExpansion() {
+ horizontalExpansion++;
+ }
+
/**
* @return the description
*/
@@ -84,5 +91,12 @@
public List<OENode> getChildren() {
return children;
}
+
+ /**
+ * @return the horizontalExpansion
+ */
+ public int getHorizontalExpansion() {
+ return horizontalExpansion;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2009-02-16 13:03:46 UTC (rev 1605)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2009-02-16 17:09:30 UTC (rev 1606)
@@ -294,11 +294,14 @@
lpClass = PosNegLPStandard.class;
}
lp = cm.learningProblem(lpClass, rc);
- SortedSet<String> posExamples = parser.getPositiveExamples();
- SortedSet<String> negExamples = parser.getNegativeExamples();
- cm.applyConfigEntry(lp, "positiveExamples", posExamples);
- if (lpClass != PosOnlyLP.class)
+ if(lpClass == PosNegLPStandard.class || lpClass == PosOnlyLP.class) {
+ SortedSet<String> posExamples = parser.getPositiveExamples();
+ cm.applyConfigEntry(lp, "positiveExamples", posExamples);
+ }
+ if(lpClass == PosNegLPStandard.class) {
+ SortedSet<String> negExamples = parser.getNegativeExamples();
cm.applyConfigEntry(lp, "negativeExamples", negExamples);
+ }
configureComponent(cm, lp, parser);
initComponent(cm, lp);
lpMonitor.stop();
Modified: trunk/src/dl-learner/org/dllearner/core/configurators/CELOEConfigurator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/configurators/CELOEConfigurator.java 2009-02-16 13:03:46 UTC (rev 1605)
+++ trunk/src/dl-learner/org/dllearner/core/configurators/CELOEConfigurator.java 2009-02-16 17:09:30 UTC (rev 1606)
@@ -155,6 +155,15 @@
public double getNoisePercentage() {
return (Double) ComponentManager.getInstance().getConfigOptionValue(cELOE, "noisePercentage") ;
}
+/**
+* maxDepth maximum depth of description.
+* mandatory: false| reinit necessary: true
+* default value: 3
+* @return int
+**/
+public int getMaxDepth() {
+return (Integer) ComponentManager.getInstance().getConfigOptionValue(cELOE, "maxDepth") ;
+}
/**
* @param useAllConstructor specifies whether the universal concept constructor is used in the learning algorithm.
@@ -255,6 +264,15 @@
ComponentManager.getInstance().applyConfigEntry(cELOE, "noisePercentage", noisePercentage);
reinitNecessary = true;
}
+/**
+* @param maxDepth maximum depth of description.
+* mandatory: false| reinit necessary: true
+* default value: 3
+**/
+public void setMaxDepth(int maxDepth) {
+ComponentManager.getInstance().applyConfigEntry(cELOE, "maxDepth", maxDepth);
+reinitNecessary = true;
+}
/**
* true, if this component needs reinitializsation.
Modified: trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java 2009-02-16 13:03:46 UTC (rev 1605)
+++ trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java 2009-02-16 17:09:30 UTC (rev 1606)
@@ -73,6 +73,10 @@
return new BooleanConfigOption("terminateOnNoiseReached", "specifies whether to terminate when noise criterion is met", terminateOnNoiseReachedDefault);
}
+ public static IntegerConfigOption getMaxDepth(int defaultValue) {
+ return new IntegerConfigOption("maxDepth", "maximum depth of description", defaultValue);
+ }
+
public static DoubleConfigOption getPercentPerLenghtUnitOption(double defaultValue) {
DoubleConfigOption option = new DoubleConfigOption("percentPerLenghtUnit", "describes the reduction in classification accuracy in percent one is willing to accept for reducing the length of the concept by one", defaultValue);
option.setLowerLimit(0.0);
@@ -153,6 +157,10 @@
return new IntegerConfigOption("maxExecutionTimeInSeconds", "algorithm will stop after specified seconds",maxExecutionTimeInSecondsDefault);
}
+ public static IntegerConfigOption maxExecutionTimeInSeconds(int defaultValue) {
+ return new IntegerConfigOption("maxExecutionTimeInSeconds", "algorithm will stop after specified seconds",defaultValue);
+ }
+
public static IntegerConfigOption minExecutionTimeInSeconds() {
return new IntegerConfigOption("minExecutionTimeInSeconds", "algorithm will run at least specified seconds",minExecutionTimeInSecondsDefault);
}
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/ClassLearningProblem.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/ClassLearningProblem.java 2009-02-16 13:03:46 UTC (rev 1605)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/ClassLearningProblem.java 2009-02-16 17:09:30 UTC (rev 1606)
@@ -28,6 +28,7 @@
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.configurators.ClassLearningProblemConfigurator;
+import org.dllearner.core.configurators.PosNegLPStandardConfigurator;
import org.dllearner.core.options.ConfigOption;
import org.dllearner.core.options.StringConfigOption;
import org.dllearner.core.owl.Description;
@@ -55,6 +56,7 @@
public ClassLearningProblem(ReasonerComponent reasoner) {
super(reasoner);
+ configurator = new ClassLearningProblemConfigurator(this);
}
public static Collection<ConfigOption<?>> createConfigOptions() {
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2009-02-16 13:03:46 UTC (rev 1605)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2009-02-16 17:09:30 UTC (rev 1606)
@@ -335,6 +335,11 @@
throw new RuntimeException();
}
+ @Override
+ public Set<Description> refine(Description description, int maxLength) {
+ return refine(description, maxLength, null, startClass);
+ }
+
/* (non-Javadoc)
* @see org.dllearner.algorithms.refinement.RefinementOperator#refine(org.dllearner.core.owl.Description, int, java.util.List)
*/
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