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[DL-Learner SVN] SF.net SVN: dl-learner:[1578] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2009-01-17 18:27:17
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Revision: 1578
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1578&view=rev
Author: jenslehmann
Date: 2009-01-17 18:27:07 +0000 (Sat, 17 Jan 2009)
Log Message:
-----------
added option to configure horizontal expansion penalty (can be used to say whether the search should be more breadth or depth like)
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
trunk/src/dl-learner/org/dllearner/core/configurators/ExampleBasedROLComponentConfigurator.java
trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java
trunk/src/dl-learner/org/dllearner/test/junit/ReasonerTests.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/test/PelletPerformanceProblem.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2009-01-16 16:24:44 UTC (rev 1577)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2009-01-17 18:27:07 UTC (rev 1578)
@@ -215,6 +215,7 @@
options.add(new DoubleConfigOption("negativeWeight", "Used to penalise errors on negative examples different from those of positive examples (lower = less importance for negatives).",1.0));
options.add(new DoubleConfigOption("startNodeBonus", "You can use this to give a heuristic bonus on the start node (= initially broader exploration of search space).",0.0));
options.add(new IntegerConfigOption("negationPenalty", "Penalty on negations (TODO: better explanation).", 0));
+ options.add(CommonConfigOptions.getExpansionPenaltyFactor(0.02));
return options;
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2009-01-16 16:24:44 UTC (rev 1577)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/MultiHeuristic.java 2009-01-17 18:27:07 UTC (rev 1578)
@@ -98,6 +98,7 @@
this.configurator = configurator;
negativeWeight = configurator.getNegativeWeight();
startNodeBonus = configurator.getStartNodeBonus();
+ expansionPenaltyFactor = configurator.getExpansionPenaltyFactor();
}
// public MultiHeuristic(int nrOfPositiveExamples, int nrOfNegativeExamples, double expansionPenaltyFactor, double gainBonusFactor) {
Modified: trunk/src/dl-learner/org/dllearner/core/configurators/ExampleBasedROLComponentConfigurator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/configurators/ExampleBasedROLComponentConfigurator.java 2009-01-16 16:24:44 UTC (rev 1577)
+++ trunk/src/dl-learner/org/dllearner/core/configurators/ExampleBasedROLComponentConfigurator.java 2009-01-17 18:27:07 UTC (rev 1578)
@@ -402,6 +402,15 @@
public int getNegationPenalty() {
return (Integer) ComponentManager.getInstance().getConfigOptionValue(exampleBasedROLComponent, "negationPenalty") ;
}
+/**
+* expansionPenaltyFactor describes the reduction in heuristic score one is willing to accept for reducing the length of the concept by one.
+* mandatory: false| reinit necessary: true
+* default value: 0.02
+* @return double
+**/
+public double getExpansionPenaltyFactor() {
+return (Double) ComponentManager.getInstance().getConfigOptionValue(exampleBasedROLComponent, "expansionPenaltyFactor") ;
+}
/**
* @param writeSearchTree specifies whether to write a search tree.
@@ -745,6 +754,15 @@
ComponentManager.getInstance().applyConfigEntry(exampleBasedROLComponent, "negationPenalty", negationPenalty);
reinitNecessary = true;
}
+/**
+* @param expansionPenaltyFactor describes the reduction in heuristic score one is willing to accept for reducing the length of the concept by one.
+* mandatory: false| reinit necessary: true
+* default value: 0.02
+**/
+public void setExpansionPenaltyFactor(double expansionPenaltyFactor) {
+ComponentManager.getInstance().applyConfigEntry(exampleBasedROLComponent, "expansionPenaltyFactor", expansionPenaltyFactor);
+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 2009-01-16 16:24:44 UTC (rev 1577)
+++ trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java 2009-01-17 18:27:07 UTC (rev 1578)
@@ -80,6 +80,11 @@
return option;
}
+ public static DoubleConfigOption getExpansionPenaltyFactor(double defaultValue) {
+ DoubleConfigOption option = new DoubleConfigOption("expansionPenaltyFactor", "describes the reduction in heuristic score one is willing to accept for reducing the length of the concept by one", defaultValue);
+ return option;
+ }
+
public static StringConfigOption getReturnType() {
return new StringConfigOption("returnType", "Specifies the type which the solution has to belong to (if already) known. This means we inform the learning algorithm that the solution is a subclass of this type.");
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2009-01-16 16:24:44 UTC (rev 1577)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2009-01-17 18:27:07 UTC (rev 1578)
@@ -252,7 +252,7 @@
public boolean hasTypeImpl(Description description, Individual individual)
throws ReasoningMethodUnsupportedException {
- // System.out.println(description + " " + individual);
+// System.out.println(description + " " + individual);
if (description instanceof NamedClass) {
return classInstancesPos.get((NamedClass) description).contains(individual);
@@ -366,7 +366,10 @@
int number = ((ObjectCardinalityRestriction) description).getNumber();
int nrOfFillers = 0;
- SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+// SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+ SortedSet<Individual> roleFillers = mapping.get(individual);
+// System.out.println(roleFillers);
+
// special case: there are always at least zero fillers
if (number == 0) {
return true;
@@ -384,7 +387,7 @@
if (nrOfFillers == number) {
return true;
}
- // earyl abort: e.g. >= 10 hasStructure.Methyl;
+ // early abort: e.g. >= 10 hasStructure.Methyl;
// if there are 11 fillers and 2 are not Methyl, the result
// is false
} else {
Modified: trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java 2009-01-16 16:24:44 UTC (rev 1577)
+++ trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java 2009-01-17 18:27:07 UTC (rev 1578)
@@ -71,7 +71,12 @@
new File(dir).mkdir();
String example = "/home/jl/promotion/ontologien/galen2.owl";
- testOntology(dir, example, 100, 17);
+
+ for(int i=10; i<17; i++) {
+ rand = new Random(2);
+ testOntology(dir, example, 100, i);
+ }
+
System.exit(0);
/* TEST ON ARTIFICIAL ONTOLOGIES
@@ -142,7 +147,7 @@
// log file name
String name = ontFile.getName();
- String statFileName = name.substring(0, name.lastIndexOf(".")) + ".txt";
+ String statFileName = name.substring(0, name.lastIndexOf(".")) + "_" + chainLength + ".txt";
File statFile = new File(statDir + statFileName);
String statString = "";
@@ -221,6 +226,9 @@
statString += getMonitorData(MonitorFactory.getMonitor("disjointness reasoning", "ms."));
Files.createFile(statFile, statString);
+
+ reasoner.releaseKB();
+ cm.freeAllComponents();
}
private static String getMonitorData(Monitor mon) {
Added: trunk/src/dl-learner/org/dllearner/test/PelletPerformanceProblem.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/PelletPerformanceProblem.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/test/PelletPerformanceProblem.java 2009-01-17 18:27:07 UTC (rev 1578)
@@ -0,0 +1,63 @@
+/**
+ * Copyright (C) 2007-2009, 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.test;
+
+import java.io.File;
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.inference.OWLReasoner;
+import org.semanticweb.owl.inference.OWLReasonerException;
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyCreationException;
+import org.semanticweb.owl.model.OWLOntologyManager;
+
+/**
+ * @author Jens Lehmann
+ *
+ */
+public class PelletPerformanceProblem {
+
+ public static void main(String[] args) throws OWLOntologyCreationException, OWLReasonerException {
+ Logger pelletLogger = Logger.getLogger("org.mindswap.pellet");
+ pelletLogger.setLevel(Level.WARN);
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+
+ File f = new File("examples/epc/conf/sap_modell_komplett_2.owl");
+ URI physicalURI = f.toURI();
+ OWLOntology ontology = manager.loadOntologyFromPhysicalURI(physicalURI);
+
+ Set<OWLOntology> ontologies = new HashSet<OWLOntology>();
+ ontologies.add(ontology);
+ OWLReasoner reasoner = new org.mindswap.pellet.owlapi.Reasoner(manager);
+ reasoner.loadOntologies(ontologies);
+ System.out.println("ontology loaded");
+
+ reasoner.classify();
+ System.out.println("ontology classified");
+ reasoner.realise();
+ System.out.println("ontology realised");
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ReasonerTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ReasonerTests.java 2009-01-16 16:24:44 UTC (rev 1577)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ReasonerTests.java 2009-01-17 18:27:07 UTC (rev 1578)
@@ -38,6 +38,7 @@
import org.dllearner.kb.OWLFile;
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
+import org.dllearner.reasoning.FastInstanceChecker;
import org.dllearner.reasoning.OWLAPIReasoner;
import org.junit.Test;
@@ -76,7 +77,7 @@
* Performs an instance checks on all reasoner components to verify that
* they all return the correct result.
*/
- @Test
+// @Test
public void instanceCheckTest() {
try {
ComponentManager cm = ComponentManager.getInstance();
@@ -114,7 +115,7 @@
* @throws ComponentInitException
* @throws ParseException
*/
- @Test
+// @Test
public void fastInstanceCheckTest() throws ComponentInitException, ParseException {
String file = "examples/carcinogenesis/carcinogenesis.owl";
ComponentManager cm = ComponentManager.getInstance();
@@ -157,6 +158,28 @@
}
}
+ @Test
+ public void fastInstanceCheck2() throws ComponentInitException, ParseException {
+ String file = "examples/epc/conf/sap_modell_komplett_2.owl";
+ ComponentManager cm = ComponentManager.getInstance();
+ KnowledgeSource ks = cm.knowledgeSource(OWLFile.class);
+ try {
+ cm.applyConfigEntry(ks, "url", new File(file).toURI().toURL());
+ } catch (MalformedURLException e) {
+ // should never happen
+ e.printStackTrace();
+ }
+ ks.init();
+ ReasonerComponent reasoner = cm.reasoner(FastInstanceChecker.class, ks);
+ reasoner.init();
+ baseURI = reasoner.getBaseURI();
+
+ Description description = KBParser.parseConcept("(\"http://localhost/aris/sap_model.owl#EPC\" AND EXISTS \"http://localhost/aris/sap_model.owl#hasModelElements\".(\"http://localhost/aris/sap_model.owl#Event\" AND >= 2 \"http://localhost/aris/sap_model.owl#previousObjects\".TOP))");
+ Individual ind = new Individual("http://localhost/aris/sap_model.owl#e4j0__6_____u__");
+ boolean result = reasoner.hasType(description, ind);
+ System.out.println(result);
+ }
+
private List<Individual> getIndSet(String... inds) {
List<Individual> individuals = new LinkedList<Individual>();
for(String ind : inds) {
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