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[DL-Learner SVN] SF.net SVN: dl-learner:[1567] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2009-01-05 12:35:32
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Revision: 1567
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1567&view=rev
Author: jenslehmann
Date: 2009-01-05 12:35:24 +0000 (Mon, 05 Jan 2009)
Log Message:
-----------
EL operator benchmark started and a number of smaller changes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/owl/KB.java
trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java
trunk/src/dl-learner/org/dllearner/kb/KBFile.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java
trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java
trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/core/owl/ContextDescription.java
trunk/src/dl-learner/org/dllearner/scripts/evaluation/
trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java
trunk/src/dl-learner/org/dllearner/scripts/evaluation/package-info.java
trunk/src/dl-learner/org/dllearner/scripts/package-info.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/scripts/package.html
Added: trunk/src/dl-learner/org/dllearner/core/owl/ContextDescription.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ContextDescription.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ContextDescription.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -0,0 +1,57 @@
+/**
+ * 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 class description in its context, i.e. including a parent link (if any).
+ * For instance, there is only one description owl:Thing, but it can occur
+ * nested within different descriptions like "createdBy SOME owl:Thing".
+ * Depending on what you want to do, you either need a Description or a
+ * ContextDescription.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class ContextDescription {
+
+ private Description description;
+
+ private Description parent;
+
+ public ContextDescription(Description description, Description parent) {
+ this.description = description;
+ this.parent = parent;
+ }
+
+ /**
+ * @return the description
+ */
+ public Description getDescription() {
+ return description;
+ }
+
+ /**
+ * @return the parent
+ */
+ public Description getParent() {
+ return parent;
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/KB.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/KB.java 2008-12-22 13:50:14 UTC (rev 1566)
+++ trunk/src/dl-learner/org/dllearner/core/owl/KB.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -1,11 +1,22 @@
package org.dllearner.core.owl;
+import java.io.File;
+import java.net.URI;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
+import org.dllearner.utilities.owl.OWLAPIAxiomConvertVisitor;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyCreationException;
+import org.semanticweb.owl.model.OWLOntologyManager;
+import org.semanticweb.owl.model.OWLOntologyStorageException;
+import org.semanticweb.owl.model.UnknownOWLOntologyException;
+import org.semanticweb.owl.util.SimpleURIMapper;
+
public class KB implements KBElement {
// private Set<Axiom> axioms = new HashSet<Axiom>();
@@ -273,4 +284,24 @@
return axioms;
}
+ public void export(File file, org.dllearner.core.OntologyFormat format){
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ URI ontologyURI = URI.create("http://example.com");
+ URI physicalURI = file.toURI();
+ SimpleURIMapper mapper = new SimpleURIMapper(ontologyURI, physicalURI);
+ manager.addURIMapper(mapper);
+ OWLOntology ontology;
+ try {
+ ontology = manager.createOntology(ontologyURI);
+ // OWLAPIReasoner.fillOWLAPIOntology(manager,ontology,kb);
+ OWLAPIAxiomConvertVisitor.fillOWLOntology(manager, ontology, this);
+ manager.saveOntology(ontology);
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (UnknownOWLOntologyException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ }
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java 2008-12-22 13:50:14 UTC (rev 1566)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Nothing.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -22,7 +22,7 @@
import java.util.Map;
/**
- * Implementation of owl:nothing/BOTTOM.
+ * Implementation of owl:Nothing/BOTTOM.
*
* @author Jens Lehmann
*
Modified: trunk/src/dl-learner/org/dllearner/kb/KBFile.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-12-22 13:50:14 UTC (rev 1566)
+++ trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -38,14 +38,6 @@
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
import org.dllearner.reasoning.DIGConverter;
-import org.dllearner.utilities.owl.OWLAPIAxiomConvertVisitor;
-import org.semanticweb.owl.apibinding.OWLManager;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLOntologyCreationException;
-import org.semanticweb.owl.model.OWLOntologyManager;
-import org.semanticweb.owl.model.OWLOntologyStorageException;
-import org.semanticweb.owl.model.UnknownOWLOntologyException;
-import org.semanticweb.owl.util.SimpleURIMapper;
/**
* KB files are an internal convenience format used in DL-Learner. Their
@@ -158,24 +150,25 @@
@Override
public void export(File file, org.dllearner.core.OntologyFormat format){
- OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
- URI ontologyURI = URI.create("http://example.com");
- URI physicalURI = file.toURI();
- SimpleURIMapper mapper = new SimpleURIMapper(ontologyURI, physicalURI);
- manager.addURIMapper(mapper);
- OWLOntology ontology;
- try {
- ontology = manager.createOntology(ontologyURI);
- // OWLAPIReasoner.fillOWLAPIOntology(manager,ontology,kb);
- OWLAPIAxiomConvertVisitor.fillOWLOntology(manager, ontology, kb);
- manager.saveOntology(ontology);
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
- } catch (UnknownOWLOntologyException e) {
- e.printStackTrace();
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- }
+ kb.export(file, format);
+// OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+// URI ontologyURI = URI.create("http://example.com");
+// URI physicalURI = file.toURI();
+// SimpleURIMapper mapper = new SimpleURIMapper(ontologyURI, physicalURI);
+// manager.addURIMapper(mapper);
+// OWLOntology ontology;
+// try {
+// ontology = manager.createOntology(ontologyURI);
+// // OWLAPIReasoner.fillOWLAPIOntology(manager,ontology,kb);
+// OWLAPIAxiomConvertVisitor.fillOWLOntology(manager, ontology, kb);
+// manager.saveOntology(ontology);
+// } catch (OWLOntologyCreationException e) {
+// e.printStackTrace();
+// } catch (UnknownOWLOntologyException e) {
+// e.printStackTrace();
+// } catch (OWLOntologyStorageException e) {
+// e.printStackTrace();
+// }
}
public URL getURL() {
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-12-22 13:50:14 UTC (rev 1566)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -71,7 +71,6 @@
import org.dllearner.parser.ParseException;
import org.dllearner.utilities.Helper;
import org.dllearner.utilities.owl.ConceptTransformation;
-import org.semanticweb.owl.inference.OWLReasonerException;
/**
* Reasoner for fast instance checks. It works by completely dematerialising the
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java 2008-12-22 13:50:14 UTC (rev 1566)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -393,7 +393,6 @@
List<ELDescriptionEdge> piVEdges = new LinkedList<ELDescriptionEdge>();
ELDescriptionNode tmp = v;
while(!tmp.isRoot()) {
-// System.out.println("blub");
piVEdges.add(tmp.getParentEdge());
tmp = tmp.getParent();
}
@@ -446,9 +445,14 @@
i.addChild(opDomains.get(edge.getLabel()));
}
+ int size = i.getChildren().size();
+ // size = 0 means we have the top concept
+ if(size == 0) {
+ return Thing.instance;
+ }
// if the intersection has just one element, we return
// the element itself instead
- if(i.getChildren().size() == 1) {
+ else if(size == 1) {
return i.getChild(0);
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java 2008-12-22 13:50:14 UTC (rev 1566)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -176,6 +176,7 @@
public boolean isDisjoint(Description d1, Description d2) {
// System.out.println("d1: " + d1);
// System.out.println("d2: " + d2);
+// System.out.println("cache: " + cachedDisjoints);
// check whether we have cached this query
Map<Description,Boolean> tmp = cachedDisjoints.get(d1);
Added: trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -0,0 +1,152 @@
+/**
+ * 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.scripts.evaluation;
+
+import java.io.File;
+import java.net.MalformedURLException;
+import java.util.ArrayList;
+import java.util.Random;
+import java.util.Set;
+
+import org.dllearner.algorithms.el.ELDescriptionTree;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.owl.Thing;
+import org.dllearner.kb.OWLFile;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.dllearner.refinementoperators.ELDown2;
+import org.dllearner.utilities.statistics.Stat;
+
+/**
+ * An evaluation of the EL refinement operator {@link ELDown2}. It creates
+ * a set of artificial ontologies with varying complexity and performs
+ * refinement steps on them.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class ELOperatorBenchmark {
+
+ private static Random rand = new Random(1);
+
+ public static void main(String[] args) throws MalformedURLException, ComponentInitException {
+ String example = "/home/jl/promotion/ontologien/galen2.owl";
+ testOntology(example);
+ System.exit(0);
+
+ /* TEST ON ARTIFICIAL ONTOLOGIES
+
+
+ // number of concepts and roles
+ int[] conceptCounts = new int[] { 5, 10 };
+ int[] roleCounts = new int[] { 5, 10};
+
+ // number of applications of operator
+ int opApplications = 10;
+
+ // statistics directory
+ String statDir = "/log/stat/el/";
+ String statFile = statDir + "stats.txt";
+ String gnuPlotApplicationTimeFile = statDir + "application.gp";
+ String gnuPlotRefinementTimeFile = statDir + "refinement.gp";
+ boolean writeOntologies = true;
+ String ontologyDir = "/log/stat/el/ontologies/";
+
+
+
+ for(int conceptCount : conceptCounts) {
+ for(int roleCount : roleCounts) {
+ // code for ontology creation
+ KB kb = new KB();
+
+ // create class hierarchy (concept 0 is owl:Thing)
+ for(int i=1; i<=conceptCount; i++) {
+ // create class
+ NamedClass nc = new NamedClass("a" + i);
+ // pick an existing class as super class
+ int j = (i == 0) ? 0 : rand.nextInt(i);
+ Description superClass;
+ if(j==0) {
+ superClass = Thing.instance;
+ } else {
+ superClass = new NamedClass("a" + j);
+ }
+ kb.addAxiom(new SubClassAxiom(nc, superClass));
+ // disjointness with siblings
+ }
+
+
+ // save ontology
+ File f = new File(ontologyDir + "c" + conceptCount + "r" + roleCount + ".owl");
+ kb.export(f, OntologyFormat.RDF_XML);
+
+
+ }
+ }
+ */
+// ELDown2 operator = new ELDown2();
+ }
+
+ private static void testOntology(String ont) throws MalformedURLException, ComponentInitException {
+ System.out.print("Reading in " + ont + " ... ");
+ ComponentManager cm = ComponentManager.getInstance();
+ // reading ontology into a reasoner
+ KnowledgeSource source = cm.knowledgeSource(OWLFile.class);
+ cm.applyConfigEntry(source, "url", new File(ont).toURI().toURL());
+ source.init();
+ ReasonerComponent reasoner = cm.reasoner(OWLAPIReasoner.class, source);
+ reasoner.init();
+ System.out.println("done.");
+ System.out.println();
+
+ int outerLoops = 10;
+ for(int loop = 0; loop < outerLoops; loop++) {
+
+ // application of operator and statistics recording
+ int nrOfApplications = 10;
+ ELDescriptionTree currTree = new ELDescriptionTree(reasoner, Thing.instance);
+ ELDown2 operator = new ELDown2(reasoner);
+ Stat runtime = new Stat();
+ Stat runtimePerRefinement = new Stat();
+
+ System.out.println("Testing operator (applying it " + nrOfApplications + " times):");
+ for(int i=0; i < nrOfApplications; i++) {
+ System.out.print("current concept: " + currTree.transformToDescription().toString(reasoner.getBaseURI(), reasoner.getPrefixes()));
+ // apply operator on current description
+ long start = System.nanoTime();
+ Set<ELDescriptionTree> refinements = operator.refine(currTree);
+ long time = System.nanoTime() - start;
+ runtime.addNumber(time/1000000d);
+ runtimePerRefinement.addNumber(time/1000000d/refinements.size());
+ System.out.println(" [has " + refinements.size() + " refinements]");
+ // pick a refinement randomly (which is kind of slow for a set, but
+ // this does not matter here)
+ int index = rand.nextInt(refinements.size());
+ currTree = new ArrayList<ELDescriptionTree>(refinements).get(index);
+ }
+ System.out.println("operator time: " + runtime.prettyPrint("ms"));
+ System.out.println("operator time per refinement: " + runtimePerRefinement.prettyPrint("ms"));
+ System.out.println();
+
+ }
+ }
+}
Added: trunk/src/dl-learner/org/dllearner/scripts/evaluation/package-info.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/evaluation/package-info.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/evaluation/package-info.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -0,0 +1,6 @@
+/**
+ * All scripts, which serve evaluation purposes, i.e. evaluation of
+ * learning algorithms, refinement operators, components etc. These
+ * are usually benchmarks testing accuracy, performance etc. of algorithms.
+ */
+package org.dllearner.scripts.evaluation;
\ No newline at end of file
Copied: trunk/src/dl-learner/org/dllearner/scripts/package-info.java (from rev 1566, trunk/src/dl-learner/org/dllearner/scripts/package.html)
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/package-info.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/package-info.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -0,0 +1,4 @@
+/**
+ * Runnable scripts, each for a different task or experiment.
+ */
+package org.dllearner.scripts;
\ No newline at end of file
Property changes on: trunk/src/dl-learner/org/dllearner/scripts/package-info.java
___________________________________________________________________
Added: svn:mergeinfo
+
Deleted: trunk/src/dl-learner/org/dllearner/scripts/package.html
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/package.html 2008-12-22 13:50:14 UTC (rev 1566)
+++ trunk/src/dl-learner/org/dllearner/scripts/package.html 2009-01-05 12:35:24 UTC (rev 1567)
@@ -1,7 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head></head>
-<body bgcolor="white">
-<p>Runnable scripts, each for a different task or experiment.</p>
-</body>
-</html>
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2008-12-22 13:50:14 UTC (rev 1566)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -19,7 +19,7 @@
*/
package org.dllearner.test.junit;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertTrue;
import java.io.File;
import java.util.Set;
@@ -30,7 +30,6 @@
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.owl.Description;
-import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
import org.dllearner.refinementoperators.ELDown2;
@@ -38,7 +37,6 @@
import org.dllearner.test.junit.TestOntologies.TestOntology;
import org.dllearner.utilities.Files;
import org.dllearner.utilities.Helper;
-import org.dllearner.utilities.JamonMonitorLogger;
import org.dllearner.utilities.owl.ConceptComparator;
import org.dllearner.utilities.owl.ConceptTransformation;
import org.dllearner.utilities.statistics.Stat;
Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java 2008-12-22 13:50:14 UTC (rev 1566)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java 2009-01-05 12:35:24 UTC (rev 1567)
@@ -24,7 +24,7 @@
/**
* Utility class for calculating the mean and standard deviation of a given set
- * of numbers.
+ * of numbers. The class also contains convenience methods for printing values.
*
* @author Jens Lehmann
*
@@ -144,4 +144,20 @@
return str;
}
+ /**
+ * Pretty prints the results under the assumption that the input
+ * values are time spans measured in nano seconds.
+ *
+ * @see System#nanoTime()
+ * @return A string summarising statistical values.
+ */
+// public String prettyPrintNanoSeconds() {
+// DecimalFormat df = new DecimalFormat();
+// String str = "av. " + df.format(getMean()) + unit;
+// str += " (deviation " + df.format(getStandardDeviation()) + unit + "; ";
+// str += "min " + df.format(getMin()) + unit + "; ";
+// str += "max " + df.format(getMax()) + unit + ")";
+// return str;
+// }
+
}
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