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[DL-Learner SVN] SF.net SVN: dl-learner:[3512] trunk/components-core/src/main/java/org/ dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
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From: <lor...@us...> - 2011-12-21 10:15:23
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Revision: 3512
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3512&view=rev
Author: lorenz_b
Date: 2011-12-21 10:15:12 +0000 (Wed, 21 Dec 2011)
Log Message:
-----------
Extended script to firstly handle the root unsatisfiable classes.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2011-12-20 11:43:21 UTC (rev 3511)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2011-12-21 10:15:12 UTC (rev 3512)
@@ -1,6 +1,9 @@
package org.dllearner.utilities;
+import java.io.BufferedOutputStream;
import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
@@ -11,8 +14,10 @@
import java.util.logging.Level;
import java.util.logging.Logger;
+import org.aksw.mole.ore.rootderived.StructureBasedRootClassFinder;
import org.mindswap.pellet.RBox;
import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLEntity;
@@ -20,6 +25,7 @@
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.RemoveAxiom;
import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
@@ -31,14 +37,14 @@
public class JustificationBasedCoherentOntologyExtractor implements CoherentOntologyExtractor{
- private static final int NUMBER_OF_JUSTIFICATIONS = 2;
+ private static final int NUMBER_OF_JUSTIFICATIONS = 5;
// private PelletReasoner reasoner;
private IncrementalClassifier reasoner;
private OWLOntology incoherentOntology;
private OWLOntology ontology;
- private Map<OWLClass, OWLOntology> cls2ModuleMap;
+ private Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
static {PelletExplanation.setup();}
@@ -54,49 +60,134 @@
OWLOntologyManager man = incoherentOntology.getOWLOntologyManager();
// man.addOntologyChangeListener(reasoner);
+ StructureBasedRootClassFinder rootFinder = new StructureBasedRootClassFinder(reasoner);
+ rootFinder.computeRootDerivedClasses();
+ Set<OWLClass> unsatClasses = rootFinder.getRootUnsatisfiableClasses();//reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ int cnt = unsatClasses.size();
- Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
-
//if the ontology is not incoherent we return it here
if(unsatClasses.isEmpty()){
return incoherentOntology;
}
-
+ //compute the logical modules for each unsatisfiable class
cls2ModuleMap = extractModules(unsatClasses);
+
+ //compute initial explanations for each unsatisfiable class
+ Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = getInitialExplanationsForUnsatClasses(unsatClasses);
while(!unsatClasses.isEmpty()){
- //for each unsatisfiable class we compute n justifications here and count how often each axiom occurs globally
- Map<OWLAxiom, Integer> axiom2CountMap = new HashMap<OWLAxiom, Integer>();
- for(OWLClass unsatClass : unsatClasses){
- Set<Set<OWLAxiom>> explanations = computeExplanations(unsatClass);
- for(Set<OWLAxiom> explanation : explanations){
- for(OWLAxiom ax : explanation){
- Integer cnt = axiom2CountMap.get(ax);
- if(cnt == null){
- cnt = 0;
- }
- cnt = cnt + 1;
- axiom2CountMap.put(ax, cnt);
- }
- }
- }
+ //get frequency for each axiom
+ Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(cls2Explanations);
+
//get a sorted list of entries with the highest axiom count first
List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
for(Entry<OWLAxiom, Integer> entry : sortedEntries){
System.out.println(entry.getKey() + ":" + entry.getValue());
}
- //we remove the most occuring axiom
+ //we remove the most frequent axiom from the ontology
OWLAxiom toRemove = sortedEntries.get(0).getKey();
+ System.out.println("Removing axiom " + toRemove);
man.removeAxiom(incoherentOntology, toRemove);
man.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
+ removeFromExplanations(cls2Explanations, toRemove);
+ removeFromModules(toRemove);
+
+ //recompute the unsatisfiable classes
reasoner.classify();
- unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ rootFinder = new StructureBasedRootClassFinder(reasoner);
+ rootFinder.computeRootDerivedClasses();
+ unsatClasses = rootFinder.getRootUnsatisfiableClasses();//reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ System.out.println("Remaining unsatisfiable classes: " + unsatClasses.size());
+
+ //save
+ if(cnt - unsatClasses.size() >= 10){
+ OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
+ try {
+ toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_" + unsatClasses.size() + ".owl")));
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ cnt = unsatClasses.size();
+ }
+
+ //recompute explanations if necessary
+ refillExplanations(unsatClasses, cls2Explanations);
+
+ System.gc();
}
+ try {
+ incoherentOntology.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_coherent.owl")));
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
System.out.println(incoherentOntology.getLogicalAxiomCount());
return getOntologyWithAnnotations(incoherentOntology);
}
+ private void removeFromModules(OWLAxiom axiom){
+ OWLOntology module;
+ for(Entry<OWLClass, OWLOntology> entry : cls2ModuleMap.entrySet()){
+ module = entry.getValue();
+ module.getOWLOntologyManager().removeAxiom(module, axiom);
+ }
+ }
+
+ private void removeFromExplanations(Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations, OWLAxiom axiom){
+ for(Entry<OWLClass, Set<Set<OWLAxiom>>> entry : cls2Explanations.entrySet()){
+ for (Iterator<Set<OWLAxiom>> iterator = entry.getValue().iterator(); iterator.hasNext();) {
+ Set<OWLAxiom> explanation = iterator.next();
+ if(explanation.contains(axiom)){
+ iterator.remove();
+ }
+ }
+ }
+ }
+
+ private void refillExplanations(Set<OWLClass> unsatClasses, Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations){
+ for(OWLClass unsatClass : unsatClasses){
+ Set<Set<OWLAxiom>> precomputedExplanations = cls2Explanations.get(unsatClass);
+ if(precomputedExplanations == null || precomputedExplanations.size() < NUMBER_OF_JUSTIFICATIONS){
+ Set<Set<OWLAxiom>> newExplanations = computeExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
+ cls2Explanations.put(unsatClass, newExplanations);
+ }
+ }
+ }
+
+ private Map<OWLAxiom, Integer> getAxiomFrequency(Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations){
+ Map<OWLAxiom, Integer> axiom2CountMap = new HashMap<OWLAxiom, Integer>();
+
+ for(Entry<OWLClass, Set<Set<OWLAxiom>>> entry : cls2Explanations.entrySet()){
+ for(Set<OWLAxiom> explanation : entry.getValue()){
+ for(OWLAxiom ax : explanation){
+ Integer cnt = axiom2CountMap.get(ax);
+ if(cnt == null){
+ cnt = 0;
+ }
+ cnt = cnt + 1;
+ axiom2CountMap.put(ax, cnt);
+ }
+ }
+ }
+
+ return axiom2CountMap;
+ }
+
+ private Map<OWLClass, Set<Set<OWLAxiom>>> getInitialExplanationsForUnsatClasses(Set<OWLClass> unsatClasses){
+ Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = new HashMap<OWLClass, Set<Set<OWLAxiom>>>();
+
+ for(OWLClass unsatClass : unsatClasses){
+ Set<Set<OWLAxiom>> explanations = computeExplanations(unsatClass);
+ cls2Explanations.put(unsatClass, explanations);
+ }
+
+ return cls2Explanations;
+ }
+
private OWLOntology getOntologyWithoutAnnotations(OWLOntology ontology){
try {
OWLOntologyManager man = ontology.getOWLOntologyManager();
@@ -124,15 +215,29 @@
}
private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass){
- PelletExplanation expGen = new PelletExplanation(cls2ModuleMap.get(unsatClass));
+ PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
return expGen.getUnsatisfiableExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
}
+ private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass, int limit){
+ PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
+ return expGen.getUnsatisfiableExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
+ }
+
+ private OWLOntology getModule(OWLClass cls){
+ OWLOntology module = cls2ModuleMap.get(cls);
+ if(module == null){
+ module = OntologyUtils.getOntologyFromAxioms(
+ ModularityUtils.extractModule(incoherentOntology, Collections.singleton((OWLEntity)cls), ModuleType.TOP_OF_BOT));
+ cls2ModuleMap.put(cls, module);
+ }
+ return module;
+ }
+
private Map<OWLClass, OWLOntology> extractModules(Set<OWLClass> classes){
Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
for(OWLClass cls : classes){
- OWLOntology module = OntologyUtils.getOntologyFromAxioms(
- ModularityUtils.extractModule(incoherentOntology, Collections.singleton((OWLEntity)cls), ModuleType.TOP_OF_BOT));
+ OWLOntology module = getModule(cls);
cls2ModuleMap.put(cls, module);
}
return cls2ModuleMap;
@@ -144,6 +249,9 @@
// OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("../components-core/cohaerent.owl"));
// System.out.println(schema.getLogicalAxiomCount());
OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("/home/lorenz/arbeit/dbpedia_0.75_no_datapropaxioms.owl"));
+// System.out.println(schema.getLogicalAxiomCount());
+// OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("log/dbpedia_coherent.owl"));
+ System.out.println(schema.getLogicalAxiomCount());
JustificationBasedCoherentOntologyExtractor extractor = new JustificationBasedCoherentOntologyExtractor();
OWLOntology coherentOntology = extractor.getCoherentOntology(schema);System.out.println(coherentOntology.getLogicalAxiomCount());
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