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[DL-Learner SVN] SF.net SVN: dl-learner:[3590] trunk/components-core/src/main/java/org/ dllearner/utilities
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From: <lor...@us...> - 2012-02-27 13:00:41
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Revision: 3590
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3590&view=rev
Author: lorenz_b
Date: 2012-02-27 13:00:31 +0000 (Mon, 27 Feb 2012)
Log Message:
-----------
Integrated parallel computation of explanations.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
trunk/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-26 10:02:29 UTC (rev 3589)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-27 13:00:31 UTC (rev 3590)
@@ -12,15 +12,19 @@
import java.net.URL;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
-import java.util.Map.Entry;
-import java.util.Set;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
import java.util.logging.Level;
import java.util.logging.Logger;
@@ -47,7 +51,6 @@
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.RemoveAxiom;
-import org.semanticweb.owlapi.owllink.builtin.requests.LoadOntologies;
import org.semanticweb.owlapi.reasoner.IllegalConfigurationException;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
@@ -61,7 +64,7 @@
import com.clarkparsia.owlapi.explanation.HSTExplanationGenerator;
import com.clarkparsia.owlapi.explanation.PelletExplanation;
import com.clarkparsia.owlapiv3.OntologyUtils;
-import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
public class JustificationBasedCoherentOntologyExtractor implements CoherentOntologyExtractor{
@@ -82,6 +85,7 @@
private Map<OWLEntity, OWLOntology> entity2ModuleMap = new HashMap<OWLEntity, OWLOntology>();
private Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
+ private Map<OWLEntity, PelletExplanation> entity2ExpGen = new HashMap<OWLEntity, PelletExplanation>();
private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
MessageDigest md5;
@@ -177,7 +181,7 @@
//compute the unsatisfiable classes
logger.info("Computing root/derived unsatisfiable classes...");
long startTime = System.currentTimeMillis();
- StructureBasedRootClassFinder rootFinder = new StructureBasedRootClassFinder(reasoner);
+ StructureBasedRootClassFinder rootFinder = new StructureBasedRootClassFinder(reasoner, this);
Set<OWLClass> unsatClasses = rootFinder.getRootUnsatisfiableClasses();
Set<OWLClass> derivedUnsatClasses = rootFinder.getDerivedUnsatisfiableClasses();
@@ -212,7 +216,7 @@
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
- entity2Explanations.putAll(getInitialExplanations(unsatClasses));
+ computeExplanations(unsatClasses);
if(computeParallel){
entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
}
@@ -274,9 +278,9 @@
//recompute explanations if necessary
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
- refillExplanations(unsatClasses, entity2Explanations);
+ computeExplanations(unsatClasses);
if(computeParallel){
- refillExplanations(unsatObjectProperties, entity2Explanations);
+ computeExplanations(unsatObjectProperties);
}
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
@@ -290,6 +294,11 @@
logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
entity2ModuleMap.putAll(extractModules(unsatObjectProperties));
+
+ logger.info("Recomputing explanations...");
+ startTime = System.currentTimeMillis();
+ computeExplanations(unsatObjectProperties);
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatObjectProperties.isEmpty()){
//we remove the most appropriate axiom from the ontology
removeAppropriateAxiom();
@@ -313,7 +322,7 @@
//recompute explanations if necessary
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
- refillExplanations(unsatObjectProperties, entity2Explanations);
+ computeExplanations(unsatObjectProperties);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
System.gc();
@@ -400,6 +409,74 @@
return getOntologyWithAnnotations(incoherentOntology);
}
+ private OWLOntology computeCoherentOntology2(OWLOntology ontology) {
+ //compute the unsatisfiable classes
+ logger.info("Computing unsatisfiable classes...");
+ long startTime = System.currentTimeMillis();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ int cnt = unsatClasses.size();
+ logger.info("Detected " + cnt + " unsatisfiable classes.");
+
+ //if the ontology is not incoherent we return it here
+ if(unsatClasses.isEmpty()){
+ return incoherentOntology;
+ }
+
+ //compute initial explanations for each unsatisfiable class
+ logger.info("Computing initial explanations...");
+ startTime = System.currentTimeMillis();
+ PelletExplanation expGen = new PelletExplanation(reasoner.getReasoner());
+ Set<Set<OWLAxiom>> explanations;
+ for(OWLClass unsatCls : unsatClasses){
+ explanations = expGen.getUnsatisfiableExplanations(unsatCls, numberOfJustifications);
+ logger.info(unsatCls);
+ entity2Explanations.put(unsatCls, explanations);
+ }
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+
+ while(!unsatClasses.isEmpty() && !unsatObjectProperties.isEmpty()){
+ //we remove the most appropriate axiom from the ontology
+ removeAppropriateAxiom();
+
+ //recompute the unsatisfiable classes
+ logger.info("Reclassifying...");
+ startTime = System.currentTimeMillis();
+ reasoner.classify();
+ unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ logger.info("Remaining unsatisfiable classes: " + unsatClasses.size());
+
+ //save
+ if(cnt - unsatClasses.size() >= 1){
+ cnt = unsatClasses.size();
+ save("log/" + fileName + "_" + cnt + "cls" + ".owl");
+ }
+
+ //recompute explanations if necessary
+ logger.info("Recomputing explanations...");
+ startTime = System.currentTimeMillis();
+ for(OWLClass unsatCls : unsatClasses){
+ if(entity2Explanations.get(unsatCls).size() < numberOfJustifications){
+ explanations = expGen.getUnsatisfiableExplanations(unsatCls, numberOfJustifications);
+ entity2Explanations.put(unsatCls, explanations);
+ }
+ }
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+
+ }
+ try {
+ incoherentOntology.getOWLOntologyManager().saveOntology(getOntologyWithAnnotations(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 removeAppropriateAxiom(){
//get frequency for each axiom
Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
@@ -496,16 +573,40 @@
return axiom2CountMap;
}
+ private void computeExplanations(Set<? extends OWLEntity> unsatEntities){
+
+ ExecutorService executor = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
+ List<Future<Void>> list = new ArrayList<Future<Void>>();
+
+ for(final OWLEntity unsatEntity : unsatEntities){
+ Set<Set<OWLAxiom>> precomputedExplanations = entity2Explanations.get(unsatEntity);
+ if(precomputedExplanations == null || precomputedExplanations.size() < numberOfJustifications){
+ executor.execute(new Runnable(){
+
+ @Override
+ public void run() {
+ Set<Set<OWLAxiom>> explanations = computeExplanations(unsatEntity);
+ entity2Explanations.put(unsatEntity, explanations);
+ }
+
+ });
+ }
+ }
+
+ executor.shutdown();
+ while (!executor.isTerminated()) {
+
+ }
+
+ }
+
+
private Map<OWLEntity, Set<Set<OWLAxiom>>> getInitialExplanations(Set<? extends OWLEntity> unsatEntities){
Map<OWLEntity, Set<Set<OWLAxiom>>> cls2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
+ Set<Set<OWLAxiom>> explanations;
for(OWLEntity unsatEntity : unsatEntities){
- Set<Set<OWLAxiom>> explanations = null;
- if(unsatEntity instanceof OWLClass){
- explanations = computeExplanations((OWLClass) unsatEntity);
- } else if(unsatEntity instanceof OWLObjectProperty){
- explanations = computeExplanations((OWLObjectProperty) unsatEntity);
- }
+ explanations = computeExplanations(unsatEntity);
cls2Explanations.put(unsatEntity, explanations);
}
@@ -539,17 +640,12 @@
}
private Set<Set<OWLAxiom>> computeExplanations(OWLEntity unsatEntity){
- PelletExplanation expGen = new PelletExplanation(getModule(unsatEntity));
- if(unsatEntity instanceof OWLClass){
- return expGen.getUnsatisfiableExplanations((OWLClass) unsatEntity, numberOfJustifications);
- } else if(unsatEntity instanceof OWLObjectProperty){
- return expGen.getUnsatisfiableExplanations(factory.getOWLObjectExactCardinality(1, (OWLObjectProperty)unsatEntity), numberOfJustifications);
- }
- return null;
+ logger.info(unsatEntity);
+ return computeExplanations(unsatEntity, numberOfJustifications);
}
private Set<Set<OWLAxiom>> computeExplanations(OWLEntity unsatEntity, int limit){
- PelletExplanation expGen = new PelletExplanation(getModule(unsatEntity));
+ PelletExplanation expGen = getExplanationGenerator(unsatEntity);
if(unsatEntity instanceof OWLClass){
return expGen.getUnsatisfiableExplanations((OWLClass) unsatEntity, limit);
} else if(unsatEntity instanceof OWLObjectProperty){
@@ -558,6 +654,14 @@
return null;
}
+ private PelletExplanation getExplanationGenerator(OWLEntity entity){
+ PelletExplanation expGen = entity2ExpGen.get(entity);
+ if(expGen == null){
+ expGen = new PelletExplanation(PelletReasonerFactory.getInstance().createNonBufferingReasoner(getModule(entity)));
+ entity2ExpGen.put(entity, expGen);
+ }
+ return expGen;
+ }
private Set<Set<OWLAxiom>> computeExplanationsBlackBox(OWLClass unsatClass, int limit){
BlackBoxExplanation singleExpGen = new BlackBoxExplanation(incoherentOntology, new HermiTReasonerFactory(), hermitReasoner);
@@ -600,7 +704,7 @@
// return module;
// }
- private OWLOntology getModule(OWLEntity entity){
+ public OWLOntology getModule(OWLEntity entity){
OWLOntology module = entity2ModuleMap.get(entity);
new File("log").mkdir();
if(module == null){
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java 2012-02-26 10:02:29 UTC (rev 3589)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java 2012-02-27 13:00:31 UTC (rev 3590)
@@ -8,6 +8,7 @@
import java.util.Map;
import java.util.Set;
+import org.apache.commons.httpclient.methods.GetMethod;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.AddAxiom;
import org.semanticweb.owlapi.model.AxiomType;
@@ -76,6 +77,8 @@
private Map<OWLClass, Set<OWLClass>> child2Parents;
private Map<OWLClass, Set<OWLClass>> parent2Children;
+ private JustificationBasedCoherentOntologyExtractor extractor;
+
// private Map<OWLClass, Map<OWLAxiom, Set<OWLClass>>> class2Dependency;
public StructureBasedRootClassFinder(OWLReasoner reasoner){
@@ -105,6 +108,33 @@
}
+ public StructureBasedRootClassFinder(OWLReasoner reasoner, JustificationBasedCoherentOntologyExtractor extractor){
+ this.extractor = extractor;
+ this.manager = OWLManager.createOWLOntologyManager();
+ this.reasoner = reasoner;
+ this.reasonerFactory = new PelletReasonerFactory();
+ try {
+ this.ontology = manager.createOntology(IRI.create("http://all"), reasoner.getRootOntology().getImportsClosure());
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyChangeException e) {
+ e.printStackTrace();
+ }
+ rootClasses = new HashSet<OWLClass>();
+ derivedClasses = new HashSet<OWLClass>();
+ unsatClasses = new HashSet<OWLClass>();
+
+ depend2Classes = new HashSet<OWLClass>();
+ depth2UniversalRestrictionPropertyMap = new HashMap<Integer, Set<OWLObjectAllValuesFrom>>();
+ depth2ExistsRestrictionPropertyMap = new HashMap<Integer, Set<OWLObjectPropertyExpression>>();
+
+ child2Parents = new HashMap<OWLClass, Set<OWLClass>>();
+ parent2Children = new HashMap<OWLClass, Set<OWLClass>>();
+
+// class2Dependency = new HashMap<OWLClass, Map<OWLAxiom, Set<OWLClass>>>();
+
+ }
+
public void computeRootDerivedClasses(){
unsatClasses.clear();
rootClasses.clear();
@@ -180,8 +210,7 @@
OWLReasoner checker = null;
for (OWLClass root : new ArrayList<OWLClass>(roots)) {
- checker = reasonerFactory.createNonBufferingReasoner(manager.createOntology(ModularityUtils.extractModule
- (ontology, root.getSignature(), ModuleType.TOP_OF_BOT)));
+ checker = reasonerFactory.createNonBufferingReasoner(extractor.getModule(root));
if (!potentialRoots.contains(root) && checker.isSatisfiable(root)) {
rootClasses.remove(root);
}
@@ -195,10 +224,9 @@
}
} catch (OWLOntologyChangeException e) {
e.printStackTrace();
- } catch (OWLOntologyCreationException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
+ }
+
+
}
private void reset(){
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