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[DL-Learner SVN] SF.net SVN: dl-learner:[3603] trunk/components-core/src/main/java/org/ dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
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From: <lor...@us...> - 2012-03-01 09:32:12
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Revision: 3603
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3603&view=rev
Author: lorenz_b
Date: 2012-03-01 09:32:01 +0000 (Thu, 01 Mar 2012)
Log Message:
-----------
Added some optimization to use local debugging if all justifications for each entity are found, so no reasoner call would be needed to check if there are still some unsatisfiable entities.
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 2012-03-01 02:50:14 UTC (rev 3602)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-03-01 09:32:01 UTC (rev 3603)
@@ -106,6 +106,7 @@
private Set<OWLTransitiveObjectPropertyAxiom> removedTransitiveAxioms;
private Set<OWLObjectProperty> unsatObjectProperties;
+ private Set<OWLClass> unsatClasses;
//whether to debug classes and properties in parallel
private boolean computeParallel = false;
@@ -196,7 +197,7 @@
logger.info("Computing root/derived unsatisfiable classes...");
long startTime = System.currentTimeMillis();
StructureBasedRootClassFinder rootFinder = new StructureBasedRootClassFinder(reasoner, this);
- Set<OWLClass> unsatClasses = rootFinder.getRootUnsatisfiableClasses();
+ unsatClasses = rootFinder.getRootUnsatisfiableClasses();
Set<OWLClass> derivedUnsatClasses = rootFinder.getDerivedUnsatisfiableClasses();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
@@ -347,8 +348,9 @@
System.gc();
}
}
-
save("log/" + fileName + "_coherent.owl");
+ logger.info("Finished. \n Coherent ontology contains " + ontology.getLogicalAxiomCount() + " logical axioms." +
+ "Removed axioms: " + diffOntology.getLogicalAxiomCount());
return ontology;
}
@@ -361,7 +363,7 @@
//compute the unsatisfiable classes
logger.info("Computing unsatisfiable classes...");
long startTime = System.currentTimeMillis();
- Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
logger.info("Detected " + unsatClasses.size() + " unsatisfiable classes.");
@@ -384,7 +386,7 @@
cnt += unsatObjectProperties.size();
}
- while(cnt > 0){
+ while(!runLocalDebugging() && cnt > 0){
//we remove the most appropriate axiom from the ontology
removeAppropriateAxiom();
@@ -399,8 +401,8 @@
logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
//save
- if((!computeParallel && (cnt-unsatClasses.size()>= 5))
- || (computeParallel && (cnt-unsatClasses.size()+unsatObjectProperties.size())>=5)){
+ if((!computeParallel && (cnt-unsatClasses.size()>= 10))
+ || (computeParallel && (cnt-unsatClasses.size()+unsatObjectProperties.size())>=10)){
cnt = unsatClasses.size();
save("log/" + fileName + "_" + unsatClasses.size() + "cls" + unsatObjectProperties.size() + "prop.owl");
if(computeParallel){
@@ -425,6 +427,8 @@
}
entity2Explanations.clear();
entity2ModuleMap.clear();
+ entitiesWithLessExplanations.clear();
+ entity2ExpGen.clear();
save("log/" + fileName + "_" + unsatClasses.size() + "cls" + unsatObjectProperties.size() + "prop.owl");
@@ -434,11 +438,11 @@
int unsatPropCnt = unsatObjectProperties.size();
logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
- logger.info("Recomputing explanations...");
+ logger.info("Computing explanations...");
startTime = System.currentTimeMillis();
computeExplanations(unsatObjectProperties);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- while(unsatPropCnt > 0){
+ while(!runLocalDebugging() && unsatPropCnt > 0){
//we remove the most appropriate axiom from the ontology
removeAppropriateAxiom();
@@ -447,7 +451,7 @@
logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
//save
- if((unsatPropCnt - unsatObjectProperties.size()) >= 5){
+ if((unsatPropCnt - unsatObjectProperties.size()) >= 10){
save("log/" + fileName + "_" + unsatClasses.size() + "cls" + unsatPropCnt + "prop.owl");
unsatPropCnt = unsatObjectProperties.size();
}
@@ -464,12 +468,52 @@
System.gc();
}
}
-
save("log/" + fileName + "_coherent.owl");
+ logger.info("Finished. \n Coherent ontology contains " + ontology.getLogicalAxiomCount() + " logical axioms." +
+ "Removed axioms: " + diffOntology.getLogicalAxiomCount());
return ontology;
}
+ /*
+ * check here if all explanations are found, i.e. for each entity the number of justifications is lower than the limit which was set
+ */
+ private boolean allExplanationsFound(){
+ boolean allExplanationsFound = false;
+ if(computeParallel){
+ allExplanationsFound = entitiesWithLessExplanations.size() == (unsatClasses.size() + unsatObjectProperties.size());
+ } else {
+ allExplanationsFound = entitiesWithLessExplanations.size() == unsatClasses.size();
+ }
+ return allExplanationsFound;
+ }
+
+ private boolean runLocalDebugging(){
+ if(allExplanationsFound()){
+ //add all explanations into one set
+ Set<Set<OWLAxiom>> explanations = new HashSet<Set<OWLAxiom>>();
+ for(Entry<OWLEntity, Set<Set<OWLAxiom>>> e: entity2Explanations.entrySet()){
+ explanations.addAll(e.getValue());
+ }
+ //get the frequency for each axiom
+ Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
+ //get a sorted list of entries with the highest axiom count first
+ List<Entry<OWLAxiom, Integer>> candidates = sort(axiom2CountMap);
+ //remove axioms until no further explanation exists
+ while(!explanations.isEmpty()){
+ removeAppropriateAxiomLocal(explanations, candidates);
+ }
+ if(computeParallel){
+ unsatClasses.clear();
+ unsatObjectProperties.clear();
+ } else {
+ unsatClasses.clear();
+ }
+ return true;
+ }
+ return false;
+ }
+
private OWLOntology computeCoherentOntology2(OWLOntology ontology) {
//compute the unsatisfiable classes
logger.info("Computing unsatisfiable classes...");
@@ -562,6 +606,40 @@
}
}
+ private void removeAppropriateAxiomLocal(Set<Set<OWLAxiom>> explanations, List<Entry<OWLAxiom, Integer>> candidates){
+ logger.info("Searching for appropriate axiom to remove...");
+ logger.info("Candidates: " + candidates.size());
+ if(candidates.size() >= 2){
+ logger.info("First: " + candidates.get(0) + "(" + getConfidence(candidates.get(0).getKey()) + ")");
+ logger.info("Second: " + candidates.get(1) + "(" + getConfidence(candidates.get(1).getKey()) + ")");
+ }
+
+ //we remove the most frequent axiom from the ontology which is not contained in the original DBpedia ontology
+ for(Iterator<Entry<OWLAxiom, Integer>> iter = candidates.iterator(); iter.hasNext();){
+ OWLAxiom axiom = iter.next().getKey();
+ if(!dbpediaOntology.containsAxiomIgnoreAnnotations(axiom)){
+ iter.remove();
+ logger.info("Removing axiom " + axiom + ".");
+ manager.removeAxiom(incoherentOntology, axiom);
+ //remove the axiom also from the loaded ontology
+ OWLAxiom originalAnnotatedAxiom = ontology.getAxiomsIgnoreAnnotations(axiom).iterator().next();
+ ontology.getOWLOntologyManager().removeAxiom(ontology, originalAnnotatedAxiom);
+ //add the removed annotated axiom to the diff ontology
+ manager.addAxiom(diffOntology, originalAnnotatedAxiom);
+ //remove each explanation which contains the axiom
+ for (Iterator<Set<OWLAxiom>> iterator = explanations.iterator(); iterator.hasNext();) {
+ Set<OWLAxiom> explanation = iterator.next();
+ if(explanation.contains(axiom)){
+ iterator.remove();
+ }
+ }
+ return;
+ } else {
+ iter.remove();
+ }
+ }
+ }
+
private void save(String fileName){
logger.info("Writing to disk...");
long startTime = System.currentTimeMillis();
@@ -951,7 +1029,6 @@
OWLOntology coherentOntology = extractor.getCoherentOntology(schema, preferRoots);
- System.out.println("Coherent ontology contains " + coherentOntology.getLogicalAxiomCount() + " logical axioms.");
}
class HermiTReasonerFactory implements OWLReasonerFactory{
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