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[DL-Learner SVN] SF.net SVN: dl-learner:[3563] trunk/components-core/src/main/java/org/ dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
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From: <lor...@us...> - 2012-02-02 13:17:22
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Revision: 3563
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3563&view=rev
Author: lorenz_b
Date: 2012-02-02 13:17:12 +0000 (Thu, 02 Feb 2012)
Log Message:
-----------
Continued integration of debugging unsatisfiable object properties.
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 2012-02-01 14:31:26 UTC (rev 3562)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-02 13:17:12 UTC (rev 3563)
@@ -66,7 +66,6 @@
private OWLOntology ontology;
private OWLDataFactory factory;
- private Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
private Map<OWLEntity, OWLOntology> entity2ModuleMap = new HashMap<OWLEntity, OWLOntology>();
private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
@@ -96,8 +95,8 @@
this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
//only for debugging
- removedTransitiveAxioms = ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
- incoherentOntology.getOWLOntologyManager().removeAxioms(ontology, removedTransitiveAxioms);
+ removedTransitiveAxioms = incoherentOntology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
+ incoherentOntology.getOWLOntologyManager().removeAxioms(incoherentOntology, removedTransitiveAxioms);
manager = incoherentOntology.getOWLOntologyManager();
factory = manager.getOWLDataFactory();
@@ -107,8 +106,10 @@
reasoner.classify();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- //compute the unsatisfiable object properties
+ //compute the unsatisfiable object properties and their corresponding modules
unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Found unsatisfiable object properties: " + unsatObjectProperties.size());
+ entity2ModuleMap.putAll(extractModules(unsatObjectProperties));
//start main process, either preferring root classes or not
if(preferRoots){
@@ -147,20 +148,22 @@
return incoherentOntology;
}
//compute the logical modules for each unsatisfiable class
- logger.info("Computing module for each unsatisfiable class...");
+ logger.info("Computing module for each unsatisfiable entity...");
startTime = System.currentTimeMillis();
- cls2ModuleMap = extractModules(unsatClasses);
+ entity2ModuleMap.putAll(extractModules(unsatClasses));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
- Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = getInitialExplanationsForUnsatClasses(unsatClasses);
+ Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
+ entity2Explanations.putAll(getInitialExplanations(unsatClasses));
+ entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
//get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(cls2Explanations);
+ Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
//get a sorted list of entries with the highest axiom count first
List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
@@ -172,7 +175,7 @@
logger.info("Removing axiom " + toRemove + ".");
man.removeAxiom(incoherentOntology, toRemove);
man.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
- removeFromExplanations(cls2Explanations, toRemove);
+ removeFromExplanations(entity2Explanations, toRemove);
removeFromModules(toRemove);
//recompute the unsatisfiable classes
@@ -194,6 +197,10 @@
logger.info("Remaining unsatisfiable classes: " + (rootCnt + derivedCnt) + "(" + rootCnt + " roots).");
+ //recompute unsatisfiable object properties
+ unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+
//save
if(cnt - (rootCnt+derivedCnt) >= 10){
cnt = rootCnt + derivedCnt;
@@ -204,7 +211,8 @@
//recompute explanations if necessary
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
- refillExplanations(unsatClasses, cls2Explanations);
+ refillExplanations(unsatClasses, entity2Explanations);
+ refillExplanations(unsatObjectProperties, entity2Explanations);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
System.gc();
@@ -237,19 +245,20 @@
//compute the logical modules for each unsatisfiable class
logger.info("Computing module for each unsatisfiable class...");
startTime = System.currentTimeMillis();
- cls2ModuleMap = extractModules(unsatClasses);
+ entity2ModuleMap = extractModules(unsatClasses);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
- Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = getInitialExplanationsForUnsatClasses(unsatClasses);
- Map<OWLObjectProperty, Set<Set<OWLAxiom>>> prop2Explanations = getInitialExplanationsForUnsatObjectProperties(unsatObjectProperties);
+ Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
+ entity2Explanations.putAll(getInitialExplanations(unsatClasses));
+ entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
//get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(cls2Explanations);
+ Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
//get a sorted list of entries with the highest axiom count first
List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
@@ -261,7 +270,7 @@
logger.info("Removing axiom " + toRemove + ".");
manager.removeAxiom(incoherentOntology, toRemove);
manager.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
- removeFromExplanations(cls2Explanations, toRemove);
+ removeFromExplanations(entity2Explanations, toRemove);
removeFromModules(toRemove);
//recompute the unsatisfiable classes
@@ -272,6 +281,10 @@
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
logger.info("Remaining unsatisfiable classes: " + unsatClasses.size());
+ //recompute unsatisfiable object properties
+ unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+
//save
if(cnt - unsatClasses.size() >= 10){
cnt = unsatClasses.size();
@@ -281,7 +294,8 @@
//recompute explanations if necessary
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
- refillExplanations(unsatClasses, cls2Explanations);
+ refillExplanations(unsatClasses, entity2Explanations);
+ refillExplanations(unsatObjectProperties, entity2Explanations);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
System.gc();
@@ -310,6 +324,8 @@
}
private Set<OWLObjectProperty> getUnsatisfiableObjectProperties(IncrementalClassifier reasoner){
+ logger.info("Computing unsatisfiable object properties...");
+ long startTime = System.currentTimeMillis();
SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>();
OWLDataFactory f = OWLManager.createOWLOntologyManager().getOWLDataFactory();
for(OWLObjectProperty p : reasoner.getRootOntology().getObjectPropertiesInSignature()){
@@ -319,19 +335,20 @@
properties.add(p);
}
}
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return properties;
}
private void removeFromModules(OWLAxiom axiom){
OWLOntology module;
- for(Entry<OWLClass, OWLOntology> entry : cls2ModuleMap.entrySet()){
+ for(Entry<? extends OWLEntity, OWLOntology> entry : entity2ModuleMap.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()){
+ private void removeFromExplanations(Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations, OWLAxiom axiom){
+ for(Entry<OWLEntity, Set<Set<OWLAxiom>>> entry : entity2Explanations.entrySet()){
for (Iterator<Set<OWLAxiom>> iterator = entry.getValue().iterator(); iterator.hasNext();) {
Set<OWLAxiom> explanation = iterator.next();
if(explanation.contains(axiom)){
@@ -341,20 +358,20 @@
}
}
- private void refillExplanations(Set<OWLClass> unsatClasses, Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations){
- for(OWLClass unsatClass : unsatClasses){
- Set<Set<OWLAxiom>> precomputedExplanations = cls2Explanations.get(unsatClass);
+ private void refillExplanations(Set<? extends OWLEntity> unsatEntities, Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations){
+ for(OWLEntity unsatClass : unsatEntities){
+ Set<Set<OWLAxiom>> precomputedExplanations = entity2Explanations.get(unsatClass);
if(precomputedExplanations == null || precomputedExplanations.size() < numberOfJustifications){
Set<Set<OWLAxiom>> newExplanations = computeExplanations(unsatClass, numberOfJustifications);
- cls2Explanations.put(unsatClass, newExplanations);
+ entity2Explanations.put(unsatClass, newExplanations);
}
}
}
- private Map<OWLAxiom, Integer> getAxiomFrequency(Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations){
+ private Map<OWLAxiom, Integer> getAxiomFrequency(Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations){
Map<OWLAxiom, Integer> axiom2CountMap = new HashMap<OWLAxiom, Integer>();
- for(Entry<OWLClass, Set<Set<OWLAxiom>>> entry : cls2Explanations.entrySet()){
+ for(Entry<OWLEntity, Set<Set<OWLAxiom>>> entry : entity2Explanations.entrySet()){
for(Set<OWLAxiom> explanation : entry.getValue()){
for(OWLAxiom ax : explanation){
Integer cnt = axiom2CountMap.get(ax);
@@ -370,28 +387,22 @@
return axiom2CountMap;
}
- private Map<OWLClass, Set<Set<OWLAxiom>>> getInitialExplanationsForUnsatClasses(Set<OWLClass> unsatClasses){
- Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = new HashMap<OWLClass, Set<Set<OWLAxiom>>>();
+ private Map<OWLEntity, Set<Set<OWLAxiom>>> getInitialExplanations(Set<? extends OWLEntity> unsatEntities){
+ Map<OWLEntity, Set<Set<OWLAxiom>>> cls2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
- for(OWLClass unsatClass : unsatClasses){
- Set<Set<OWLAxiom>> explanations = computeExplanations(unsatClass);
- cls2Explanations.put(unsatClass, 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);
+ }
+ cls2Explanations.put(unsatEntity, explanations);
}
return cls2Explanations;
}
- private Map<OWLObjectProperty, Set<Set<OWLAxiom>>> getInitialExplanationsForUnsatObjectProperties(Set<OWLObjectProperty> unsatObjProperties){
- Map<OWLObjectProperty, Set<Set<OWLAxiom>>> prop2Explanations = new HashMap<OWLObjectProperty, Set<Set<OWLAxiom>>>();
-
- for(OWLObjectProperty unsatClass : unsatObjProperties){
- Set<Set<OWLAxiom>> explanations = computeExplanations(unsatClass);
- prop2Explanations.put(unsatClass, explanations);
- }
-
- return prop2Explanations;
- }
-
private OWLOntology getOntologyWithoutAnnotations(OWLOntology ontology){
try {
OWLOntologyManager man = ontology.getOWLOntologyManager();
@@ -418,20 +429,26 @@
return ontology;
}
- private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass){
- PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
- return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
+ 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;
}
- private Set<Set<OWLAxiom>> computeExplanations(OWLObjectProperty unsatProp){
- PelletExplanation expGen = new PelletExplanation(getModule(unsatProp));
- return expGen.getUnsatisfiableExplanations(factory.getOWLObjectExactCardinality(1, unsatProp), numberOfJustifications);
+ private Set<Set<OWLAxiom>> computeExplanations(OWLEntity unsatEntity, int limit){
+ PelletExplanation expGen = new PelletExplanation(getModule(unsatEntity));
+ if(unsatEntity instanceof OWLClass){
+ return expGen.getUnsatisfiableExplanations((OWLClass) unsatEntity, limit);
+ } else if(unsatEntity instanceof OWLObjectProperty){
+ return expGen.getUnsatisfiableExplanations(factory.getOWLObjectExactCardinality(1, (OWLObjectProperty)unsatEntity), limit);
+ }
+ return null;
}
- private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass, int limit){
- PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
- return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
- }
private Set<Set<OWLAxiom>> computeExplanationsBlackBox(OWLClass unsatClass, int limit){
BlackBoxExplanation singleExpGen = new BlackBoxExplanation(incoherentOntology, new HermiTReasonerFactory(), hermitReasoner);
@@ -446,33 +463,33 @@
// return expGen.getUnsatisfiableExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
// }
- private OWLOntology getModule(OWLClass cls){
- OWLOntology module = cls2ModuleMap.get(cls);
- new File("log").mkdir();
- if(module == null){
- md5.reset();
- md5.update((ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toString() + cls.toStringID()).getBytes());
- String hash = MD5.asHex(md5.digest());
- String filename = "log/" + hash + ".owl";
- File file = new File(filename);
- if(file.exists()){
- module = loadModule(file);
- } else {
- module = OntologyUtils.getOntologyFromAxioms(
- ModularityUtils.extractModule(incoherentOntology, Collections.singleton((OWLEntity)cls), ModuleType.TOP_OF_BOT));
- try {
- manager.saveOntology(module, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(filename)));
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
- }
-
- cls2ModuleMap.put(cls, module);
- }
- return module;
- }
+// private OWLOntology getModule(OWLClass cls){
+// OWLOntology module = cls2ModuleMap.get(cls);
+// new File("log").mkdir();
+// if(module == null){
+// md5.reset();
+// md5.update((ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toString() + cls.toStringID()).getBytes());
+// String hash = MD5.asHex(md5.digest());
+// String filename = "log/" + hash + ".owl";
+// File file = new File(filename);
+// if(file.exists()){
+// module = loadModule(file);
+// } else {
+// module = OntologyUtils.getOntologyFromAxioms(
+// ModularityUtils.extractModule(incoherentOntology, Collections.singleton((OWLEntity)cls), ModuleType.TOP_OF_BOT));
+// try {
+// manager.saveOntology(module, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(filename)));
+// } catch (OWLOntologyStorageException e) {
+// e.printStackTrace();
+// } catch (FileNotFoundException e) {
+// e.printStackTrace();
+// }
+// }
+//
+// cls2ModuleMap.put(cls, module);
+// }
+// return module;
+// }
private OWLOntology getModule(OWLEntity entity){
OWLOntology module = entity2ModuleMap.get(entity);
@@ -531,12 +548,16 @@
// return prop2ModuleMap;
// }
- private <T extends OWLEntity> Map<T, OWLOntology> extractModules(Set<T> entities){
- Map<T, OWLOntology> entity2ModuleMap = new HashMap<T, OWLOntology>();
- for(T entity : entities){
+ private Map<OWLEntity, OWLOntology> extractModules(Set<? extends OWLEntity> entities){
+ logger.info("Computing modules...");
+ long startTime = System.currentTimeMillis();
+ Map<OWLEntity, OWLOntology> entity2ModuleMap = new HashMap<OWLEntity, OWLOntology>();
+ for(OWLEntity entity : entities){
+ logger.info(" for " + entity.toStringID());
OWLOntology module = getModule(entity);
entity2ModuleMap.put(entity, module);
}
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return entity2ModuleMap;
}
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