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[DL-Learner SVN] SF.net SVN: dl-learner:[3972] trunk/scripts/src/main/java/org/dllearner/ scripts/pattern/OWLAxiomPatternUsageEvaluation.java
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From: <lor...@us...> - 2013-05-10 06:39:35
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Revision: 3972
http://sourceforge.net/p/dl-learner/code/3972
Author: lorenz_b
Date: 2013-05-10 06:39:31 +0000 (Fri, 10 May 2013)
Log Message:
-----------
Added filtering of trivial axioms in pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 15:57:17 UTC (rev 3971)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-10 06:39:31 UTC (rev 3972)
@@ -49,7 +49,6 @@
import org.dllearner.reasoning.SPARQLReasoner;
import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
-import org.semanticweb.elk.reasoner.saturation.classes.SuperClassExpression;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
import org.semanticweb.owlapi.io.ToStringRenderer;
@@ -121,7 +120,7 @@
private double threshold = 0.6;
private OWLAnnotationProperty confidenceProperty = df.getOWLAnnotationProperty(IRI.create("http://dl-learner.org/pattern/confidence"));
- private long maxFragmentExtractionTime = TimeUnit.SECONDS.toMillis(10);
+ private long maxFragmentExtractionTime = TimeUnit.SECONDS.toMillis(60);
private OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
private long maxExecutionTime = TimeUnit.SECONDS.toMillis(20);
private int queryLimit = 10000;
@@ -134,66 +133,6 @@
}
- public void run(SparqlEndpoint endpoint, OWLOntology ontology, File outputFile, int maxNrOfTestedClasses){
- ks = new SparqlEndpointKS(endpoint, cache);
- SPARQLReasoner reasoner = new SPARQLReasoner(ks, cache);
-
- //get the axiom patterns to evaluate
- List<OWLAxiom> patterns = getPatternsToEvaluate(ontology);
-
- //get all classes in KB
- Collection<NamedClass> classes = reasoner.getTypes(ns);
- List<NamedClass> classesList = new ArrayList<NamedClass>(classes);
- Collections.shuffle(classesList, new Random(123));
- classesList = classesList.subList(0, maxNrOfTestedClasses);
- classes = classesList;
-
- //for each pattern
- for (OWLAxiom pattern : patterns) {
- File file = new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations.ttl");
- if(!file.exists()){
- //if pattern is equivalent classes axiom, we need to get the subclass axiom where the named class is the subclass
- if(pattern.isOfType(AxiomType.EQUIVALENT_CLASSES)){
- Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)pattern).asOWLSubClassOfAxioms();
- for (OWLSubClassOfAxiom axiom : subClassOfAxioms) {
- if(!axiom.getSubClass().isAnonymous()){
- pattern = axiom;
- break;
- }
- }
- }
- if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
- logger.info("Processing " + pattern + "...");
- Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
- //for each class
- int i = 1;
- for (NamedClass cls : classes) {
- logger.info("Processing " + cls + "...");
-
- Map<OWLAxiom, Score> result = evaluateUsingFragmentExtraction(pattern, cls);
- axioms2Score.putAll(result);
-
- for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Score score = entry.getValue();
- if(score.getAccuracy() >= threshold){
- logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
- }
- }
-
- //wait some time to avoid flooding of endpoint
- try {
- Thread.sleep(waitingTime);
- } catch (InterruptedException e) {
- e.printStackTrace();
- }
-// if(i++ == 3) break;
- }
- save(pattern, axioms2Score, file);
- }
- }
- }
- }
public void runUsingFragmentExtraction(SparqlEndpoint endpoint, OWLOntology patternOntology, File outputFile, int maxNrOfTestedClasses){
ks = new SparqlEndpointKS(endpoint, cache);
@@ -210,6 +149,7 @@
Collections.shuffle(classesList, new Random(123));
classesList = classesList.subList(0, maxNrOfTestedClasses);
classes = classesList;
+// classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
//get the maximum modal depth in the pattern axioms
int maxModalDepth = maxModalDepth(patterns);
@@ -238,26 +178,18 @@
OWLOntology ontology = null;
if(!file.exists()){
logger.info("Applying pattern " + pattern + "...");
- // if pattern is equivalent classes axiom, we need to get the
- // subclass axiom where the named class is the subclass
- Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
+ Set<OWLAxiom> learnedAxioms = new HashSet<OWLAxiom>();
// for each class
for (NamedClass cls : classes) {
logger.info("...on class " + cls + "...");
Model fragment = class2Fragment.get(cls);
Map<OWLAxiom, Score> result = applyPattern(pattern,
df.getOWLClass(IRI.create(cls.getName())), fragment);
- axioms2Score.putAll(result);
-
- for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Score score = entry.getValue();
- if (score.getAccuracy() >= threshold) {
- logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
- }
- }
+ Set<OWLAxiom> annotatedAxioms = asAnnotatedAxioms(result);
+ filterOutTrivialAxioms(annotatedAxioms);
+ printAxioms(annotatedAxioms, threshold);
}
- ontology = save(pattern, axioms2Score, file);
+ ontology = save(pattern, learnedAxioms, file);
} else {
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
try {
@@ -282,8 +214,32 @@
}
}
+ private Set<OWLAxiom> asAnnotatedAxioms(Map<OWLAxiom, Score> axioms2Score){
+ Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
+ for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Score score = entry.getValue();
+ if(score.getAccuracy() >= threshold){
+ annotatedAxioms.add(axiom.getAnnotatedAxiom(Collections.singleton(df.getOWLAnnotation(confidenceProperty, df.getOWLLiteral(score.getAccuracy())))));
+
+ }
+ }
+ return annotatedAxioms;
+ }
+
+ private void printAxioms(Set<OWLAxiom> axioms, double threshold){
+ for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ OWLAxiom axiom = iter.next();
+ double accuracy = getAccuracy(axiom);
+ if (accuracy >= threshold) {
+ logger.info(axiom + "(" + format.format(accuracy) + ")");
+ }
+ }
+ }
+
private List<OWLAxiom> createSample(OWLOntology ontology){
Set<OWLAxiom> axioms = ontology.getAxioms();
+ filterOutTrivialAxioms(axioms);
for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
OWLAxiom axiom = iter.next();
double accuracy = getAccuracy(axiom);
@@ -300,49 +256,53 @@
}
if(remove){
iter.remove();
- } else {
- if(axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)){
- Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)axiom).asOWLSubClassOfAxioms();
- for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
- if(!subClassOfAxiom.getSubClass().isAnonymous()){
- axiom = subClassOfAxiom;
+ }
+ }
+ }
+ List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>(axioms);
+ Collections.shuffle(axiomList, new Random(123));
+ return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
+ }
+
+ private void filterOutTrivialAxioms(Set<OWLAxiom> axioms) {
+ for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ OWLAxiom axiom = iter.next();
+ if (axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom) axiom).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom subClassOfAxiom : subClassOfAxioms) {
+ if (!subClassOfAxiom.getSubClass().isAnonymous()) {
+ axiom = subClassOfAxiom;
+ break;
+ }
+ }
+ }
+ // check for some trivial axioms
+ if (axiom.isOfType(AxiomType.SUBCLASS_OF)) {
+ OWLClassExpression subClass = ((OWLSubClassOfAxiom) axiom).getSubClass();
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom) axiom).getSuperClass();
+ if (superClass.isOWLThing()) {
+ iter.remove();
+ } else if (subClass.equals(superClass)) {
+ iter.remove();
+ } else if (superClass instanceof OWLObjectIntersectionOf) {
+ List<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperandsAsList();
+
+ if (operands.size() == 1) {// how can this happen?
+ iter.remove();
+ } else if (operands.size() > ((OWLObjectIntersectionOf) superClass).getOperands().size()) {// duplicates
+ iter.remove();
+ } else {
+ for (OWLClassExpression op : operands) {
+ if (op.isOWLThing() || op.equals(subClass)) {
+ iter.remove();
break;
}
}
}
- //check for some trivial axioms
- if(axiom.isOfType(AxiomType.SUBCLASS_OF)){
- OWLClassExpression subClass = ((OWLSubClassOfAxiom)axiom).getSubClass();
- OWLClassExpression superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
- if(superClass.isOWLThing()){
- iter.remove();
- } else if(subClass.equals(superClass)){
- iter.remove();
- } else if(superClass instanceof OWLObjectIntersectionOf){
- List<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperandsAsList();
-
-
- if(operands.size() == 1){//how can this happen?
- iter.remove();
- } else if(operands.size() > ((OWLObjectIntersectionOf) superClass).getOperands().size()){//duplicates
- iter.remove();
- } else {
- for (OWLClassExpression op : operands) {
- if(op.isOWLThing() || op.equals(subClass)){
- iter.remove();
- break;
- }
- }
- }
- }
- }
}
-
}
+
}
- List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>(axioms);
- Collections.shuffle(axiomList, new Random(123));
- return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
}
private double getAccuracy(OWLAxiom axiom){
@@ -432,12 +392,13 @@
}
}
logger.info("...got " + fragment.size() + " triples.");
- class2Fragment.put(cls, fragment);
try {
fragment.write(new FileOutputStream(file), "TURTLE");
} catch (FileNotFoundException e) {
e.printStackTrace();
}
+ filterModel(fragment);
+ class2Fragment.put(cls, fragment);
}
return class2Fragment;
}
@@ -453,6 +414,8 @@
}
if(st.getPredicate().hasURI("http://xmlns.com/foaf/0.1/depiction") || st.getPredicate().hasURI("http://dbpedia.org/ontology/thumbnail")){
statements2Remove.add(st);
+ } else if(!st.getPredicate().equals(RDF.type) && !st.getPredicate().getURI().startsWith("http://dbpedia.org/ontology/")){
+ statements2Remove.add(st);
}
}
model.remove(statements2Remove);
@@ -672,6 +635,9 @@
} else if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
patternSubClass = ((OWLSubClassOfAxiom) pattern).getSubClass();
patternSuperClass = ((OWLSubClassOfAxiom) pattern).getSuperClass();
+ } else if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
+ patternSubClass = ((OWLSubClassOfAxiom) pattern).getSubClass();
+ patternSuperClass = ((OWLSubClassOfAxiom) pattern).getSuperClass();
} else {
logger.warn("Pattern " + pattern + " not supported yet.");
return axioms2Score;
@@ -722,6 +688,7 @@
int total = resources.size();
for (OWLAxiom axiom : instantiations.elementSet()) {
int frequency = instantiations.count(axiom);
+// System.out.println(axiom + ":" + frequency);
Score score = computeScore(total, Math.min(total, frequency));
axioms2Score.put(axiom, score);
}
@@ -825,19 +792,10 @@
return template.asQuery();
}
- private OWLOntology save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score, File file){
+ private OWLOntology save(OWLAxiom pattern, Set<OWLAxiom> learnedAxioms, File file){
try {
- Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
- for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Score score = entry.getValue();
- if(score.getAccuracy() >= threshold){
- annotatedAxioms.add(axiom.getAnnotatedAxiom(Collections.singleton(df.getOWLAnnotation(confidenceProperty, df.getOWLLiteral(score.getAccuracy())))));
-
- }
- }
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- OWLOntology ontology = man.createOntology(annotatedAxioms);
+ OWLOntology ontology = man.createOntology(learnedAxioms);
man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(file));
return ontology;
} catch (OWLOntologyCreationException e) {
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