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[DL-Learner SVN] SF.net SVN: dl-learner:[3966] trunk/scripts/src/main/java/org/dllearner/ scripts/pattern/OWLAxiomPatternUsageEvaluation.java
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From: <lor...@us...> - 2013-05-09 13:21:31
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Revision: 3966
http://sourceforge.net/p/dl-learner/code/3966
Author: lorenz_b
Date: 2013-05-09 13:21:27 +0000 (Thu, 09 May 2013)
Log Message:
-----------
Refactored 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 03:51:49 UTC (rev 3965)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-09 13:21:27 UTC (rev 3966)
@@ -6,6 +6,7 @@
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.SocketTimeoutException;
import java.net.URI;
@@ -17,6 +18,7 @@
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
@@ -47,11 +49,13 @@
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;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
@@ -59,7 +63,9 @@
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
+import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLObjectComplementOf;
+import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
@@ -71,11 +77,14 @@
import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+import com.google.common.base.Charsets;
+import com.google.common.base.Joiner;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
import com.google.common.hash.HashCode;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
+import com.google.common.io.Files;
import com.hp.hpl.jena.query.ParameterizedSparqlString;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
@@ -115,6 +124,9 @@
private OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
private long maxExecutionTime = TimeUnit.SECONDS.toMillis(20);
private int queryLimit = 10000;
+ private boolean sampling = true;
+ private double sampleThreshold = 0.8;
+ private int sampleSize = 100;
public OWLAxiomPatternUsageEvaluation() {
}
@@ -181,12 +193,12 @@
}
}
- public void runUsingFragmentExtraction(SparqlEndpoint endpoint, OWLOntology ontology, File outputFile, int maxNrOfTestedClasses){
+ public void runUsingFragmentExtraction(SparqlEndpoint endpoint, OWLOntology patternOntology, 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);
+ List<OWLAxiom> patterns = getPatternsToEvaluate(patternOntology);
//get all classes in KB
Collection<NamedClass> classes = reasoner.getTypes(ns);
@@ -207,6 +219,7 @@
for (OWLAxiom pattern : patterns) {
//run if not already exists a result on disk
File file = new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations.ttl");
+ OWLOntology ontology = null;
if(!file.exists()){
logger.info("Applying pattern " + pattern + "...");
// if pattern is equivalent classes axiom, we need to get the
@@ -228,11 +241,75 @@
}
}
}
- save(pattern, axioms2Score, file);
+ ontology = save(pattern, axioms2Score, file);
+ } else {
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ try {
+ ontology = man.loadOntologyFromOntologyDocument(file);
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
}
+ if(sampling){
+ List<OWLAxiom> sample = createSample(ontology);
+ List<String> lines = new ArrayList<String>();
+ for (OWLAxiom axiom : sample) {
+ double accuracy = getAccuracy(axiom);
+ lines.add(axiomRenderer.render(axiom) + "," + format.format(accuracy));
+ }
+ try {
+ Files.write(Joiner.on("\n").join(lines), new File(axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations-sample.csv"), Charsets.UTF_8);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
}
}
+ private List<OWLAxiom> createSample(OWLOntology ontology){
+ Set<OWLAxiom> axioms = ontology.getAxioms();
+ for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ OWLAxiom axiom = iter.next();
+ double accuracy = getAccuracy(axiom);
+ if(accuracy < sampleThreshold){
+ iter.remove();
+ }
+ //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){
+ Set<OWLClassExpression> operands = ((OWLObjectIntersectionOf) superClass).getOperands();
+ for (OWLClassExpression op : operands) {
+ if(op.isOWLThing()){
+ iter.remove();
+ break;
+ }
+ }
+ } else if(superClass.toString().contains("Concept") || superClass.toString().contains("subject")){
+ iter.remove();
+ }
+ }
+ }
+ 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){
+ Set<OWLAnnotation> annotations = axiom.getAnnotations(confidenceProperty);
+ if(!annotations.isEmpty()){
+ OWLAnnotation annotation = annotations.iterator().next();
+ double accuracy = ((OWLLiteral)annotation.getValue()).parseDouble();
+ return accuracy;
+ }
+ return -1;
+ }
+
private int maxModalDepth(List<OWLAxiom> patterns) {
int maxModalDepth = 1;
for (OWLAxiom pattern : patterns) {
@@ -329,6 +406,9 @@
if(st.getPredicate().equals(RDF.type) && !st.getObject().asResource().getURI().startsWith("http://dbpedia.org/ontology/")){
statements2Remove.add(st);
}
+ if(st.getPredicate().hasURI("http://xmlns.com/foaf/0.1/depiction") || st.getPredicate().hasURI("http://dbpedia.org/ontology/thumbnail")){
+ statements2Remove.add(st);
+ }
}
model.remove(statements2Remove);
}
@@ -700,7 +780,7 @@
return template.asQuery();
}
- private void save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score, File file){
+ private OWLOntology save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score, File file){
try {
Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
@@ -714,6 +794,7 @@
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology ontology = man.createOntology(annotatedAxioms);
man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(file));
+ return ontology;
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (OWLOntologyStorageException e) {
@@ -721,6 +802,7 @@
} catch (FileNotFoundException e) {
e.printStackTrace();
}
+ return null;
}
private void save(Set<EvaluatedAxiom> evaluatedAxioms){
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