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[DL-Learner SVN] SF.net SVN: dl-learner:[4224] trunk/components-core/src
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From: <lor...@us...> - 2014-02-16 15:59:46
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Revision: 4224
http://sourceforge.net/p/dl-learner/code/4224
Author: lorenz_b
Date: 2014-02-16 15:59:43 +0000 (Sun, 16 Feb 2014)
Log Message:
-----------
Added ISLE experiments.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java
trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithmDisjunctive.java
trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/StableHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/RelevanceMapGenerator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/syntactic/SolrSyntacticIndex.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/AbstractRelevanceMetric.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/PMIRelevanceMetric.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/RelevanceUtils.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/SignificantPMIRelevanceMetric.java
trunk/components-core/src/main/java/org/dllearner/core/EvaluatedDescription.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlEndpoint.java
trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/ELDown3.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
trunk/components-core/src/test/java/org/dllearner/algorithms/isle/DBpediaExperiment.java
trunk/components-core/src/test/java/org/dllearner/algorithms/isle/KnowledgebaseSampleGenerator.java
trunk/components-core/src/test/java/org/dllearner/algorithms/isle/metrics/RelevanceMetricsTest.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -19,7 +19,10 @@
package org.dllearner.algorithms.celoe;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
import java.io.File;
+import java.io.FileInputStream;
import java.util.Collection;
import java.util.Iterator;
import java.util.LinkedList;
@@ -29,6 +32,7 @@
import java.util.TreeSet;
import org.apache.log4j.Logger;
+import org.dllearner.algorithms.elcopy.ELLearningAlgorithm;
import org.dllearner.core.AbstractCELA;
import org.dllearner.core.AbstractHeuristic;
import org.dllearner.core.AbstractKnowledgeSource;
@@ -45,6 +49,7 @@
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Restriction;
import org.dllearner.core.owl.Thing;
+import org.dllearner.kb.OWLAPIOntology;
import org.dllearner.kb.OWLFile;
import org.dllearner.learningproblems.ClassLearningProblem;
import org.dllearner.learningproblems.PosNegLP;
@@ -62,9 +67,19 @@
import org.dllearner.utilities.owl.ConceptTransformation;
import org.dllearner.utilities.owl.DescriptionMinimizer;
import org.dllearner.utilities.owl.EvaluatedDescriptionSet;
+import org.dllearner.utilities.owl.OWLEntityTypeAdder;
import org.dllearner.utilities.owl.PropertyContext;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLOntology;
import org.springframework.beans.factory.annotation.Autowired;
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.ResultSetFormatter;
+import com.hp.hpl.jena.query.Syntax;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
@@ -578,6 +593,7 @@
// System.out.println("refining: " + node);
int horizExp = node.getHorizontalExpansion();
TreeSet<Description> refinements = (TreeSet<Description>) operator.refine(node.getDescription(), horizExp+1);
+ System.out.println(refinements);
node.incHorizontalExpansion();
node.setRefinementCount(refinements.size());
nodes.add(node);
@@ -1120,16 +1136,44 @@
}
public static void main(String[] args) throws Exception{
- AbstractKnowledgeSource ks = new OWLFile("../examples/family/father_oe.owl");
+ String cls = "http://purl.org/procurement/public-contracts#Tender";
+ String file = "/home/me/work/datasets/e-procurement/dl-learner-sample-with-classes-pco.rdf";
+ Model model = ModelFactory.createDefaultModel();
+ model.read(new FileInputStream(file), null);
+ OWLEntityTypeAdder.addEntityTypes(model);
+ Query query = QueryFactory.create("SELECT (COUNT(distinct ?s) as ?cnt) WHERE {" +
+ "?s a <" + cls + ">.}", Syntax.syntaxARQ);
+ System.out.println(ResultSetFormatter.asText(QueryExecutionFactory.create(query, model).execSelect()));
+ query = QueryFactory.create("SELECT ?p (COUNT(distinct ?s) AS ?cnt) WHERE {" +
+ "?s ?p ?o. ?p a <http://www.w3.org/2002/07/owl#ObjectProperty>." +
+ "?s a <" + cls + ">. " +
+// "OPTIONAL{?x ?p ?o1. " +
+// "FILTER NOT EXISTS{?x a <" + cls + ">.}}" +
+
+ "}GROUP BY ?p ORDER BY DESC(?cnt)", Syntax.syntaxARQ);
+
+ System.out.println(ResultSetFormatter.asText(QueryExecutionFactory.create(query, model).execSelect()));
+
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ model.write(baos, "TURTLE");
+ OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray()));
+
+ AbstractKnowledgeSource ks = new OWLAPIOntology(ontology);
ks.init();
AbstractReasonerComponent rc = new FastInstanceChecker(ks);
rc.init();
ClassLearningProblem lp = new ClassLearningProblem(rc);
- lp.setClassToDescribe(new NamedClass("http://example.com/father#father"));
+ lp.setClassToDescribe(new NamedClass("http://purl.org/procurement/public-contracts#Tender"));
lp.init();
+// ELLearningAlgorithm alg = new ELLearningAlgorithm(lp, rc);
+// alg.setNoisePercentage(30);
+// alg.setClassToDescribe(new NamedClass("http://purl.org/procurement/public-contracts#Tender"));
+// alg.init();
+
+
CELOE alg = new CELOE(lp, rc);
alg.setMaxExecutionTimeInSeconds(10);
alg.init();
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -117,7 +117,6 @@
// private TreeSet<Description> descriptions;
private SortedSet<Description> descriptions;
- private EvaluatedDescriptionSet bestEvaluatedDescriptions;
// if true, then each solution is evaluated exactly instead of approximately
// private boolean exactBestDescriptionEvaluation = false;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -47,6 +47,7 @@
import org.dllearner.learningproblems.ScorePosNeg;
import org.dllearner.refinementoperators.ELDown3;
import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.owl.EvaluatedDescriptionSet;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
@@ -88,6 +89,10 @@
@ConfigOption(name = "startClass", defaultValue="owl:Thing", description="You can specify a start class for the algorithm. To do this, you have to use Manchester OWL syntax without using prefixes.")
private Description startClass;
+ private int maxClassExpressionDepth = 2;
+
+ private int maxNrOfResults = 10;
+
private Set<NamedClass> ignoredConcepts = null;
private NamedClass classToDescribe;
@@ -155,8 +160,11 @@
}
operator = new ELDown3(reasoner, instanceBasedDisjoints);
+ operator.setMaxClassExpressionDepth(maxClassExpressionDepth);
noise = noisePercentage/100d;
+
+ bestEvaluatedDescriptions = new EvaluatedDescriptionSet(maxNrOfResults);
}
@Override
@@ -229,7 +237,8 @@
} else {
node.setCoveredNegatives(negCovers);
}
- node.setScore(accuracy);
+// node.setScore(accuracy);
+// System.out.println(description + ":" + accuracy);
// link to parent (unless start node)
if(parentNode == null) {
startNode = node;
@@ -481,5 +490,19 @@
public void setTreeSearchTimeSeconds(double treeSearchTimeSeconds) {
this.treeSearchTimeSeconds = treeSearchTimeSeconds;
}
+
+ /**
+ * @param maxNrOfResults the maxNrOfResults to set
+ */
+ public void setMaxNrOfResults(int maxNrOfResults) {
+ this.maxNrOfResults = maxNrOfResults;
+ }
+
+ /**
+ * @param maxClassExpressionDepth the maxClassExpressionDepth to set
+ */
+ public void setMaxClassExpressionDepth(int maxClassExpressionDepth) {
+ this.maxClassExpressionDepth = maxClassExpressionDepth;
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithmDisjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithmDisjunctive.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithmDisjunctive.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -242,9 +242,13 @@
// form union of trees found so far with
if(treeCount==0) {
bestEvaluatedDescription = learningProblem.evaluate(bestDescription);
+ bestEvaluatedDescriptions.add(bestEvaluatedDescription);
} else {
- bestCombinedDescription = new Union(bestEvaluatedDescription.getDescription(), bestDescription);
+ if(!bestEvaluatedDescription.equals(Thing.instance)){
+ bestCombinedDescription = new Union(bestEvaluatedDescription.getDescription(), bestDescription);
+ }
bestEvaluatedDescription = learningProblem.evaluate(bestCombinedDescription);
+ bestEvaluatedDescriptions.add(bestEvaluatedDescription);
}
// remove already covered examples
@@ -405,7 +409,7 @@
// return (bestNode.getCoveredNegatives() == 0);
// stop if there are no more positive examples to cover
- if(currentPosExamples.size()==0) {
+ if(stopOnFirstDefinition && currentPosExamples.size()==0) {
return true;
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/StableHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/StableHeuristic.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/StableHeuristic.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -36,8 +36,8 @@
@Override
public int compare(SearchTreeNode o1, SearchTreeNode o2) {
- double diff = o2.getScore() - o1.getScore();
-// diff = -diff;
+ int diff = o2.getCoveredNegatives() - o1.getCoveredNegatives();
+// diff = Double.compare(o1.getScore(), o2.getScore());
if(diff>0) {
return 1;
} else if(diff<0) {
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/RelevanceMapGenerator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/RelevanceMapGenerator.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/RelevanceMapGenerator.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -8,6 +8,11 @@
import java.io.ObjectOutputStream;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
@@ -17,7 +22,6 @@
import org.dllearner.core.owl.NamedClass;
import org.semanticweb.owlapi.model.OWLOntology;
-import com.google.common.hash.HashCode;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
@@ -35,12 +39,13 @@
public static String cacheDirectory = "cache/relevance";
public static Map<Entity, Double> generateRelevanceMap(NamedClass cls, OWLOntology ontology, RelevanceMetric relevanceMetric, boolean cached){
+ logger.info("Relevance Metric: " + relevanceMetric.getClass().getSimpleName());
Map<Entity, Double> relevanceMap = null;
File folder = new File(cacheDirectory);
folder.mkdirs();
File file = null;
try {
- file = new File(folder, URLEncoder.encode(cls.getName(), "UTF-8") + ".rel");
+ file = new File(folder, URLEncoder.encode(cls.getName() + "-" + relevanceMetric.getClass().getSimpleName(), "UTF-8") + ".rel");
} catch (UnsupportedEncodingException e2) {
e2.printStackTrace();
}
@@ -69,6 +74,22 @@
return relevanceMap;
}
+ public static Map<RelevanceMetric, Map<Entity, Double>> generateRelevanceMaps(NamedClass cls, OWLOntology ontology, List<RelevanceMetric> relevanceMetrics, boolean cached){
+ Map<RelevanceMetric, Map<Entity, Double>> metric2Map = new LinkedHashMap<>();
+ for (RelevanceMetric relevanceMetric : relevanceMetrics) {
+ try {
+ long start = System.currentTimeMillis();
+ metric2Map.put(relevanceMetric, generateRelevanceMap(cls, ontology, relevanceMetric, cached));
+ long end = System.currentTimeMillis();
+ logger.info("Operation took " + (end - start) + "ms");
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+ return metric2Map;
+ }
+
public static Map<Entity, Double> generateRelevanceMap(NamedClass cls, OWLOntology ontology, RelevanceMetric relevanceMetric){
return generateRelevanceMap(cls, ontology, relevanceMetric, false);
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/syntactic/SolrSyntacticIndex.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/syntactic/SolrSyntacticIndex.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/syntactic/SolrSyntacticIndex.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -4,14 +4,24 @@
package org.dllearner.algorithms.isle.index.syntactic;
import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectOutputStream;
+import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.TreeSet;
import java.util.Map.Entry;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
import java.util.Set;
+import org.apache.log4j.Logger;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrServer;
import org.apache.solr.client.solrj.SolrServerException;
@@ -28,11 +38,14 @@
import org.dllearner.algorithms.isle.textretrieval.RDFSLabelEntityTextRetriever;
import org.dllearner.core.owl.Entity;
import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.utilities.owl.OWLAPIConverter;
import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import com.google.common.base.Joiner;
+import com.google.common.collect.Sets;
/**
* @author Lorenz Buehmann
@@ -40,6 +53,8 @@
*/
public class SolrSyntacticIndex implements Index{
+ private static final Logger logger = Logger.getLogger(SolrSyntacticIndex.class.getName());
+
private SolrServer solr;
private AnnotationEntityTextRetriever textRetriever;
private String searchField;
@@ -48,13 +63,78 @@
long totalNumberOfDocuments = -1;
Map<Entity, Long> cache = new HashMap<>();
+ Map<List<Entity>, Long> cache2 = new HashMap<>();
+ private OWLOntology ontology;
public SolrSyntacticIndex(OWLOntology ontology, String solrServerURL, String searchField) {
+ this.ontology = ontology;
this.searchField = searchField;
solr = new HttpSolrServer(solrServerURL);
textRetriever = new RDFSLabelEntityTextRetriever(ontology);
}
+ public void buildIndex(Set<NamedClass> classes){
+ logger.info("Building cache...");
+
+ ExecutorService executor = Executors.newFixedThreadPool(6);
+
+ final Set<OWLEntity> owlEntities = new TreeSet<OWLEntity>();
+ owlEntities.addAll(ontology.getClassesInSignature());
+ owlEntities.addAll(ontology.getDataPropertiesInSignature());
+ owlEntities.addAll(ontology.getObjectPropertiesInSignature());
+
+ final Map<Set<Entity>, Long> cache = new HashMap<>();
+
+
+ for (final NamedClass cls : classes) {
+ executor.submit(new Runnable() {
+
+ @Override
+ public void run() {
+ Set<Entity> entities;
+ logger.info(cls);
+ Set<Entity> otherEntities = OWLAPIConverter.getEntities(owlEntities);
+ otherEntities.remove(cls);
+ //fA
+ long fA = getNumberOfDocumentsFor(cls);
+ entities = new HashSet<>();
+ entities.add(cls);
+ cache.put(entities, fA);
+ for (Entity entity : otherEntities) {
+ //fB
+ long fB = getNumberOfDocumentsFor(entity);
+ entities = new HashSet<>();
+ entities.add(entity);
+ cache.put(entities, fB);
+ //fAB
+ long fAB = getNumberOfDocumentsFor(cls, entity);
+ entities = new HashSet<>();
+ entities.add(cls);
+ entities.add(entity);
+ cache.put(entities, fAB);
+ }
+ }
+ });
+ }
+ executor.shutdown();
+ try {
+ executor.awaitTermination(10, TimeUnit.DAYS);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+ try {
+ ObjectOutputStream oos = new ObjectOutputStream(new FileOutputStream("frequencies.obj"));
+ oos.writeObject(cache);
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ }
+
+
+
/* (non-Javadoc)
* @see org.dllearner.algorithms.isle.index.Index#getDocuments(org.dllearner.core.owl.Entity)
*/
@@ -109,7 +189,7 @@
* @see org.dllearner.algorithms.isle.index.Index#getNumberOfDocumentsFor(org.dllearner.core.owl.Entity)
*/
@Override
- public long getNumberOfDocumentsFor(Entity entity) {
+ public synchronized long getNumberOfDocumentsFor(Entity entity) {
if(cache.containsKey(entity)){
return cache.get(entity);
}
@@ -146,7 +226,11 @@
* @see org.dllearner.algorithms.isle.index.Index#getNumberOfDocumentsFor(org.dllearner.core.owl.Entity[])
*/
@Override
- public long getNumberOfDocumentsFor(Entity... entities) {
+ public synchronized long getNumberOfDocumentsFor(Entity... entities) {
+ List<Entity> entitiesList = Arrays.asList(entities);
+ if(cache2.containsKey(entitiesList)){
+ return cache2.get(entitiesList);
+ }
Set<String> queryStringParts = new HashSet<>();
@@ -177,6 +261,7 @@
try {
QueryResponse response = solr.query(query);
SolrDocumentList list = response.getResults();
+ cache2.put(entitiesList, list.getNumFound());
return list.getNumFound();
} catch (SolrServerException e) {
e.printStackTrace();
@@ -234,6 +319,11 @@
System.out.println(n);
n = index.getNumberOfDocumentsForTyped(new NamedClass("http://dbpedia.org/ontology/Person"), new NamedClass("http://dbpedia.org/ontology/birthPlace"));
System.out.println(n);
+
+ System.out.println(index.getNumberOfDocumentsFor(
+ new NamedClass("http://dbpedia.org/ontology/Person"), new ObjectProperty("http://dbpedia.org/ontology/birthPlace")));
+ System.out.println(index.getNumberOfDocumentsFor(
+ new NamedClass("http://dbpedia.org/ontology/Person"), new ObjectProperty("http://dbpedia.org/ontology/birthPlace")));
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/AbstractRelevanceMetric.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/AbstractRelevanceMetric.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/AbstractRelevanceMetric.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -7,7 +7,7 @@
import java.util.Map;
import org.dllearner.algorithms.isle.index.Index;
-import org.semanticweb.owlapi.model.OWLEntity;
+import org.dllearner.core.owl.Entity;
/**
* @author Lorenz Buehmann
@@ -20,33 +20,32 @@
public AbstractRelevanceMetric(Index index) {
this.index = index;
}
-
- public Map<OWLEntity,Double> normalizeMinMax( Map<OWLEntity,Double> hmEntity2Score ){
- Map<OWLEntity,Double> hmEntity2Norm = new HashMap<OWLEntity,Double>();
- double dMin = Double.MAX_VALUE;
- Double dMax = Double.MIN_VALUE;
- for( OWLEntity e : hmEntity2Score.keySet() )
- {
- double dValue = hmEntity2Score.get(e);
- if( dValue < dMin ){
- dMin = dValue;
+
+ public static Map<Entity, Double> normalizeMinMax(Map<Entity, Double> hmEntity2Score) {
+ Map<Entity, Double> hmEntity2Norm = new HashMap<Entity, Double>();
+
+ double min = Double.MAX_VALUE;
+ double max = Double.MIN_VALUE;
+
+ for (Entity e : hmEntity2Score.keySet()) {
+ double value = hmEntity2Score.get(e);
+ if (value < min) {
+ min = value;
+ } else if (value > max) {
+ max = value;
}
- else if( dValue > dMax ){
- dMax = dValue;
- }
}
// System.out.println( "min="+ dMin +" max="+ dMax );
- for( OWLEntity e : hmEntity2Score.keySet() )
- {
- double dValue = hmEntity2Score.get(e);
- double dNorm = 0;
- if( dMin == dMax ){
- dNorm = dValue;
- }
- else {
- dNorm = ( dValue - dMin ) / ( dMax - dMin );
+ for (Entity e : hmEntity2Score.keySet()) {
+ double value = hmEntity2Score.get(e);
+ double normalized = 0;
+ if (min == max) {
+ normalized = value;
+ normalized = 0.5;
+ } else {
+ normalized = (value - min) / (max - min);
}
- hmEntity2Norm.put( e, dNorm );
+ hmEntity2Norm.put(e, normalized);
}
return hmEntity2Norm;
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/PMIRelevanceMetric.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/PMIRelevanceMetric.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/PMIRelevanceMetric.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -17,7 +17,7 @@
}
@Override
- public synchronized double getRelevance(Entity entityA, Entity entityB){
+ public double getRelevance(Entity entityA, Entity entityB){
long nrOfDocumentsA = index.getNumberOfDocumentsFor(entityA);
long nrOfDocumentsB = index.getNumberOfDocumentsFor(entityB);
long nrOfDocumentsAB = index.getNumberOfDocumentsFor(entityA, entityB);
@@ -28,13 +28,17 @@
double pB = nrOfDocuments == 0 ? 0 : ((double) nrOfDocumentsB / (double) nrOfDocuments);
double pAB = nrOfDocuments == 0 ? 0 : ((double) nrOfDocumentsAB / (double) nrOfDocuments);
+ if(pAB == 0 || (pA * pB) == 0){
+ return 0;
+ }
+
double pmi = Math.log(pAB / pA * pB);
return pmi;
}
@Override
- public synchronized double getNormalizedRelevance(Entity entityA, Entity entityB){
+ public double getNormalizedRelevance(Entity entityA, Entity entityB){
long nrOfDocumentsA = index.getNumberOfDocumentsFor(entityA);
long nrOfDocumentsB = index.getNumberOfDocumentsFor(entityB);
long nrOfDocumentsAB = index.getNumberOfDocumentsFor(entityA, entityB);
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/RelevanceUtils.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/RelevanceUtils.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/RelevanceUtils.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -3,10 +3,12 @@
*/
package org.dllearner.algorithms.isle.metrics;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
+import java.util.TreeSet;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
@@ -25,6 +27,7 @@
private static final Logger logger = Logger.getLogger(RelevanceUtils.class.getName());
static int maxNrOfThreads = Math.max(1, Runtime.getRuntime().availableProcessors() - 1);
+ static boolean normalize = true;
/**
* Returns a map containing the relevance score based on the given metric between the entity and each other entity.
@@ -43,8 +46,9 @@
executor.submit(new Runnable() {
@Override
public void run() {
- double relevance = metric.getNormalizedRelevance(entity, otherEntity);
- logger.info(otherEntity + ":" + relevance);
+// double relevance = metric.getNormalizedRelevance(entity, otherEntity);
+ double relevance = metric.getRelevance(entity, otherEntity);
+// logger.info(otherEntity + ":" + relevance);
relevantEntities.put(otherEntity, relevance);
}
});
@@ -55,17 +59,21 @@
} catch (InterruptedException e) {
e.printStackTrace();
}
-
+ //normalize the values
+ if(normalize){
+ return AbstractRelevanceMetric.normalizeMinMax(relevantEntities);
+ }
return relevantEntities;
}
public static Map<Entity, Double> getRelevantEntities(Entity entity, OWLOntology ontology, RelevanceMetric metric){
- Set<OWLEntity> owlEntities = new HashSet<OWLEntity>();
+ Set<OWLEntity> owlEntities = new TreeSet<OWLEntity>();
owlEntities.addAll(ontology.getClassesInSignature());
owlEntities.addAll(ontology.getDataPropertiesInSignature());
owlEntities.addAll(ontology.getObjectPropertiesInSignature());
Set<Entity> otherEntities = OWLAPIConverter.getEntities(owlEntities);
+// Set<Entity> otherEntities = OWLAPIConverter.getEntities(new HashSet<OWLEntity>(new ArrayList<OWLEntity>(owlEntities).subList(0, 20)));
otherEntities.remove(entity);
return getRelevantEntities(entity, otherEntities, metric);
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/SignificantPMIRelevanceMetric.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/SignificantPMIRelevanceMetric.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/SignificantPMIRelevanceMetric.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -34,6 +34,10 @@
double N = index.getTotalNumberOfDocuments();
+ if(fA == 0 || fB == 0 || fAB == 0){
+ return 0;
+ }
+
double pmi = Math.log(fAB / (fA*fB/N + Math.sqrt(fA)*Math.sqrt(Math.log(delta)/-2)));
return pmi;
Modified: trunk/components-core/src/main/java/org/dllearner/core/EvaluatedDescription.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/EvaluatedDescription.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/core/EvaluatedDescription.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -24,6 +24,7 @@
import org.dllearner.core.owl.Description;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
+import org.dllearner.utilities.owl.ConceptComparator;
import org.dllearner.utilities.owl.OWLAPIDescriptionConvertVisitor;
import org.dllearner.utilities.owl.OWLAPIRenderers;
import org.json.JSONException;
@@ -37,12 +38,13 @@
* @author Jens Lehmann
*
*/
-public class EvaluatedDescription implements Serializable{
+public class EvaluatedDescription implements Serializable, Comparable<EvaluatedDescription>{
/**
*
*/
private static final long serialVersionUID = 1106431570510815033L;
+ private static ConceptComparator conceptComparator = new ConceptComparator();
protected Description description;
protected Score score;
@@ -139,4 +141,16 @@
return description.toString() + " " + dfPercent.format(getAccuracy());
}
+ /* (non-Javadoc)
+ * @see java.lang.Comparable#compareTo(java.lang.Object)
+ */
+ @Override
+ public int compareTo(EvaluatedDescription o) {
+ int diff = Double.compare(score.getAccuracy(), o.score.getAccuracy());
+ if(diff == 0){
+ conceptComparator.compare(description, o.getDescription());
+ }
+ return diff;
+ }
+
}
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -61,6 +61,12 @@
qef = new QueryExecutionFactoryPaginated(qef, 10000);
}
+ public ConciseBoundedDescriptionGeneratorImpl(Model model, int maxRecursionDepth) {
+ this.maxRecursionDepth = maxRecursionDepth;
+
+ qef = new QueryExecutionFactoryModel(model);
+ }
+
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir) {
this(endpoint, cacheDir, MAX_RECURSION_DEPTH_DEFAULT);
}
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlEndpoint.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlEndpoint.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlEndpoint.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -504,6 +504,43 @@
}
return new SparqlEndpoint(u);
}
+
+ @Override
+ public int hashCode() {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + ((defaultGraphURIs == null) ? 0 : defaultGraphURIs.hashCode());
+ result = prime * result + ((namedGraphURIs == null) ? 0 : namedGraphURIs.hashCode());
+ result = prime * result + ((url == null) ? 0 : url.hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ SparqlEndpoint other = (SparqlEndpoint) obj;
+ if (defaultGraphURIs == null) {
+ if (other.defaultGraphURIs != null)
+ return false;
+ } else if (!defaultGraphURIs.equals(other.defaultGraphURIs))
+ return false;
+ if (namedGraphURIs == null) {
+ if (other.namedGraphURIs != null)
+ return false;
+ } else if (!namedGraphURIs.equals(other.namedGraphURIs))
+ return false;
+ if (url == null) {
+ if (other.url != null)
+ return false;
+ } else if (!url.equals(other.url))
+ return false;
+ return true;
+ }
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -554,7 +554,9 @@
DatatypeSomeRestriction dsr = (DatatypeSomeRestriction) description;
DatatypeProperty dp = (DatatypeProperty) dsr.getRestrictedPropertyExpression();
DataRange dr = dsr.getDataRange();
- if(dr.isDatatype() && ((Datatype)dr).isTopDatatype()){
+ if(dr.isDatatype()
+// && ((Datatype)dr).isTopDatatype()
+ ){
if(dpPos.get(dp).containsKey(individual)){
return true;
} else {
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -82,6 +82,7 @@
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFNode;
@@ -657,7 +658,7 @@
String query = String.format(
"SELECT ?type WHERE {<%s> a ?type . "
+ "FILTER NOT EXISTS{<%s> a ?moreSpecificType ."
- + "?moreSpecificType <http://www.w3.org/2000/01/rdf-schema#subClassOf>+ ?type.}}", individual.getName(), individual.getName());
+ + "?moreSpecificType <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?type.}}", individual.getName(), individual.getName());
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -858,7 +859,8 @@
Set<NamedClass> siblings = new TreeSet<NamedClass>();
String query = "SELECT ?sub WHERE { <" + cls.getName() + "> <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
query += "?sub <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
- query += "FILTER( !SAMETERM(?sub, <" + cls.getName() + ">)) . }";
+// query += "FILTER NOT EXISTS{?sub2 <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super. ?sub <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super.}";
+ query += "FILTER( !SAMETERM(?sub, <" + cls.getName() + ">) && !SAMETERM(?super, <http://www.w3.org/2000/01/rdf-schema#Resource>)) . }";
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
Modified: trunk/components-core/src/main/java/org/dllearner/refinementoperators/ELDown3.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/refinementoperators/ELDown3.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/refinementoperators/ELDown3.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -111,6 +111,8 @@
private ELDescriptionTreeComparator treeComp = new ELDescriptionTreeComparator();
private ELDescriptionEdgeComparator edgeComp = new ELDescriptionEdgeComparator();
private TreeAndRoleSetComparator mComp = new TreeAndRoleSetComparator();
+
+ private int maxClassExpressionDepth = 2;
public ELDown3(AbstractReasonerComponent rs) {
this(rs, true);
@@ -180,7 +182,7 @@
refinements.addAll(refineLabel(tree, v, position));
}
refinements.addAll(refineEdge(tree, v, position));
- if(v.isClassNode() && v.getLevel() < 4){
+ if(v.isClassNode() && v.getLevel() <= maxClassExpressionDepth){
refinements.addAll(attachSubtree2(tree, v, position));
refinements.addAll(attachSubtreeDatatypeProperties(tree, v, position));
}
@@ -655,6 +657,13 @@
}
return false;
}
+
+ /**
+ * @param maxClassExpressionDepth the maxClassExpressionDepth to set
+ */
+ public void setMaxClassExpressionDepth(int maxClassExpressionDepth) {
+ this.maxClassExpressionDepth = maxClassExpressionDepth;
+ }
@Override
public void init() throws ComponentInitException {
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -194,6 +194,7 @@
Set<Description> superClasses = sr.getSuperClasses(nc);
superClasses.remove(new NamedClass(Thing.instance.getURI()));
superClasses.remove(Thing.instance);
+ superClasses.remove(new NamedClass("http://www.w3.org/2000/01/rdf-schema#Resource"));
superClasses = filterByNamespace(superClasses);
logger.info("Super classes: " + superClasses);
@@ -211,7 +212,7 @@
logger.info("Negative examples(" + superClassNegativeExamples.size() + "): " + superClassNegativeExamples);
negativeExamples.addAll(superClassNegativeExamples);
} else if(strategy == RANDOM){//get some random examples
-
+ String query = "SELECT ?s WHERE {?s a ?type. FILTER NOT EXIST{?type rdfs:subClassOf* }}";
}
}
return negativeExamples;
Modified: trunk/components-core/src/test/java/org/dllearner/algorithms/isle/DBpediaExperiment.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/algorithms/isle/DBpediaExperiment.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/test/java/org/dllearner/algorithms/isle/DBpediaExperiment.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -9,9 +9,17 @@
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
+import java.io.FileNotFoundException;
import java.io.IOException;
+import java.io.InputStream;
import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.net.URLEncoder;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.SQLException;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Arrays;
@@ -23,19 +31,27 @@
import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
+import java.util.TreeSet;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
+import java.util.prefs.Preferences;
import org.apache.log4j.Logger;
-import org.coode.owlapi.rdfxml.parser.DataSomeValuesFromTranslator;
import org.dllearner.algorithms.celoe.CELOE;
-import org.dllearner.algorithms.el.ELLearningAlgorithmDisjunctive;
import org.dllearner.algorithms.elcopy.ELLearningAlgorithm;
import org.dllearner.algorithms.isle.index.Index;
import org.dllearner.algorithms.isle.index.RelevanceMapGenerator;
import org.dllearner.algorithms.isle.index.syntactic.SolrSyntacticIndex;
+import org.dllearner.algorithms.isle.metrics.ChiSquareRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.DiceRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.JaccardRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.LLRRelevanceMetric;
import org.dllearner.algorithms.isle.metrics.PMIRelevanceMetric;
import org.dllearner.algorithms.isle.metrics.RelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.SCIRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.SignificantPMIRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.TTestRelevanceMetric;
import org.dllearner.core.AbstractCELA;
import org.dllearner.core.AbstractLearningProblem;
import org.dllearner.core.AbstractReasonerComponent;
@@ -65,6 +81,8 @@
import org.dllearner.refinementoperators.RhoDRDown;
import org.dllearner.utilities.PrefixCCMap;
import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2;
+import org.ini4j.IniPreferences;
+import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
@@ -78,6 +96,7 @@
import com.google.common.base.Charsets;
import com.google.common.collect.Sets;
+import com.google.common.hash.HashCode;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import com.google.common.io.Files;
@@ -108,9 +127,9 @@
private static final Logger logger = Logger.getLogger(DBpediaExperiment.class.getName());
private DecimalFormat dfPercent = new DecimalFormat("0.00%");
- HashFunction hf = Hashing.md5();
+ final HashFunction hf = Hashing.md5();
- SparqlEndpoint endpoint = SparqlEndpoint.getEndpointDBpedia();
+ SparqlEndpoint endpoint = SparqlEndpoint.getEndpointDBpediaLiveAKSW();
String namespace = "http://dbpedia.org/ontology/";
OWLOntology schema;
@@ -120,7 +139,7 @@
String cacheDirectory = "cache/isle";
String testFolder = "experiments/isle/logs/";
- private SPARQLReasoner reasoner;
+ private SPARQLReasoner sparqlReasoner;
private AutomaticNegativeExampleFinderSPARQL2 negativeExampleFinder;
final int maxNrOfPositiveExamples = 100;
@@ -129,25 +148,33 @@
int maxCBDDepth = 1;
//learning algorithm settings
- private int maxNrOfResults = 50;
+ private int maxNrOfResults = 100;
private int maxExecutionTimeInSeconds = 10;
- private double noiseInPercentage = 70;
+ private double noiseInPercentage = 50;
private boolean useNegation = false;
private boolean useAllConstructor = false;
- private RelevanceMetric relevanceMetric;
-
String experimentsFolder = "experiments/isle/";
File resultsFolder = new File(experimentsFolder + "result/");
private boolean useEL = true;
private boolean forceLongDescriptions = true;
+
+ private List<RelevanceMetric> relevanceMetrics;
+
+ private PreparedStatement ps;
public DBpediaExperiment() {
- reasoner = new SPARQLReasoner(new SparqlEndpointKS(endpoint), cacheDirectory);
- negativeExampleFinder = new AutomaticNegativeExampleFinderSPARQL2(endpoint, reasoner);
+ try {
+ endpoint = new SparqlEndpoint(new URL("http://[2001:638:902:2010:0:168:35:138]/sparql"), "http://dbpedia.org");
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ }
+
+ sparqlReasoner = new SPARQLReasoner(new SparqlEndpointKS(endpoint), cacheDirectory);
+ negativeExampleFinder = new AutomaticNegativeExampleFinderSPARQL2(endpoint, sparqlReasoner);
KnowledgebaseSampleGenerator.maxCBDDepth = maxCBDDepth;
new File(experimentsFolder + "samples/").mkdirs();
KnowledgebaseSampleGenerator.cacheDir = experimentsFolder + "samples/";
@@ -155,18 +182,88 @@
loadSchema();
- relevanceMetric = new PMIRelevanceMetric(getSyntacticIndex());
+ Index syntacticIndex = getSyntacticIndex();
+ relevanceMetrics = new ArrayList<>();
+ relevanceMetrics.add(new PMIRelevanceMetric(syntacticIndex));
+ relevanceMetrics.add(new ChiSquareRelevanceMetric(syntacticIndex));
+ relevanceMetrics.add(new DiceRelevanceMetric(syntacticIndex));
+ relevanceMetrics.add(new JaccardRelevanceMetric(syntacticIndex));
+ relevanceMetrics.add(new LLRRelevanceMetric(syntacticIndex));
+ relevanceMetrics.add(new SCIRelevanceMetric(syntacticIndex));
+ relevanceMetrics.add(new SignificantPMIRelevanceMetric(syntacticIndex, 0.5));
+ relevanceMetrics.add(new TTestRelevanceMetric(syntacticIndex));
+
resultsFolder.mkdirs();
+
+ initDBConnection();
}
+ /**
+ * Setup the database connection, create the table if not exists and prepare the INSERT statement.
+ */
+ private void initDBConnection() {
+ try {
+ InputStream is = this.getClass().getClassLoader().getResourceAsStream("db_settings.ini");
+ Preferences prefs = new IniPreferences(is);
+ String dbServer = prefs.node("database").get("server", null);
+ String dbName = prefs.node("database").get("name", null);
+ String dbUser = prefs.node("database").get("user", null);
+ String dbPass = prefs.node("database").get("pass", null);
+
+ Class.forName("com.mysql.jdbc.Driver");
+ String url = "jdbc:mysql://" + dbServer + "/" + dbName;
+ Connection conn = DriverManager.getConnection(url, dbUser, dbPass);
+
+ java.sql.Statement st = conn.createStatement();
+ String sql = "CREATE TABLE IF NOT EXISTS ISLE_Evaluation ("
+ + "id VARCHAR(100),"
+ + "class TEXT NOT NULL,"
+ + "position TINYINT NOT NULL,"
+ + "expression TEXT NOT NULL,"
+ + "fscore DECIMAL(8,6) NOT NULL,";
+ for (RelevanceMetric metric : relevanceMetrics) {
+ sql += metric.getClass().getSimpleName().replace("RelevanceMetric", "") + " DECIMAL(8,6) NOT NULL,";
+ }
+ sql += "PRIMARY KEY(id),"
+ + "INDEX(class(200))) DEFAULT CHARSET=utf8";
+ st.execute(sql);
+
+ sql = "INSERT INTO ISLE_Evaluation (id, class, position, expression, fscore";
+ for (RelevanceMetric metric : relevanceMetrics) {
+ sql += "," + metric.getClass().getSimpleName().replace("RelevanceMetric", "");
+ }
+ sql += ") VALUES(?,?,?,?,?";
+ for(int i = 0 ; i < relevanceMetrics.size(); i++){
+ sql += ",?";
+ }
+ sql += ")";
+ ps = conn.prepareStatement(sql);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ } catch (InvalidFileFormatException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
public void run(){
Set<NamedClass> classes = getClasses();
- classes = reasoner.getMostSpecificClasses();
+ classes = sparqlReasoner.getMostSpecificClasses();
List<NamedClass> classList = new ArrayList<>(classes);
// Collections.reverse(classList);
+// classList = classList.subList(0, 10);
- for (NamedClass cls : classList) {
+ new SolrSyntacticIndex(schema, solrServerURL, searchField).buildIndex(classes);
+
+ ExecutorService executor = Executors.newFixedThreadPool(6);
+
+ for (final NamedClass cls : classList) {
try {
File resultsFile = new File(resultsFolder, URLEncoder.encode(cls.getName(), "UTF-8") + ".csv");
if(resultsFile.exists()){
@@ -175,12 +272,23 @@
} catch (UnsupportedEncodingException e1) {
e1.printStackTrace();
}
- try {
- run(cls);
- } catch (Exception e) {
- logger.error("Error when learning class " + cls, e);
- }
+ executor.submit(new Runnable() {
+ @Override
+ public void run() {
+ try {
+ DBpediaExperiment.this.run(cls);
+ } catch (Exception e) {
+ logger.error("Error when learning class " + cls, e);
+ }
+ }
+ });
}
+ executor.shutdown();
+ try {
+ executor.awaitTermination(10, TimeUnit.DAYS);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
}
public void run(NamedClass cls){
@@ -198,14 +306,15 @@
SortedSet<Individual> negativeExamples = getNegativeExamples(cls, positiveExamples);
//generate a sample of the knowledge base based on the examples
- OWLOntology knowledgebaseSample = loadKnowledgebaseSample(Sets.union(positiveExamples, negativeExamples));
-// Map<Entity, Double> entityRelevance = RelevanceMapGenerator.generateRelevanceMap(cls, schema, relevanceMetric, true);
- try {
- Thread.sleep(2000);
- } catch (InterruptedException e) {
- e.printStackTrace();
- }
-
+ OWLOntology knowledgebaseSample = loadKnowledgebaseSample(cls, Sets.union(positiveExamples, negativeExamples));
+// try {
+// Thread.sleep(2000);
+// } catch (InterruptedException e) {
+// e.printStackTrace();
+// }
+
+ return;
+ /**
//set up the learning
try {
// set KB
@@ -230,22 +339,6 @@
}
lp.init();
- /**
- Monitor mon = MonitorFactory.getTimeMonitor("time");
- Individual ex = positiveExamples.iterator().next();
- Description r = new DatatypeSomeRestriction(new DatatypeProperty("http://dbpedia.org/ontology/Astronaut/timeInSpace"), new Datatype("http://www.w3.org/2000/01/rdf-schema#Literal"));
- mon.start();
- reasoner.hasType(r, ex);
-// lp.getAccuracyOrTooWeak(r, 0.3d);
- mon.stop();
- System.out.println(mon.getLastValue());
- r = new ObjectSomeRestriction(new ObjectProperty("http://dbpedia.org/ontology/nationality"), new NamedClass("http://dbpedia.org/ontology/Country"));
- mon.start();
- reasoner.hasType(r, ex);
-// lp.getAccuracyOrTooWeak(r, 0.3d);
- mon.stop();
- System.out.println(mon.getLastValue());
- **/
// 1. run basic algorithm
//set up the refinement operator and the allowed OWL constructs
@@ -265,6 +358,7 @@
((ELLearningAlgorithm)la).setIgnoredConcepts(Sets.newHashSet(cls));
((ELLearningAlgorithm)la).setClassToDescribe(cls);
((ELLearningAlgorithm)la).setTreeSearchTimeSeconds(maxExecutionTimeInSeconds);
+ ((ELLearningAlgorithm)la).setMaxNrOfResults(maxNrOfResults);
// la = new ELLearningAlgorithmDisjunctive(lp, reasoner);
} else {
//build CELOE la
@@ -273,6 +367,7 @@
laTmp.setOperator(rop);
laTmp.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
laTmp.setStartClass(startClass);
+ laTmp.setNoisePercentage(noiseInPercentage);
new File(testFolder).mkdirs();
laTmp.setSearchTreeFile(testFolder + "searchTree.txt");
laTmp.setWriteSearchTree(true);
@@ -285,19 +380,36 @@
}
la.init();
la.start();
- Map<Entity, Double> entityRelevance = RelevanceMapGenerator.generateRelevanceMap(cls, schema, relevanceMetric, true);
-
+ //compute the relevance scores
+ Map<RelevanceMetric, Map<Entity, Double>> entityRelevances = RelevanceMapGenerator.generateRelevanceMaps(cls, schema, relevanceMetrics, true);
+ //Write to DB
+ try {
+ write2DB(reasoner, lp, cls, la.getCurrentlyBestEvaluatedDescriptions(), entityRelevances);
+ } catch (SQLException e1) {
+ e1.printStackTrace();
+ }
+ //write to CSV file
int current = 1;
StringBuilder sb = new StringBuilder();
+ //the header line
+ sb.append("class expression,fmeasure");
+ for (RelevanceMetric metric : relevanceMetrics) {
+ sb.append(",").append(metric.getClass().getSimpleName());
+ }
+ sb.append("\n");
+ //the entries
for(EvaluatedDescription ed : la.getCurrentlyBestEvaluatedDescriptions().descendingSet()) {
if(lp instanceof PosNegLPStandard) {
double fMeasure = ((PosNegLPStandard)lp).getFMeasureOrTooWeakExact(ed.getDescription(),1);
sb.append(replaceDataPropertyRanges(ed.getDescription()).toManchesterSyntaxString(reasoner.getBaseURI(), reasoner.getPrefixes()) + ","
// + ((PosNegLPStandard)lp).getPredAccuracyOrTooWeakExact(ed.getDescription(),1) + ","
+ fMeasure);
- double relevanceScore = getRelevanceScore(ed.getDescription(), entityRelevance);
- sb.append(",").append(relevanceScore);
- sb.append(",").append(fMeasure + relevanceScore);
+ for (RelevanceMetric metric : relevanceMetrics) {
+ double relevanceScore = getRelevanceScore(ed.getDescription(), entityRelevances.get(metric));
+ sb.append(",").append(relevanceScore);
+ }
+
+// sb.append(",").append(fMeasure + relevanceScore);
sb.append("\n");
}
@@ -322,6 +434,7 @@
} catch (ComponentInitException e) {
e.printStackTrace();
}
+ */
}
/**
@@ -414,7 +527,7 @@
private SortedSet<Individual> getPositiveExamples(NamedClass cls){
logger.info("Generating positive examples...");
- SortedSet<Individual> individuals = reasoner.getIndividuals(cls, 1000);
+ SortedSet<Individual> individuals = sparqlReasoner.getIndividuals(cls, 1000);
List<Individual> individualsList = new ArrayList<>(individuals);
// Collections.shuffle(individualsList, new Random(1234));
individuals.clear();
@@ -440,15 +553,14 @@
logger.info("Done. Number of logical axioms: " + schema.getLogicalAxiomCount());
}
- private OWLOntology loadKnowledgebaseSample(Set<Individual> individuals){
+ private OWLOntology loadKnowledgebaseSample(NamedClass nc, Set<Individual> individuals){
logger.info("Generating knowledge base sample...");
Model sampleModel = KnowledgebaseSampleGenerator.createKnowledgebaseSample(endpoint, namespace, individuals);
sampleModel.setNsPrefix("dbo", "http://dbpedia.org/ontology/");
logger.info("Done. Size: " + sampleModel.size() + " triples");
cleanUp(sampleModel);
logger.info("Clean up. Size: " + sampleModel.size() + " triples");
-// Query query = QueryFactory.create("SELECT ?p (COUNT(distinct ?s) AS ?cnt) WHERE {?s ?p ?o. ?s a <http://dbpedia.org/ontology/Cardinal>} GROUP BY ?p ORDER BY DESC(?cnt)", Syntax.syntaxARQ);
-// System.out.println(ResultSetFormatter.asText(QueryExecutionFactory.create(query, sampleModel).execSelect()));
+ showPropertyDistribution(nc, sampleModel);
try {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
@@ -462,6 +574,7 @@
man.removeAxioms(ontology, ontology.getAxioms(AxiomType.DATA_PROPERTY_RANGE));
man.removeAxioms(ontology, ontology.getAxioms(AxiomType.DISJOINT_CLASSES));
man.removeAxioms(ontology, ontology.getAxioms(AxiomType.SAME_INDIVIDUAL));
+// man.removeAxioms(ontology, ontology.getAxioms(AxiomType.OBJECT_PROPERTY_RANGE));
man.removeAxiom(ontology, df.getOWLObjectPropertyDomainAxiom(
df.getOWLObjectProperty(IRI.create("http://dbpedia.org/ontology/mission")),
df.getOWLClass(IRI.create("http://dbpedia.org/ontology/Aircraft"))));
@@ -480,6 +593,17 @@
return null;
}
+ private void showPropertyDistribution(NamedClass cls, Model model){
+ Query query = QueryFactory.create("SELECT ?p (COUNT(distinct ?s) AS ?cnt) (COUNT(distinct ?x) AS ?negCnt) WHERE {" +
+ "?s ?p ?o. {?p a <http://www.w3.org/2002/07/owl#ObjectProperty>} UNION {?p a <http://www.w3.org/2002/07/owl#DatatypeProperty>}" +
+ "?s a <" + cls.getName() + ">. " +
+ "OPTIONAL{?x ?p ?o1. " +
+ "FILTER NOT EXISTS{?x a <" + cls.getName() + ">.}}} "
+ + "GROUP BY ?p ORDER BY DESC(?cnt)", Syntax.syntaxARQ);
+
+ System.out.println(ResultSetFormatter.asText(QueryExecutionFactory.create(query, model).execSelect()));
+ }
+
private void cleanUp(Model model){
String dbo = "http://dbpedia.org/ontology/";
Set<String> blackList = Sets.newHashSet(
@@ -591,6 +715,33 @@
return classes;
}
+ private synchronized void write2DB(FastInstanceChecker reasoner, AbstractLearningProblem lp, NamedClass cls, TreeSet<? extends EvaluatedDescription> evaluatedDescriptions, Map<RelevanceMetric, Map<Entity, Double>> entityRelevances) throws SQLException{
+ int position = 1;
+ for(EvaluatedDescription ed : evaluatedDescriptions.descendingSet()) {
+ String clsName = cls.getName();
+ String expression = replaceDataPropertyRanges(ed.getDescription()).toManchesterSyntaxString(reasoner.getBaseURI(), reasoner.getPrefixes());
+ HashCode hc = hf.newHasher()
+ .putString(clsName, Charsets.UTF_8)
+ .putString(expression, Charsets.UTF_8)
+ .hash();
+ String id = hc.toString();
+ double fMeasure = ((PosNegLPStandard)lp).getAccuracyOrTooWeakExact(ed.getDescription(), noiseInPercentage/100d);
+ ps.setString(1, id);
+ ps.setString(2, cls.getName());
+ ps.setInt(3, position++);
+ ps.setString(4, expression);
+ ps.setDouble(5, fMeasure);
+ int col = 6;
+ for (RelevanceMetric metric : relevanceMetrics) {
+ double relevanceScore = getRelevanceScore(ed.getDescription(), entityRelevances.get(metric));
+ ps.setDouble(col++, relevanceScore);
+ }
+
+ ps.addBatch();
+ }
+ ps.executeBatch();
+ }
+
public static void main(String[] args) throws Exception {
// ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
// String cls = "http://dbpedia.org/ontology/Astronaut";
@@ -607,8 +758,11 @@
// la.setPattern(DLLearnerAxiomConvertVisitor.getDLLearnerAxiom(pattern));
// la.start();
+ long start = System.currentTimeMillis();
+ new DBpediaExperiment().run();
+// new DBpediaExperiment().run(new NamedClass("http://dbpedia.org/ontology/SoccerClub"));
+ long end = System.currentTimeMillis();
+ logger.info("Operation took " + (end - start) + "ms");
- new DBpediaExperiment().run();
-// new DBpediaExperiment().run(new NamedClass("http://dbpedia.org/ontology/Astronaut"));
}
}
Modified: trunk/components-core/src/test/java/org/dllearner/algorithms/isle/KnowledgebaseSampleGenerator.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/algorithms/isle/KnowledgebaseSampleGenerator.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/test/java/org/dllearner/algorithms/isle/KnowledgebaseSampleGenerator.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -136,7 +136,7 @@
Model cbd;
for (Individual individual : individuals) {
try {
- Thread.sleep(500);
+ Thread.sleep(100);
} catch (InterruptedException e) {
e.printStackTrace();
}
Modified: trunk/components-core/src/test/java/org/dllearner/algorithms/isle/metrics/RelevanceMetricsTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/algorithms/isle/metrics/RelevanceMetricsTest.java 2014-02-13 11:47:52 UTC (rev 4223)
+++ trunk/components-core/src/test/java/org/dllearner/algorithms/isle/metrics/RelevanceMetricsTest.java 2014-02-16 15:59:43 UTC (rev 4224)
@@ -62,7 +62,7 @@
relevance = metric.getRelevance(entity1, entity2);
System.out.println(relevance);
- // dbo:Person and dbo:Animal
+ // dbo:Person and dbo:birthPlace
entity1 = new NamedClass(DBPEDIA_NS + "Person");
entity2 = new ObjectProperty(DBPEDIA_NS + "birthPlace");
relevance = metric.getRelevance(entity1, entity2);
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