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[DL-Learner SVN] SF.net SVN: dl-learner:[3834] trunk/components-core
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From: <lor...@us...> - 2012-08-23 13:19:14
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Revision: 3834
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3834&view=rev
Author: lorenz_b
Date: 2012-08-23 13:19:03 +0000 (Thu, 23 Aug 2012)
Log Message:
-----------
Started feature to explain score in enrichment algorithms and return pos and neg examples.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner2.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2012-08-23 13:13:39 UTC (rev 3833)
+++ trunk/components-core/pom.xml 2012-08-23 13:19:03 UTC (rev 3834)
@@ -242,7 +242,12 @@
<artifactId>jsexp</artifactId>
<version>0.1.0</version>
</dependency>
-
+
+ <dependency>
+ <groupId>xerces</groupId>
+ <artifactId>xercesImpl</artifactId>
+ <version>2.8.0</version>
+ </dependency>
</dependencies>
<dependencyManagement>
<dependencies>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2012-08-23 13:13:39 UTC (rev 3833)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2012-08-23 13:19:03 UTC (rev 3834)
@@ -20,6 +20,11 @@
package org.dllearner.algorithms.properties;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
import org.dllearner.core.AbstractAxiomLearningAlgorithm;
import org.dllearner.core.ComponentAnn;
@@ -27,12 +32,14 @@
import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.config.ObjectPropertyEditor;
import org.dllearner.core.owl.FunctionalObjectPropertyAxiom;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import com.hp.hpl.jena.query.ParameterizedSparqlString;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Model;
@@ -51,6 +58,8 @@
public FunctionalObjectPropertyAxiomLearner(SparqlEndpointKS ks){
this.ks = ks;
+ posExamplesQueryTemplate = new ParameterizedSparqlString("SELECT ?s WHERE {?s ?p ?o1. FILTER NOT EXISTS {?s ?p ?o2. FILTER(?o1 != ?o2)} }");
+ negExamplesQueryTemplate = new ParameterizedSparqlString("SELECT ?s WHERE {?s ?p ?o1. ?s ?p ?o2. FILTER(?o1 != ?o2)}");
}
public ObjectProperty getPropertyToDescribe() {
@@ -59,6 +68,8 @@
public void setPropertyToDescribe(ObjectProperty propertyToDescribe) {
this.propertyToDescribe = propertyToDescribe;
+ posExamplesQueryTemplate.setIri("p", propertyToDescribe.getURI().toString());
+ negExamplesQueryTemplate.setIri("p", propertyToDescribe.getURI().toString());
}
@Override
@@ -86,36 +97,36 @@
}
private void runSPARQL1_0_Mode() {
- Model model = ModelFactory.createDefaultModel();
+ workingModel = ModelFactory.createDefaultModel();
int limit = 1000;
int offset = 0;
String baseQuery = "CONSTRUCT {?s <%s> ?o.} WHERE {?s <%s> ?o} LIMIT %d OFFSET %d";
String query = String.format(baseQuery, propertyToDescribe.getName(), propertyToDescribe.getName(), limit, offset);
Model newModel = executeConstructQuery(query);
while(!terminationCriteriaSatisfied() && newModel.size() != 0){System.out.println(query);
- model.add(newModel);
+ workingModel.add(newModel);
// get number of instances of s with <s p o>
query = String.format(
"SELECT (COUNT(DISTINCT ?s) AS ?all) WHERE {?s <%s> ?o.}",
propertyToDescribe.getName());
- ResultSet rs = executeSelectQuery(query, model);
+ ResultSet rs = executeSelectQuery(query, workingModel);
QuerySolution qs;
int all = 1;
while (rs.hasNext()) {
qs = rs.next();
all = qs.getLiteral("all").getInt();
}
- System.out.println(all);
+
// get number of instances of s with <s p o> <s p o1> where o != o1
query = "SELECT (COUNT(DISTINCT ?s) AS ?functional) WHERE {?s <%s> ?o1. FILTER NOT EXISTS {?s <%s> ?o2. FILTER(?o1 != ?o2)} }";
query = query.replace("%s", propertyToDescribe.getURI().toString());
- rs = executeSelectQuery(query, model);
+ rs = executeSelectQuery(query, workingModel);
int functional = 1;
while (rs.hasNext()) {
qs = rs.next();
functional = qs.getLiteral("functional").getInt();
}
- System.out.println(functional);
+
if (all > 0) {
currentlyBestAxioms.clear();
currentlyBestAxioms.add(new EvaluatedAxiom(
@@ -155,13 +166,21 @@
}
public static void main(String[] args) throws Exception{
- FunctionalObjectPropertyAxiomLearner l = new FunctionalObjectPropertyAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW()));
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/wikiPageExternalLink"));
- l.setMaxExecutionTimeInSeconds(10);
-// l.setForceSPARQL_1_0_Mode(true);
+ FunctionalObjectPropertyAxiomLearner l = new FunctionalObjectPropertyAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia()));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/league"));
+ l.setMaxExecutionTimeInSeconds(20);
+ l.setForceSPARQL_1_0_Mode(true);
l.init();
l.start();
- System.out.println(l.getCurrentlyBestEvaluatedAxioms(5));
+ List<EvaluatedAxiom> axioms = l.getCurrentlyBestEvaluatedAxioms(5);
+ System.out.println(axioms);
+
+ for(EvaluatedAxiom axiom : axioms){
+ printSubset(l.getPositiveExamples(axiom), 10);
+ printSubset(l.getNegativeExamples(axiom), 10);
+ l.explainScore(axiom);
+ }
+
}
}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner2.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner2.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner2.java 2012-08-23 13:19:03 UTC (rev 3834)
@@ -0,0 +1,221 @@
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.dllearner.algorithms.properties;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedSet;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.core.AbstractAxiomLearningAlgorithm;
+import org.dllearner.core.ComponentAnn;
+import org.dllearner.core.EvaluatedAxiom;
+import org.dllearner.core.config.ConfigOption;
+import org.dllearner.core.config.ObjectPropertyEditor;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.ObjectPropertyDomainAxiom;
+import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.hp.hpl.jena.query.ParameterizedSparqlString;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.vocabulary.RDFS;
+
+@ComponentAnn(name="objectproperty domain axiom learner", shortName="opldomain", version=0.1)
+public class ObjectPropertyDomainAxiomLearner2 extends AbstractAxiomLearningAlgorithm {
+
+ private static final Logger logger = LoggerFactory.getLogger(ObjectPropertyDomainAxiomLearner2.class);
+
+ private Map<Individual, SortedSet<Description>> individual2Types;
+
+
+ @ConfigOption(name="propertyToDescribe", description="", propertyEditorClass=ObjectPropertyEditor.class)
+ private ObjectProperty propertyToDescribe;
+
+ public ObjectPropertyDomainAxiomLearner2(SparqlEndpointKS ks){
+ this.ks = ks;
+ super.posExamplesQueryTemplate = new ParameterizedSparqlString("SELECT DISTINCT ?s WHERE {?s a ?type}");
+ super.negExamplesQueryTemplate = new ParameterizedSparqlString("SELECT DISTINCT ?s WHERE {?s ?p ?o. FILTER NOT EXISTS{?s a ?type}}");
+
+ }
+
+ public ObjectProperty getPropertyToDescribe() {
+ return propertyToDescribe;
+ }
+
+ public void setPropertyToDescribe(ObjectProperty propertyToDescribe) {
+ this.propertyToDescribe = propertyToDescribe;
+// negExamplesQueryTemplate.clearParams();
+// posExamplesQueryTemplate.clearParams();
+ }
+
+ @Override
+ public void start() {
+ iterativeQueryTemplate.setIri("p", propertyToDescribe.getName());
+ logger.info("Start learning...");
+ startTime = System.currentTimeMillis();
+ fetchedRows = 0;
+ currentlyBestAxioms = new ArrayList<EvaluatedAxiom>();
+
+ if(returnOnlyNewAxioms){
+ //get existing domains
+ Description existingDomain = reasoner.getDomain(propertyToDescribe);
+ if(existingDomain != null){
+ existingAxioms.add(new ObjectPropertyDomainAxiom(propertyToDescribe, existingDomain));
+ if(reasoner.isPrepared()){
+ if(reasoner.getClassHierarchy().contains(existingDomain)){
+ for(Description sup : reasoner.getClassHierarchy().getSuperClasses(existingDomain)){
+ existingAxioms.add(new ObjectPropertyDomainAxiom(propertyToDescribe, existingDomain));
+ logger.info("Existing domain(inferred): " + sup);
+ }
+ }
+
+ }
+ }
+ }
+
+ runSPARQL1_0_Mode();
+ logger.info("...finished in {}ms.", (System.currentTimeMillis()-startTime));
+ }
+
+ private void runSPARQL1_0_Mode() {
+ workingModel = ModelFactory.createDefaultModel();
+ int limit = 1000;
+ int offset = 0;
+ String baseQuery = "CONSTRUCT {?s a ?type.} WHERE {?s <%s> ?o. ?s a ?type.} LIMIT %d OFFSET %d";
+ String query = String.format(baseQuery, propertyToDescribe.getName(), limit, offset);
+ Model newModel = executeConstructQuery(query);
+ while(!terminationCriteriaSatisfied() && newModel.size() != 0){
+ workingModel.add(newModel);
+ // get number of distinct subjects
+ query = "SELECT (COUNT(DISTINCT ?s) AS ?all) WHERE {?s a ?type.}";
+ ResultSet rs = executeSelectQuery(query, workingModel);
+ QuerySolution qs;
+ int all = 1;
+ while (rs.hasNext()) {
+ qs = rs.next();
+ all = qs.getLiteral("all").getInt();
+ }
+
+ // get class and number of instances
+ query = "SELECT ?type (COUNT(DISTINCT ?s) AS ?cnt) WHERE {?s a ?type.} GROUP BY ?type";
+ rs = executeSelectQuery(query, workingModel);
+
+ if (all > 0) {
+ currentlyBestAxioms.clear();
+ while(rs.hasNext()){
+ qs = rs.next();
+ Resource type = qs.get("type").asResource();
+ //omit owl:Thing as trivial domain
+ if(type.equals(OWL.Thing)){
+ continue;
+ }
+ currentlyBestAxioms.add(new EvaluatedAxiom(
+ new ObjectPropertyDomainAxiom(propertyToDescribe, new NamedClass(type.getURI())),
+ computeScore(all, qs.get("cnt").asLiteral().getInt())));
+ }
+
+ }
+ offset += limit;
+ query = String.format(baseQuery, propertyToDescribe.getName(), limit, offset);
+ newModel = executeConstructQuery(query);
+ fillWithInference(newModel);
+ }
+ }
+
+ private void fillWithInference(Model model){
+ Model additionalModel = ModelFactory.createDefaultModel();
+ if(reasoner.isPrepared()){
+ for(StmtIterator iter = model.listStatements(null, RDF.type, (RDFNode)null); iter.hasNext();){
+ Statement st = iter.next();
+ Description cls = new NamedClass(st.getObject().asResource().getURI());
+ if(reasoner.getClassHierarchy().contains(cls)){
+ for(Description sup : reasoner.getClassHierarchy().getSuperClasses(cls)){
+ additionalModel.add(st.getSubject(), st.getPredicate(), model.createResource(sup.toString()));
+ }
+ }
+ }
+ }
+ model.add(additionalModel);
+ }
+
+ @Override
+ protected SortedSet<Individual> getPositiveExamples(EvaluatedAxiom evAxiom) {
+ ObjectPropertyDomainAxiom axiom = (ObjectPropertyDomainAxiom) evAxiom.getAxiom();
+ posExamplesQueryTemplate.setIri("type", axiom.getDomain().toString());
+ return super.getPositiveExamples(evAxiom);
+ }
+
+ @Override
+ protected SortedSet<Individual> getNegativeExamples(EvaluatedAxiom evAxiom) {
+ ObjectPropertyDomainAxiom axiom = (ObjectPropertyDomainAxiom) evAxiom.getAxiom();
+ negExamplesQueryTemplate.setIri("type", axiom.getDomain().toString());
+ return super.getNegativeExamples(evAxiom);
+ }
+
+ public static void main(String[] args) throws Exception{
+ org.apache.log4j.Logger.getRootLogger().addAppender(new ConsoleAppender(new SimpleLayout()));
+ org.apache.log4j.Logger.getRootLogger().setLevel(Level.INFO);
+ org.apache.log4j.Logger.getLogger(DataPropertyDomainAxiomLearner.class).setLevel(Level.INFO);
+
+ SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
+
+ SPARQLReasoner reasoner = new SPARQLReasoner(ks);
+ reasoner.prepareSubsumptionHierarchy();
+
+
+ ObjectPropertyDomainAxiomLearner2 l = new ObjectPropertyDomainAxiomLearner2(ks);
+ l.setReasoner(reasoner);
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/league"));
+ l.setMaxFetchedRows(20000);
+ l.setMaxExecutionTimeInSeconds(20);
+ l.addFilterNamespace("http://dbpedia.org/ontology/");
+// l.setReturnOnlyNewAxioms(true);
+ l.init();
+ l.start();
+
+ List<EvaluatedAxiom> axioms = l.getCurrentlyBestEvaluatedAxioms(10, 0.3);
+ System.out.println(axioms);
+ for(EvaluatedAxiom axiom : axioms){
+ printSubset(l.getPositiveExamples(axiom), 10);
+ printSubset(l.getNegativeExamples(axiom), 10);
+ l.explainScore(axiom);
+ }
+ }
+
+}
Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-08-23 13:13:39 UTC (rev 3833)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-08-23 13:19:03 UTC (rev 3834)
@@ -24,6 +24,7 @@
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -37,6 +38,7 @@
import org.dllearner.core.owl.Axiom;
import org.dllearner.core.owl.ClassHierarchy;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
import org.dllearner.kb.SparqlEndpointKS;
@@ -116,6 +118,11 @@
protected ParameterizedSparqlString iterativeQueryTemplate;
+ protected Model workingModel;
+ protected ParameterizedSparqlString posExamplesQueryTemplate;
+ protected ParameterizedSparqlString negExamplesQueryTemplate;
+
+
public AbstractAxiomLearningAlgorithm() {
existingAxioms = new TreeSet<Axiom>(new AxiomComparator());
}
@@ -255,7 +262,7 @@
}
- protected Model executeConstructQuery(String query) {
+ protected Model executeConstructQuery(String query) {System.out.println(query);
logger.debug("Sending query\n{} ...", query);
if(ks.isRemote()){
SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
@@ -266,7 +273,12 @@
queryExecution.setNamedGraphURIs(endpoint.getNamedGraphURIs());
try {
Model model = queryExecution.execConstruct();
+ fetchedRows += model.size();
timeout = false;
+ if(model.size() == 0){
+ fullDataLoaded = true;
+ }
+
return model;
} catch (QueryExceptionHTTP e) {
if(e.getCause() instanceof SocketTimeoutException){
@@ -277,8 +289,13 @@
return ModelFactory.createDefaultModel();
}
} else {
- QueryExecution qexec = QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
- return qexec.execConstruct();
+ QueryExecution queryExecution = QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
+ Model model = queryExecution.execConstruct();
+ fetchedRows += model.size();
+ if(model.size() == 0){
+ fullDataLoaded = true;
+ }
+ return model;
}
}
@@ -456,6 +473,67 @@
filterNamespaces.add(namespace);
}
+ protected SortedSet<Individual> getPositiveExamples(EvaluatedAxiom axiom){
+ if(workingModel != null){
+ SortedSet<Individual> posExamples = new TreeSet<Individual>();
+
+ ResultSet rs = executeSelectQuery(posExamplesQueryTemplate.toString(), workingModel);
+ while(rs.hasNext()){
+ posExamples.add(new Individual(rs.next().get("s").asResource().getURI()));
+ }
+
+ return posExamples;
+ } else {
+ throw new UnsupportedOperationException("Getting positive examples is not possible.");
+ }
+ }
+
+ protected SortedSet<Individual> getNegativeExamples(EvaluatedAxiom axiom){
+ if(workingModel != null){
+ SortedSet<Individual> negExamples = new TreeSet<Individual>();
+
+ ResultSet rs = executeSelectQuery(negExamplesQueryTemplate.toString(), workingModel);
+ while(rs.hasNext()){
+ negExamples.add(new Individual(rs.next().get("s").asResource().getURI()));
+ }
+
+ return negExamples;
+ } else {
+ throw new UnsupportedOperationException("Getting negative examples is not possible.");
+ }
+ }
+
+ protected void explainScore(EvaluatedAxiom evAxiom){
+ int posExampleCnt = getPositiveExamples(evAxiom).size();
+ int negExampleCnt = getNegativeExamples(evAxiom).size();
+ int total = posExampleCnt + negExampleCnt;
+ StringBuilder sb = new StringBuilder();
+ String lb = "\n";
+ sb.append("######################################").append(lb);
+ sb.append("Explanation:").append(lb);
+ sb.append("Score(").append(evAxiom.getAxiom()).append(") = ").append(evAxiom.getScore().getAccuracy()).append(lb);
+ sb.append("Total number of resources:\t").append(total).append(lb);
+ sb.append("Number of positive examples:\t").append(posExampleCnt).append(lb);
+ sb.append("Number of negative examples:\t").append(negExampleCnt).append(lb);
+ sb.append("Complete data processed:\t").append(fullDataLoaded).append(lb);
+ sb.append("######################################");
+ System.out.println(sb.toString());
+ }
+
+ protected static <E> void printSubset(Collection<E> collection, int maxSize){
+ StringBuffer sb = new StringBuffer();
+ int i = 0;
+ Iterator<E> iter = collection.iterator();
+ while(iter.hasNext() && i < maxSize){
+ sb.append(iter.next().toString()).append(", ");
+ i++;
+ }
+ if(iter.hasNext()){
+ sb.append("...(").append(collection.size()-i).append(" more)");
+ }
+ System.out.println(sb.toString());
+ }
+
protected <K,T extends Set<V>, V> void addToMap(Map<K, T> map, K key, V value ){
T values = map.get(key);
if(values == null){
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