Menu
▾
▴
[DL-Learner SVN] SF.net SVN: dl-learner:[4261] trunk/scripts/src/main
|
From: <lor...@us...> - 2014-05-07 11:25:58
|
Revision: 4261
http://sourceforge.net/p/dl-learner/code/4261
Author: lorenz_b
Date: 2014-05-07 11:25:54 +0000 (Wed, 07 May 2014)
Log Message:
-----------
Added eprocurement eval script.
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java
trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java
trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java
trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/UserEvaluation.java
trunk/scripts/src/main/resources/db_settings.ini
Added: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java 2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,91 @@
+package org.dllearner.scripts;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.text.DecimalFormat;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import org.dllearner.utilities.MapUtils;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.AxiomType;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+
+public class OWLAxiomsHTMLWriter {
+
+ public static void main(String[] args) throws Exception{
+ if(args.length != 2){
+ System.out.println("Usage: OWLAxiomsHTMLWriter <ontology> <targetFile>");
+ }
+ ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
+
+ String ontologyURL = args[0];
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLDataFactory dataFactory = man.getOWLDataFactory();
+ OWLOntology ontology = man.loadOntologyFromOntologyDocument(new File(ontologyURL));
+ OWLAnnotationProperty anProp = dataFactory.getOWLAnnotationProperty(IRI.create("http://www.dl-learner.org/ontologies/enrichment.owl#confidence"));
+
+ StringBuilder sb = new StringBuilder();
+ DecimalFormat dfPercent = new DecimalFormat("0.00%");
+ sb.append("<html>\n");
+ sb.append("<table border=\"3\">\n");
+ sb.append("<thead><tr><th>Source Class</th><th>Equivalent Class Expression</th><th>Accuracy</th></tr></thead>\n");
+ sb.append("<tbody>\n");
+
+ SortedMap<OWLClass, Map<OWLClassExpression, Double>> map = new TreeMap<OWLClass, Map<OWLClassExpression,Double>>();
+ for (OWLEquivalentClassesAxiom axiom : ontology.getAxioms(AxiomType.EQUIVALENT_CLASSES)) {
+ List<OWLClassExpression> classExpressionsAsList = axiom.getClassExpressionsAsList();
+ OWLClass left = classExpressionsAsList.get(0).asOWLClass();
+ if(!left.toStringID().startsWith("http://dbpedia.org/ontology/"))continue;//skip not DBpedia
+ OWLClassExpression right = classExpressionsAsList.get(1);
+ OWLLiteral lit = (OWLLiteral) axiom.getAnnotations(anProp).iterator().next().getValue();
+ double accuracy = lit.parseDouble();
+ Map<OWLClassExpression, Double> equivalentClasses = map.get(left);
+ if(equivalentClasses == null){
+ equivalentClasses = new HashMap<OWLClassExpression, Double>();
+ map.put(left, equivalentClasses);
+ }
+ equivalentClasses.put(right, accuracy);
+ }
+
+ for (Entry<OWLClass, Map<OWLClassExpression, Double>> entry : map.entrySet()) {
+ OWLClass cls = entry.getKey();
+ Map<OWLClassExpression, Double> equivalentClasses = entry.getValue();
+ List<Entry<OWLClassExpression, Double>> sorted = MapUtils.sortByValues(equivalentClasses);
+ sb.append("<tr><th rowspan=\"" + (sorted.size()+1) + "\">" + cls.toString() + "</th>\n");
+ for (Entry<OWLClassExpression, Double> expr : sorted) {
+ OWLClassExpression classExpression = expr.getKey();
+ Double value = expr.getValue();
+ sb.append("<tr>");
+ sb.append("<td>" + classExpression.toString() + "</td>");
+ sb.append("<td>" + dfPercent.format(value.doubleValue()) + "</td>");
+ sb.append("</tr>\n");
+ }
+
+ }
+
+ sb.append("</tbody>\n");
+ sb.append("</table>\n");
+ sb.append("</html>\n");
+
+ FileOutputStream fos = new FileOutputStream(new File(args[1]));
+ fos.write(sb.toString().getBytes());
+ fos.close();
+ }
+
+}
Added: trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java 2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,299 @@
+/**
+ *
+ */
+package org.dllearner.scripts;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FilenameFilter;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.algorithms.celoe.OEHeuristicRuntime;
+import org.dllearner.algorithms.elcopy.ELLearningAlgorithm;
+import org.dllearner.algorithms.qtl.QueryTreeFactory;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl;
+import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.kb.OWLAPIOntology;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.dllearner.refinementoperators.RhoDRDown;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.util.SimpleShortFormProvider;
+
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+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;
+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;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class RAChallenge {
+
+
+ private static boolean useEL = false;
+
+ static Map<String, String> prefixes = new HashMap<>();
+
+ private static String baseURI = "http://bio2rdf.org/ra.challenge:";
+
+ static {
+
+// prefixes.put("ra", "http://bio2rdf.org/ra.challenge:");
+ prefixes.put("ra-voc", "http://bio2rdf.org/ra.challenge_vocabulary:");
+ prefixes.put("dbsnp", "http://bio2rdf.org/dbsnp:");
+ prefixes.put("xsd", "http://www.w3.org/2001/XMLSchema#");
+ prefixes.put("foaf", "http://xmlns.com/foaf/0.1/");
+ prefixes.put("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
+ prefixes.put("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
+ prefixes.put("drug-voc", "http://bio2rdf.org/drugbank_vocabulary:");
+
+
+ }
+
+ public static void main(String[] args) throws Exception{
+ //load the data
+ File dataDir = new File(args[0]);
+ File[] files = dataDir.listFiles(new FilenameFilter() {
+ @Override
+ public boolean accept(File dir, String name) {
+ return name.endsWith(".nt") || name.endsWith(".ttl") || name.endsWith(".rdf") || name.endsWith(".owl");
+ }
+ });
+ System.out.println("loading data...");
+ Model model = ModelFactory.createDefaultModel();
+ for (File file : files) {
+ model.read(new FileInputStream(file), null, "TURTLE");
+ }
+
+ analyzeData(model);
+
+ //get the positive and negative examples via SPARQL
+ //<http://bio2rdf.org/ra.challenge:1877000> <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
+ System.out.println("extracting pos/neg examples...");
+ SortedSet<Individual> posExamples = new TreeSet<Individual>();
+ SortedSet<Individual> negExamples = new TreeSet<Individual>();
+ String query = "SELECT ?s WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>} limit 400";
+ QueryExecution qe = QueryExecutionFactory.create(query, model);
+ ResultSet rs = qe.execSelect();
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ posExamples.add(new Individual(qs.getResource("s").getURI()));
+ }
+ query = "SELECT ?s WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"false\"^^<http://www.w3.org/2001/XMLSchema#boolean>} limit 400";
+ qe = QueryExecutionFactory.create(query, model);
+ rs = qe.execSelect();
+ while(rs.hasNext()){
+ qs = rs.next();
+ negExamples.add(new Individual(qs.getResource("s").getURI()));
+ }
+ qe.close();
+ System.out.println("#pos examples: " + posExamples.size());
+ System.out.println("#neg examples: " + negExamples.size());
+
+ //remove triples with property non-responder
+ model.remove(model.listStatements(null, model.createProperty("http://bio2rdf.org/ra.challenge_vocabulary:non-responder"), (RDFNode)null));
+
+ //enrich with additional data
+ enrich(model);
+
+ //check the LGG
+// computeLGG(model, posExamples);
+
+ //convert JENA model to OWL API ontology
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ model.write(baos , "N-TRIPLES");
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology ontology = man.loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray()));
+
+ //init knowledge source
+ KnowledgeSource ks = new OWLAPIOntology(ontology);
+
+ //init reasoner
+ System.out.println("initializing reasoner...");
+ OWLAPIReasoner baseReasoner = new OWLAPIReasoner(ks);
+// baseReasoner.setReasonerTypeString("elk");
+ baseReasoner.init();
+ FastInstanceChecker rc = new FastInstanceChecker(ks);
+ rc.setReasonerComponent(baseReasoner);
+ rc.setBaseURI(baseURI);
+ rc.setPrefixes(prefixes);
+ rc.init();
+
+ //init learning problem
+ System.out.println("initializing learning problem...");
+ PosNegLPStandard lp = new PosNegLPStandard(rc, posExamples, negExamples);
+ lp.setUseApproximations(true);
+ lp.init();
+
+ //init learning algorithm
+ System.out.println("initializing learning algorithm...");
+ AbstractCELA la;
+ if(useEL){
+ la = new ELLearningAlgorithm(lp, rc);
+ ((ELLearningAlgorithm) la).setNoisePercentage(30);
+ ((ELLearningAlgorithm) la).setMaxNrOfResults(50);
+ ((ELLearningAlgorithm) la).setTreeSearchTimeSeconds(10);
+ } else {
+ OEHeuristicRuntime heuristic = new OEHeuristicRuntime();
+ heuristic.setExpansionPenaltyFactor(0.1);
+ la = new CELOE(lp, rc);
+ ((CELOE) la).setHeuristic(heuristic);
+ ((CELOE) la).setMaxExecutionTimeInSeconds(100);
+ ((CELOE) la).setNoisePercentage(50);
+ ((CELOE) la).setMaxNrOfResults(50);
+ ((CELOE) la).setWriteSearchTree(true);
+ ((CELOE) la).setReplaceSearchTree(true);
+ ((CELOE) la).setStartClass(new NamedClass("http://xmlns.com/foaf/0.1/Person"));
+ RhoDRDown op = new RhoDRDown();
+ op.setUseHasValueConstructor(true);
+ op.setUseObjectValueNegation(true);
+ op.setReasoner(rc);
+ op.init();
+// ((CELOE) la).setOperator(op);
+ }
+ la.init();
+
+ la.start();
+ }
+
+ /**
+ * Do some statistical queries.
+ * @param model
+ */
+ private static void analyzeData(Model model){
+ String query = "SELECT (COUNT(DISTINCT ?s)AS ?cnt) WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o.} ";
+ QueryExecution qe = QueryExecutionFactory.create(query, model);
+ ResultSet rs = qe.execSelect();
+ System.out.println(ResultSetFormatter.asText(rs));
+
+ query = "SELECT ?o (COUNT(?s) AS ?cnt) WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+// + "OPTIONAL{?s_res <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>.FILTER(?s=s_res)} "
+// + "?s_non_res <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"false\"^^<http://www.w3.org/2001/XMLSchema#boolean>"
+ + "}"
+ + " GROUP BY ?o ORDER BY DESC(?cnt)";
+ qe = QueryExecutionFactory.create(query, model);
+ rs = qe.execSelect();
+ System.out.println(ResultSetFormatter.asText(rs));
+
+ query = "SELECT ?o (COUNT(?s) AS ?cnt) WHERE {"
+ + "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+ + "?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>."
+ + "}"
+ + " GROUP BY ?o ORDER BY DESC(?cnt)";
+ qe = QueryExecutionFactory.create(query, model);
+ rs = qe.execSelect();
+ System.out.println(ResultSetFormatter.asText(rs));
+
+ query = "SELECT ?o (COUNT(?s) AS ?total) (Min(?cnt_res) as ?responder) (Min(?cnt_non_res) as ?non_responder) WHERE {"
+ + "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+ + "{SELECT ?o (COUNT(?s) AS ?cnt_res) WHERE {"
+ + "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+ + "?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>."
+ + "} GROUP BY ?o}"
+ + "{SELECT ?o (COUNT(?s) AS ?cnt_non_res) WHERE {"
+ + "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+ + "?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"false\"^^<http://www.w3.org/2001/XMLSchema#boolean>."
+ + "}"
+ + " GROUP BY ?o}} GROUP BY ?o ORDER BY DESC(?total)";
+ qe = QueryExecutionFactory.create(query, model);
+ rs = qe.execSelect();
+ System.out.println(ResultSetFormatter.asText(rs));
+ }
+
+ private static void computeLGG(Model model, SortedSet<Individual> posExamples){
+ QueryTreeFactory<String> queryTreeFactory = new QueryTreeFactoryImpl();
+
+ List<QueryTree<String>> posExampleTrees = new ArrayList<QueryTree<String>>();
+ for (Individual ex : posExamples) {
+ QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex.getName(), model);
+ posExampleTrees.add(tree);
+ }
+
+ LGGGenerator<String> lggGenerator = new LGGGeneratorImpl<String>();
+ QueryTree<String> lgg = lggGenerator.getLGG(posExampleTrees);
+ String lggString = lgg.getStringRepresentation(true);
+ lggString = lggString.replace(baseURI, "");
+ for (Entry<String, String> entry : prefixes.entrySet()) {
+ String key = entry.getKey();
+ String value = entry.getValue();
+ lggString = lggString.replace(value, key + ":");
+ }
+ System.out.println(lggString);
+
+ OWLClassExpression classExpression = lgg.asOWLClassExpression();
+ ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
+ ToStringRenderer.getInstance().setShortFormProvider(new SimpleShortFormProvider());
+ System.out.println(classExpression);
+ }
+
+ private static void enrich(Model model) throws MalformedURLException, FileNotFoundException{
+ System.out.println("enriching data...");
+ SparqlEndpoint endpoint = new SparqlEndpoint(new URL("http://cu.drugbank.bio2rdf.org/sparql"));
+
+// StmtIterator stmtIterator = model.listStatements(null, RDF.type, (RDFNode)null);
+// Model classes = ModelFactory.createDefaultModel();
+// while(stmtIterator.hasNext()){
+// Statement st = stmtIterator.next();
+// classes.add(classes.createStatement(st.getObject().asResource(), RDF.type, OWL.Class));
+// }
+// classes.write(new FileOutputStream("classes.nt"), "TURTLE");
+
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(endpoint, "cache/drugbank");
+ List<RDFNode> drugs = model.listObjectsOfProperty(model.getProperty("http://bio2rdf.org/ra.challenge_vocabulary:drug")).toList();
+ Model drugbankData = ModelFactory.createDefaultModel();
+ Model cbd;
+ for (RDFNode drug : drugs) {
+ cbd = cbdGen.getConciseBoundedDescription(drug.asResource().getURI(), 0, true);
+ drugbankData.add(cbd);
+ }
+ drugbankData.setNsPrefix("drug-voc", "http://bio2rdf.org/drugbank_vocabulary:");
+ drugbankData.setNsPrefix("drug-res", "http://bio2rdf.org/drugbank_resource:");
+ drugbankData.setNsPrefix("drug", "http://bio2rdf.org/drugbank:");
+
+ drugbankData.write(new FileOutputStream("drugbank.ttl"), "TURTLE", null);
+ model.add(drugbankData);
+
+
+ }
+}
Added: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java 2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,290 @@
+/**
+ *
+ */
+package org.dllearner.scripts.evaluation;
+
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SIBLING;
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SUPERCLASS;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.SortedSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.algorithms.elcopy.ELLearningAlgorithm;
+import org.dllearner.algorithms.qtl.QueryTreeFactory;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl;
+import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.AbstractKnowledgeSource;
+import org.dllearner.core.AbstractLearningProblem;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
+import org.dllearner.kb.OWLAPIOntology;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.dllearner.refinementoperators.RhoDRDown;
+import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2;
+import org.dllearner.utilities.owl.OWLEntityTypeAdder;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import com.google.common.collect.Sets;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDFS;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class EProcurementUseCase {
+
+
+ private static final Logger logger = Logger.getLogger(EProcurementUseCase.class.getName());
+ static final int maxNrOfPositiveExamples = 100;
+ static final int maxNrOfNegativeExamples = 200;
+ static boolean posOnly = false;
+ static int maxCBDDepth = 2;
+ static int maxNrOfResults = 100;
+ static int maxExecutionTimeInSeconds = 200;
+ static double noiseInPercentage = 50;
+ static boolean useNegation = false;
+ static boolean useAllConstructor = false;
+ static String testFolder = "logs/eprocurement";
+
+ static boolean useEL = false;
+ private static int maxClassExpressionDepth = 2;
+
+ static Map<String, String> prefixes = new HashMap<String, String>();;
+ static {
+ prefixes.put("pc", "http://purl.org/procurement/public-contracts#");
+ prefixes.put("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
+ prefixes.put("skos", "http://www.w3.org/2004/02/skos/core#");
+ prefixes.put("dcterms", "http://purl.org/dc/terms/");
+ prefixes.put("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
+ prefixes.put("activities", "http://purl.org/procurement/public-contracts-activities#");
+ prefixes.put("gr", "http://purl.org/goodrelations/v1#");
+ prefixes.put("schema", "http://schema.org/");
+
+
+ }
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) throws Exception{
+ NamedClass posClass = new NamedClass("http://purl.org/procurement/public-contracts#SuccessfulTender");
+ NamedClass negClass = new NamedClass("http://purl.org/procurement/public-contracts#UnsuccessfulTender");
+
+ //1. setup the knowledge base
+ Model model = ModelFactory.createDefaultModel();
+ //the data
+ model.read(new FileInputStream("../test/eprocurement/dl-learner-sample-with-classes-pco.rdf"), null);
+ //the schema
+ Model schema = ModelFactory.createDefaultModel();
+ schema.read(new FileInputStream("../test/eprocurement/pco.rdf"), null);
+ schema.add(schema.getResource("http://purl.org/procurement/public-contracts#SuccessfulTender"),
+ OWL.disjointWith,
+ schema.getResource("http://purl.org/procurement/public-contracts#UnsuccessfulTender"));
+ schema.add(schema.getResource("http://purl.org/procurement/public-contracts#SuccessfulTender"),
+ RDFS.subClassOf,
+ schema.getResource("http://purl.org/procurement/public-contracts#Tender"));
+ schema.add(schema.getResource("http://purl.org/procurement/public-contracts#UnsuccessfulTender"),
+ RDFS.subClassOf,
+ schema.getResource("http://purl.org/procurement/public-contracts#Tender"));
+// schema.read(new URL("http://opendata.cz/pco/public-contracts.ttl").openStream(), null, "TURTLE");
+ model.add(schema);
+ // get positive examples
+ SortedSet<Individual> positiveExamples = getExamples(model, posClass);
+ // get negative examples
+// SortedSet<Individual> negativeExamples = getNegativeExamples(model, cls, positiveExamples);
+ SortedSet<Individual> negativeExamples = getExamples(model, negClass);
+ //get the lgg of the pos. examples
+// showLGG(model, positiveExamples);
+ // build a sample of the kb
+ model = getSample(model, Sets.union(positiveExamples, negativeExamples));
+ //add inferred entity types
+ OWLEntityTypeAdder.addEntityTypes(model);
+ //the ontology
+ model.add(schema);
+ //convert all into DL-Learner kb object
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ model.write(baos, "TURTLE");
+ OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray()));
+ AbstractKnowledgeSource ks = new OWLAPIOntology(ontology);
+ ks.init();
+
+
+
+ //2. setup the reasoner
+ AbstractReasonerComponent rc = new FastInstanceChecker(ks);
+ rc.init();
+
+ //3. setup the learning problem
+ AbstractLearningProblem lp;
+// lp = new ClassLearningProblem(rc);
+// ((ClassLearningProblem)lp).setClassToDescribe(cls);
+// ((ClassLearningProblem)lp).setEquivalence(true);
+ lp = new PosNegLPStandard(rc, positiveExamples, negativeExamples);
+ lp.init();
+
+ //4. setup the learning algorithm
+ AbstractCELA la;
+ if(useEL){
+ la = new ELLearningAlgorithm(lp, rc);
+ ((ELLearningAlgorithm)la).setNoisePercentage(noiseInPercentage);
+// ((ELLearningAlgorithm)la).setStartClass(startClass);
+ ((ELLearningAlgorithm)la).setIgnoredConcepts(Sets.newHashSet(posClass));
+ ((ELLearningAlgorithm)la).setClassToDescribe(posClass);
+ ((ELLearningAlgorithm)la).setTreeSearchTimeSeconds(maxExecutionTimeInSeconds);
+ ((ELLearningAlgorithm)la).setMaxNrOfResults(maxNrOfResults);
+ ((ELLearningAlgorithm)la).setMaxClassExpressionDepth(maxClassExpressionDepth );
+// la = new ELLearningAlgorithmDisjunctive(lp, reasoner);
+ } else {
+ //set up the refinement operator and the allowed OWL constructs
+ RhoDRDown rop = new RhoDRDown();
+ rop.setReasoner(rc);
+ rop.setUseNegation(useNegation);
+ rop.setUseAllConstructor(useAllConstructor);
+ rop.init();
+ //build CELOE la
+ CELOE laTmp = new CELOE(lp, rc);
+ laTmp.setMaxNrOfResults(maxNrOfResults);
+ laTmp.setOperator(rop);
+ laTmp.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
+// laTmp.setStartClass(startClass);
+ laTmp.setNoisePercentage(noiseInPercentage);
+ new File(testFolder).mkdirs();
+ laTmp.setSearchTreeFile(testFolder + "searchTree.txt");
+ laTmp.setWriteSearchTree(true);
+// isle.setTerminateOnNoiseReached(true);
+ laTmp.setIgnoredConcepts(Collections.singleton(posClass));
+ laTmp.setReplaceSearchTree(true);
+ laTmp.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
+ laTmp.setExpandAccuracy100Nodes(true);
+ la = laTmp;
+ }
+ la.init();
+
+ //5. run
+ la.start();
+
+
+ }
+
+ private static void showLGG(Model model, SortedSet<Individual> positiveExamples){
+ LGGGenerator<String> lggGen = new LGGGeneratorImpl<String>();
+ QueryTree<String> lgg = lggGen.getLGG(buildTrees(model, positiveExamples));
+ String s = lgg.getStringRepresentation();
+ for (Entry<String, String> entry : prefixes.entrySet()) {
+ s = s.replace(entry.getValue(), entry.getKey() + ":");
+ }
+ System.out.println(s);
+ ((QueryTreeImpl<String>) lgg).asGraph();
+ }
+
+ private static SortedSet<Individual> getExamples(Model model, NamedClass cls){
+ logger.info("Generating examples...");
+ SortedSet<Individual> individuals = new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model)).getIndividuals(cls, 1000);
+ List<Individual> individualsList = new ArrayList<>(individuals);
+// Collections.shuffle(individualsList, new Random(1234));
+ individuals.clear();
+ individuals.addAll(individualsList.subList(0, Math.min(maxNrOfPositiveExamples, individualsList.size())));
+ logger.info("Done. Got " + individuals.size() + ": " + individuals);
+ return individuals;
+ }
+
+ private static SortedSet<Individual> getPositiveExamples(Model model, NamedClass cls){
+ logger.info("Generating positive examples...");
+ SortedSet<Individual> individuals = new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model)).getIndividuals(cls, 1000);
+ List<Individual> individualsList = new ArrayList<>(individuals);
+// Collections.shuffle(individualsList, new Random(1234));
+ individuals.clear();
+ individuals.addAll(individualsList.subList(0, Math.min(maxNrOfPositiveExamples, individualsList.size())));
+ logger.info("Done. Got " + individuals.size() + ": " + individuals);
+ return individuals;
+ }
+
+ private static SortedSet<Individual> getNegativeExamples(Model model, NamedClass classToDescribe, Set<Individual> positiveExamples){
+ logger.info("Generating positive examples...");
+ SortedSet<Individual> individuals = new AutomaticNegativeExampleFinderSPARQL2(new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model))).getNegativeExamples(classToDescribe, positiveExamples, Arrays.asList(SIBLING, SUPERCLASS), maxNrOfNegativeExamples);
+ logger.info("Done. Got " + individuals.size() + ": " + individuals);
+ return individuals;
+ }
+
+ private static Model getSample(Model model, Individual individual){
+ logger.info("Generating sample...");
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(model, maxCBDDepth);
+ Model sample = cbdGen.getConciseBoundedDescription(individual.getName(), maxCBDDepth, true);
+ logger.info("Done. Got " + sample.size() + " triples.");
+ return sample;
+ }
+
+ private static Model getSample(Model model, Set<Individual> individuals){
+ logger.info("Generating sample...");
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(model, maxCBDDepth);
+ Model sample = ModelFactory.createDefaultModel();
+ Model cbd;
+ for (Individual individual : individuals) {
+// System.out.println("##########################");
+// System.out.println(individual);
+ try {
+ cbd = cbdGen.getConciseBoundedDescription(individual.getName(), maxCBDDepth, true);
+// showTree(individual, model);
+ sample.add(cbd);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+ logger.info("Done. Got " + sample.size() + " triples.");
+ return sample;
+ }
+
+ private static QueryTree<String> buildTree(Individual ind, Model model){
+ QueryTreeFactory<String> qf = new QueryTreeFactoryImpl();
+ QueryTreeImpl<String> queryTree = qf.getQueryTree(ind.getName(), model);
+ return queryTree;
+ }
+
+ private static List<QueryTree<String>> buildTrees(Model model, Collection<Individual> individuals){
+ List<QueryTree<String>> trees = new ArrayList<QueryTree<String>>();
+ for (Individual individual : individuals) {
+ trees.add(buildTree(individual, getSample(model, individual)));
+ }
+ return trees;
+ }
+
+ private static void showTree(Individual ind, Model model){
+ QueryTree<String> tree = buildTree(ind, model);
+ String s = tree.getStringRepresentation();
+
+ for (Entry<String, String> entry : prefixes.entrySet()) {
+ s = s.replace(entry.getValue(), entry.getKey() + ":");
+ }
+ System.out.println(s);
+ }
+
+
+}
Added: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java 2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,516 @@
+/**
+ *
+ */
+package org.dllearner.scripts.evaluation;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Random;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.qtl.QTL2;
+import org.dllearner.algorithms.qtl.QTL2Disjunctive;
+import org.dllearner.algorithms.qtl.QueryTreeFactory;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
+import org.dllearner.cli.CrossValidation;
+import org.dllearner.cli.SPARQLCrossValidation;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
+import org.dllearner.kb.OWLAPIOntology;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChange;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import com.google.common.collect.Lists;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class QTLEvaluation {
+
+ int nrOfFolds = 10;
+ private int nrOfPosExamples = 100;
+ private int nrOfNegExamples = 100;
+
+ List<String> posExamples = Lists.newArrayList(
+ "http://dl-learner.org/carcinogenesis#d1",
+ "http://dl-learner.org/carcinogenesis#d10",
+ "http://dl-learner.org/carcinogenesis#d101",
+ "http://dl-learner.org/carcinogenesis#d102",
+ "http://dl-learner.org/carcinogenesis#d103",
+ "http://dl-learner.org/carcinogenesis#d106",
+ "http://dl-learner.org/carcinogenesis#d107",
+ "http://dl-learner.org/carcinogenesis#d108",
+ "http://dl-learner.org/carcinogenesis#d11",
+ "http://dl-learner.org/carcinogenesis#d12",
+ "http://dl-learner.org/carcinogenesis#d13",
+ "http://dl-learner.org/carcinogenesis#d134",
+ "http://dl-learner.org/carcinogenesis#d135",
+ "http://dl-learner.org/carcinogenesis#d136",
+ "http://dl-learner.org/carcinogenesis#d138",
+ "http://dl-learner.org/carcinogenesis#d140",
+ "http://dl-learner.org/carcinogenesis#d141",
+ "http://dl-learner.org/carcinogenesis#d144",
+ "http://dl-learner.org/carcinogenesis#d145",
+ "http://dl-learner.org/carcinogenesis#d146",
+ "http://dl-learner.org/carcinogenesis#d147",
+ "http://dl-learner.org/carcinogenesis#d15",
+ "http://dl-learner.org/carcinogenesis#d17",
+ "http://dl-learner.org/carcinogenesis#d19",
+ "http://dl-learner.org/carcinogenesis#d192",
+ "http://dl-learner.org/carcinogenesis#d193",
+ "http://dl-learner.org/carcinogenesis#d195",
+ "http://dl-learner.org/carcinogenesis#d196",
+ "http://dl-learner.org/carcinogenesis#d197",
+ "http://dl-learner.org/carcinogenesis#d198",
+ "http://dl-learner.org/carcinogenesis#d199",
+ "http://dl-learner.org/carcinogenesis#d2",
+ "http://dl-learner.org/carcinogenesis#d20",
+ "http://dl-learner.org/carcinogenesis#d200",
+ "http://dl-learner.org/carcinogenesis#d201",
+ "http://dl-learner.org/carcinogenesis#d202",
+ "http://dl-learner.org/carcinogenesis#d203",
+ "http://dl-learner.org/carcinogenesis#d204",
+ "http://dl-learner.org/carcinogenesis#d205",
+ "http://dl-learner.org/carcinogenesis#d21",
+ "http://dl-learner.org/carcinogenesis#d22",
+ "http://dl-learner.org/carcinogenesis#d226",
+ "http://dl-learner.org/carcinogenesis#d227",
+ "http://dl-learner.org/carcinogenesis#d228",
+ "http://dl-learner.org/carcinogenesis#d229",
+ "http://dl-learner.org/carcinogenesis#d231",
+ "http://dl-learner.org/carcinogenesis#d232",
+ "http://dl-learner.org/carcinogenesis#d234",
+ "http://dl-learner.org/carcinogenesis#d236",
+ "http://dl-learner.org/carcinogenesis#d239",
+ "http://dl-learner.org/carcinogenesis#d23_2",
+ "http://dl-learner.org/carcinogenesis#d242",
+ "http://dl-learner.org/carcinogenesis#d245",
+ "http://dl-learner.org/carcinogenesis#d247",
+ "http://dl-learner.org/carcinogenesis#d249",
+ "http://dl-learner.org/carcinogenesis#d25",
+ "http://dl-learner.org/carcinogenesis#d252",
+ "http://dl-learner.org/carcinogenesis#d253",
+ "http://dl-learner.org/carcinogenesis#d254",
+ "http://dl-learner.org/carcinogenesis#d255",
+ "http://dl-learner.org/carcinogenesis#d26",
+ "http://dl-learner.org/carcinogenesis#d272",
+ "http://dl-learner.org/carcinogenesis#d275",
+ "http://dl-learner.org/carcinogenesis#d277",
+ "http://dl-learner.org/carcinogenesis#d279",
+ "http://dl-learner.org/carcinogenesis#d28",
+ "http://dl-learner.org/carcinogenesis#d281",
+ "http://dl-learner.org/carcinogenesis#d283",
+ "http://dl-learner.org/carcinogenesis#d284",
+ "http://dl-learner.org/carcinogenesis#d288",
+ "http://dl-learner.org/carcinogenesis#d29",
+ "http://dl-learner.org/carcinogenesis#d290",
+ "http://dl-learner.org/carcinogenesis#d291",
+ "http://dl-learner.org/carcinogenesis#d292",
+ "http://dl-learner.org/carcinogenesis#d30",
+ "http://dl-learner.org/carcinogenesis#d31",
+ "http://dl-learner.org/carcinogenesis#d32",
+ "http://dl-learner.org/carcinogenesis#d33",
+ "http://dl-learner.org/carcinogenesis#d34",
+ "http://dl-learner.org/carcinogenesis#d35",
+ "http://dl-learner.org/carcinogenesis#d36",
+ "http://dl-learner.org/carcinogenesis#d37",
+ "http://dl-learner.org/carcinogenesis#d38",
+ "http://dl-learner.org/carcinogenesis#d42",
+ "http://dl-learner.org/carcinogenesis#d43",
+ "http://dl-learner.org/carcinogenesis#d44",
+ "http://dl-learner.org/carcinogenesis#d45",
+ "http://dl-learner.org/carcinogenesis#d46",
+ "http://dl-learner.org/carcinogenesis#d47",
+ "http://dl-learner.org/carcinogenesis#d48",
+ "http://dl-learner.org/carcinogenesis#d49",
+ "http://dl-learner.org/carcinogenesis#d5",
+ "http://dl-learner.org/carcinogenesis#d51",
+ "http://dl-learner.org/carcinogenesis#d52",
+ "http://dl-learner.org/carcinogenesis#d53",
+ "http://dl-learner.org/carcinogenesis#d55",
+ "http://dl-learner.org/carcinogenesis#d58",
+ "http://dl-learner.org/carcinogenesis#d6",
+ "http://dl-learner.org/carcinogenesis#d7",
+ "http://dl-learner.org/carcinogenesis#d84",
+ "http://dl-learner.org/carcinogenesis#d85_2",
+ "http://dl-learner.org/carcinogenesis#d86",
+ "http://dl-learner.org/carcinogenesis#d87",
+ "http://dl-learner.org/carcinogenesis#d88",
+ "http://dl-learner.org/carcinogenesis#d89",
+ "http://dl-learner.org/carcinogenesis#d9",
+ "http://dl-learner.org/carcinogenesis#d91",
+ "http://dl-learner.org/carcinogenesis#d92",
+ "http://dl-learner.org/carcinogenesis#d93",
+ "http://dl-learner.org/carcinogenesis#d95",
+ "http://dl-learner.org/carcinogenesis#d96",
+ "http://dl-learner.org/carcinogenesis#d98",
+ "http://dl-learner.org/carcinogenesis#d99",
+ "http://dl-learner.org/carcinogenesis#d100",
+ "http://dl-learner.org/carcinogenesis#d104",
+ "http://dl-learner.org/carcinogenesis#d105",
+ "http://dl-learner.org/carcinogenesis#d109",
+ "http://dl-learner.org/carcinogenesis#d137",
+ "http://dl-learner.org/carcinogenesis#d139",
+ "http://dl-learner.org/carcinogenesis#d14",
+ "http://dl-learner.org/carcinogenesis#d142",
+ "http://dl-learner.org/carcinogenesis#d143",
+ "http://dl-learner.org/carcinogenesis#d148",
+ "http://dl-learner.org/carcinogenesis#d16",
+ "http://dl-learner.org/carcinogenesis#d18",
+ "http://dl-learner.org/carcinogenesis#d191",
+ "http://dl-learner.org/carcinogenesis#d206",
+ "http://dl-learner.org/carcinogenesis#d230",
+ "http://dl-learner.org/carcinogenesis#d233",
+ "http://dl-learner.org/carcinogenesis#d235",
+ "http://dl-learner.org/carcinogenesis#d237",
+ "http://dl-learner.org/carcinogenesis#d238",
+ "http://dl-learner.org/carcinogenesis#d23_1",
+ "http://dl-learner.org/carcinogenesis#d24",
+ "http://dl-learner.org/carcinogenesis#d240",
+ "http://dl-learner.org/carcinogenesis#d241",
+ "http://dl-learner.org/carcinogenesis#d243",
+ "http://dl-learner.org/carcinogenesis#d244",
+ "http://dl-learner.org/carcinogenesis#d246",
+ "http://dl-learner.org/carcinogenesis#d248",
+ "http://dl-learner.org/carcinogenesis#d250",
+ "http://dl-learner.org/carcinogenesis#d251",
+ "http://dl-learner.org/carcinogenesis#d27",
+ "http://dl-learner.org/carcinogenesis#d273",
+ "http://dl-learner.org/carcinogenesis#d274",
+ "http://dl-learner.org/carcinogenesis#d278",
+ "http://dl-learner.org/carcinogenesis#d286",
+ "http://dl-learner.org/carcinogenesis#d289",
+ "http://dl-learner.org/carcinogenesis#d3",
+ "http://dl-learner.org/carcinogenesis#d39",
+ "http://dl-learner.org/carcinogenesis#d4",
+ "http://dl-learner.org/carcinogenesis#d40",
+ "http://dl-learner.org/carcinogenesis#d41",
+ "http://dl-learner.org/carcinogenesis#d50",
+ "http://dl-learner.org/carcinogenesis#d54",
+ "http://dl-learner.org/carcinogenesis#d56",
+ "http://dl-learner.org/carcinogenesis#d57",
+ "http://dl-learner.org/carcinogenesis#d8",
+ "http://dl-learner.org/carcinogenesis#d85_1",
+ "http://dl-learner.org/carcinogenesis#d90",
+ "http://dl-learner.org/carcinogenesis#d94",
+ "http://dl-learner.org/carcinogenesis#d97",
+ "http://dl-learner.org/carcinogenesis#d296",
+ "http://dl-learner.org/carcinogenesis#d305",
+ "http://dl-learner.org/carcinogenesis#d306",
+ "http://dl-learner.org/carcinogenesis#d307",
+ "http://dl-learner.org/carcinogenesis#d308",
+ "http://dl-learner.org/carcinogenesis#d311",
+ "http://dl-learner.org/carcinogenesis#d314",
+ "http://dl-learner.org/carcinogenesis#d315",
+ "http://dl-learner.org/carcinogenesis#d316",
+ "http://dl-learner.org/carcinogenesis#d320",
+ "http://dl-learner.org/carcinogenesis#d322",
+ "http://dl-learner.org/carcinogenesis#d323",
+ "http://dl-learner.org/carcinogenesis#d325",
+ "http://dl-learner.org/carcinogenesis#d329",
+ "http://dl-learner.org/carcinogenesis#d330",
+ "http://dl-learner.org/carcinogenesis#d331",
+ "http://dl-learner.org/carcinogenesis#d332",
+ "http://dl-learner.org/carcinogenesis#d333",
+ "http://dl-learner.org/carcinogenesis#d336",
+ "http://dl-learner.org/carcinogenesis#d337"
+ );
+
+ List<String> negExamples = Lists.newArrayList(
+ "http://dl-learner.org/carcinogenesis#d110",
+ "http://dl-learner.org/carcinogenesis#d111",
+ "http://dl-learner.org/carcinogenesis#d114",
+ "http://dl-learner.org/carcinogenesis#d116",
+ "http://dl-learner.org/carcinogenesis#d117",
+ "http://dl-learner.org/carcinogenesis#d119",
+ "http://dl-learner.org/carcinogenesis#d121",
+ "http://dl-learner.org/carcinogenesis#d123",
+ "http://dl-learner.org/carcinogenesis#d124",
+ "http://dl-learner.org/carcinogenesis#d125",
+ "http://dl-learner.org/carcinogenesis#d127",
+ "http://dl-learner.org/carcinogenesis#d128",
+ "http://dl-learner.org/carcinogenesis#d130",
+ "http://dl-learner.org/carcinogenesis#d133",
+ "http://dl-learner.org/carcinogenesis#d150",
+ "http://dl-learner.org/carcinogenesis#d151",
+ "http://dl-learner.org/carcinogenesis#d154",
+ "http://dl-learner.org/carcinogenesis#d155",
+ "http://dl-learner.org/carcinogenesis#d156",
+ "http://dl-learner.org/carcinogenesis#d159",
+ "http://dl-learner.org/carcinogenesis#d160",
+ "http://dl-learner.org/carcinogenesis#d161",
+ "http://dl-learner.org/carcinogenesis#d162",
+ "http://dl-learner.org/carcinogenesis#d163",
+ "http://dl-learner.org/carcinogenesis#d164",
+ "http://dl-learner.org/carcinogenesis#d165",
+ "http://dl-learner.org/carcinogenesis#d166",
+ "http://dl-learner.org/carcinogenesis#d169",
+ "http://dl-learner.org/carcinogenesis#d170",
+ "http://dl-learner.org/carcinogenesis#d171",
+ "http://dl-learner.org/carcinogenesis#d172",
+ "http://dl-learner.org/carcinogenesis#d173",
+ "http://dl-learner.org/carcinogenesis#d174",
+ "http://dl-learner.org/carcinogenesis#d178",
+ "http://dl-learner.org/carcinogenesis#d179",
+ "http://dl-learner.org/carcinogenesis#d180",
+ "http://dl-learner.org/carcinogenesis#d181",
+ "http://dl-learner.org/carcinogenesis#d183",
+ "http://dl-learner.org/carcinogenesis#d184",
+ "http://dl-learner.org/carcinogenesis#d185",
+ "http://dl-learner.org/carcinogenesis#d186",
+ "http://dl-learner.org/carcinogenesis#d188",
+ "http://dl-learner.org/carcinogenesis#d190",
+ "http://dl-learner.org/carcinogenesis#d194",
+ "http://dl-learner.org/carcinogenesis#d207",
+ "http://dl-learner.org/carcinogenesis#d208_1",
+ "http://dl-learner.org/carcinogenesis#d209",
+ "http://dl-learner.org/carcinogenesis#d210",
+ "http://dl-learner.org/carcinogenesis#d211",
+ "http://dl-learner.org/carcinogenesis#d212",
+ "http://dl-learner.org/carcinogenesis#d213",
+ "http://dl-learner.org/carcinogenesis#d214",
+ "http://dl-learner.org/carcinogenesis#d215",
+ "http://dl-learner.org/carcinogenesis#d217",
+ "http://dl-learner.org/carcinogenesis#d218",
+ "http://dl-learner.org/carcinogenesis#d219",
+ "http://dl-learner.org/carcinogenesis#d220",
+ "http://dl-learner.org/carcinogenesis#d224",
+ "http://dl-learner.org/carcinogenesis#d256",
+ "http://dl-learner.org/carcinogenesis#d257",
+ "http://dl-learner.org/carcinogenesis#d258",
+ "http://dl-learner.org/carcinogenesis#d261",
+ "http://dl-learner.org/carcinogenesis#d262",
+ "http://dl-learner.org/carcinogenesis#d263",
+ "http://dl-learner.org/carcinogenesis#d264",
+ "http://dl-learner.org/carcinogenesis#d265",
+ "http://dl-learner.org/carcinogenesis#d266",
+ "http://dl-learner.org/carcinogenesis#d267",
+ "http://dl-learner.org/carcinogenesis#d269",
+ "http://dl-learner.org/carcinogenesis#d271",
+ "http://dl-learner.org/carcinogenesis#d276",
+ "http://dl-learner.org/carcinogenesis#d280",
+ "http://dl-learner.org/carcinogenesis#d285",
+ "http://dl-learner.org/carcinogenesis#d287",
+ "http://dl-learner.org/carcinogenesis#d293",
+ "http://dl-learner.org/carcinogenesis#d294",
+ "http://dl-learner.org/carcinogenesis#d59",
+ "http://dl-learner.org/carcinogenesis#d60",
+ "http://dl-learner.org/carcinogenesis#d61",
+ "http://dl-learner.org/carcinogenesis#d63",
+ "http://dl-learner.org/carcinogenesis#d64",
+ "http://dl-learner.org/carcinogenesis#d65",
+ "http://dl-learner.org/carcinogenesis#d69",
+ "http://dl-learner.org/carcinogenesis#d70",
+ "http://dl-learner.org/carcinogenesis#d71",
+ "http://dl-learner.org/carcinogenesis#d72",
+ "http://dl-learner.org/carcinogenesis#d73",
+ "http://dl-learner.org/carcinogenesis#d74",
+ "http://dl-learner.org/carcinogenesis#d75",
+ "http://dl-learner.org/carcinogenesis#d76",
+ "http://dl-learner.org/carcinogenesis#d77",
+ "http://dl-learner.org/carcinogenesis#d78",
+ "http://dl-learner.org/carcinogenesis#d79",
+ "http://dl-learner.org/carcinogenesis#d80",
+ "http://dl-learner.org/carcinogenesis#d81",
+ "http://dl-learner.org/carcinogenesis#d82",
+ "http://dl-learner.org/carcinogenesis#d112",
+ "http://dl-learner.org/carcinogenesis#d113",
+ "http://dl-learner.org/carcinogenesis#d115",
+ "http://dl-learner.org/carcinogenesis#d118",
+ "http://dl-learner.org/carcinogenesis#d120",
+ "http://dl-learner.org/carcinogenesis#d122",
+ "http://dl-learner.org/carcinogenesis#d126",
+ "http://dl-learner.org/carcinogenesis#d129",
+ "http://dl-learner.org/carcinogenesis#d131",
+ "http://dl-learner.org/carcinogenesis#d132",
+ "http://dl-learner.org/carcinogenesis#d149",
+ "http://dl-learner.org/carcinogenesis#d152",
+ "http://dl-learner.org/carcinogenesis#d153",
+ "http://dl-learner.org/carcinogenesis#d157",
+ "http://dl-learner.org/carcinogenesis#d158",
+ "http://dl-learner.org/carcinogenesis#d167",
+ "http://dl-learner.org/carcinogenesis#d168",
+ "http://dl-learner.org/carcinogenesis#d175",
+ "http://dl-learner.org/carcinogenesis#d176",
+ "http://dl-learner.org/carcinogenesis#d177",
+ "http://dl-learner.org/carcinogenesis#d182",
+ "http://dl-learner.org/carcinogenesis#d187",
+ "http://dl-learner.org/carcinogenesis#d189",
+ "http://dl-learner.org/carcinogenesis#d208_2",
+ "http://dl-learner.org/carcinogenesis#d216",
+ "http://dl-learner.org/carcinogenesis#d221",
+ "http://dl-learner.org/carcinogenesis#d222",
+ "http://dl-learner.org/carcinogenesis#d223",
+ "http://dl-learner.org/carcinogenesis#d225",
+ "http://dl-learner.org/carcinogenesis#d259",
+ "http://dl-learner.org/carcinogenesis#d260",
+ "http://dl-learner.org/carcinogenesis#d268",
+ "http://dl-learner.org/carcinogenesis#d270",
+ "http://dl-learner.org/carcinogenesis#d282",
+ "http://dl-learner.org/carcinogenesis#d295",
+ "http://dl-learner.org/carcinogenesis#d62",
+ "http://dl-learner.org/carcinogenesis#d66",
+ "http://dl-learner.org/carcinogenesis#d67",
+ "http://dl-learner.org/carcinogenesis#d68",
+ "http://dl-learner.org/carcinogenesis#d83",
+ "http://dl-learner.org/carcinogenesis#d297",
+ "http://dl-learner.org/carcinogenesis#d298",
+ "http://dl-learner.org/carcinogenesis#d299",
+ "http://dl-learner.org/carcinogenesis#d300",
+ "http://dl-learner.org/carcinogenesis#d302",
+ "http://dl-learner.org/carcinogenesis#d303",
+ "http://dl-learner.org/carcinogenesis#d304",
+ "http://dl-learner.org/carcinogenesis#d309",
+ "http://dl-learner.org/carcinogenesis#d312",
+ "http://dl-learner.org/carcinogenesis#d313",
+ "http://dl-learner.org/carcinogenesis#d317",
+ "http://dl-learner.org/carcinogenesis#d318",
+ "http://dl-learner.org/carcinogenesis#d319",
+ "http://dl-learner.org/carcinogenesis#d324",
+ "http://dl-learner.org/carcinogenesis#d326",
+ "http://dl-learner.org/carcinogenesis#d327",
+ "http://dl-learner.org/carcinogenesis#d328",
+ "http://dl-learner.org/carcinogenesis#d334",
+ "http://dl-learner.org/carcinogenesis#d335"
+ );
+
+ private Model model;
+ private OWLOntology ontology;
+ private QueryTreeFactory<String> queryTreeFactory;
+ private List<QueryTree<String>> posExampleTrees;
+ private List<QueryTree<String>> negExampleTrees;
+ private PosNegLP lp;
+
+
+
+ public QTLEvaluation() throws ComponentInitException {
+ queryTreeFactory = new QueryTreeFactoryImpl();
+ queryTreeFactory.setMaxDepth(3);
+
+ loadDataset();
+
+ loadExamples();
+ }
+
+ private void loadDataset(){
+ File file = new File("../examples/carcinogenesis/carcinogenesis.owl");
+ model = ModelFactory.createDefaultModel();
+ try {
+ model.read(new FileInputStream(file), null, "RDF/XML");
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ try {
+ ontology = man.loadOntologyFromOntologyDocument(file);
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void loadExamples() throws ComponentInitException{
+
+ Collections.shuffle(posExamples, new Random(1));
+ Collections.shuffle(negExamples, new Random(2));
+ posExamples = posExamples.subList(0, Math.min(posExamples.size(), nrOfPosExamples));
+ negExamples = negExamples.subList(0, Math.min(negExamples.size(), nrOfNegExamples));
+
+// posExamples.clear();
+// String string = "http://dl-learner.org/carcinogenesis#d101, http://dl-learner.org/carcinogenesis#d103, http://dl-learner.org/carcinogenesis#d107, http://dl-learner.org/carcinogenesis#d108, http://dl-learner.org/carcinogenesis#d135, http://dl-learner.org/carcinogenesis#d139, http://dl-learner.org/carcinogenesis#d14, http://dl-learner.org/carcinogenesis#d141, http://dl-learner.org/carcinogenesis#d143, http://dl-learner.org/carcinogenesis#d147, http://dl-learner.org/carcinogenesis#d17, http://dl-learner.org/carcinogenesis#d19, http://dl-learner.org/carcinogenesis#d193, http://dl-learner.org/carcinogenesis#d198, http://dl-learner.org/carcinogenesis#d228, http://dl-learner.org/carcinogenesis#d236, http://dl-learner.org/carcinogenesis#d242, http://dl-learner.org/carcinogenesis#d244, http://dl-learner.org/carcinogenesis#d273, http://dl-learner.org/carcinogenesis#d275, http://dl-learner.org/carcinogenesis#d28, http://dl-learner.org/carcinogenesis#d283, http://dl-learner.org/carcinogenesis#d286, http://dl-learner.org/carcinogenesis#d291, http://dl-learner.org/carcinogenesis#d292, http://dl-learner.org/carcinogenesis#d307, http://dl-learner.org/carcinogenesis#d31, http://dl-learner.org/carcinogenesis#d325, http://dl-learner.org/carcinogenesis#d33, http://dl-learner.org/carcinogenesis#d333, http://dl-learner.org/carcinogenesis#d34, http://dl-learner.org/carcinogenesis#d36, http://dl-learner.org/carcinogenesis#d38, http://dl-learner.org/carcinogenesis#d4, http://dl-learner.org/carcinogenesis#d40, http://dl-learner.org/carcinogenesis#d44, http://dl-learner.org/carcinogenesis#d51, http://dl-learner.org/carcinogenesis#d85_2, http://dl-learner.org/carcinogenesis#d98, http://dl-learner.org/carcinogenesis#d99";
+// String[] split = string.split(",");
+// for (String s : split) {
+// posExamples.add(s.trim());
+// }
+// negExamples.clear();
+// string = "http://dl-learner.org/carcinogenesis#d112, http://dl-learner.org/carcinogenesis#d116, http://dl-learner.org/carcinogenesis#d117, http://dl-learner.org/carcinogenesis#d119, http://dl-learner.org/carcinogenesis#d157, http://dl-learner.org/carcinogenesis#d160, http://dl-learner.org/carcinogenesis#d161, http://dl-learner.org/carcinogenesis#d162, http://dl-learner.org/carcinogenesis#d163, http://dl-learner.org/carcinogenesis#d167, http://dl-learner.org/carcinogenesis#d169, http://dl-learner.org/carcinogenesis#d175, http://dl-learner.org/carcinogenesis#d177, http://dl-learner.org/carcinogenesis#d184, http://dl-learner.org/carcinogenesis#d194, http://dl-learner.org/carcinogenesis#d208_2, http://dl-learner.org/carcinogenesis#d209, http://dl-learner.org/carcinogenesis#d217, http://dl-learner.org/carcinogenesis#d256, http://dl-learner.org/carcinogenesis#d257, http://dl-learner.org/carcinogenesis#d260, http://dl-learner.org/carcinogenesis#d271, http://dl-learner.org/carcinogenesis#d276, http://dl-learner.org/carcinogenesis#d282, http://dl-learner.org/carcinogenesis#d287, http://dl-learner.org/carcinogenesis#d294, http://dl-learner.org/carcinogenesis#d298, http://dl-learner.org/carcinogenesis#d300, http://dl-learner.org/carcinogenesis#d309, http://dl-learner.org/carcinogenesis#d319, http://dl-learner.org/carcinogenesis#d326, http://dl-learner.org/carcinogenesis#d328, http://dl-learner.org/carcinogenesis#d334, http://dl-learner.org/carcinogenesis#d60, http://dl-learner.org/carcinogenesis#d61, http://dl-learner.org/carcinogenesis#d66, http://dl-learner.org/carcinogenesis#d75, http://dl-learner.org/carcinogenesis#d79, http://dl-learner.org/carcinogenesis#d80, http://dl-learner.org/carcinogenesis#d83";
+// split = string.split(",");
+// for (String s : split) {
+// negExamples.add(s.trim());
+// }
+
+ posExampleTrees = new ArrayList<QueryTree<String>>();
+ for (String ex : posExamples) {
+ QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model);
+ posExampleTrees.add(tree);
+ }
+
+ negExampleTrees = new ArrayList<QueryTree<String>>();
+ for (String ex : negExamples) {
+ QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model);
+ negExampleTrees.add(tree);
+ }
+
+ int cnt = 1;
+ for(QueryTree<String> tree : posExampleTrees){
+// System.out.println("TREE " + cnt);
+// tree.dump();
+//
+// System.out.println("-----------------------------");
+ cnt++;
+// System.out.println(((QueryTreeImpl<String>)tree).toQuery());
+ }
+
+ SortedSet<Individual> pos = new TreeSet<Individual>();
+ for (String ex : posExamples) {
+ pos.add(new Individual(ex));
+ }
+ SortedSet<Individual> neg = new TreeSet<Individual>();
+ for (String ex : negExamples) {
+ neg.add(new Individual(ex));
+ }
+ lp = new PosNegLPStandard();
+ lp.setPositiveExamples(pos);
+ lp.setNegativeExamples(neg);
+ }
+
+ public void run(boolean multiThreaded) throws ComponentInitException, LearningProblemUnsupportedException{
+ long startTime = System.currentTimeMillis();
+ FastInstanceChecker reasoner = new FastInstanceChecker(new OWLAPIOntology(ontology));
+ reasoner.init();
+ lp.setReasoner(reasoner);
+ lp.init();
+ QTL2Disjunctive la = new QTL2Disjunctive(lp, reasoner);
+ la.init();
+ la.start();
+
+// CrossValidation.outputFile = new File("log/qtl-cv.log");
+// CrossValidation.writeToFile = true;
+// CrossValidation.multiThreaded = multiThreaded;
+// CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
+ long endTime = System.currentTimeMillis();
+ System.err.println((endTime - startTime) + "ms");
+ }
+
+
+ public static void main(String[] args) throws Exception {
+ boolean multiThreaded = Boolean.valueOf(args[0]);
+ new QTLEvaluation().run(multiThreaded);
+ }
+
+}
Added: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java 2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,281 @@
+/**
+ *
+ */
+package org.dllearner.scripts.pattern;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Random;
+import java.util.Set;
+import java.util.TreeMap;
+import java.util.prefs.Preferences;
+
+import org.ini4j.IniPreferences;
+import org.ini4j.InvalidFileFormatException;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+
+import com.google.common.base.Charsets;
+import com.google.common.base.Joiner;
+import com.google.common.collect.LinkedListMultimap;
+import com.google.common.collect.Multimap;
+import com.google.common.io.Files;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class FixPointDetection {
+
+ private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
+
+ public FixPointDetection() {
+ initDBConnection();
+
+ File dir = new File("pattern-fixpoint");
+ dir.mkdir();
+ }
+
+ private Connection conn;
+ private PreparedStatement ps;
+
+ 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;
+ conn = DriverManager.getConnection(url, dbUser, dbPass);
+ } 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();
+ }
+
+ try {
+ ps = conn.prepareStatement("SELECT occurrences FROM Ontology_Pattern WHERE pattern_id=? AND ontology_id=?");
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+
+
+ private List<Integer> getProcessedOntologies() throws SQLException{
+ List<Integer> ids = new ArrayList<Integer>();
+ ResultSet rs = conn.createStatement().executeQuery("SELECT DISTINCT id FROM Ontology");
+ while(rs.next()){
+ int id = rs.getInt(1);
+ ...
[truncated message content] |
