Menu
▾
▴
dl-learner-svn
|
From: <lor...@us...> - 2011-12-07 21:50:18
|
Revision: 3487
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3487&view=rev
Author: lorenz_b
Date: 2011-12-07 21:50:12 +0000 (Wed, 07 Dec 2011)
Log Message:
-----------
Started greedy algorithm implementation to build cohaerent ontology.
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
Added: trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2011-12-07 21:50:12 UTC (rev 3487)
@@ -0,0 +1,99 @@
+package org.dllearner.utilities;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import org.apache.commons.collections15.BidiMap;
+import org.apache.commons.collections15.bidimap.DualHashBidiMap;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.AxiomType;
+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 org.semanticweb.owlapi.reasoner.OWLReasoner;
+
+public class GreedyCohaerencyExtractor {
+
+ public GreedyCohaerencyExtractor() {
+ // TODO Auto-generated constructor stub
+ }
+
+ public OWLOntology getCoharentOntology(OWLOntology ontology) throws OWLOntologyCreationException{
+ BidiMap<AxiomType<? extends OWLAxiom>, Integer> axiomType2CountMap = getAxiomTypeCount(ontology);
+
+ Map<AxiomType<? extends OWLAxiom>, List<OWLAxiom>> axiomType2AxiomsMap = new HashMap<AxiomType<? extends OWLAxiom>, List<OWLAxiom>>();
+ for(AxiomType<? extends OWLAxiom> type : AxiomType.AXIOM_TYPES){
+ axiomType2AxiomsMap.put(type, new ArrayList<OWLAxiom>(ontology.getAxioms(type)));
+ }
+
+ int lcm = lcm(new ArrayList<Integer>(axiomType2CountMap.values()));
+
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology cohaerentOntology = man.createOntology();
+
+ for(int i = 0; i < lcm; i++){
+ for(Entry<AxiomType<? extends OWLAxiom>, Integer> entry : axiomType2CountMap.entrySet()){
+ if((i % entry.getValue()) == 0){
+ man.addAxiom(cohaerentOntology, axiomType2AxiomsMap.get(entry.getKey()).remove(0));
+ }
+ }
+ }
+ return cohaerentOntology;
+ }
+
+ public OWLOntology getCoharentOntology(OWLReasoner reasoner) throws OWLOntologyCreationException{
+ return getCoharentOntology(reasoner.getRootOntology());
+ }
+
+ private BidiMap<AxiomType<? extends OWLAxiom>, Integer> getAxiomTypeCount(OWLOntology ontology){
+ BidiMap<AxiomType<? extends OWLAxiom>, Integer> axiomType2CountMap = new DualHashBidiMap<AxiomType<? extends OWLAxiom>, Integer>();
+
+ for(AxiomType<? extends OWLAxiom> type : AxiomType.AXIOM_TYPES){
+ axiomType2CountMap.put(type, ontology.getAxiomCount(type));
+ }
+
+ return axiomType2CountMap;
+ }
+
+ private int lcm(int x1,int x2) {
+ if(x1<=0 || x2<=0) {
+ throw new IllegalArgumentException("Cannot compute the least "+
+ "common multiple of two "+
+ "numbers if one, at least,"+
+ "is negative.");
+ }
+ int max,min;
+ if (x1>x2) {
+ max = x1;
+ min = x2;
+ } else {
+ max = x2;
+ min = x1;
+ }
+ for(int i=1; i<=min; i++) {
+ if( (max*i)%min == 0 ) {
+ return i*max;
+ }
+ }
+ throw new Error("Cannot find the least common multiple of numbers "+
+ x1+" and "+x2);
+ }
+
+ private int lcm(List<Integer> values) {
+ if(values.size() == 1){
+ return values.get(0);
+ } else {
+ List<Integer> list = new ArrayList<Integer>();
+ list.add(lcm(values.get(0), values.get(1)));
+ if(values.size() > 2){
+ list.addAll(values.subList(2, values.size()));
+ }
+ return lcm(list);
+ }
+ }
+
+}
Property changes on: trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-12-07 22:23:10
|
Revision: 3488
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3488&view=rev
Author: lorenz_b
Date: 2011-12-07 22:23:04 +0000 (Wed, 07 Dec 2011)
Log Message:
-----------
Continued greedy algorithm implementation to build cohaerent ontology.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2011-12-07 21:50:12 UTC (rev 3487)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2011-12-07 22:23:04 UTC (rev 3488)
@@ -16,6 +16,8 @@
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import com.clarkparsia.modularity.IncrementalClassifier;
+
public class GreedyCohaerencyExtractor {
public GreedyCohaerencyExtractor() {
@@ -23,6 +25,9 @@
}
public OWLOntology getCoharentOntology(OWLOntology ontology) throws OWLOntologyCreationException{
+ IncrementalClassifier reasoner = new IncrementalClassifier(ontology);
+ reasoner.classify();
+
BidiMap<AxiomType<? extends OWLAxiom>, Integer> axiomType2CountMap = getAxiomTypeCount(ontology);
Map<AxiomType<? extends OWLAxiom>, List<OWLAxiom>> axiomType2AxiomsMap = new HashMap<AxiomType<? extends OWLAxiom>, List<OWLAxiom>>();
@@ -33,12 +38,22 @@
int lcm = lcm(new ArrayList<Integer>(axiomType2CountMap.values()));
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ man.addOntologyChangeListener(reasoner);
OWLOntology cohaerentOntology = man.createOntology();
+ boolean isCohaerent = true;
for(int i = 0; i < lcm; i++){
- for(Entry<AxiomType<? extends OWLAxiom>, Integer> entry : axiomType2CountMap.entrySet()){
- if((i % entry.getValue()) == 0){
- man.addAxiom(cohaerentOntology, axiomType2AxiomsMap.get(entry.getKey()).remove(0));
+ if(isCohaerent){
+ for(Entry<AxiomType<? extends OWLAxiom>, Integer> entry : axiomType2CountMap.entrySet()){
+ if((i % entry.getValue()) == 0){
+ OWLAxiom ax = axiomType2AxiomsMap.get(entry.getKey()).remove(0);
+ man.addAxiom(cohaerentOntology, ax);
+ isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().isEmpty();
+ if(!isCohaerent){
+ man.removeAxiom(cohaerentOntology, ax);
+ break;
+ }
+ }
}
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-27 16:02:38
|
Revision: 3591
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3591&view=rev
Author: lorenz_b
Date: 2012-02-27 16:02:32 +0000 (Mon, 27 Feb 2012)
Log Message:
-----------
Continued.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-27 13:00:31 UTC (rev 3590)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-27 16:02:32 UTC (rev 3591)
@@ -31,6 +31,10 @@
private static final double STEP_SIZE = 0.001;
private static final int ALLOWED_UNSATISFIABLE_CLASSES = 5;
+ private OWLOntologyManager manager;
+ private OWLOntology cohaerentOntology;
+ private IncrementalClassifier reasoner;
+
public GreedyCohaerencyExtractor() {
// TODO Auto-generated constructor stub
}
@@ -55,11 +59,11 @@
}
- OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- OWLOntology cohaerentOntology = man.createOntology();
+ manager = OWLManager.createOWLOntologyManager();
+ cohaerentOntology = manager.createOntology();
- IncrementalClassifier reasoner = new IncrementalClassifier(cohaerentOntology);
- man.addOntologyChangeListener(reasoner);
+ reasoner = new IncrementalClassifier(cohaerentOntology);
+ manager.addOntologyChangeListener(reasoner);
reasoner.classify();
@@ -80,14 +84,20 @@
// break;
// }
// }
- Set<OWLAxiom> toAdd = new HashSet<OWLAxiom>(axiomType2AxiomsMap.get(type[i]).subList(0, x));
- man.addAxioms(cohaerentOntology, toAdd);
+
+ /*Set<OWLAxiom> toAdd = new HashSet<OWLAxiom>(axiomType2AxiomsMap.get(type[i]).subList(0, x));
+ manager.addAxioms(cohaerentOntology, toAdd);
axiomType2AxiomsMap.get(type[i]).removeAll(toAdd);
isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
if(!isCohaerent){
- man.removeAxioms(cohaerentOntology, toAdd);System.out.println("Incohaerency detected");
+ manager.removeAxioms(cohaerentOntology, toAdd);System.out.println("Incohaerency detected");
break;
- }
+ }*/
+
+ List<OWLAxiom> toAdd = axiomType2AxiomsMap.get(type[i]).subList(0, x);
+ addAxioms(toAdd);
+ axiomType2AxiomsMap.get(type[i]).removeAll(toAdd);
+
cnt[i] = cnt[i] - x;
}
}
@@ -95,7 +105,7 @@
}
try {
- man.saveOntology(cohaerentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(new File("coherent.owl"))));
+ manager.saveOntology(cohaerentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(new File("coherent.owl"))));
} catch (OWLOntologyStorageException e) {
e.printStackTrace();
} catch (FileNotFoundException e) {
@@ -105,6 +115,36 @@
return cohaerentOntology;
}
+ private Set<OWLAxiom> addAxioms(List<OWLAxiom> axioms){
+ Set<OWLAxiom> addedAxioms = new HashSet<OWLAxiom>();
+
+ Set<OWLAxiom> axiomSet = new HashSet<OWLAxiom>(axioms);
+ manager.addAxioms(cohaerentOntology, axiomSet);
+ reasoner.classify();
+ boolean isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
+ if(!isCohaerent){
+ System.out.println("Incohaerency detected. Splitting...");
+ manager.removeAxioms(cohaerentOntology, axiomSet);
+ if(axioms.size() == 1){
+ return addedAxioms;
+ }
+
+ int size = axioms.size();
+ int pivot = size/2;
+
+ List<OWLAxiom> left = axioms.subList(0, pivot);
+ List<OWLAxiom> right = axioms.subList(pivot, size-1);
+
+ addedAxioms.addAll(addAxioms(left));
+ addedAxioms.addAll(addAxioms(right));
+
+ } else {
+ addedAxioms.addAll(axioms);
+ }
+
+ return addedAxioms;
+ }
+
public OWLOntology getCoharentOntology(OWLReasoner reasoner) throws OWLOntologyCreationException{
return getCoharentOntology(reasoner.getRootOntology());
}
@@ -125,7 +165,7 @@
public static void main(String[] args) throws Exception{
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("/home/lorenz/arbeit/dbpedia_0.75_no_datapropaxioms.owl"));
+ OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("/home/lorenz/arbeit/papers/ESWC2012/dbpedia_0.75_no_datapropaxioms.owl"));
GreedyCohaerencyExtractor ge = new GreedyCohaerencyExtractor();
ge.getCoharentOntology(schema);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-28 13:07:54
|
Revision: 3593
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3593&view=rev
Author: lorenz_b
Date: 2012-02-28 13:07:43 +0000 (Tue, 28 Feb 2012)
Log Message:
-----------
Updated algorithm.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-28 02:25:27 UTC (rev 3592)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-28 13:07:43 UTC (rev 3593)
@@ -1,9 +1,12 @@
package org.dllearner.utilities;
+import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
@@ -14,6 +17,12 @@
import org.apache.commons.collections15.BidiMap;
import org.apache.commons.collections15.bidimap.DualHashBidiMap;
+import org.apache.commons.compress.compressors.CompressorStreamFactory;
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.FileAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.AxiomType;
@@ -28,31 +37,37 @@
public class GreedyCohaerencyExtractor {
- private static final double STEP_SIZE = 0.001;
+ private static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(JustificationBasedCoherentOntologyExtractor.class);
+
+ private double stepSize = 0.001;
private static final int ALLOWED_UNSATISFIABLE_CLASSES = 5;
private OWLOntologyManager manager;
- private OWLOntology cohaerentOntology;
+ private OWLOntology coherentOntology;
private IncrementalClassifier reasoner;
public GreedyCohaerencyExtractor() {
// TODO Auto-generated constructor stub
}
- public OWLOntology getCoharentOntology(OWLOntology ontology) throws OWLOntologyCreationException{
+ public OWLOntology getCoherentOntology(OWLOntology ontology, String target, double stepSize) throws OWLOntologyCreationException{
+ stepSize = stepSize/100;
BidiMap<AxiomType<? extends OWLAxiom>, Integer> axiomType2CountMap = getAxiomTypeCount(ontology);
Map<AxiomType<? extends OWLAxiom>, List<OWLAxiom>> axiomType2AxiomsMap = new HashMap<AxiomType<? extends OWLAxiom>, List<OWLAxiom>>();
for(AxiomType<? extends OWLAxiom> type : AxiomType.AXIOM_TYPES){
axiomType2AxiomsMap.put(type, new ArrayList<OWLAxiom>(ontology.getAxioms(type)));
}
- System.out.println(ontology.getLogicalAxiomCount());
- double[] stepSize = new double[axiomType2CountMap.entrySet().size()];
+ //omit annotation axioms here
+ axiomType2AxiomsMap.remove(AxiomType.ANNOTATION_ASSERTION);
+
+ logger.info("Source ontology contains " + ontology.getLogicalAxiomCount() + " logical axioms.");
+ double[] stepSizeArray = new double[axiomType2CountMap.entrySet().size()];
double[] cnt = new double[axiomType2CountMap.entrySet().size()];
AxiomType[] type = new AxiomType[axiomType2CountMap.entrySet().size()];
int i=0;
for(Entry<AxiomType<? extends OWLAxiom>, Integer> entry : axiomType2CountMap.entrySet()){
- stepSize[i] = STEP_SIZE * entry.getValue();
+ stepSizeArray[i] = stepSize * entry.getValue();
type[i] = entry.getKey();
cnt[i] = 0;
i++;
@@ -60,71 +75,67 @@
manager = OWLManager.createOWLOntologyManager();
- cohaerentOntology = manager.createOntology();
+ coherentOntology = manager.createOntology();
- reasoner = new IncrementalClassifier(cohaerentOntology);
- manager.addOntologyChangeListener(reasoner);
+ reasoner = new IncrementalClassifier(coherentOntology);
+ reasoner.setMultiThreaded(false);
+// manager.addOntologyChangeListener(reasoner);
reasoner.classify();
- boolean isCohaerent = true;
- for(double j = 0; j < 1; j += STEP_SIZE){System.out.println(j);
- if(isCohaerent){
- for(i = 0; i < stepSize.length; i++){
- cnt[i] = cnt[i] + stepSize[i];
+ boolean isCoherent = true;
+ for(double j = 0; j < 1; j += stepSize){//increase by stepsize p until 100%
+ if(isCoherent){
+ for(i = 0; i < stepSizeArray.length; i++){//for each axiomtype
+ cnt[i] = cnt[i] + stepSizeArray[i];//sum up value which was computed by p * #axioms
int x = (int)cnt[i];
- System.out.println("Adding " + x + " " + type[i] + " axioms from " + axiomType2CountMap.get(type[i]));
-// System.out.println(axiomType2AxiomsMap.get(type[i]).size());
-// for(int k = 0; k < x; k++){
-// OWLAxiom ax = axiomType2AxiomsMap.get(type[i]).remove(0);
-// man.addAxiom(cohaerentOntology, ax);
-// isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().isEmpty();
-// if(!isCohaerent){
-// man.removeAxiom(cohaerentOntology, ax);
+ if(x > 0){
+ logger.info("Adding " + x + " " + type[i] + " axioms from " + axiomType2CountMap.get(type[i]));
+ Set<OWLAxiom> toAdd = new HashSet<OWLAxiom>(axiomType2AxiomsMap.get(type[i]).subList(0, x));
+ manager.addAxioms(coherentOntology, toAdd);
+ axiomType2AxiomsMap.get(type[i]).removeAll(toAdd);
+ isCoherent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
+ if(!isCoherent){
+ manager.removeAxioms(coherentOntology, toAdd);
+ logger.info("Incoherency detected. Undoing changes.");
+ isCoherent = true;
// break;
-// }
-// }
+ }
+ }
- /*Set<OWLAxiom> toAdd = new HashSet<OWLAxiom>(axiomType2AxiomsMap.get(type[i]).subList(0, x));
- manager.addAxioms(cohaerentOntology, toAdd);
- axiomType2AxiomsMap.get(type[i]).removeAll(toAdd);
- isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
- if(!isCohaerent){
- manager.removeAxioms(cohaerentOntology, toAdd);System.out.println("Incohaerency detected");
- break;
- }*/
-
- List<OWLAxiom> toAdd = axiomType2AxiomsMap.get(type[i]).subList(0, x);
+ //same procedure with divide and conquer optimization
+ /*List<OWLAxiom> toAdd = axiomType2AxiomsMap.get(type[i]).subList(0, x);
addAxioms(toAdd);
axiomType2AxiomsMap.get(type[i]).removeAll(toAdd);
+ */
cnt[i] = cnt[i] - x;
}
}
- System.out.println(cohaerentOntology.getLogicalAxiomCount());
+ logger.info("Coherent ontology contains " + coherentOntology.getLogicalAxiomCount() + " logical axioms.");
}
try {
- manager.saveOntology(cohaerentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(new File("coherent.owl"))));
+ manager.saveOntology(coherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(new File(target))));
} catch (OWLOntologyStorageException e) {
e.printStackTrace();
} catch (FileNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
- return cohaerentOntology;
+ return coherentOntology;
}
private Set<OWLAxiom> addAxioms(List<OWLAxiom> axioms){
Set<OWLAxiom> addedAxioms = new HashSet<OWLAxiom>();
Set<OWLAxiom> axiomSet = new HashSet<OWLAxiom>(axioms);
- manager.addAxioms(cohaerentOntology, axiomSet);
+ manager.addAxioms(coherentOntology, axiomSet);
reasoner.classify();
boolean isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
if(!isCohaerent){
System.out.println("Incohaerency detected. Splitting...");
- manager.removeAxioms(cohaerentOntology, axiomSet);
+ manager.removeAxioms(coherentOntology, axiomSet);
if(axioms.size() == 1){
return addedAxioms;
}
@@ -145,8 +156,8 @@
return addedAxioms;
}
- public OWLOntology getCoharentOntology(OWLReasoner reasoner) throws OWLOntologyCreationException{
- return getCoharentOntology(reasoner.getRootOntology());
+ public OWLOntology getCoherentOntology(OWLReasoner reasoner, String target, double stepSize) throws OWLOntologyCreationException{
+ return getCoherentOntology(reasoner.getRootOntology(), target, stepSize);
}
private BidiMap<AxiomType<? extends OWLAxiom>, Integer> getAxiomTypeCount(OWLOntology ontology){
@@ -164,11 +175,30 @@
}
public static void main(String[] args) throws Exception{
+ Logger.getRootLogger().setLevel(Level.INFO);
+ Logger.getRootLogger().removeAllAppenders();
+ Logger.getRootLogger().addAppender(new ConsoleAppender(new SimpleLayout()));
+ Logger.getRootLogger().addAppender(new FileAppender(new SimpleLayout(), "log/greedy_out.log"));
+
+ if(args.length != 3){
+ System.out.println("USAGE: GreedyCoherencyExtractor <incoherent.owl> <target.owl> <stepsizeInPercent>");
+ System.exit(0);
+ }
+ String filename = args[0];
+ String target = args[1];
+ double stepSize = Double.parseDouble(args[2]);
+
+ System.out.println("Loading ontology...");
+ InputStream is = new BufferedInputStream(new FileInputStream(filename));
+ if(args[0].endsWith("bz2")){
+ is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ }
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("/home/lorenz/arbeit/papers/ESWC2012/dbpedia_0.75_no_datapropaxioms.owl"));
+ OWLOntology schema = man.loadOntologyFromOntologyDocument(is);
+ System.out.println("...done.");
GreedyCohaerencyExtractor ge = new GreedyCohaerencyExtractor();
- ge.getCoharentOntology(schema);
+ ge.getCoherentOntology(schema, target, stepSize);
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-28 13:39:32
|
Revision: 3594
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3594&view=rev
Author: lorenz_b
Date: 2012-02-28 13:39:21 +0000 (Tue, 28 Feb 2012)
Log Message:
-----------
Fixed bug.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-28 13:07:43 UTC (rev 3593)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-28 13:39:21 UTC (rev 3594)
@@ -58,8 +58,6 @@
for(AxiomType<? extends OWLAxiom> type : AxiomType.AXIOM_TYPES){
axiomType2AxiomsMap.put(type, new ArrayList<OWLAxiom>(ontology.getAxioms(type)));
}
- //omit annotation axioms here
- axiomType2AxiomsMap.remove(AxiomType.ANNOTATION_ASSERTION);
logger.info("Source ontology contains " + ontology.getLogicalAxiomCount() + " logical axioms.");
double[] stepSizeArray = new double[axiomType2CountMap.entrySet().size()];
@@ -195,6 +193,7 @@
}
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology schema = man.loadOntologyFromOntologyDocument(is);
+ man.removeAxioms(schema, schema.getAxioms(AxiomType.ANNOTATION_ASSERTION));
System.out.println("...done.");
GreedyCohaerencyExtractor ge = new GreedyCohaerencyExtractor();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-28 15:46:10
|
Revision: 3596
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3596&view=rev
Author: lorenz_b
Date: 2012-02-28 15:46:01 +0000 (Tue, 28 Feb 2012)
Log Message:
-----------
Added property coherency check into script.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-28 15:32:59 UTC (rev 3595)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/GreedyCohaerencyExtractor.java 2012-02-28 15:46:01 UTC (rev 3596)
@@ -12,6 +12,8 @@
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.SortedSet;
+import java.util.TreeSet;
import java.util.Map.Entry;
import java.util.Set;
@@ -27,6 +29,8 @@
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
@@ -40,18 +44,22 @@
private static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(JustificationBasedCoherentOntologyExtractor.class);
private double stepSize = 0.001;
- private static final int ALLOWED_UNSATISFIABLE_CLASSES = 5;
+ private int allowedUnsatClasses = 5;
+ private int allowedUnsatProperties = 5;
private OWLOntologyManager manager;
private OWLOntology coherentOntology;
+ private OWLDataFactory factory;
private IncrementalClassifier reasoner;
public GreedyCohaerencyExtractor() {
// TODO Auto-generated constructor stub
}
- public OWLOntology getCoherentOntology(OWLOntology ontology, String target, double stepSize) throws OWLOntologyCreationException{
+ public OWLOntology getCoherentOntology(OWLOntology ontology, String target, double stepSize, int allowedUnsatClasses, int allowedUnsatProperties) throws OWLOntologyCreationException{
stepSize = stepSize/100;
+ this.allowedUnsatClasses = allowedUnsatClasses;
+ this.allowedUnsatProperties = allowedUnsatProperties;
BidiMap<AxiomType<? extends OWLAxiom>, Integer> axiomType2CountMap = getAxiomTypeCount(ontology);
Map<AxiomType<? extends OWLAxiom>, List<OWLAxiom>> axiomType2AxiomsMap = new HashMap<AxiomType<? extends OWLAxiom>, List<OWLAxiom>>();
@@ -73,6 +81,7 @@
manager = OWLManager.createOWLOntologyManager();
+ factory = manager.getOWLDataFactory();
coherentOntology = manager.createOntology();
reasoner = new IncrementalClassifier(coherentOntology);
@@ -92,7 +101,7 @@
Set<OWLAxiom> toAdd = new HashSet<OWLAxiom>(axiomType2AxiomsMap.get(type[i]).subList(0, x));
manager.addAxioms(coherentOntology, toAdd);
axiomType2AxiomsMap.get(type[i]).removeAll(toAdd);
- isCoherent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
+ isCoherent = isCoherent();
if(!isCoherent){
manager.removeAxioms(coherentOntology, toAdd);
logger.info("Incoherency detected. Undoing changes.");
@@ -124,14 +133,35 @@
return coherentOntology;
}
+ private boolean isCoherent(){
+ return (reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= allowedUnsatClasses)
+ && (getUnsatisfiableObjectProperties(reasoner).size() <= allowedUnsatProperties);
+ }
+
+ private Set<OWLObjectProperty> getUnsatisfiableObjectProperties(IncrementalClassifier reasoner){
+ logger.info("Computing unsatisfiable object properties...");
+ long startTime = System.currentTimeMillis();
+ SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>();
+ OWLDataFactory f = OWLManager.createOWLOntologyManager().getOWLDataFactory();
+ for(OWLObjectProperty p : reasoner.getRootOntology().getObjectPropertiesInSignature()){
+// boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectExactCardinality(1, p));
+ boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectSomeValuesFrom(p, factory.getOWLThing()));
+ if(!satisfiable){
+ properties.add(p);
+ }
+ }
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return properties;
+ }
+
private Set<OWLAxiom> addAxioms(List<OWLAxiom> axioms){
Set<OWLAxiom> addedAxioms = new HashSet<OWLAxiom>();
Set<OWLAxiom> axiomSet = new HashSet<OWLAxiom>(axioms);
manager.addAxioms(coherentOntology, axiomSet);
reasoner.classify();
- boolean isCohaerent = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() <= ALLOWED_UNSATISFIABLE_CLASSES;
- if(!isCohaerent){
+ boolean isCoherent = isCoherent();
+ if(!isCoherent){
System.out.println("Incohaerency detected. Splitting...");
manager.removeAxioms(coherentOntology, axiomSet);
if(axioms.size() == 1){
@@ -154,8 +184,8 @@
return addedAxioms;
}
- public OWLOntology getCoherentOntology(OWLReasoner reasoner, String target, double stepSize) throws OWLOntologyCreationException{
- return getCoherentOntology(reasoner.getRootOntology(), target, stepSize);
+ public OWLOntology getCoherentOntology(OWLReasoner reasoner, String target, double stepSize, int allowedUnsatClasses, int allowedUnsatProperties) throws OWLOntologyCreationException{
+ return getCoherentOntology(reasoner.getRootOntology(), target, stepSize, allowedUnsatClasses, allowedUnsatProperties);
}
private BidiMap<AxiomType<? extends OWLAxiom>, Integer> getAxiomTypeCount(OWLOntology ontology){
@@ -178,13 +208,15 @@
Logger.getRootLogger().addAppender(new ConsoleAppender(new SimpleLayout()));
Logger.getRootLogger().addAppender(new FileAppender(new SimpleLayout(), "log/greedy_out.log"));
- if(args.length != 3){
- System.out.println("USAGE: GreedyCoherencyExtractor <incoherent.owl> <target.owl> <stepsizeInPercent>");
+ if(args.length != 5){
+ System.out.println("USAGE: GreedyCoherencyExtractor <incoherent.owl> <target.owl> <stepsizeInPercent> <nrOfallowedUnsatClasses> <nrOfallowedUnsatProperties>");
System.exit(0);
}
String filename = args[0];
String target = args[1];
double stepSize = Double.parseDouble(args[2]);
+ int nrOfallowedUnsatClasses = Integer.parseInt(args[3]);
+ int nrOfallowedUnsatProperties = Integer.parseInt(args[4]);
System.out.println("Loading ontology...");
InputStream is = new BufferedInputStream(new FileInputStream(filename));
@@ -197,7 +229,7 @@
System.out.println("...done.");
GreedyCohaerencyExtractor ge = new GreedyCohaerencyExtractor();
- ge.getCoherentOntology(schema, target, stepSize);
+ ge.getCoherentOntology(schema, target, stepSize, nrOfallowedUnsatClasses, nrOfallowedUnsatProperties);
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X