Menu
▾
▴
[DL-Learner SVN] SF.net SVN: dl-learner:[1165] trunk/src/dl-learner/org/dllearner
|
From: <ku...@us...> - 2008-09-01 00:00:23
|
Revision: 1165
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1165&view=rev
Author: kurzum
Date: 2008-09-01 00:00:09 +0000 (Mon, 01 Sep 2008)
Log Message:
-----------
servercommit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/scripts/SemanticBible2.java
trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java
Modified: trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-08-31 19:55:38 UTC (rev 1164)
+++ trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-09-01 00:00:09 UTC (rev 1165)
@@ -28,6 +28,7 @@
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Comparator;
@@ -687,8 +688,43 @@
return new LinkedList<Class<? extends LearningAlgorithm>>(learningAlgorithms);
}
+
+ /**
+ * Retuns a list of all instanciated and registered Components
+ * @return
+ */
public List<Component> getLiveComponents(){
return pool.getComponents();
}
+
+ /**
+ * Retuns a list of all instanciated and registered LearningAlgorithm
+ * @return
+ */
+ public List<LearningAlgorithm> getLiveLearningAlgorithms(){
+ List<LearningAlgorithm> list = new ArrayList<LearningAlgorithm>();
+ for (Component component : cm.getLiveComponents()) {
+ if(component instanceof LearningAlgorithm){
+ list.add((LearningAlgorithm) component);
+ }
+
+ }
+ return list;
+ }
+
+ /**
+ * Retuns a list of all instanciated and registered KnowledgeSource
+ * @return
+ */
+ public List<KnowledgeSource> getLiveKnowledgeSources(){
+ List<KnowledgeSource> list = new ArrayList<KnowledgeSource>();
+ for (Component component : cm.getLiveComponents()) {
+ if(component instanceof KnowledgeSource){
+ list.add((KnowledgeSource) component);
+ }
+
+ }
+ return list;
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java 2008-08-31 19:55:38 UTC (rev 1164)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java 2008-09-01 00:00:09 UTC (rev 1165)
@@ -35,6 +35,7 @@
private Configuration configuration;
private ExtractionAlgorithm extractionAlgorithm;
+ private int nrOfExtractedTriples = 0;
private static Logger logger = Logger
.getLogger(Manager.class);
@@ -85,6 +86,7 @@
logger.info("Finished extracting, start conversion");
StringBuffer nt = new StringBuffer(100000);
Object[] arr = tripleCollector.toArray();
+ nrOfExtractedTriples = arr.length;
for (int i = 0; i < arr.length; i++) {
nt.append((String) arr[i] + "\n");
if (i % 1000 == 0)
@@ -105,4 +107,8 @@
return configuration;
}
+ public int getNrOfExtractedTriples() {
+ return nrOfExtractedTriples;
+ }
+
}
\ No newline at end of file
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-08-31 19:55:38 UTC (rev 1164)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-09-01 00:00:09 UTC (rev 1165)
@@ -129,6 +129,9 @@
// received ontology as KB, the internal format
private KB kb;
+ //mainly used for statistic
+ private int nrOfExtractedTriples = 0;
+
public static String getName() {
return "SPARQL Endpoint";
}
@@ -368,6 +371,7 @@
} catch (Exception e) {
e.printStackTrace();
}
+ nrOfExtractedTriples = m.getNrOfExtractedTriples();
logger.info("SparqlModul: ****Finished " + totalTime.getAndSet("") );
if(debugExitAfterExtraction){
@@ -505,6 +509,10 @@
return cacheDir;
}
+ public int getNrOfExtractedTriples() {
+ return nrOfExtractedTriples;
+ }
+
/*public static void main(String[] args) throws MalformedURLException {
String query = "SELECT ?pred ?obj\n"
+ "WHERE {<http://dbpedia.org/resource/Leipzig> ?pred ?obj}";
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBible2.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBible2.java 2008-08-31 19:55:38 UTC (rev 1164)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBible2.java 2008-09-01 00:00:09 UTC (rev 1165)
@@ -20,9 +20,12 @@
package org.dllearner.scripts;
import java.io.File;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import java.util.Locale;
import java.util.SortedSet;
import java.util.StringTokenizer;
import java.util.TreeSet;
@@ -36,20 +39,23 @@
import org.dllearner.core.Component;
import org.dllearner.core.ComponentManager;
import org.dllearner.core.EvaluatedDescription;
+import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.utilities.Files;
import org.dllearner.utilities.JamonMonitorLogger;
-import org.dllearner.utilities.StringFormatter;
import org.dllearner.utilities.datastructures.SetManipulation;
+import org.dllearner.utilities.learn.ConfWriter;
import org.dllearner.utilities.owl.ReasoningServiceFactory;
import org.dllearner.utilities.owl.ReasoningServiceFactory.AvailableReasoners;
import org.dllearner.utilities.statistics.SimpleClock;
+import org.dllearner.utilities.statistics.Stat;
-import com.jamonapi.Monitor;
+import com.jamonapi.MonitorFactory;
public class SemanticBible2 {
@@ -66,7 +72,26 @@
public static String tmpFilename = dir + "tmp.conf";
static File log = new File(dir+"results.txt");
+ private static Stat accFragment = new Stat();
+ private static Stat accOnOnto = new Stat();
+ private static Stat accPosExOnOnto = new Stat();
+ private static Stat accNegExOnOnto = new Stat();
+ private static Stat timeFragment = new Stat();
+ private static Stat nrOfExtractedTriples = new Stat();
+ private static Stat dLengthFragment = new Stat();
+ private static Stat dDepthFragment = new Stat();
+ private static Stat timeWhole = new Stat();
+ private static Stat accWhole = new Stat();
+ private static Stat dLengthWhole = new Stat();
+ private static Stat dDepthWhole = new Stat();
+
+ private static int normalNoisePercentage = 0;
+ private static int normalMaxExecution = 500;
+ private static int sparqllMaxExecution = 250;
+
+
+
//private static Class usedReasoner = FastInstanceChecker.class;
private static boolean useSPARQL = true;
@@ -76,6 +101,7 @@
*/
public static void main(String[] args) {
SimpleClock total = new SimpleClock();
+
initLogger();
logger.warn("Start");
File tmpFile = new File(tmpFilename);
@@ -84,86 +110,123 @@
List<File> confs = getFilesContaining(useSPARQL,"ten","all", "99+");
//analyzeFiles(confs);
- Files.createFile(log,
- "accOnFragment"+del+
- "accOnOnt"+del+
- "timeFragme"+del+
- "coveredPos"+del+
- "coveredNeg"+del+
- "timeWhole"+cr);
+
reasoningService = ReasoningServiceFactory.getReasoningService(ontologyPath, AvailableReasoners.OWLAPIREASONERPELLET);
ComponentManager cm =ComponentManager.getInstance();
try{
for (File f : confs) {
+ Cache.getDefaultCache().clearCache();
String fileContent = Files.readFile(f);
-
- String logLine ="";
SortedSet<Individual> posEx = SetManipulation.stringToInd(getIndividuals(fileContent, true));
SortedSet<Individual> negEx = SetManipulation.stringToInd(getIndividuals(fileContent, false));
StringBuffer sbuf = new StringBuffer(fileContent);
- sbuf.insert(0, (useSPARQL)?sparqlOptions():normalOptions());
+ sbuf.insert(0, sparqlOptions());
Files.createFile(tmpFile, sbuf.toString());
- //System.out.println(tmpFile.getCanonicalPath());
- Monitor m = JamonMonitorLogger.getTimeMonitor(SemanticBible2.class, "learn on fragment").start();
SimpleClock sc = new SimpleClock();
Start.main(new String[] { tmpFilename });
- long time = sc.getTime();
- m.stop();
- LearningAlgorithm la = getLearningAlgorithm();
+ timeFragment.addNumber((double) sc.getTime());
+
+ LearningAlgorithm la = cm.getLiveLearningAlgorithms().remove(0);
EvaluatedDescription onFragment =(la.getCurrentlyBestEvaluatedDescription());
- logLine += StringFormatter.doubleToPercent(onFragment.getAccuracy())+del;
+ accFragment.addNumber(onFragment.getAccuracy());
+ dDepthFragment.addNumber((double)onFragment.getDescriptionDepth());
+ dLengthFragment.addNumber((double)onFragment.getDescriptionLength());
+
SortedSet<Individual> retrieved = reasoningService.retrieval(onFragment.getDescription());
EvaluatedDescription onOnto = reEvaluateDescription(
onFragment.getDescription(), retrieved, posEx, negEx);
- /*if(onOnto.getAccuracy()!=1.0){
- Files.appendFile(log, onOnto.toString()+"\n");
- System.out.println(onOnto.toString());
-
- System.out.println(onOnto.getCoveredPositives());
- System.out.println(onOnto.getCoveredNegatives().size());
-
- System.out.println(onOnto.getNotCoveredPositives());
- System.out.println(onOnto.getNotCoveredNegatives());
- System.out.println("p then n");
- System.out.println(posEx);
- System.out.println(negEx);
- System.out.println(retrieved);
- System.out.println((5-onOnto.getCoveredNegatives().size())+"");
- double n = (double) (5-onOnto.getCoveredNegatives().size());
- System.out.println();
- System.out.println((n/5.0));
- System.exit(0);
- }*/
- logLine += StringFormatter.doubleToPercent(onOnto.getAccuracy())+del;
- logLine += time+del;
- logLine += StringFormatter.doubleToPercent((double)(onOnto.getCoveredPositives().size()/5))+del;
+ double reachedAccuracy = onOnto.getAccuracy();
+ accOnOnto.addNumber(onOnto.getAccuracy());
+
+ int tmp = (int)(Math.floor(onOnto.getAccuracy()*100));
+ normalNoisePercentage = 100-tmp;
+ accPosExOnOnto.addNumber((double)(onOnto.getCoveredPositives().size()/5));
double n = (double) (5-onOnto.getCoveredNegatives().size());
- logLine += StringFormatter.doubleToPercent(n/5.0)+del;
- logLine += " size of retrieve: "+retrieved.size()+del;
- logLine += f.toString();
- Files.appendFile(log, logLine+cr);
- Cache.getDefaultCache().clearCache();
+ accNegExOnOnto.addNumber(n/5.0);
+ SparqlKnowledgeSource s=null;
+ for(KnowledgeSource ks : cm.getLiveKnowledgeSources()){
+ if (ks instanceof SparqlKnowledgeSource) {
+ s = (SparqlKnowledgeSource) ks;
+ }
+ }
+
+ double nrtrip = (double)(s.getNrOfExtractedTriples());
+ nrOfExtractedTriples.addNumber(nrtrip);
+
+
+
cm.freeAllComponents();
+ /*************comp**/
+ logger.warn("learning normal");
+
+ StringBuffer sbufNormal = new StringBuffer();
+ sbufNormal.append(normalOptions());
+ sbufNormal.append(ConfWriter.listExamples(true, posEx));
+ sbufNormal.append(ConfWriter.listExamples(false, negEx));
+ //sbufNormal.append(ConfWriter.)
+ Files.createFile(tmpFile, sbufNormal.toString());
+ SimpleClock scNormal = new SimpleClock();
+ Start.main(new String[] { tmpFilename });
+ timeWhole.addNumber((double) scNormal.getTime());
+
+ la = cm.getLiveLearningAlgorithms().remove(0);
+
+ EvaluatedDescription normalOnOnto =(la.getCurrentlyBestEvaluatedDescription());
+ accWhole.addNumber(normalOnOnto.getAccuracy());
+ dDepthWhole.addNumber((double)normalOnOnto.getDescriptionDepth());
+ dLengthWhole.addNumber((double)normalOnOnto.getDescriptionLength());
+
+ cm.freeAllComponents();
+
+ //writeLog();
+ //System.exit(0);
}//end for
}catch (Exception e) {
e.printStackTrace();
}
+ writeLog();
total.printAndSet("Finished");
//logger.warn("Finished");
}
+ public static void writeLog(){
+ String l = "a";
+ l +=
+
+ l+="accFragment\t\t"+accFragment.getMeanAsPercentage()+" +-"+accFragment.getStandardDeviation()+"\n";
+ l+="accOnOnto\t\t"+accOnOnto.getMeanAsPercentage()+" +-"+accOnOnto.getStandardDeviation()+"\n";
+ l+="accPosExOnOnto\t\t"+accPosExOnOnto.getMeanAsPercentage()+" +-"+accPosExOnOnto.getStandardDeviation()+"\n";
+ l+="accNegExOnOnto\t\t"+accNegExOnOnto.getMeanAsPercentage()+" +-"+accNegExOnOnto.getStandardDeviation()+"\n";
+ l+="timeFragment\t\t"+timeFragment.getMean()+" +-"+timeFragment.getStandardDeviation()+"\n";
+ l+="nrOfExtractedTriples\t\t"+nrOfExtractedTriples.getMean()+" +-"+nrOfExtractedTriples.getStandardDeviation()+"\n";
+ l+="dLengthFragment\t\t"+dLengthFragment.getMean()+" +-"+dLengthFragment.getStandardDeviation()+"\n";
+ l+="dDepthFragment\t\t"+dDepthFragment.getMean()+" +-"+dDepthFragment.getStandardDeviation()+"\n";
+
+ l+="timeWhole\t\t"+timeWhole.getMean()+" +-"+timeWhole.getStandardDeviation()+"\n";
+ l+="accWhole\t\t"+accWhole.getMeanAsPercentage()+" +-"+accWhole.getStandardDeviation()+"\n";
+ l+="dLengthWhole\t\t"+dLengthWhole.getMean()+" +-"+dLengthWhole.getStandardDeviation()+"\n";
+ l+="dDepthWhole\t\t"+dDepthWhole.getMean()+" +-"+dDepthWhole.getStandardDeviation()+"\n";
+
+ Files.createFile(log, l);
+
+// write JaMON report in HTML file
+ File jamonlog = new File("sembib/jamon.html");
+ Files.createFile(jamonlog, MonitorFactory.getReport());
+ Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
+ }
+
public static EvaluatedDescription reEvaluateDescription(Description d, SortedSet<Individual> retrieved ,SortedSet<Individual> posEx ,SortedSet<Individual> negEx ){
SortedSet<Individual> PosAsPos = new TreeSet<Individual>();
SortedSet<Individual> PosAsNeg = new TreeSet<Individual>();
@@ -304,7 +367,7 @@
public static String sparqlOptions (){
String s="// SPARQL options\n"+
- "sparql.recursionDepth = 3;\n"+
+ "sparql.recursionDepth = 2;\n"+
"sparql.useLits = true;\n"+
"sparql.predefinedEndpoint = \"LOCALJOSEKIBIBLE\";\n"+
"import(\"lalala\",\"SPARQL\");\n"+
@@ -316,7 +379,9 @@
public static String normalOptions (){
String s="\n"+
"import(\"NTNcombined.owl\");\n"+
- "refexamples.maxExecutionTimeInSeconds = 1800;\n"+
+ "refexamples.maxExecutionTimeInSeconds = "+normalMaxExecution+";\n";
+
+ s+="refexamples.noisePercentage = "+normalNoisePercentage+";\n"+
getCombinedOptions()+
"";
return s;
Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java 2008-08-31 19:55:38 UTC (rev 1164)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java 2008-09-01 00:00:09 UTC (rev 1165)
@@ -20,6 +20,8 @@
package org.dllearner.utilities.statistics;
+import java.text.DecimalFormat;
+
/**
* Utility class for calculating the mean and standard deviation of a given set
* of numbers.
@@ -34,6 +36,8 @@
private double squareSum = 0;
private double min = Double.MAX_VALUE;
private double max = Double.MIN_NORMAL;
+ //used to give a good percentage output
+ private DecimalFormat df = new DecimalFormat( ".00%" );
/**
* Add a number to this object.
@@ -77,6 +81,15 @@
public double getMean() {
return sum / count;
}
+
+ /**
+ * Gets the mean of all numbers as percentage
+ * *100 so 0.5678 -> "56.78%"
+ * @return
+ */
+ public String getMeanAsPercentage(){
+ return df.format(getMean());
+ }
/**
* Gets the standard deviation of all numbers.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
