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[DL-Learner SVN] SF.net SVN: dl-learner: [942] trunk/src/dl-learner/org/dllearner
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From: <Jen...@us...> - 2008-06-05 10:43:29
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Revision: 942
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=942&view=rev
Author: JensLehmann
Date: 2008-06-05 03:43:24 -0700 (Thu, 05 Jun 2008)
Log Message:
-----------
updated statistics and cross validation script
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java
trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/algorithms/gp/GP.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -163,19 +163,20 @@
options.add(new BooleanConfigOption("elitism", "specifies whether to use elitism in selection", true));
StringConfigOption algorithmType = new StringConfigOption("algorithmType", "algorithm type", "steadyState");
algorithmType.setAllowedValues(new String[] {"generational", "steadyState"});
- DoubleConfigOption mutationProb = new DoubleConfigOption("mutationProbablitiy", "mutation probability", 0.03);
+ options.add(algorithmType);
+ DoubleConfigOption mutationProb = new DoubleConfigOption("mutationProbability", "mutation probability", 0.03);
mutationProb.setLowerLimit(0.0);
mutationProb.setUpperLimit(1.0);
options.add(mutationProb);
- DoubleConfigOption crossoverProb = new DoubleConfigOption("crossoverProbablitiy", "crossover probability", 0.95);
+ DoubleConfigOption crossoverProb = new DoubleConfigOption("crossoverProbability", "crossover probability", 0.95);
crossoverProb.setLowerLimit(0.0);
crossoverProb.setUpperLimit(1.0);
options.add(crossoverProb);
- DoubleConfigOption hillClimbingProb = new DoubleConfigOption("hillClimbingProbablitiy", "hill climbing probability", 0.0);
+ DoubleConfigOption hillClimbingProb = new DoubleConfigOption("hillClimbingProbability", "hill climbing probability", 0.0);
hillClimbingProb.setLowerLimit(0.0);
hillClimbingProb.setUpperLimit(1.0);
options.add(hillClimbingProb);
- DoubleConfigOption refinementProb = new DoubleConfigOption("refinementProbablitiy", "refinement operator probability (values higher than 0 turn this into a hybrid GP algorithm - see publication)", 0.00);
+ DoubleConfigOption refinementProb = new DoubleConfigOption("refinementProbability", "refinement operator probability (values higher than 0 turn this into a hybrid GP algorithm - see publication)", 0.00);
refinementProb.setLowerLimit(0.0);
refinementProb.setUpperLimit(1.0);
options.add(refinementProb);
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -104,6 +104,7 @@
private LearningAlgorithm la;
private LearningProblem lp;
private ReasoningService rs;
+ private ReasonerComponent rc;
/**
* Entry point for CLI interface.
@@ -183,10 +184,10 @@
// step 2: detect used reasoner
ConfFileOption reasonerOption = parser.getConfOptionsByName("reasoner");
- ReasonerComponent reasoner = cm.reasoner(getReasonerClass(reasonerOption), sources);
- configureComponent(cm, reasoner, componentPrefixMapping, parser);
- initComponent(cm, reasoner);
- rs = cm.reasoningService(reasoner);
+ rc = cm.reasoner(getReasonerClass(reasonerOption), sources);
+ configureComponent(cm, rc, componentPrefixMapping, parser);
+ initComponent(cm, rc);
+ rs = cm.reasoningService(rc);
// step 3: detect learning problem
ConfFileOption problemOption = parser.getConfOptionsByName("problem");
@@ -754,6 +755,10 @@
return lp;
}
+ public ReasonerComponent getReasonerComponent() {
+ return rc;
+ }
+
public ReasoningService getReasoningService() {
return rs;
}
@@ -829,4 +834,6 @@
return laClass;
}
+
+
}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -35,7 +35,6 @@
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.ReasoningMethodUnsupportedException;
-import org.dllearner.core.ReasoningService;
import org.dllearner.core.config.ConfigEntry;
import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.config.InvalidConfigOptionValueException;
@@ -100,7 +99,7 @@
private SortedSet<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
private SortedSet<Individual> individuals;
- private ReasoningService rs;
+// private ReasoningService rs;
private OWLAPIReasoner rc;
private Set<KnowledgeSource> sources;
@@ -177,7 +176,7 @@
atomicRoles = rc.getAtomicRoles();
individuals = rc.getIndividuals();
- rs = new ReasoningService(rc);
+// rs = new ReasoningService(rc);
// TODO: some code taken from Helper.createFlatABox, but pasted here
// because additional things need to
@@ -187,9 +186,9 @@
logger.debug("dematerialising concepts");
- for (NamedClass atomicConcept : rs.getAtomicConcepts()) {
+ for (NamedClass atomicConcept : rc.getAtomicConcepts()) {
- SortedSet<Individual> pos = rs.retrieval(atomicConcept);
+ SortedSet<Individual> pos = rc.retrieval(atomicConcept);
classInstancesPos.put(atomicConcept, pos);
if(defaultNegation) {
@@ -199,7 +198,7 @@
// on the carcinogenesis data set (and probably others), so we have to
// be careful here
Negation negatedAtomicConcept = new Negation(atomicConcept);
- classInstancesNeg.put(atomicConcept, rs.retrieval(negatedAtomicConcept));
+ classInstancesNeg.put(atomicConcept, rc.retrieval(negatedAtomicConcept));
}
@@ -521,32 +520,32 @@
* @see org.dllearner.core.Reasoner#prepareSubsumptionHierarchy(java.util.Set)
*/
public void prepareSubsumptionHierarchy(Set<NamedClass> allowedConcepts) {
- rs.prepareSubsumptionHierarchy();
+ rc.prepareSubsumptionHierarchy(allowedConcepts);
}
@Override
public SubsumptionHierarchy getSubsumptionHierarchy() {
- return rs.getSubsumptionHierarchy();
+ return rc.getSubsumptionHierarchy();
}
@Override
public void prepareRoleHierarchy(Set<ObjectProperty> allowedRoles) {
- rs.prepareRoleHierarchy(allowedRoles);
+ rc.prepareRoleHierarchy(allowedRoles);
}
@Override
public ObjectPropertyHierarchy getRoleHierarchy() {
- return rs.getRoleHierarchy();
+ return rc.getRoleHierarchy();
}
@Override
public void prepareDatatypePropertyHierarchy(Set<DatatypeProperty> allowedRoles) {
- rs.prepareDatatypePropertyHierarchy(allowedRoles);
+ rc.prepareDatatypePropertyHierarchy(allowedRoles);
}
@Override
public DatatypePropertyHierarchy getDatatypePropertyHierarchy() {
- return rs.getDatatypePropertyHierarchy();
+ return rc.getDatatypePropertyHierarchy();
}
@Override
@@ -554,7 +553,7 @@
// Negation neg = new Negation(subConcept);
// Intersection c = new Intersection(neg,superConcept);
// return fastRetrieval.calculateSets(c).getPosSet().isEmpty();
- return rs.subsumes(superConcept, subConcept);
+ return rc.subsumes(superConcept, subConcept);
}
/**
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -474,6 +474,9 @@
private TreeSet<Description> getMoreSpecialConcepts(Description concept) {
Set<Set<OWLClass>> classes = null;
try {
+// System.out.println(OWLAPIDescriptionConvertVisitor.getOWLDescription(concept));
+// System.out.println(getSubsumptionHierarchy());
+// System.out.println(reasoner);
classes = reasoner.getSubClasses(OWLAPIDescriptionConvertVisitor.getOWLDescription(concept));
} catch (OWLReasonerException e) {
e.printStackTrace();
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -34,6 +34,7 @@
import org.apache.log4j.Logger;
import org.dllearner.algorithms.refinement.RefinementOperator;
+import org.dllearner.core.ReasoningMethodUnsupportedException;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.BooleanValueRestriction;
import org.dllearner.core.owl.DataRange;
Modified: trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -115,7 +115,8 @@
}
LearningProblem lp = start.getLearningProblem();
- ReasoningService rs = start.getReasoningService();
+// ReasoningService rs = start.getReasoningService();
+// start.getReasoningService().releaseKB();
// the training and test sets used later on
List<Set<Individual>> trainingSetsPos = new LinkedList<Set<Individual>>();
@@ -194,7 +195,6 @@
try {
start = new Start(file);
} catch (ComponentInitException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
}
lp = start.getLearningProblem();
@@ -206,17 +206,17 @@
// System.out.println("neg: " + neg.size());
// System.exit(0);
- // es fehlt init zwischendurch
-
- if(la == null)
- la = start.getLearningAlgorithm();
+ la = start.getLearningAlgorithm();
// init again, because examples have changed
try {
+// start.getReasonerComponent().init();
+ lp.init();
la.init();
} catch (ComponentInitException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
+
long algorithmStartTime = System.nanoTime();
la.start();
long algorithmDuration = System.nanoTime() - algorithmStartTime;
@@ -224,6 +224,7 @@
Description concept = la.getBestSolution();
+ ReasoningService rs = start.getReasoningService();
Set<Individual> tmp = rs.instanceCheck(concept, testSetsPos.get(currFold));
Set<Individual> tmp2 = Helper.difference(testSetsPos.get(currFold), tmp);
Set<Individual> tmp3 = rs.instanceCheck(concept, testSetsNeg.get(currFold));
@@ -258,7 +259,7 @@
System.out.println(" runtime: " + df.format(algorithmDuration/(double)1000000000) + "s");
// free all resources
- start.getReasoningService().releaseKB();
+ rs.releaseKB();
cm.freeAllComponents();
}
@@ -312,7 +313,7 @@
return splits;
}
- private String statOutput(DecimalFormat df, Stat stat, String unit) {
+ public static String statOutput(DecimalFormat df, Stat stat, String unit) {
String str = "av. " + df.format(stat.getMean()) + unit;
str += " (deviation " + df.format(stat.getStandardDeviation()) + unit + "; ";
str += "min " + df.format(stat.getMin()) + unit + "; ";
Modified: trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java 2008-06-05 05:35:11 UTC (rev 941)
+++ trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java 2008-06-05 10:43:24 UTC (rev 942)
@@ -22,6 +22,7 @@
import java.io.File;
import java.net.MalformedURLException;
import java.net.URL;
+import java.text.DecimalFormat;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -49,6 +50,8 @@
*/
public class PaperStatistics {
+ private static DecimalFormat df = new DecimalFormat();
+
/**
* Points to the current statistic generation function.
*
@@ -82,7 +85,7 @@
// learning examples:
// - trains
- // - arches
+ // - arches => left out, insufficiently many examples
// - moral (simple)
// - moral (complex)
// - poker (pair)
@@ -95,22 +98,22 @@
String statBaseDir = "log/stat/";
File[] confFiles = new File[1];
-// confFiles[0] = new File(exampleBaseDir + "trains", "trains_owl");
- confFiles[0] = new File(exampleBaseDir + "arch", "arch");
-// confFiles[2] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_owl");
-// confFiles[3] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_complex_owl");
-// confFiles[4] = new File(exampleBaseDir + "poker", "pair_owl");
-// confFiles[5] = new File(exampleBaseDir + "poker", "straight_owl");
-// confFiles[6] = new File(exampleBaseDir + "forte", "forte_uncle_owl");
+ confFiles[0] = new File(exampleBaseDir + "trains", "trains_owl");
+// confFiles[0] = new File(exampleBaseDir + "arch", "arch");
+ confFiles[1] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_owl");
+ confFiles[2] = new File(exampleBaseDir + "moral_reasoner", "moral_43examples_complex_owl");
+ confFiles[3] = new File(exampleBaseDir + "poker", "pair_owl");
+ confFiles[4] = new File(exampleBaseDir + "poker", "straight_owl");
+ confFiles[5] = new File(exampleBaseDir + "forte", "forte_uncle_owl");
String[] examples = new String[7];
examples[0] = "trains";
- examples[1] = "arches";
- examples[2] = "moral reasoner (43 examples, simple)";
- examples[3] = "moral reasoner (43 examples, complex)";
- examples[4] = "poker (49 examples, pair)";
- examples[5] = "poker (55 examples, straight)";
- examples[6] = "uncle (FORTE data set)";
+// examples[0] = "arches";
+ examples[1] = "moral reasoner (43 examples, simple)";
+ examples[2] = "moral reasoner (43 examples, complex)";
+ examples[3] = "poker (49 examples, pair)";
+ examples[4] = "poker (55 examples, straight)";
+ examples[5] = "uncle (FORTE data set)";
int startExampleNr = 0;
// for any example, we create conf files for each configuration to be tested
@@ -121,6 +124,8 @@
algorithmPostfix[3] = "_hybrid";
int startAlgorithmNr = 0;
+ int[] folds = new int[] {5,5,5,5,5,5};
+
File statFile = new File(statBaseDir, "statistics.txt");
String statString = "**automatically generated statistics**\n\n";
@@ -132,16 +137,22 @@
File confFile = new File(confFiles[exampleNr] + algorithmPostfix[algorithmNr] + ".conf");
- CrossValidation cv = new CrossValidation(confFile, 5, false);
- Stat classification = new Stat();
- Stat length = new Stat();
- Stat runtime = new Stat();
+ System.out.println("running " + folds[exampleNr] + " fold cross validation on " + confFile);
+ CrossValidation cv = new CrossValidation(confFile, folds[exampleNr], false);
+ Stat accuracy = cv.getAccuracy();
+ Stat length = cv.getLength();
+ Stat runtime = cv.getRuntime();
+
statString += "conf file: " + confFile + "\n";
- statString += "classification: " + classification.getMean() + "% (standard deviation: " + classification.getStandardDeviation() + "%)\n";
- statString += "concept length: " + length.getMean() + " (standard deviation: " + length.getStandardDeviation() + ")\n";
- statString += "runtime: " + Helper.prettyPrintNanoSeconds(Math.round(runtime.getMean())) + " (standard deviation: " + Helper.prettyPrintNanoSeconds(Math.round(runtime.getStandardDeviation())) + ")\n\n";
+// statString += "classification: " + classification.getMean() + "% (standard deviation: " + classification.getStandardDeviation() + "%)\n";
+// statString += "concept length: " + length.getMean() + " (standard deviation: " + length.getStandardDeviation() + ")\n";
+// statString += "runtime: " + runtime.getMean() + " (standard deviation: " + runtime.getStandardDeviation() + ")\n\n";
+ statString += "accuracy: " + CrossValidation.statOutput(df, accuracy, "%") + "\n";
+ statString += "length: " + CrossValidation.statOutput(df, length, "") + "\n";
+ statString += "runtime: " + CrossValidation.statOutput(df, runtime, "s") + "\n\n";
+
Files.createFile(statFile, statString);
} // end algorithm loop
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