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[DL-Learner SVN] SF.net SVN: dl-learner:[3715] trunk
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From: <tc...@us...> - 2012-05-17 03:10:07
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Revision: 3715
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3715&view=rev
Author: tcanvn
Date: 2012-05-17 03:09:57 +0000 (Thu, 17 May 2012)
Log Message:
-----------
change the PADCEL algorithm's name (PADCEL --> ParCEL). Package name, examples, CLI and test units have been updated
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown2008.java
trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELAbstract.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELComplenessComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELCompletenessComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELCorrectnessComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELCoverageGreedyReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELCoveredNegativeExampleComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELDefaultHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELDefinitionGenerationTimeComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELDefinitionLengthComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELDefinitionLengthReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELEvaluationResult.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELExtraNode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELGenerationTimeReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELImprovedCovegareGreedyReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELNode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELOntologyUtil.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELPosNegLP.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELRefinementOperatorFactory.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELRefinementOperatorPool.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELScore.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELStringUtilities.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELTaskComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELWorker.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELWorkerMat.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELWorkerThreadFactory.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELearnerMBean.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/ParCELearnerMat.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/split/
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/split/ParCELDoubleSplitterAbstract.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/split/ParCELDoubleSplitterV1.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/split/ValueCount.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCEL/split/ValuesSet.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCELEx/
trunk/components-core/src/main/java/org/dllearner/algorithms/ParCELEx/ParCELExAbstract.java
trunk/examples/carcinogenesis/carcinogenesis_parcel.conf
trunk/examples/family-benchmark/Aunt_parcel.conf
trunk/examples/family-benchmark/Brother_parcel.conf
trunk/examples/family-benchmark/Cousin_parcel.conf
trunk/examples/family-benchmark/Daughter_parcel.conf
trunk/examples/family-benchmark/Father_parcel.conf
trunk/examples/family-benchmark/Grandson_parcel.conf
trunk/examples/family-benchmark/Uncle_parcel.conf
trunk/examples/forte/uncle_owl_large_parcel.conf
trunk/examples/moral_reasoner/moral_all_examples_simple_owl_parcel.conf
trunk/examples/poker/straight_owl_parcel.conf
trunk/examples/showering-duration/uca1_150_parcel.conf
trunk/examples/showering-duration/uca2_300_parcel.conf
trunk/interfaces/src/main/java/org/dllearner/cli/ParCELCrossValidation.java
trunk/interfaces/src/test/java/org/dllearner/cli/ParCELCLITestAbstract.java
trunk/interfaces/src/test/java/org/dllearner/cli/ParCELCarcinoGenesisTest.java
trunk/interfaces/src/test/java/org/dllearner/cli/ParCELFamilyBenchmarkTest.java
trunk/interfaces/src/test/java/org/dllearner/cli/ParCELMultiExamplesTest.java
Removed Paths:
-------------
trunk/components-core/src/main/java/nz/ac/massey/abd/
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELAbstract.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELComplenessComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCompletenessComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCorrectnessComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCoverageGreedyReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCoveredNegativeExampleComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefaultHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionGenerationTimeComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionLengthComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionLengthReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELEvaluationResult.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELExtraNode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELGenerationTimeReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELImprovedCovegareGreedyReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELNode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELOntologyUtil.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELPosNegLP.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELReducer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELRefinementOperatorFactory.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELRefinementOperatorPool.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELScore.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELStringUtilities.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELTaskComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELWorker.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELWorkerThreadFactory.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELearnerMBean.java
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/split/
trunk/components-core/src/main/java/org/dllearner/algorithms/PADCELEx/
trunk/examples/carcinogenesis/carcinogenesis_padcel.conf
trunk/examples/family-benchmark/Aunt_padcel.conf
trunk/examples/family-benchmark/Brother_padcel.conf
trunk/examples/family-benchmark/Cousin_padcel.conf
trunk/examples/family-benchmark/Daughter_padcel.conf
trunk/examples/family-benchmark/Father_padcel.conf
trunk/examples/family-benchmark/Grandson_padcel.conf
trunk/examples/family-benchmark/Uncle_padcel.conf
trunk/examples/forte/uncle_owl_large_padcel.conf
trunk/examples/moral_reasoner/moral_all_examples_simple_owl_padcel.conf
trunk/examples/poker/straight_owl_padcel.conf
trunk/examples/showering-duration/uca1_150_padcel.conf
trunk/examples/showering-duration/uca2_300_padcel.conf
trunk/interfaces/src/main/java/org/dllearner/cli/PADCELCrossValidation.java
trunk/interfaces/src/test/java/org/dllearner/cli/PADCELCLITestAbstract.java
trunk/interfaces/src/test/java/org/dllearner/cli/PADCELCarcinoGenesisTest.java
trunk/interfaces/src/test/java/org/dllearner/cli/PADCELFamilyBenchmarkTest.java
trunk/interfaces/src/test/java/org/dllearner/cli/PADCELMultiExamplesTest.java
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELAbstract.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELAbstract.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELAbstract.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,142 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.concurrent.ConcurrentSkipListSet;
-
-import org.dllearner.core.AbstractCELA;
-import org.dllearner.core.AbstractReasonerComponent;
-import org.dllearner.core.config.ConfigOption;
-import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.NamedClass;
-
-/**
- * Abstract class for all PDL-Learner algorithms family
- *
- * @author An C. Tran
- *
- */
-public abstract class PADCELAbstract extends AbstractCELA {
-
- // ----------------------------------
- // configuration options
- // ----------------------------------
- @ConfigOption(name = "numberOfWorkers", defaultValue = "2", description = "This option is used to set the number of workers will be created to serve the leaner. This should be = 2 * total number of cores of CPUs")
- protected int numberOfWorkers = 4; // max number of workers will be created
-
- @ConfigOption(name = "maxExecutionTimeInSeconds", defaultValue = "0", description = "maximum execution of the algorithm in seconds")
- protected int maxExecutionTimeInSeconds = 0;
-
- @ConfigOption(name = "noisePercentage", defaultValue = "0.0", description = "The percentage of noise within the examples")
- protected double noisePercentage = 0.0;
-
- @ConfigOption(name = "maxNoOfSplits", defaultValue = "10", description = "Max number of splits will be applied for data properties with double range")
- protected int maxNoOfSplits = 10;
-
- @ConfigOption(name = "ignoredConcepts", defaultValue = "", description = "set of concepts that will be ignored in learning the target concept")
- protected Set<NamedClass> ignoredConcepts = null;
-
-
- /**
- * All generated descriptions thread-safe set is used to avoid concurrently
- * accessing
- */
- protected ConcurrentSkipListSet<Description> allDescriptions = null;
-
- /**
- * Search tree. It hold all evaluated descriptions that are not correct and
- * not weak ==> candidate for partial definitions Nodes in the search tree
- * must be ordered using heuristic so that it can help the searching more
- * efficiently (best search rather than 'blind' breadth first of depth
- * first) NOTE: node = (description + accuracy/correctness/completeness/...
- * value)
- */
- protected ConcurrentSkipListSet<PADCELNode> searchTree = null; // thread safe
- // set
-
- /**
- * partial definitions (they should be sorted so that we can get the best
- * partial definition at any time
- */
- protected SortedSet<PADCELExtraNode> partialDefinitions = null;
-
- /**
- * Default constructor
- */
- public PADCELAbstract() {
- super();
- }
-
- /**
- * ========================================================================
- * Constructor for the learning algorithm
- *
- * @param learningProblem
- * Must be a PDLLPosNegLP
- * @param reasoningService
- * A reasoner
- */
- public PADCELAbstract(PADCELPosNegLP learningProblem, AbstractReasonerComponent reasoningService) {
- super(learningProblem, reasoningService);
- }
-
- public abstract Description getUnionCurrenlyBestDescription();
-
- public abstract int getNoOfCompactedPartialDefinition();
-
- public abstract Set<PADCELExtraNode> getPartialDefinitions();
-
- public abstract double getCurrentlyOveralMaxCompleteness();
-
- public long getNumberOfPartialDefinitions() {
- return this.partialDefinitions.size();
- }
-
-
- // ------------------------------------------------
- // setters and getters for configuration options
- // ------------------------------------------------
-
- public void setNumberOfWorkers(int numberOfWorkers) {
- this.numberOfWorkers = numberOfWorkers;
- }
-
- public int getNumberOfWorkers() {
- return numberOfWorkers;
- }
-
- public void setMaxExecutionTimeInSeconds(int maxExecutionTime) {
- this.maxExecutionTimeInSeconds = maxExecutionTime;
- }
-
- public int getMaxExecutionTimeInSeconds() {
- return maxExecutionTimeInSeconds;
- }
-
- public void setNoisePercentage(double noise) {
- this.noisePercentage = noise;
- }
-
- public double getNoisePercentage() {
- return this.noisePercentage;
- }
-
-
- public int getMaxNoOfSplits() {
- return maxNoOfSplits;
- }
-
- public void setMaxNoOfSplits(int maxNoOfSplits) {
- this.maxNoOfSplits = maxNoOfSplits;
- }
-
- public Set<NamedClass> getIgnoredConcepts() {
- return ignoredConcepts;
- }
-
- public void setIgnoredConcepts(Set<NamedClass> ignoredConcepts) {
- this.ignoredConcepts = ignoredConcepts;
- }
-
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELComplenessComparator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELComplenessComparator.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELComplenessComparator.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,37 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.Comparator;
-
-import org.dllearner.utilities.owl.ConceptComparator;
-
-/**
- * Comparator for PDLLNode based on the completeness of the description If two
- * nodes has the same completeness, description length will be taken into the
- * consideration and finally the ConceptComparator
- *
- * @author An C. Tran
- *
- */
-
-public class PADCELComplenessComparator implements Comparator<PADCELNode> {
-
- @Override
- public int compare(PADCELNode node1, PADCELNode node2) {
- int v1 = node1.getCoveredPositiveExamples().size();
- int v2 = node2.getCoveredPositiveExamples().size();
- if (v1 > v2)
- return -1;
- else if (v1 < v2)
- return 1;
- else {
- if (node1.getDescription().getLength() < node2.getDescription().getLength())
- return -1;
- else if (node1.getDescription().getLength() > node2.getDescription().getLength())
- return 1;
- else
- return new ConceptComparator().compare(node1.getDescription(),
- node2.getDescription());
- }
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCompletenessComparator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCompletenessComparator.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCompletenessComparator.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,38 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.Comparator;
-
-import org.dllearner.utilities.owl.ConceptComparator;
-
-/**
- * Use to compare 2 ExtraPLOENode nodes based on their completeness (coverage). The description
- * length and ConceptComparator will be used it they have equal coverage
- *
- * @author An C. Tran
- *
- */
-public class PADCELCompletenessComparator implements Comparator<PADCELExtraNode> {
-
- @Override
- public int compare(PADCELExtraNode node1, PADCELExtraNode node2) {
-
- int v1 = node1.getCoveredPositiveExamples().size();
- int v2 = node2.getCoveredPositiveExamples().size();
-
- if (v1 > v2)
- return -1;
- else if (v1 < v2)
- return 1;
- else {
- int len1 = node1.getDescription().getLength();
- int len2 = node2.getDescription().getLength();
- if (len1 < len2)
- return -1;
- else if (len1 > len2)
- return 1;
- else
- return new ConceptComparator().compare(node1.getDescription(),
- node2.getDescription());
- }
- }
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCorrectnessComparator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCorrectnessComparator.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCorrectnessComparator.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,38 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.Comparator;
-
-import org.dllearner.utilities.owl.ConceptComparator;
-
-/**
- * Use to compare 2 ExtraPLOENode nodes based on their correctness. The description length and
- * ConceptComparator will be used it they have equal coverage
- *
- * @author An C. Tran
- *
- */
-public class PADCELCorrectnessComparator implements Comparator<PADCELExtraNode> {
-
- @Override
- public int compare(PADCELExtraNode node1, PADCELExtraNode node2) {
- double correctness1 = node1.getCorrectness();
- double correctness2 = node2.getCorrectness();
-
- if (correctness1 > correctness2)
- return -1; // smaller will be on the top
- else if (correctness1 < correctness2)
- return 1;
- else {
- int len1 = node1.getDescription().getLength();
- int len2 = node2.getDescription().getLength();
-
- if (len1 < len2)
- return -1;
- else if (len1 > len2)
- return 1;
- else
- return new ConceptComparator().compare(node1.getDescription(),
- node2.getDescription());
- }
- }
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCoverageGreedyReducer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCoverageGreedyReducer.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCoverageGreedyReducer.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,82 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.dllearner.core.owl.Individual;
-
-/**
- * This class implements a simple strategy for compacting the partial definition set In this
- * strategy, the partial definition will be chosen based on their accuracy. The partial definition
- * with the best accuracy will be chosen first and the rests will not be re-calculated before the
- * next reduction
- *
- * @author An C. Tran
- *
- */
-public class PADCELCoverageGreedyReducer implements PADCELReducer {
-
- /**
- * Compact partial definitions
- *
- * @param partialDefinitions
- * Set of partial definitions
- * @param positiveExamples
- * Set of positive examples (used to check whether partial definition is useful
- * @param uncoveredPositiveExamples
- * Number of uncovered positive examples allowed
- *
- * @return Subset of partial definitions that cover all positive examples
- */
- @Override
- public SortedSet<PADCELExtraNode> compact(SortedSet<PADCELExtraNode> partialDefinitions,
- Set<Individual> positiveExamples) {
- return compact(partialDefinitions, positiveExamples, 0);
- }
-
- /**
- * Compact partial definition with noise allowed
- *
- * @param partialDefinitions
- * Set of partial definitions
- * @param positiveExamples
- * Set of positive examples (used to check whether partial definition is useful
- * @param uncoveredPositiveExamples
- * Number of uncovered positive examples allowed
- *
- * @return Subset of partial definitions that cover (positive examples \ uncovered positive
- * examples)
- */
- @Override
- public SortedSet<PADCELExtraNode> compact(SortedSet<PADCELExtraNode> partialDefinitions,
- Set<Individual> positiveExamples, int uncoveredPositiveExamples) {
-
- Set<Individual> positiveExamplesTmp = new HashSet<Individual>();
- positiveExamplesTmp.addAll(positiveExamples);
-
- TreeSet<PADCELExtraNode> minimisedPartialDefinition = new TreeSet<PADCELExtraNode>(
- new PADCELCorrectnessComparator());
-
- Iterator<PADCELExtraNode> partialDefinitionIterator = partialDefinitions.iterator();
- while ((positiveExamplesTmp.size() > uncoveredPositiveExamples)
- && (partialDefinitionIterator.hasNext())) {
- PADCELExtraNode node = partialDefinitionIterator.next();
-
- int positiveExamplesRemoved = positiveExamplesTmp.size();
- positiveExamplesTmp.removeAll(node.getCoveredPositiveExamples());
-
- positiveExamplesRemoved -= positiveExamplesTmp.size();
-
- if (positiveExamplesRemoved > 0) {
- node.setCorrectness(positiveExamplesRemoved);
- minimisedPartialDefinition.add(node);
- }
- }
-
- return minimisedPartialDefinition;
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCoveredNegativeExampleComparator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCoveredNegativeExampleComparator.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELCoveredNegativeExampleComparator.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,38 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.Comparator;
-
-import org.dllearner.utilities.owl.ConceptComparator;
-
-/**
- * Use to compare 2 ExtraPLOENode nodes based on the number of covered negative examples. The
- * description length and ConceptComparator will be used it they have equal coverage
- *
- * @author An C. Tran
- *
- */
-public class PADCELCoveredNegativeExampleComparator implements Comparator<PADCELExtraNode> {
-
- @Override
- public int compare(PADCELExtraNode node1, PADCELExtraNode node2) {
- int coveredNeg1 = node1.getCoveredNegativeExamples().size();
- int coveredNeg2 = node2.getCoveredPositiveExamples().size();
-
- if (coveredNeg1 > coveredNeg2)
- return -1; // smaller will be on the top
- else if (coveredNeg1 < coveredNeg2)
- return 1;
- else {
- int len1 = node1.getDescription().getLength();
- int len2 = node2.getDescription().getLength();
-
- if (len1 < len2)
- return -1;
- else if (len1 > len2)
- return 1;
- else
- return new ConceptComparator().compare(node1.getDescription(),
- node2.getDescription());
- }
- }
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefaultHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefaultHeuristic.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefaultHeuristic.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,95 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import org.dllearner.utilities.owl.ConceptComparator;
-
-/**
- * Implements the heuristic used to expand the search tree. Dimensions used: <br>
- * + correctness: main value<br>
- * + horizontal expansion: penalty<br>
- * + accuracy gained from the parent node: bonus<br>
- * + refinement nodes: penalty<br>
- * + concept type + name (org.dllearner.utilities.owl.ConceptComparator)
- *
- * @author An C. Tran
- *
- */
-public class PADCELDefaultHeuristic implements PADCELHeuristic {
-
- // penalty for long descriptions
- protected double expansionPenaltyFactor = 0.1;
-
- // bonus for gained accuracy
- protected double gainBonusFactor = 0.2;
-
- // penalty if a node description has very many refinements since exploring
- // such a node is computationally very expensive
- protected double nodeRefinementPenalty = 0.0001;
-
- // award for node with high accuracy
- protected double accuracyAwardFactor = 0.01;
-
- // syntactic comparison as final comparison criterion
- protected ConceptComparator conceptComparator = new ConceptComparator();
-
- /**
- * Compare two node
- *
- * @param node1
- * Node to compare
- * @param node2
- * Node to compare
- *
- * @return 1 if node1 "greater" than node2 and vice versa
- */
- public int compare(PADCELNode node1, PADCELNode node2) {
- double diff = getNodeScore(node1) - getNodeScore(node2);
-
- if (diff > 0) { // node1 has better score than node2
- return 1;
- } else if (diff < 0) {
- return -1;
- } else {
- int comp = conceptComparator.compare(node1.getDescription(), node2.getDescription());
-
- // this allows duplicate descriptions exists in the set
- if (comp != 0)
- return comp;
- else
- return -1;
-
- }
- }
-
- /**
- * Calculate score for a node which is used as the searching heuristic
- *
- * @param node
- * Node to be scored
- *
- * @return Score of the node
- */
- protected double getNodeScore(PADCELNode node) {
-
- // the scoring mainly bases on correctness
- double score = node.getCorrectness();
-
- // bonus for the accuracy gained
- if (!node.isRoot()) {
- double parentAccuracy = ((PADCELNode) (node.getParent())).getAccuracy();
- score += (parentAccuracy - node.getAccuracy()) * gainBonusFactor;
- }
-
- // award node with high accuracy
- score += node.getAccuracy() * accuracyAwardFactor;
-
- // penalty for horizontal expansion
- score -= node.getHorizontalExpansion() * expansionPenaltyFactor;
- // score -= node.getDescription().getLength() * expansionPenaltyFactor;
-
- return score;
- }
-
- public double getScore(PADCELNode node) {
- return this.getNodeScore(node);
- }
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionGenerationTimeComparator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionGenerationTimeComparator.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionGenerationTimeComparator.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,37 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-/**
- * Compare two node based on their generation time.
- * This will be used in the Generation Time Greedy Compactness strategy
- * GOLR
- *
- * @author An C. Tran
- */
-
-import java.util.Comparator;
-
-import org.dllearner.utilities.owl.ConceptComparator;
-
-public class PADCELDefinitionGenerationTimeComparator implements Comparator<PADCELExtraNode> {
-
- @Override
- public int compare(PADCELExtraNode node1, PADCELExtraNode node2) {
- double genTime1 = node1.getGenerationTime();
- double genTime2 = node2.getGenerationTime();
-
- if (genTime1 < genTime2)
- return -1;
- else if (genTime1 > genTime2)
- return 1;
- else {
- if (node1.getDescription().getLength() < node2.getDescription().getLength())
- return -1;
- else if (node1.getDescription().getLength() > node2.getDescription().getLength())
- return 1;
- else
- return new ConceptComparator().compare(node1.getDescription(),
- node2.getDescription());
- }
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionLengthComparator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionLengthComparator.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionLengthComparator.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,29 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.Comparator;
-
-import org.dllearner.utilities.owl.ConceptComparator;
-
-/**
- * Compare two node based on their definition length. This will be used in the Definition Length
- * Greedy Compactness strategy
- *
- * @author An C. Tran
- *
- */
-
-public class PADCELDefinitionLengthComparator implements Comparator<PADCELExtraNode> {
-
- @Override
- public int compare(PADCELExtraNode node1, PADCELExtraNode node2) {
- int len1 = node1.getDescription().getLength();
- int len2 = node2.getDescription().getLength();
- if (len1 < len2)
- return -1;
- else if (len1 > len2)
- return 1;
- else
- return new ConceptComparator().compare(node1.getDescription(), node2.getDescription());
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionLengthReducer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionLengthReducer.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELDefinitionLengthReducer.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,59 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.dllearner.core.owl.Individual;
-
-/**
- * Compact set of partial definitions using Definition Length Grredy Reduction strategy
- *
- * @author An C. Tran
- *
- */
-public class PADCELDefinitionLengthReducer implements PADCELReducer {
-
- @Override
- public SortedSet<PADCELExtraNode> compact(SortedSet<PADCELExtraNode> partialDefinitions,
- Set<Individual> positiveExamples) {
- return compact(partialDefinitions, positiveExamples, 0);
- }
-
- @Override
- public SortedSet<PADCELExtraNode> compact(SortedSet<PADCELExtraNode> partialDefinitions,
- Set<Individual> positiveExamples, int uncoveredPositiveExamples) {
- Set<Individual> positiveExamplesTmp = new HashSet<Individual>();
- positiveExamplesTmp.addAll(positiveExamples);
-
- TreeSet<PADCELExtraNode> newSortedPartialDefinitions = new TreeSet<PADCELExtraNode>(
- new PADCELDefinitionLengthComparator());
- synchronized (partialDefinitions) {
- newSortedPartialDefinitions.addAll(partialDefinitions);
- }
-
- TreeSet<PADCELExtraNode> minimisedPartialDefinition = new TreeSet<PADCELExtraNode>(
- new PADCELDefinitionGenerationTimeComparator());
-
- Iterator<PADCELExtraNode> partialDefinitionIterator = newSortedPartialDefinitions.iterator();
- while ((positiveExamplesTmp.size() > uncoveredPositiveExamples)
- && (partialDefinitionIterator.hasNext())) {
- PADCELExtraNode node = partialDefinitionIterator.next();
-
- int positiveExamplesRemoved = positiveExamplesTmp.size();
- positiveExamplesTmp.removeAll(node.getCoveredPositiveExamples());
-
- positiveExamplesRemoved -= positiveExamplesTmp.size();
-
- if (positiveExamplesRemoved > 0) {
- node.setCorrectness(positiveExamplesRemoved);
- minimisedPartialDefinition.add(node);
- }
- }
-
- return minimisedPartialDefinition;
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELEvaluationResult.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELEvaluationResult.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELEvaluationResult.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,132 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.Set;
-
-import org.dllearner.core.owl.Individual;
-
-/**
- * This class represents the result of an evaluation result return from the PDLL learning problem
- * (PDLLPosNegLP) <br>
- * Information included in a PDLL evaluation includes:
- * <ol>
- * <li>- accuracy: double</li>
- * <li>- correctness: double</li>
- * <li>- completeness: double</li>
- * <li>- covered positive examples: Set<Individual></li>
- * <li>- covered negative examples: Set<Individual></li>
- * </ol>
- *
- * @author An C. Tran
- *
- */
-public class PADCELEvaluationResult {
-
- protected double accuracy = -1;
- protected double correctness = -1;
- protected double completeness = -1;
- protected Set<Individual> coveredPossitiveExamples = null;
- protected Set<Individual> coveredNegativeExamples = null;
-
- /**
- * Default constructor, use default value for all properties
- */
- public PADCELEvaluationResult() {
-
- }
-
- /**
- * This use to create an evaluation result that is not for a correct definition. So, we don't
- * need to hold the set of covered positive examples
- *
- * @param accuracy
- * @param correctness
- */
- public PADCELEvaluationResult(double accuracy, double correctness, double completeness) {
- this.accuracy = accuracy;
- this.correctness = correctness;
- this.completeness = completeness;
- }
-
- /**
- * Used to create an evaluation result for a correct definition.<br>
- * Covered positive examples have to be kept to be used in the result compactness later on.<br>
- * This is usually used in case of partial definition
- *
- * @param accuracy
- * @param correctness
- * @param completeness
- * @param coveredPossitiveExamples
- */
- public PADCELEvaluationResult(double accuracy, double correctness, double completeness,
- Set<Individual> coveredPossitiveExamples) {
- this.accuracy = accuracy;
- this.correctness = correctness;
- this.completeness = completeness;
- this.coveredPossitiveExamples = coveredPossitiveExamples;
- }
-
- /**
- * Used to create an evaluation result for a correct definition.<br>
- * Both covered positive examples and covered negative examples will be kept to be used in the
- * result compactness later on.
- *
- * @param accuracy
- * @param correctness
- * @param completeness
- * @param coveredPositiveExamples
- * @param coveredNegativeExamples
- */
- public PADCELEvaluationResult(double accuracy, double correctness, double completeness,
- Set<Individual> coveredPositiveExamples, Set<Individual> coveredNegativeExamples) {
-
- this.accuracy = accuracy;
- this.correctness = correctness;
- this.completeness = completeness;
- this.coveredPossitiveExamples = coveredPositiveExamples;
- this.coveredNegativeExamples = coveredNegativeExamples;
- }
-
- // ---------------------------------------
- // Getters and setters
- // ---------------------------------------
- public double getAccuracy() {
- return accuracy;
- }
-
- public void setAccuracy(double accuracy) {
- this.accuracy = accuracy;
- }
-
- public double getCorrectness() {
- return correctness;
- }
-
- public void setCorrectness(double correctness) {
- this.correctness = correctness;
- }
-
- public double getCompleteness() {
- return completeness;
- }
-
- public void setCompleteness(double completeness) {
- this.completeness = completeness;
- }
-
- public Set<Individual> getCoveredPossitiveExamples() {
- return coveredPossitiveExamples;
- }
-
- public void setCoveredPossitiveExamples(Set<Individual> coveredPossitiveExamples) {
- this.coveredPossitiveExamples = coveredPossitiveExamples;
- }
-
- public Set<Individual> getCoveredNegativeExamples() {
- return coveredNegativeExamples;
- }
-
- public void setCoveredNegativeExamples(Set<Individual> coveredNegativeExamples) {
- this.coveredNegativeExamples = coveredNegativeExamples;
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELExtraNode.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELExtraNode.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELExtraNode.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,132 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.dllearner.algorithms.celoe.OENode;
-import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.Individual;
-
-/**
- * Generation time and node type is added into PADCELNode. This information is necessary for some
- * reduction algorithms
- *
- * @author An C. Tran
- *
- */
-public class PADCELExtraNode extends PADCELNode {
-
- private double generationTime = Double.MIN_VALUE; // time in ms that the node was generated
- private int type = -1;
-
- Set<OENode> compositeNodes = new HashSet<OENode>();
-
- /**
- * ============================================================================================
- * Constructor with correctness of the description
- *
- * @param parentNode
- * Parent node of this node
- * @param description
- * Description of the node
- * @param accuracy
- * Accuracy of the node
- * @param distance
- * Distance between the node and the learning problem
- * @param correctness
- * Correctness of the node
- */
- public PADCELExtraNode(OENode parentNode, Description description, double accuracy,
- double correctness) {
- super(parentNode, description, accuracy, correctness);
- }
-
- public PADCELExtraNode(OENode parentNode, Description description, double accuracy) {
- super(parentNode, description, accuracy);
- }
-
- public PADCELExtraNode(PADCELNode node) {
- super(node.getParent(), node.getDescription(), node.getAccuracy(), node.getCorrectness());
- setCoveredPositiveExamples(node.getCoveredPositiveExamples());
- setCoveredNegativeExamples(node.getCoveredNegativeExamples());
- }
-
- public PADCELExtraNode(PADCELNode node, Set<Individual> cp, double generationTime) {
- super(node.getParent(), node.getDescription(), node.getAccuracy(), node.getCorrectness());
- super.coveredPositiveExamples = cp;
- this.generationTime = generationTime;
- }
-
- /**
- * ============================================================================================
- * Constructor with the correctness and the generation time of the description
- *
- * @param parentNode
- * Parent node of this node
- * @param description
- * Description of the node
- * @param accuracy
- * Accuracy of the node
- * @param distance
- * Distance between the node and the learning problem
- * @param correctness
- * Correctness of the node
- * @param genTime
- * Time in ms that the work used to generate this node
- */
- public PADCELExtraNode(PADCELNode parentNode, Description description, double accuracy,
- double correctness, double genTime) {
- super(parentNode, description, accuracy, correctness);
- this.coveredPositiveExamples = null;
- this.generationTime = genTime;
- }
-
- /**
- * ============================================================================================
- * Constructor with the set of positive examples covered by the description of the node
- *
- * @param parentNode
- * @param description
- * @param accuracy
- * @param distance
- * @param correctness
- * @param cn
- * Covered positive examples
- */
- public PADCELExtraNode(PADCELNode parentNode, Description description, double accuracy,
- double correctness, Set<Individual> cp) {
- super(parentNode, description, accuracy, correctness);
- super.setCoveredPositiveExamples(cp);
- }
-
- // -------------------------
- // getters and setters
- // -------------------------
- public void setCoveredPositiveExamples(Set<Individual> cpn) {
- super.setCoveredPositiveExamples(cpn);
- }
-
- public double getGenerationTime() {
- return generationTime;
- }
-
- public void setGenerationTime(double d) {
- this.generationTime = d;
- }
-
- public void setType(int t) {
- this.type = t;
- }
-
- public int getType() {
- return this.type;
- }
-
- public void setCompositeList(Set<PADCELExtraNode> compositeNodes) {
- this.compositeNodes.addAll(compositeNodes);
- }
-
- public Set<OENode> getCompositeNodes() {
- return this.compositeNodes;
- }
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELGenerationTimeReducer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELGenerationTimeReducer.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELGenerationTimeReducer.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,62 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.dllearner.core.owl.Individual;
-
-/**
- * Compact two a partial definitions set using Generation Time Greedy strategy
- *
- * @author An C. Tran
- *
- */
-
-public class PADCELGenerationTimeReducer implements PADCELReducer {
-
- @Override
- public SortedSet<PADCELExtraNode> compact(SortedSet<PADCELExtraNode> partialDefinitions,
- Set<Individual> positiveExamples) {
- return compact(partialDefinitions, positiveExamples, 0);
- }
-
- @Override
- public SortedSet<PADCELExtraNode> compact(SortedSet<PADCELExtraNode> partialDefinitions,
- Set<Individual> positiveExamples, int uncoveredPositiveExamples) {
- Set<Individual> positiveExamplesTmp = new HashSet<Individual>();
- positiveExamplesTmp.addAll(positiveExamples);
-
- TreeSet<PADCELExtraNode> newSortedPartialDefinitions = new TreeSet<PADCELExtraNode>(
- new PADCELDefinitionGenerationTimeComparator());
-
- synchronized (partialDefinitions) {
- newSortedPartialDefinitions.addAll(partialDefinitions);
- }
-
- TreeSet<PADCELExtraNode> minimisedPartialDefinition = new TreeSet<PADCELExtraNode>(
- new PADCELDefinitionGenerationTimeComparator());
-
- Iterator<PADCELExtraNode> partialDefinitionIterator = newSortedPartialDefinitions.iterator();
-
- while ((positiveExamplesTmp.size() > uncoveredPositiveExamples)
- && (partialDefinitionIterator.hasNext())) {
- PADCELExtraNode node = partialDefinitionIterator.next();
-
- int positiveExamplesRemoved = positiveExamplesTmp.size();
- positiveExamplesTmp.removeAll(node.getCoveredPositiveExamples());
-
- positiveExamplesRemoved -= positiveExamplesTmp.size();
-
- if (positiveExamplesRemoved > 0) {
- node.setCorrectness(positiveExamplesRemoved);
- minimisedPartialDefinition.add(node);
- }
- }
-
- return minimisedPartialDefinition;
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELHeuristic.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELHeuristic.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,16 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.Comparator;
-
-/**
- * Interface for heuristics used in PADCEL
- *
- * @author An C. Tran
- *
- */
-public interface PADCELHeuristic extends Comparator<PADCELNode> {
-
- public int compare(PADCELNode node1, PADCELNode node2);
-
- public double getScore(PADCELNode node);
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELImprovedCovegareGreedyReducer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELImprovedCovegareGreedyReducer.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELImprovedCovegareGreedyReducer.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,115 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.util.HashSet;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.apache.log4j.Logger;
-import org.dllearner.core.owl.Individual;
-
-/**
- * This class implements "wise" coverage greedy strategy for compacting the partial definitions In
- * this strategy, the partial definitions will be chosen based on their coverage. When a partial
- * definition has been chosen, coverage of other partial definition will be recalculated
- *
- * @author An C. Tran
- *
- */
-
-public class PADCELImprovedCovegareGreedyReducer implements PADCELReducer {
-
- Logger logger = Logger.getLogger(this.getClass());
-
- /**
- * Compact partial definition with noise allowed
- *
- * @param partialDefinitions
- * Set of partial definitions
- * @param positiveExamples
- * Set of positive examples (used to check whether partial definition is useful
- * @param uncoveredPositiveExamples
- * Number of uncovered positive examples allowed
- *
- * @return Subset of partial definitions that cover all positive examples
- */
- @Override
- public SortedSet<PADCELExtraNode> compact(SortedSet<PADCELExtraNode> partialDefinitions,
- Set<Individual> positiveExamples) {
- return this.compact(partialDefinitions, positiveExamples, 0);
- }
-
- /**
- * Compact partial definition with noise allowed
- *
- * @param partialDefinitions
- * Set of partial definitions
- * @param positiveExamples
- * Set of positive examples (used to check whether partial definition is useful
- * @param uncoveredPositiveExamples
- * Number of uncovered positive examples allowed
- *
- * @return Subset of partial definitions that cover (positive examples \ uncovered positive
- * examples)
- */
- @Override
- public SortedSet<PADCELExtraNode> compact(SortedSet<PADCELExtraNode> partialDefinitions,
- Set<Individual> positiveExamples, int uncoveredPositiveExamples) {
- Set<Individual> positiveExamplesTmp = new HashSet<Individual>();
- positiveExamplesTmp.addAll(positiveExamples);
-
- TreeSet<PADCELExtraNode> reducedPartialDefinition = new TreeSet<PADCELExtraNode>(
- new PADCELCompletenessComparator());
-
- if (partialDefinitions.size() == 0)
- return reducedPartialDefinition;
-
- synchronized (partialDefinitions) {
- Object[] partialDefs = partialDefinitions.toArray();
-
- // the highest accurate partial definition
- // reducedPartialDefinition.add((PDLLExtraNode)partialDefs[0]);
- // positiveExamplesTmp.removeAll(((PDLLExtraNode)partialDefs[0]).getCoveredPositiveExamples());
-
- for (int i = 0; (positiveExamplesTmp.size() > uncoveredPositiveExamples)
- && (i < partialDefinitions.size()); i++) {
-
- // count the number of different positive examples covered
- int counti = 0;
- for (Individual indi : ((PADCELExtraNode) partialDefs[i])
- .getCoveredPositiveExamples()) {
- if (positiveExamplesTmp.contains(indi))
- counti++;
- } // count the number of different covered positive examples by
- // i
-
- for (int j = i + 1; j < partialDefinitions.size(); j++) {
- int countj = 0;
-
- for (Individual indj : ((PADCELExtraNode) partialDefs[j])
- .getCoveredPositiveExamples())
- if (positiveExamplesTmp.contains(indj))
- countj++;
-
- // TODO: revise this code: Swapping should be done only one
- // time at the end
- // swap the partial definition so that the "best" partial
- // definition will be in the top
- if (countj > counti) {
- PADCELExtraNode tmp = (PADCELExtraNode) partialDefs[j];
- partialDefs[j] = partialDefs[i];
- partialDefs[i] = tmp;
- counti = countj;
- }
- }
-
- reducedPartialDefinition.add((PADCELExtraNode) partialDefs[i]);
- positiveExamplesTmp.removeAll(((PADCELExtraNode) partialDefs[i])
- .getCoveredPositiveExamples());
- }
- }
-
- return reducedPartialDefinition;
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELNode.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELNode.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELNode.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,113 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.text.DecimalFormat;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.dllearner.algorithms.celoe.OENode;
-import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.Individual;
-
-/**
- * Represents a node in the search tree used in the PDLLeanring<br>
- * A node includes description and its corresponding properties such as: correctness, accuracy,
- * distance between the description the leaning problem, parent node of the description. It also
- * contains a flag which indicates the node is processed or not.
- *
- * @author An C. Tran
- *
- */
-public class PADCELNode extends OENode {
-
- private double correctness = -1.0;
- private double completeness = -1.0;
-
- protected Set<Individual> coveredPositiveExamples = new HashSet<Individual>();
- protected Set<Individual> coveredNegativeExamples = new HashSet<Individual>();
-
- private DecimalFormat dfPercent = new DecimalFormat("0.00%");
-
- public PADCELNode(OENode parentNode, Description description, double accuracy) {
- super(parentNode, description, accuracy);
- }
-
- public PADCELNode(OENode parentNode, Description description, double accuracy, double correctness) {
- super(parentNode, description, accuracy);
- this.correctness = correctness;
- }
-
- public PADCELNode(OENode parentNode, Description description, double accuracy,
- double correctness, double completeness) {
- super(parentNode, description, accuracy);
- this.correctness = correctness;
- this.completeness = completeness;
- }
-
- public PADCELNode(OENode parentNode, Description description) {
- super(parentNode, description, 0);
- }
-
- public PADCELNode(OENode parentNode, Description description,
- Set<Individual> coveredPositiveExamples, Set<Individual> coveredNegativeExamples) {
- super(parentNode, description, 0);
- this.coveredPositiveExamples.addAll(coveredPositiveExamples);
- this.coveredNegativeExamples.addAll(coveredNegativeExamples);
- }
-
- public void setCorrectness(double cor) {
- this.correctness = cor;
- }
-
- public double getCorrectness() {
- return this.correctness;
- }
-
- public void setCompleteness(double comp) {
- this.completeness = comp;
- }
-
- public double getCompleteness() {
- return this.completeness;
- }
-
- public void setAccuracy(double acc) {
- this.accuracy = acc;
- }
-
- public Set<Individual> getCoveredPositiveExamples() {
- return this.coveredPositiveExamples;
- }
-
- public Set<Individual> getCoveredNegativeExamples() {
- return this.coveredNegativeExamples;
- }
-
- public void setCoveredPositiveExamples(Set<Individual> coveredPositiveExamples) {
- if (coveredPositiveExamples != null)
- this.coveredPositiveExamples.addAll(coveredPositiveExamples);
- else
- this.coveredPositiveExamples.clear();
- }
-
- public void setCoveredNegativeExamples(Set<Individual> coveredNegativeExamples) {
- if (coveredNegativeExamples != null)
- this.coveredNegativeExamples.addAll(coveredNegativeExamples);
- else
- this.coveredNegativeExamples.clear();
- }
-
- @Override
- public String toString() {
- String ret = this.getDescription().toString(null, null) + " [";
- ret += "acc:" + dfPercent.format(this.getAccuracy()) + ", ";
- ret += "cor:" + dfPercent.format(this.getCorrectness()) + ", ";
- ret += "comp:" + dfPercent.format(this.completeness) + "]";
- return ret;
-
- }
-
- public void setDescription(Description newDescription) {
- this.description = newDescription;
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELOntologyUtil.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELOntologyUtil.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELOntologyUtil.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,87 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.model.OWLOntologyStorageException;
-
-/**
- * Some utility functions for ontology manipulation
- *
- * @author An C. Tran
- *
- */
-
-public class PADCELOntologyUtil {
-
- /**
- * ==========================================================================================
- * Get ontology given its file path
- *
- * @param ontologyFilePath
- *
- * @return Opened ontology
- * @throws OWLOntologyCreationException
- */
- public static OWLOntology loadOntology(String ontologyFilePath)
- throws OWLOntologyCreationException {
- OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
- OWLOntology ontology;
-
- String flash = (System.getProperty("os.name").contains("Windows")) ? "/" : "";
-
- File f = new File(ontologyFilePath);
-
- if (!ontologyFilePath.contains("file:"))
- ontologyFilePath = "file:" + flash + f.getAbsolutePath();
-
- ontologyFilePath = ontologyFilePath.replace('\\', '/');
-
- ontology = manager.loadOntology(IRI.create(ontologyFilePath));
-
- return ontology;
- }
-
- /**
- * ============================================================================================
- * Persist the ontology
- *
- * @param ontology
- * Ontology which need to be persisted
- *
- * @throws OWLOntologyStorageException
- */
- public static void persistOntology(OWLOntology ontology) throws OWLOntologyStorageException {
- OWLOntologyManager manager = ontology.getOWLOntologyManager();
- manager.saveOntology(ontology);
- }
-
- /**
- * ============================================================================================
- * Persist ontology to another ontology
- *
- * @param ontology
- * Ontology contains changes
- * @param newFilePath
- * Path to the new ontology file
- *
- * @throws OWLOntologyStorageException
- * @throws IOException
- */
- public static void persistOntology(OWLOntology ontology, String newFilePath)
- throws OWLOntologyStorageException, IOException {
- OWLOntologyManager manager = ontology.getOWLOntologyManager();
-
- File f = new File(newFilePath);
- FileOutputStream fo = new FileOutputStream(f);
-
- manager.saveOntology(ontology, fo);
- fo.close();
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELPosNegLP.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELPosNegLP.java 2012-05-15 07:20:52 UTC (rev 3714)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/PADCEL/PADCELPosNegLP.java 2012-05-17 03:09:57 UTC (rev 3715)
@@ -1,493 +0,0 @@
-package org.dllearner.algorithms.PADCEL;
-
-/**
- * PDLL Learning problem: provides correctness, completeness, and accuracy calculation.
- * Predictive accuracy calculation is used.
- *
- * @author An C. Tran
- */
-
-import java.util.Set;
-
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.LinkedList;
-
-import org.apache.log4j.Logger;
-import org.dllearner.core.AbstractLearningProblem;
-import org.dllearner.core.ComponentAnn;
-import org.dllearner.core.ComponentInitException;
-import org.dllearner.core.AbstractReasonerComponent;
-import org.dllearner.core.EvaluatedDescription;
-import org.dllearner.core.options.ConfigOption;
-import org.dllearner.core.options.StringSetConfigOption;
-import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.Individual;
-
-@ComponentAnn(name = "PDLLPosNegLP", shortName = "pdllPosNegLP", version = 0.1, description = "PDLL positive negative learning problem")
-public class PADCELPosNegLP extends AbstractLearningProblem {
-
- protected Set<Individual> positiveExamples;
- protected Set<Individual> negativeExamples;
-
- protected Set<Individual> uncoveredPositiveExamples;
-
- private Logger logger = Logger.getLogger(this.getClass());
-
- // reasoner component is declared in AbstractLearningProblem class
-
- /**
- * Constructor, used in case that positive and negative examples are provided when this
- * component is initialized
- *
- * @param reasoningService
- * Reasoner, provides reasoning service. Used to checking the instance type
- * @param positiveExamples
- * Positive examples
- * @param negativeExamples
- * Negative examples
- */
- public PADCELPosNegLP(AbstractReasonerComponent reasoningService,
- Set<Individual> positiveExamples, Set<Individual> negativeExamples) {
- super(reasoningService);
- this.positiveExamples = positiveExamples;
- this.negativeExamples = negativeExamples;
- this.uncoveredPositiveExamples = this.positiveExamples;
- }
-
- /**
- * This constructor is used when the learning configuration file is used
- *
- * @param reasoningService
- */
- public PADCELPosNegLP(AbstractReasonerComponent reasoningService) {
- super(reasoningService);
- }
-
- /**
- * This constructor can be used by SpringDefinition to create bean object Properties of new bean
- * may be initialised later using setters
- */
- public PADCELPosNegLP() {
- super();
-
- if (logger.isDebugEnabled())
- logger.debug("Learning problem created: " + this);
- }
-
- /**
- * Get list of positive examples covered by a description
- *
- * @param description
- * Description
- *
- * @return Set of positive examples covered by the description
- */
- protected Set<Individual> coveredPositiveExamples(Description description) {
- Set<Individual> coveredPositiveExamples = new HashSet<Individual>();
-
- for (Individual example : positiveExamples)
- if (reasoner.hasType(description, example))
- coveredPositiveExamples.add(example);
-
- return coveredPositiveExamples;
- }
-
- /**
- * Get number of positive examples covered by a description
- *
- * @param description
- * Description
- * @return Number if positive examples covered by the description
- */
- protected int getNumberCoveredPositiveExamples(Description description) {
- int coveredPos = 0;
-
- for (Individual example : positiveExamples)
- if (reasoner.hasType(description, example))
- coveredPos++;
-
- return coveredPos;
- }
-
- /**
- * Get number of negative examples covered by a description
- *
- * @param description
- * Description to test
- *
- * @return Number of negative examples covered by the description
- */
- protected int getNumberOfCoveredNegativeExamples(Description description) {
- int coveredNeg = 0;
- for (Individual example : negativeExamples) {
- if (reasoner.hasType(description, example)) {
- coveredNeg++;
- }
- }
-
- return coveredNeg;
- }
-
- /**
- * Calculate predictive accuracy of a description pred-accuracy(D) =
- * (covered-positive-examples(D) + uncovered-negative-examples(D)) / all-examples
- *
-...
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