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Diffstat (limited to 'elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClusteringTest.java')
-rw-r--r-- | elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClusteringTest.java | 138 |
1 files changed, 138 insertions, 0 deletions
diff --git a/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClusteringTest.java b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClusteringTest.java new file mode 100644 index 00000000..c94557dd --- /dev/null +++ b/elki/src/test/java/de/lmu/ifi/dbs/elki/algorithm/clustering/hierarchical/AnderbergHierarchicalClusteringTest.java @@ -0,0 +1,138 @@ +package de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2015 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +import org.junit.Test; + +import de.lmu.ifi.dbs.elki.JUnit4Test; +import de.lmu.ifi.dbs.elki.algorithm.AbstractSimpleAlgorithmTest; +import de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction.ExtractFlatClusteringFromHierarchy; +import de.lmu.ifi.dbs.elki.data.Clustering; +import de.lmu.ifi.dbs.elki.database.Database; +import de.lmu.ifi.dbs.elki.result.Result; +import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil; +import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.ListParameterization; +import de.lmu.ifi.dbs.elki.workflow.AlgorithmStep; + +/** + * Perform agglomerative hierarchical clustering, using the anderberg improved + * algorithm. + * + * @author Erich Schubert + * @since 0.6.0 + */ +public class AnderbergHierarchicalClusteringTest extends AbstractSimpleAlgorithmTest implements JUnit4Test { + // TODO: add more data sets. + + /** + * Run agglomerative hierarchical clustering with fixed parameters and compare + * the result to a golden standard. + */ + @Test + public void testSingleLink() { + Database db = makeSimpleDatabase(UNITTEST + "single-link-effect.ascii", 638); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(ExtractFlatClusteringFromHierarchy.Parameterizer.MINCLUSTERS_ID, 3); + params.addParameter(AlgorithmStep.Parameterizer.ALGORITHM_ID, AnderbergHierarchicalClustering.class); + params.addParameter(AGNES.Parameterizer.LINKAGE_ID, SingleLinkageMethod.class); + ExtractFlatClusteringFromHierarchy c = ClassGenericsUtil.parameterizeOrAbort(ExtractFlatClusteringFromHierarchy.class, params); + testParameterizationOk(params); + + // run clustering algorithm on database + Result result = c.run(db); + Clustering<?> clustering = findSingleClustering(result); + testFMeasure(db, clustering, 0.6829722); + testClusterSizes(clustering, new int[] { 9, 200, 429 }); + } + + /** + * Run agglomerative hierarchical clustering with fixed parameters and compare + * the result to a golden standard. + */ + @Test + public void testWard() { + Database db = makeSimpleDatabase(UNITTEST + "single-link-effect.ascii", 638); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(ExtractFlatClusteringFromHierarchy.Parameterizer.MINCLUSTERS_ID, 3); + params.addParameter(AlgorithmStep.Parameterizer.ALGORITHM_ID, AnderbergHierarchicalClustering.class); + ExtractFlatClusteringFromHierarchy c = ClassGenericsUtil.parameterizeOrAbort(ExtractFlatClusteringFromHierarchy.class, params); + testParameterizationOk(params); + + // run clustering algorithm on database + Result result = c.run(db); + Clustering<?> clustering = findSingleClustering(result); + testFMeasure(db, clustering, 0.93866265); + testClusterSizes(clustering, new int[] { 200, 211, 227 }); + } + + /** + * Run agglomerative hierarchical clustering with fixed parameters and compare + * the result to a golden standard. + */ + @Test + public void testGroupAverage() { + Database db = makeSimpleDatabase(UNITTEST + "single-link-effect.ascii", 638); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(ExtractFlatClusteringFromHierarchy.Parameterizer.MINCLUSTERS_ID, 3); + params.addParameter(AlgorithmStep.Parameterizer.ALGORITHM_ID, AnderbergHierarchicalClustering.class); + params.addParameter(AGNES.Parameterizer.LINKAGE_ID, GroupAverageLinkageMethod.class); + ExtractFlatClusteringFromHierarchy c = ClassGenericsUtil.parameterizeOrAbort(ExtractFlatClusteringFromHierarchy.class, params); + testParameterizationOk(params); + + // run clustering algorithm on database + Result result = c.run(db); + Clustering<?> clustering = findSingleClustering(result); + testFMeasure(db, clustering, 0.93866265); + testClusterSizes(clustering, new int[] { 200, 211, 227 }); + } + + /** + * Run agglomerative hierarchical clustering with fixed parameters and compare + * the result to a golden standard. + */ + @Test + public void testCompleteLink() { + Database db = makeSimpleDatabase(UNITTEST + "single-link-effect.ascii", 638); + + // Setup algorithm + ListParameterization params = new ListParameterization(); + params.addParameter(ExtractFlatClusteringFromHierarchy.Parameterizer.MINCLUSTERS_ID, 3); + params.addParameter(AlgorithmStep.Parameterizer.ALGORITHM_ID, AnderbergHierarchicalClustering.class); + params.addParameter(AGNES.Parameterizer.LINKAGE_ID, CompleteLinkageMethod.class); + ExtractFlatClusteringFromHierarchy c = ClassGenericsUtil.parameterizeOrAbort(ExtractFlatClusteringFromHierarchy.class, params); + testParameterizationOk(params); + + // run clustering algorithm on database + Result result = c.run(db); + Clustering<?> clustering = findSingleClustering(result); + testFMeasure(db, clustering, 0.938167802); + testClusterSizes(clustering, new int[] { 200, 217, 221 }); + } +} |