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authorAndrej Shadura <andrewsh@debian.org>2019-03-09 22:30:41 +0000
committerAndrej Shadura <andrewsh@debian.org>2019-03-09 22:30:41 +0000
commit38212b3127e90751fb39cda34250bc11be62b76c (patch)
treedc1397346030e9695bd763dddc93b3be527cd643 /elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMediansLloyd.java
parent337087b668d3a54f3afee3a9adb597a32e9f7e94 (diff)
Import Upstream version 0.7.0
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diff --git a/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMediansLloyd.java b/elki/src/main/java/de/lmu/ifi/dbs/elki/algorithm/clustering/kmeans/KMediansLloyd.java
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+package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans;
+
+/*
+ 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 java.util.ArrayList;
+import java.util.List;
+
+import de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization.KMeansInitialization;
+import de.lmu.ifi.dbs.elki.data.Cluster;
+import de.lmu.ifi.dbs.elki.data.Clustering;
+import de.lmu.ifi.dbs.elki.data.NumberVector;
+import de.lmu.ifi.dbs.elki.data.model.MeanModel;
+import de.lmu.ifi.dbs.elki.database.Database;
+import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory;
+import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil;
+import de.lmu.ifi.dbs.elki.database.datastore.WritableIntegerDataStore;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
+import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs;
+import de.lmu.ifi.dbs.elki.database.relation.Relation;
+import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction;
+import de.lmu.ifi.dbs.elki.logging.Logging;
+import de.lmu.ifi.dbs.elki.logging.progress.IndefiniteProgress;
+import de.lmu.ifi.dbs.elki.logging.statistics.LongStatistic;
+import de.lmu.ifi.dbs.elki.logging.statistics.StringStatistic;
+import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector;
+import de.lmu.ifi.dbs.elki.utilities.documentation.Reference;
+import de.lmu.ifi.dbs.elki.utilities.documentation.Title;
+
+/**
+ * k-medians clustering algorithm, but using Lloyd-style bulk iterations instead
+ * of the more complicated approach suggested by Kaufman and Rousseeuw (see
+ * {@link KMedoidsPAM} instead).
+ *
+ * Reference:
+ * <p>
+ * Clustering via Concave Minimization<br />
+ * P. S. Bradley, O. L. Mangasarian, W. N. Street<br />
+ * in: Advances in Neural Information Processing Systems (NIPS)
+ * </p>
+ *
+ * @author Erich Schubert
+ *
+ * @apiviz.has MeanModel
+ *
+ * @param <V> vector datatype
+ */
+@Title("K-Medians")
+@Reference(title = "Clustering via Concave Minimization", //
+authors = "P. S. Bradley, O. L. Mangasarian, W. N. Street", //
+booktitle = "Advances in Neural Information Processing Systems", //
+url = "https://papers.nips.cc/paper/1260-clustering-via-concave-minimization.pdf")
+public class KMediansLloyd<V extends NumberVector> extends AbstractKMeans<V, MeanModel> {
+ /**
+ * The logger for this class.
+ */
+ private static final Logging LOG = Logging.getLogger(KMediansLloyd.class);
+
+ /**
+ * Key for statistics logging.
+ */
+ private static final String KEY = KMediansLloyd.class.getName();
+
+ /**
+ * Constructor.
+ *
+ * @param distanceFunction distance function
+ * @param k k parameter
+ * @param maxiter Maxiter parameter
+ * @param initializer Initialization method
+ */
+ public KMediansLloyd(NumberVectorDistanceFunction<? super V> distanceFunction, int k, int maxiter, KMeansInitialization<? super V> initializer) {
+ super(distanceFunction, k, maxiter, initializer);
+ }
+
+ @Override
+ public Clustering<MeanModel> run(Database database, Relation<V> relation) {
+ if(relation.size() <= 0) {
+ return new Clustering<>("k-Medians Clustering", "kmedians-clustering");
+ }
+ // Choose initial medians
+ if(LOG.isStatistics()) {
+ LOG.statistics(new StringStatistic(KEY + ".initialization", initializer.toString()));
+ }
+ List<Vector> medians = initializer.chooseInitialMeans(database, relation, k, getDistanceFunction(), Vector.FACTORY);
+ // Setup cluster assignment store
+ List<ModifiableDBIDs> clusters = new ArrayList<>();
+ for(int i = 0; i < k; i++) {
+ clusters.add(DBIDUtil.newHashSet((int) (relation.size() * 2. / k)));
+ }
+ WritableIntegerDataStore assignment = DataStoreUtil.makeIntegerStorage(relation.getDBIDs(), DataStoreFactory.HINT_TEMP | DataStoreFactory.HINT_HOT, -1);
+ double[] distsum = new double[k];
+
+ IndefiniteProgress prog = LOG.isVerbose() ? new IndefiniteProgress("K-Medians iteration", LOG) : null;
+ int iteration = 0;
+ for(; maxiter <= 0 || iteration < maxiter; iteration++) {
+ LOG.incrementProcessed(prog);
+ boolean changed = assignToNearestCluster(relation, medians, clusters, assignment, distsum);
+ // Stop if no cluster assignment changed.
+ if(!changed) {
+ break;
+ }
+ // Recompute medians.
+ medians = medians(clusters, medians, relation);
+ }
+ LOG.setCompleted(prog);
+ if(LOG.isStatistics()) {
+ LOG.statistics(new LongStatistic(KEY + ".iterations", iteration));
+ }
+ // Wrap result
+ Clustering<MeanModel> result = new Clustering<>("k-Medians Clustering", "kmedians-clustering");
+ for(int i = 0; i < clusters.size(); i++) {
+ MeanModel model = new MeanModel(medians.get(i));
+ result.addToplevelCluster(new Cluster<>(clusters.get(i), model));
+ }
+ return result;
+ }
+
+ @Override
+ protected Logging getLogger() {
+ return LOG;
+ }
+
+ /**
+ * Parameterization class.
+ *
+ * @author Erich Schubert
+ *
+ * @apiviz.exclude
+ */
+ public static class Parameterizer<V extends NumberVector> extends AbstractKMeans.Parameterizer<V> {
+ @Override
+ protected Logging getLogger() {
+ return LOG;
+ }
+
+ @Override
+ protected KMediansLloyd<V> makeInstance() {
+ return new KMediansLloyd<>(distanceFunction, k, maxiter, initializer);
+ }
+ }
+}