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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/initialization/PAMInitialMeans.java
parent337087b668d3a54f3afee3a9adb597a32e9f7e94 (diff)
Import Upstream version 0.7.0
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+package de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.initialization;
+
+/*
+ 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.data.NumberVector;
+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.WritableDoubleDataStore;
+import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDVar;
+import de.lmu.ifi.dbs.elki.database.ids.DBIDs;
+import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery;
+import de.lmu.ifi.dbs.elki.database.relation.Relation;
+import de.lmu.ifi.dbs.elki.distance.distancefunction.NumberVectorDistanceFunction;
+import de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction;
+import de.lmu.ifi.dbs.elki.logging.Logging;
+import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress;
+import de.lmu.ifi.dbs.elki.math.MathUtil;
+import de.lmu.ifi.dbs.elki.utilities.documentation.Reference;
+import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer;
+
+/**
+ * PAM initialization for k-means (and of course, PAM).
+ *
+ * Reference:
+ * <p>
+ * Clustering my means of Medoids<br />
+ * Kaufman, L. and Rousseeuw, P.J.<br />
+ * in: Statistical Data Analysis Based on the L_1–Norm and Related Methods
+ * </p>
+ *
+ * @author Erich Schubert
+ *
+ * @param <O> Object type for KMedoids initialization
+ */
+@Reference(title = "Clustering my means of Medoids", //
+authors = "Kaufman, L. and Rousseeuw, P.J.", //
+booktitle = "Statistical Data Analysis Based on the L_1–Norm and Related Methods")
+public class PAMInitialMeans<O> implements KMeansInitialization<NumberVector>, KMedoidsInitialization<O> {
+ /**
+ * Class logger.
+ */
+ private static final Logging LOG = Logging.getLogger(PAMInitialMeans.class);
+
+ /**
+ * Constructor.
+ */
+ public PAMInitialMeans() {
+ super();
+ }
+
+ @Override
+ public <T extends NumberVector, V extends NumberVector> List<V> chooseInitialMeans(Database database, Relation<T> relation, int k, NumberVectorDistanceFunction<? super T> distanceFunction, NumberVector.Factory<V> factory) {
+ // Ugly cast; but better than code duplication.
+ @SuppressWarnings("unchecked")
+ Relation<O> rel = (Relation<O>) relation;
+ // Get a distance query
+ @SuppressWarnings("unchecked")
+ final PrimitiveDistanceFunction<? super O> distF = (PrimitiveDistanceFunction<? super O>) distanceFunction;
+ final DistanceQuery<O> distQ = database.getDistanceQuery(rel, distF);
+ DBIDs medids = chooseInitialMedoids(k, rel.getDBIDs(), distQ);
+ List<V> medoids = new ArrayList<>(k);
+ for(DBIDIter iter = medids.iter(); iter.valid(); iter.advance()) {
+ medoids.add(factory.newNumberVector(relation.get(iter)));
+ }
+ return medoids;
+ }
+
+ @Override
+ public DBIDs chooseInitialMedoids(int k, DBIDs ids, DistanceQuery<? super O> distQ) {
+ ArrayModifiableDBIDs medids = DBIDUtil.newArray(k);
+ DBIDVar bestid = DBIDUtil.newVar();
+ WritableDoubleDataStore mindist = null;
+
+ // First mean is chosen by having the smallest distance sum to all others.
+ {
+ double best = Double.POSITIVE_INFINITY;
+ WritableDoubleDataStore newd = null;
+ FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Choosing initial mean", ids.size(), LOG) : null;
+ for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
+ if(newd == null) {
+ newd = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
+ }
+ int sum = 0;
+ for(DBIDIter iter2 = ids.iter(); iter2.valid(); iter2.advance()) {
+ double d = distQ.distance(iter, iter2);
+ sum += d;
+ newd.putDouble(iter2, d);
+ }
+ if(sum < best) {
+ best = sum;
+ bestid.set(iter);
+ if(mindist != null) {
+ mindist.destroy();
+ }
+ mindist = newd;
+ newd = null;
+ }
+ LOG.incrementProcessed(prog);
+ }
+ LOG.ensureCompleted(prog);
+ if(newd != null) {
+ newd.destroy();
+ }
+ medids.add(bestid);
+ }
+ assert(mindist != null);
+
+ // Subsequent means optimize the full criterion.
+ FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Choosing initial centers", k, LOG) : null;
+ LOG.incrementProcessed(prog); // First one was just chosen.
+ for(int i = 1; i < k; i++) {
+ double best = Double.POSITIVE_INFINITY;
+ WritableDoubleDataStore bestd = null, newd = null;
+ for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
+ if(medids.contains(iter)) {
+ continue;
+ }
+ if(newd == null) {
+ newd = DataStoreUtil.makeDoubleStorage(ids, DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP);
+ }
+ double sum = 0.;
+ for(DBIDIter iter2 = ids.iter(); iter2.valid(); iter2.advance()) {
+ double v = MathUtil.min(distQ.distance(iter, iter2), mindist.doubleValue(iter2));
+ sum += v;
+ newd.put(iter2, v);
+ }
+ if(sum < best) {
+ best = sum;
+ bestid.set(iter);
+ if(bestd != null) {
+ bestd.destroy();
+ }
+ bestd = newd;
+ newd = null;
+ }
+ }
+ if(bestd == null) {
+ throw new AbortException("No median found that improves the criterion function?!? Too many infinite distances.");
+ }
+ medids.add(bestid);
+ if(newd != null) {
+ newd.destroy();
+ }
+ mindist.destroy();
+ mindist = bestd;
+ LOG.incrementProcessed(prog);
+ }
+ LOG.ensureCompleted(prog);
+
+ mindist.destroy();
+ return medids;
+ }
+
+ /**
+ * Parameterization class.
+ *
+ * @author Erich Schubert
+ *
+ * @apiviz.exclude
+ */
+ public static class Parameterizer<V> extends AbstractParameterizer {
+ @Override
+ protected PAMInitialMeans<V> makeInstance() {
+ return new PAMInitialMeans<>();
+ }
+ }
+} \ No newline at end of file