Author: luc
Date: Sat May 2 19:34:51 2009
New Revision: 770979
URL: http://svn.apache.org/viewvc?rev=770979&view=rev
Log:
added a clustering package with an implementation of k-means++
JIRA: MATH-266
Added:
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Cluster.java
(with props)
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Clusterable.java
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/EuclideanIntegerPoint.java
(with props)
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java
(with props)
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/package.html
(with props)
commons/proper/math/trunk/src/test/org/apache/commons/math/stat/clustering/
commons/proper/math/trunk/src/test/org/apache/commons/math/stat/clustering/KMeansPlusPlusClustererTest.java
(with props)
Modified:
commons/proper/math/trunk/src/site/xdoc/changes.xml
Added:
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Cluster.java
URL:
http://svn.apache.org/viewvc/commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Cluster.java?rev=770979&view=auto
==============================================================================
---
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Cluster.java
(added)
+++
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Cluster.java
Sat May 2 19:34:51 2009
@@ -0,0 +1,74 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.math.stat.clustering;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Cluster holding a set of {...@link Clusterable} points.
+ * @param <T> the type of points that can be clustered
+ * @version $Revision$ $Date$
+ * @since 2.0
+ */
+public class Cluster<T extends Clusterable<T>> implements Serializable {
+
+ /** Serializable version identifier. */
+ private static final long serialVersionUID = -1741417096265465690L;
+
+ /** The points contained in this cluster. */
+ final List<T> points;
+
+ /** Center of the cluster. */
+ final T center;
+
+ /**
+ * Build a cluster centered at a specified point.
+ * @param center the point which is to be the center of this cluster
+ */
+ public Cluster(final T center) {
+ this.center = center;
+ points = new ArrayList<T>();
+ }
+
+ /**
+ * Add a point to this cluster.
+ * @param point point to add
+ */
+ public void addPoint(final T point) {
+ points.add(point);
+ }
+
+ /**
+ * Get the points contained in the cluster.
+ * @return points contained in the cluster
+ */
+ public List<T> getPoints() {
+ return points;
+ }
+
+ /**
+ * Get the point chosen to be the center of this cluster.
+ * @return chosen cluster center
+ */
+ public T getCenter() {
+ return center;
+ }
+
+}
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Added:
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Clusterable.java
URL:
http://svn.apache.org/viewvc/commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Clusterable.java?rev=770979&view=auto
==============================================================================
---
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Clusterable.java
(added)
+++
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/Clusterable.java
Sat May 2 19:34:51 2009
@@ -0,0 +1,47 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.math.stat.clustering;
+
+import java.io.Serializable;
+import java.util.Collection;
+
+/**
+ * Interface for points that can be clustered together.
+ * @param <T> the type of point that can be clustered
+ * @version $Revision$ $Date$
+ * @since 2.0
+ */
+public interface Clusterable<T> extends Serializable {
+
+ /**
+ * Returns the distance from the given point.
+ *
+ * @param p the point to compute the distance from
+ * @return the distance from the given point
+ */
+ double distanceFrom(T p);
+
+ /**
+ * Returns the centroid of the given Collection of points.
+ *
+ * @param p the Collection of points to compute the centroid of
+ * @return the centroid of the given Collection of Points
+ */
+ T centroidOf(Collection<T> p);
+
+}
Added:
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/EuclideanIntegerPoint.java
URL:
http://svn.apache.org/viewvc/commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/EuclideanIntegerPoint.java?rev=770979&view=auto
==============================================================================
---
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/EuclideanIntegerPoint.java
(added)
+++
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/EuclideanIntegerPoint.java
Sat May 2 19:34:51 2009
@@ -0,0 +1,98 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.math.stat.clustering;
+
+import java.util.Collection;
+
+import org.apache.commons.math.util.MathUtils;
+
+/**
+ * A simple implementation of {...@link Clusterable} for points with integer
coordinates.
+ * @version $Revision$ $Date$
+ * @since 2.0
+ */
+public class EuclideanIntegerPoint implements
Clusterable<EuclideanIntegerPoint> {
+
+ /** Serializable version identifier. */
+ private static final long serialVersionUID = 3946024775784901369L;
+
+ /** Point coordinates. */
+ private final int[] point;
+
+ /**
+ * @param point the n-dimensional point in integer space
+ */
+ public EuclideanIntegerPoint(final int[] point) {
+ this.point = point;
+ }
+
+ /**
+ * Returns the n-dimensional point in integer space
+ */
+ public int[] getPoint() {
+ return point;
+ }
+
+ /** {...@inheritdoc} */
+ public double distanceFrom(final EuclideanIntegerPoint p) {
+ return MathUtils.distance(point, p.getPoint());
+ }
+
+ /** {...@inheritdoc} */
+ public EuclideanIntegerPoint centroidOf(final
Collection<EuclideanIntegerPoint> points) {
+ int[] centroid = new int[getPoint().length];
+ for (EuclideanIntegerPoint p : points) {
+ for (int i = 0; i < centroid.length; i++) {
+ centroid[i] += p.getPoint()[i];
+ }
+ }
+ for (int i = 0; i < centroid.length; i++) {
+ centroid[i] /= points.size();
+ }
+ return new EuclideanIntegerPoint(centroid);
+ }
+
+ /** {...@inheritdoc} */
+ @Override
+ public boolean equals(final Object other) {
+ if (!(other instanceof EuclideanIntegerPoint)) {
+ return false;
+ }
+ final int[] otherPoint = ((EuclideanIntegerPoint) other).getPoint();
+ if (point.length != otherPoint.length) {
+ return false;
+ }
+ for (int i = 0; i < point.length; i++) {
+ if (point[i] != otherPoint[i]) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /** {...@inheritdoc} */
+ @Override
+ public int hashCode() {
+ int hashCode = 0;
+ for (Integer i : point) {
+ hashCode += i.hashCode() * 13 + 7;
+ }
+ return hashCode;
+ }
+
+}
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Added:
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java
URL:
http://svn.apache.org/viewvc/commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java?rev=770979&view=auto
==============================================================================
---
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java
(added)
+++
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java
Sat May 2 19:34:51 2009
@@ -0,0 +1,161 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.math.stat.clustering;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Random;
+
+/**
+ * Clustering algorithm based on David Arthur and Sergei Vassilvitski
k-means++ algorithm.
+ * @see <a href="http://en.wikipedia.org/wiki/K-means%2B%2B";>K-means++
(wikipedia)</a>
+ * @version $Revision$ $Date$
+ * @since 2.0
+ */
+public class KMeansPlusPlusClusterer<T extends Clusterable<T>> {
+
+ /** Random generator for choosing initial centers. */
+ private final Random random;
+
+ /** Build a clusterer.
+ * @param random random generator to use for choosing initial centers
+ */
+ public KMeansPlusPlusClusterer(final Random random) {
+ this.random = random;
+ }
+
+ /**
+ * Runs the K-means++ clustering algorithm.
+ *
+ * @param points the points to cluster
+ * @param k the number of clusters to split the data into
+ * @param maxIterations the maximum number of iterations to run the
algorithm
+ * for. If negative, no maximum will be used
+ * @return a list of clusters containing the points
+ */
+ public List<Cluster<T>> cluster(final Collection<T> points,
+ final int k, final int maxIterations) {
+ // create the initial clusters
+ List<Cluster<T>> clusters = chooseInitialCenters(points, k, random);
+ assignPointsToClusters(clusters, points);
+
+ // iterate through updating the centers until we're done
+ final int max = (maxIterations < 0) ? Integer.MAX_VALUE :
maxIterations;
+ for (int count = 0; count < max; count++) {
+ boolean clusteringChanged = false;
+ List<Cluster<T>> newClusters = new ArrayList<Cluster<T>>();
+ for (final Cluster<T> cluster : clusters) {
+ final T newCenter =
cluster.getCenter().centroidOf(cluster.getPoints());
+ if (!newCenter.equals(cluster.getCenter())) {
+ clusteringChanged = true;
+ }
+ newClusters.add(new Cluster<T>(newCenter));
+ }
+ if (!clusteringChanged) {
+ return clusters;
+ }
+ assignPointsToClusters(newClusters, points);
+ clusters = newClusters;
+ }
+ return clusters;
+ }
+
+ /**
+ * Adds the given points to the closest {...@link Cluster}.
+ *
+ * @param clusters the {...@link Cluster}s to add the points to
+ * @param points the points to add to the given {...@link Cluster}s
+ */
+ private static <T extends Clusterable<T>> void
+ assignPointsToClusters(final Collection<Cluster<T>> clusters, final
Collection<T> points) {
+ for (final T p : points) {
+ Cluster<T> cluster = getNearestCluster(clusters, p);
+ cluster.addPoint(p);
+ }
+ }
+
+ /**
+ * Use K-means++ to choose the initial centers.
+ *
+ * @param points the points to choose the initial centers from
+ * @param k the number of centers to choose
+ * @param random random generator to use
+ * @return the initial centers
+ */
+ private static <T extends Clusterable<T>> List<Cluster<T>>
+ chooseInitialCenters(final Collection<T> points, final int k, final
Random random) {
+
+ final List<T> pointSet = new ArrayList<T>(points);
+ final List<Cluster<T>> resultSet = new ArrayList<Cluster<T>>();
+
+ // Choose one center uniformly at random from among the data points.
+ final T firstPoint = pointSet.remove(random.nextInt(pointSet.size()));
+ resultSet.add(new Cluster<T>(firstPoint));
+
+ final double[] dx2 = new double[pointSet.size()];
+ while (resultSet.size() < k) {
+ // For each data point x, compute D(x), the distance between x and
+ // the nearest center that has already been chosen.
+ int sum = 0;
+ for (int i = 0; i < pointSet.size(); i++) {
+ final T p = pointSet.get(i);
+ final Cluster<T> nearest = getNearestCluster(resultSet, p);
+ final double d = p.distanceFrom(nearest.getCenter());
+ sum += d * d;
+ dx2[i] = sum;
+ }
+
+ // Add one new data point as a center. Each point x is chosen with
+ // probability proportional to D(x)2
+ final double r = random.nextDouble() * sum;
+ for (int i = 0 ; i < dx2.length; i++) {
+ if (dx2[i] >= r) {
+ final T p = pointSet.remove(i);
+ resultSet.add(new Cluster<T>(p));
+ break;
+ }
+ }
+ }
+
+ return resultSet;
+
+ }
+
+ /**
+ * Returns the nearest {...@link Cluster} to the given point
+ *
+ * @param clusters the {...@link Cluster}s to search
+ * @param point the point to find the nearest {...@link Cluster} for
+ * @return the nearest {...@link Cluster} to the given point
+ */
+ private static <T extends Clusterable<T>> Cluster<T>
+ getNearestCluster(final Collection<Cluster<T>> clusters, final T
point) {
+ double minDistance = Double.MAX_VALUE;
+ Cluster<T> minCluster = null;
+ for (final Cluster<T> c : clusters) {
+ final double distance = point.distanceFrom(c.getCenter());
+ if (distance < minDistance) {
+ minDistance = distance;
+ minCluster = c;
+ }
+ }
+ return minCluster;
+ }
+
+}
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Added:
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/package.html
URL:
http://svn.apache.org/viewvc/commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/package.html?rev=770979&view=auto
==============================================================================
---
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/package.html
(added)
+++
commons/proper/math/trunk/src/java/org/apache/commons/math/stat/clustering/package.html
Sat May 2 19:34:51 2009
@@ -0,0 +1,20 @@
+<html>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ -->
+ <!-- $Revision$ $Date$ -->
+ <body>Clustering algorithms</body>
+</html>
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Modified: commons/proper/math/trunk/src/site/xdoc/changes.xml
URL:
http://svn.apache.org/viewvc/commons/proper/math/trunk/src/site/xdoc/changes.xml?rev=770979&r1=770978&r2=770979&view=diff
==============================================================================
--- commons/proper/math/trunk/src/site/xdoc/changes.xml (original)
+++ commons/proper/math/trunk/src/site/xdoc/changes.xml Sat May 2 19:34:51 2009
@@ -39,6 +39,9 @@
</properties>
<body>
<release version="2.0" date="TBD" description="TBD">
+ <action dev="luc" type="add" issue="MATH-266" due-to="Benjamin McCann">
+ Added a clustering package with an implementation of the k-means++
algorithm
+ </action>
<action dev="luc" type="fix" issue="MATH-265" due-to="Benjamin McCann">
Added distance1, distance and distanceInf utility methods for double
and
int arrays in MathUtils
Added:
commons/proper/math/trunk/src/test/org/apache/commons/math/stat/clustering/KMeansPlusPlusClustererTest.java
URL:
http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/org/apache/commons/math/stat/clustering/KMeansPlusPlusClustererTest.java?rev=770979&view=auto
==============================================================================
---
commons/proper/math/trunk/src/test/org/apache/commons/math/stat/clustering/KMeansPlusPlusClustererTest.java
(added)
+++
commons/proper/math/trunk/src/test/org/apache/commons/math/stat/clustering/KMeansPlusPlusClustererTest.java
Sat May 2 19:34:51 2009
@@ -0,0 +1,97 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.math.stat.clustering;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Random;
+
+import org.junit.Test;
+
+public class KMeansPlusPlusClustererTest {
+
+ @Test
+ public void dimension2() {
+ KMeansPlusPlusClusterer<EuclideanIntegerPoint> transformer =
+ new KMeansPlusPlusClusterer<EuclideanIntegerPoint>(new
Random(1746432956321l));
+ EuclideanIntegerPoint[] points = new EuclideanIntegerPoint[] {
+
+ // first expected cluster
+ new EuclideanIntegerPoint(new int[] { -15, 3 }),
+ new EuclideanIntegerPoint(new int[] { -15, 4 }),
+ new EuclideanIntegerPoint(new int[] { -15, 5 }),
+ new EuclideanIntegerPoint(new int[] { -14, 3 }),
+ new EuclideanIntegerPoint(new int[] { -14, 5 }),
+ new EuclideanIntegerPoint(new int[] { -13, 3 }),
+ new EuclideanIntegerPoint(new int[] { -13, 4 }),
+ new EuclideanIntegerPoint(new int[] { -13, 5 }),
+
+ // second expected cluster
+ new EuclideanIntegerPoint(new int[] { -1, 0 }),
+ new EuclideanIntegerPoint(new int[] { -1, -1 }),
+ new EuclideanIntegerPoint(new int[] { 0, -1 }),
+ new EuclideanIntegerPoint(new int[] { 1, -1 }),
+ new EuclideanIntegerPoint(new int[] { 1, -2 }),
+
+ // third expected cluster
+ new EuclideanIntegerPoint(new int[] { 13, 3 }),
+ new EuclideanIntegerPoint(new int[] { 13, 4 }),
+ new EuclideanIntegerPoint(new int[] { 14, 4 }),
+ new EuclideanIntegerPoint(new int[] { 14, 7 }),
+ new EuclideanIntegerPoint(new int[] { 16, 5 }),
+ new EuclideanIntegerPoint(new int[] { 16, 6 }),
+ new EuclideanIntegerPoint(new int[] { 17, 4 }),
+ new EuclideanIntegerPoint(new int[] { 17, 7 })
+
+ };
+ List<Cluster<EuclideanIntegerPoint>> clusters =
+ transformer.cluster(Arrays.asList(points), 3, 10);
+
+ assertEquals(3, clusters.size());
+ boolean cluster1Found = false;
+ boolean cluster2Found = false;
+ boolean cluster3Found = false;
+ for (Cluster<EuclideanIntegerPoint> cluster : clusters) {
+ int[] center = cluster.getCenter().getPoint();
+ if (center[0] < 0) {
+ cluster1Found = true;
+ assertEquals(8, cluster.getPoints().size());
+ assertEquals(-14, center[0]);
+ assertEquals( 4, center[1]);
+ } else if (center[1] < 0) {
+ cluster2Found = true;
+ assertEquals(5, cluster.getPoints().size());
+ assertEquals( 0, center[0]);
+ assertEquals(-1, center[1]);
+ } else {
+ cluster3Found = true;
+ assertEquals(8, cluster.getPoints().size());
+ assertEquals(15, center[0]);
+ assertEquals(5, center[1]);
+ }
+ }
+ assertTrue(cluster1Found);
+ assertTrue(cluster2Found);
+ assertTrue(cluster3Found);
+
+ }
+
+}
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