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Java example source code file (KMeansPlusPlusClusterer.java)

This example Java source code file (KMeansPlusPlusClusterer.java) is included in the alvinalexander.com "Java Source Code Warehouse" project. The intent of this project is to help you "Learn Java by Example" TM.

Learn more about this Java project at its project page.

Java - Java tags/keywords

arraylist, centroidcluster, clusterable, collection, convergenceexception, distancemeasure, emptyclusterstrategy, farthest_point, kmeansplusplusclusterer, largest_points_number, largest_variance, list, randomgenerator, util

The KMeansPlusPlusClusterer.java Java example source code

/*
 * 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.math3.ml.clustering;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;

import org.apache.commons.math3.exception.ConvergenceException;
import org.apache.commons.math3.exception.MathIllegalArgumentException;
import org.apache.commons.math3.exception.NumberIsTooSmallException;
import org.apache.commons.math3.exception.util.LocalizedFormats;
import org.apache.commons.math3.ml.distance.DistanceMeasure;
import org.apache.commons.math3.ml.distance.EuclideanDistance;
import org.apache.commons.math3.random.JDKRandomGenerator;
import org.apache.commons.math3.random.RandomGenerator;
import org.apache.commons.math3.stat.descriptive.moment.Variance;
import org.apache.commons.math3.util.MathUtils;

/**
 * Clustering algorithm based on David Arthur and Sergei Vassilvitski k-means++ algorithm.
 * @param <T> type of the points to cluster
 * @see <a href="http://en.wikipedia.org/wiki/K-means%2B%2B">K-means++ (wikipedia)
 * @since 3.2
 */
public class KMeansPlusPlusClusterer<T extends Clusterable> extends Clusterer {

    /** Strategies to use for replacing an empty cluster. */
    public enum EmptyClusterStrategy {

        /** Split the cluster with largest distance variance. */
        LARGEST_VARIANCE,

        /** Split the cluster with largest number of points. */
        LARGEST_POINTS_NUMBER,

        /** Create a cluster around the point farthest from its centroid. */
        FARTHEST_POINT,

        /** Generate an error. */
        ERROR

    }

    /** The number of clusters. */
    private final int k;

    /** The maximum number of iterations. */
    private final int maxIterations;

    /** Random generator for choosing initial centers. */
    private final RandomGenerator random;

    /** Selected strategy for empty clusters. */
    private final EmptyClusterStrategy emptyStrategy;

    /** Build a clusterer.
     * <p>
     * The default strategy for handling empty clusters that may appear during
     * algorithm iterations is to split the cluster with largest distance variance.
     * <p>
     * The euclidean distance will be used as default distance measure.
     *
     * @param k the number of clusters to split the data into
     */
    public KMeansPlusPlusClusterer(final int k) {
        this(k, -1);
    }

    /** Build a clusterer.
     * <p>
     * The default strategy for handling empty clusters that may appear during
     * algorithm iterations is to split the cluster with largest distance variance.
     * <p>
     * The euclidean distance will be used as default distance measure.
     *
     * @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.
     */
    public KMeansPlusPlusClusterer(final int k, final int maxIterations) {
        this(k, maxIterations, new EuclideanDistance());
    }

    /** Build a clusterer.
     * <p>
     * The default strategy for handling empty clusters that may appear during
     * algorithm iterations is to split the cluster with largest distance variance.
     *
     * @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.
     * @param measure the distance measure to use
     */
    public KMeansPlusPlusClusterer(final int k, final int maxIterations, final DistanceMeasure measure) {
        this(k, maxIterations, measure, new JDKRandomGenerator());
    }

    /** Build a clusterer.
     * <p>
     * The default strategy for handling empty clusters that may appear during
     * algorithm iterations is to split the cluster with largest distance variance.
     *
     * @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.
     * @param measure the distance measure to use
     * @param random random generator to use for choosing initial centers
     */
    public KMeansPlusPlusClusterer(final int k, final int maxIterations,
                                   final DistanceMeasure measure,
                                   final RandomGenerator random) {
        this(k, maxIterations, measure, random, EmptyClusterStrategy.LARGEST_VARIANCE);
    }

    /** Build a clusterer.
     *
     * @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.
     * @param measure the distance measure to use
     * @param random random generator to use for choosing initial centers
     * @param emptyStrategy strategy to use for handling empty clusters that
     * may appear during algorithm iterations
     */
    public KMeansPlusPlusClusterer(final int k, final int maxIterations,
                                   final DistanceMeasure measure,
                                   final RandomGenerator random,
                                   final EmptyClusterStrategy emptyStrategy) {
        super(measure);
        this.k             = k;
        this.maxIterations = maxIterations;
        this.random        = random;
        this.emptyStrategy = emptyStrategy;
    }

    /**
     * Return the number of clusters this instance will use.
     * @return the number of clusters
     */
    public int getK() {
        return k;
    }

    /**
     * Returns the maximum number of iterations this instance will use.
     * @return the maximum number of iterations, or -1 if no maximum is set
     */
    public int getMaxIterations() {
        return maxIterations;
    }

    /**
     * Returns the random generator this instance will use.
     * @return the random generator
     */
    public RandomGenerator getRandomGenerator() {
        return random;
    }

    /**
     * Returns the {@link EmptyClusterStrategy} used by this instance.
     * @return the {@link EmptyClusterStrategy}
     */
    public EmptyClusterStrategy getEmptyClusterStrategy() {
        return emptyStrategy;
    }

    /**
     * Runs the K-means++ clustering algorithm.
     *
     * @param points the points to cluster
     * @return a list of clusters containing the points
     * @throws MathIllegalArgumentException if the data points are null or the number
     *     of clusters is larger than the number of data points
     * @throws ConvergenceException if an empty cluster is encountered and the
     * {@link #emptyStrategy} is set to {@code ERROR}
     */
    @Override
    public List<CentroidCluster cluster(final Collection points)
        throws MathIllegalArgumentException, ConvergenceException {

        // sanity checks
        MathUtils.checkNotNull(points);

        // number of clusters has to be smaller or equal the number of data points
        if (points.size() < k) {
            throw new NumberIsTooSmallException(points.size(), k, false);
        }

        // create the initial clusters
        List<CentroidCluster clusters = chooseInitialCenters(points);

        // create an array containing the latest assignment of a point to a cluster
        // no need to initialize the array, as it will be filled with the first assignment
        int[] assignments = new int[points.size()];
        assignPointsToClusters(clusters, points, assignments);

        // 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 emptyCluster = false;
            List<CentroidCluster newClusters = new ArrayList>();
            for (final CentroidCluster<T> cluster : clusters) {
                final Clusterable newCenter;
                if (cluster.getPoints().isEmpty()) {
                    switch (emptyStrategy) {
                        case LARGEST_VARIANCE :
                            newCenter = getPointFromLargestVarianceCluster(clusters);
                            break;
                        case LARGEST_POINTS_NUMBER :
                            newCenter = getPointFromLargestNumberCluster(clusters);
                            break;
                        case FARTHEST_POINT :
                            newCenter = getFarthestPoint(clusters);
                            break;
                        default :
                            throw new ConvergenceException(LocalizedFormats.EMPTY_CLUSTER_IN_K_MEANS);
                    }
                    emptyCluster = true;
                } else {
                    newCenter = centroidOf(cluster.getPoints(), cluster.getCenter().getPoint().length);
                }
                newClusters.add(new CentroidCluster<T>(newCenter));
            }
            int changes = assignPointsToClusters(newClusters, points, assignments);
            clusters = newClusters;

            // if there were no more changes in the point-to-cluster assignment
            // and there are no empty clusters left, return the current clusters
            if (changes == 0 && !emptyCluster) {
                return clusters;
            }
        }
        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
     * @param assignments points assignments to clusters
     * @return the number of points assigned to different clusters as the iteration before
     */
    private int assignPointsToClusters(final List<CentroidCluster clusters,
                                       final Collection<T> points,
                                       final int[] assignments) {
        int assignedDifferently = 0;
        int pointIndex = 0;
        for (final T p : points) {
            int clusterIndex = getNearestCluster(clusters, p);
            if (clusterIndex != assignments[pointIndex]) {
                assignedDifferently++;
            }

            CentroidCluster<T> cluster = clusters.get(clusterIndex);
            cluster.addPoint(p);
            assignments[pointIndex++] = clusterIndex;
        }

        return assignedDifferently;
    }

    /**
     * Use K-means++ to choose the initial centers.
     *
     * @param points the points to choose the initial centers from
     * @return the initial centers
     */
    private List<CentroidCluster chooseInitialCenters(final Collection points) {

        // Convert to list for indexed access. Make it unmodifiable, since removal of items
        // would screw up the logic of this method.
        final List<T> pointList = Collections.unmodifiableList(new ArrayList (points));

        // The number of points in the list.
        final int numPoints = pointList.size();

        // Set the corresponding element in this array to indicate when
        // elements of pointList are no longer available.
        final boolean[] taken = new boolean[numPoints];

        // The resulting list of initial centers.
        final List<CentroidCluster resultSet = new ArrayList>();

        // Choose one center uniformly at random from among the data points.
        final int firstPointIndex = random.nextInt(numPoints);

        final T firstPoint = pointList.get(firstPointIndex);

        resultSet.add(new CentroidCluster<T>(firstPoint));

        // Must mark it as taken
        taken[firstPointIndex] = true;

        // To keep track of the minimum distance squared of elements of
        // pointList to elements of resultSet.
        final double[] minDistSquared = new double[numPoints];

        // Initialize the elements.  Since the only point in resultSet is firstPoint,
        // this is very easy.
        for (int i = 0; i < numPoints; i++) {
            if (i != firstPointIndex) { // That point isn't considered
                double d = distance(firstPoint, pointList.get(i));
                minDistSquared[i] = d*d;
            }
        }

        while (resultSet.size() < k) {

            // Sum up the squared distances for the points in pointList not
            // already taken.
            double distSqSum = 0.0;

            for (int i = 0; i < numPoints; i++) {
                if (!taken[i]) {
                    distSqSum += minDistSquared[i];
                }
            }

            // 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() * distSqSum;

            // The index of the next point to be added to the resultSet.
            int nextPointIndex = -1;

            // Sum through the squared min distances again, stopping when
            // sum >= r.
            double sum = 0.0;
            for (int i = 0; i < numPoints; i++) {
                if (!taken[i]) {
                    sum += minDistSquared[i];
                    if (sum >= r) {
                        nextPointIndex = i;
                        break;
                    }
                }
            }

            // If it's not set to >= 0, the point wasn't found in the previous
            // for loop, probably because distances are extremely small.  Just pick
            // the last available point.
            if (nextPointIndex == -1) {
                for (int i = numPoints - 1; i >= 0; i--) {
                    if (!taken[i]) {
                        nextPointIndex = i;
                        break;
                    }
                }
            }

            // We found one.
            if (nextPointIndex >= 0) {

                final T p = pointList.get(nextPointIndex);

                resultSet.add(new CentroidCluster<T> (p));

                // Mark it as taken.
                taken[nextPointIndex] = true;

                if (resultSet.size() < k) {
                    // Now update elements of minDistSquared.  We only have to compute
                    // the distance to the new center to do this.
                    for (int j = 0; j < numPoints; j++) {
                        // Only have to worry about the points still not taken.
                        if (!taken[j]) {
                            double d = distance(p, pointList.get(j));
                            double d2 = d * d;
                            if (d2 < minDistSquared[j]) {
                                minDistSquared[j] = d2;
                            }
                        }
                    }
                }

            } else {
                // None found --
                // Break from the while loop to prevent
                // an infinite loop.
                break;
            }
        }

        return resultSet;
    }

    /**
     * Get a random point from the {@link Cluster} with the largest distance variance.
     *
     * @param clusters the {@link Cluster}s to search
     * @return a random point from the selected cluster
     * @throws ConvergenceException if clusters are all empty
     */
    private T getPointFromLargestVarianceCluster(final Collection<CentroidCluster clusters)
            throws ConvergenceException {

        double maxVariance = Double.NEGATIVE_INFINITY;
        Cluster<T> selected = null;
        for (final CentroidCluster<T> cluster : clusters) {
            if (!cluster.getPoints().isEmpty()) {

                // compute the distance variance of the current cluster
                final Clusterable center = cluster.getCenter();
                final Variance stat = new Variance();
                for (final T point : cluster.getPoints()) {
                    stat.increment(distance(point, center));
                }
                final double variance = stat.getResult();

                // select the cluster with the largest variance
                if (variance > maxVariance) {
                    maxVariance = variance;
                    selected = cluster;
                }

            }
        }

        // did we find at least one non-empty cluster ?
        if (selected == null) {
            throw new ConvergenceException(LocalizedFormats.EMPTY_CLUSTER_IN_K_MEANS);
        }

        // extract a random point from the cluster
        final List<T> selectedPoints = selected.getPoints();
        return selectedPoints.remove(random.nextInt(selectedPoints.size()));

    }

    /**
     * Get a random point from the {@link Cluster} with the largest number of points
     *
     * @param clusters the {@link Cluster}s to search
     * @return a random point from the selected cluster
     * @throws ConvergenceException if clusters are all empty
     */
    private T getPointFromLargestNumberCluster(final Collection<? extends Cluster clusters)
            throws ConvergenceException {

        int maxNumber = 0;
        Cluster<T> selected = null;
        for (final Cluster<T> cluster : clusters) {

            // get the number of points of the current cluster
            final int number = cluster.getPoints().size();

            // select the cluster with the largest number of points
            if (number > maxNumber) {
                maxNumber = number;
                selected = cluster;
            }

        }

        // did we find at least one non-empty cluster ?
        if (selected == null) {
            throw new ConvergenceException(LocalizedFormats.EMPTY_CLUSTER_IN_K_MEANS);
        }

        // extract a random point from the cluster
        final List<T> selectedPoints = selected.getPoints();
        return selectedPoints.remove(random.nextInt(selectedPoints.size()));

    }

    /**
     * Get the point farthest to its cluster center
     *
     * @param clusters the {@link Cluster}s to search
     * @return point farthest to its cluster center
     * @throws ConvergenceException if clusters are all empty
     */
    private T getFarthestPoint(final Collection<CentroidCluster clusters) throws ConvergenceException {

        double maxDistance = Double.NEGATIVE_INFINITY;
        Cluster<T> selectedCluster = null;
        int selectedPoint = -1;
        for (final CentroidCluster<T> cluster : clusters) {

            // get the farthest point
            final Clusterable center = cluster.getCenter();
            final List<T> points = cluster.getPoints();
            for (int i = 0; i < points.size(); ++i) {
                final double distance = distance(points.get(i), center);
                if (distance > maxDistance) {
                    maxDistance     = distance;
                    selectedCluster = cluster;
                    selectedPoint   = i;
                }
            }

        }

        // did we find at least one non-empty cluster ?
        if (selectedCluster == null) {
            throw new ConvergenceException(LocalizedFormats.EMPTY_CLUSTER_IN_K_MEANS);
        }

        return selectedCluster.getPoints().remove(selectedPoint);

    }

    /**
     * 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 index of the nearest {@link Cluster} to the given point
     */
    private int getNearestCluster(final Collection<CentroidCluster clusters, final T point) {
        double minDistance = Double.MAX_VALUE;
        int clusterIndex = 0;
        int minCluster = 0;
        for (final CentroidCluster<T> c : clusters) {
            final double distance = distance(point, c.getCenter());
            if (distance < minDistance) {
                minDistance = distance;
                minCluster = clusterIndex;
            }
            clusterIndex++;
        }
        return minCluster;
    }

    /**
     * Computes the centroid for a set of points.
     *
     * @param points the set of points
     * @param dimension the point dimension
     * @return the computed centroid for the set of points
     */
    private Clusterable centroidOf(final Collection<T> points, final int dimension) {
        final double[] centroid = new double[dimension];
        for (final T p : points) {
            final double[] point = p.getPoint();
            for (int i = 0; i < centroid.length; i++) {
                centroid[i] += point[i];
            }
        }
        for (int i = 0; i < centroid.length; i++) {
            centroid[i] /= points.size();
        }
        return new DoublePoint(centroid);
    }

}

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