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weka.estimators.UnivariateMixtureEstimator Maven / Gradle / Ivy

/*
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU 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 General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see .
 */

/*
 *    UnivariateMixtureEstimator.java
 *    Copyright (C) 2014 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.estimators;

import java.io.Serializable;
import java.util.Arrays;
import java.util.Enumeration;
import java.util.Random;
import java.util.ArrayList;
import java.util.Vector;

import weka.core.ContingencyTables;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.Statistics;
import weka.core.Utils;

/**
 * Simple weighted mixture density estimator. Uses a mixture of Gaussians
 * and applies the leave-one-out bootstrap for model selection. Can alternatively use normalized entropy.
 *
 * @author Eibe Frank ([email protected])
 * @version $Revision: 8034 $
 */
public class UnivariateMixtureEstimator implements UnivariateDensityEstimator,
UnivariateIntervalEstimator,
UnivariateQuantileEstimator,
OptionHandler,
Serializable {

  /** Constant for normal distribution. */
  private static double m_normConst = Math.log(Math.sqrt(2 * Math.PI));

  /**
   * Fast univariate mixture model implementation.
   */
  public class MM {

    /** Means */
    protected double[] m_Means = null;

    /** Standard deviations */
    protected double[] m_StdDevs = null;

    /** The priors, on log scale */
    protected double[] m_LogPriors = null;

    /** The number of actual components */
    protected int m_K;

    /**
     * Returns string describing the estimator.
     */
    public String toString() {

      StringBuffer sb = new StringBuffer();
      sb.append("Mixture model estimator\n\n");
      for (int i = 0; i < m_LogPriors.length; i++) {
        sb.append("Mean: " + m_Means[i] + "\tStd. dev.: " + m_StdDevs[i] + "\tPrior prob.: " +
          Math.exp(m_LogPriors[i]) + "\n");
      }

      return sb.toString();
    }

    /**
     * Returns smallest distance to given elements.
     * Assumes m_Means has at least one element (i.e. m_K >= 1).
     */
    protected double smallestDistance(double val) {

      double min = Math.abs(val - m_Means[0]);
      for (int i = 1; i < m_K; i++) {
        if (Math.abs(val - m_Means[i]) < min) {
          min = Math.abs(val - m_Means[i]);
        }
      }
      return min;
    }

    /**
     * Returns the index of the nearest mean.
     * Assumes m_Means has at least one element (i.e. m_K >= 1).
     */
    protected int nearestMean(double val) {

      double min = Math.abs(val - m_Means[0]);
      int index = 0;
      for (int i = 1; i < m_K; i++) {
        if (Math.abs(val - m_Means[i]) < min) {
          min = Math.abs(val - m_Means[i]);
          index = i;
        }
      }
      return index;
    }

    /**
     * Initializes the model. Assumes K >= 1, values.length >= 1,
     * and values.length = weights.length.
     */
    public void initializeModel(int K, double[] values, double[] weights, Random r) {

      // Initialize means using farthest points
      m_Means = new double[K];

      // Randomly choose first point
      double furthestVal = values[r.nextInt(values.length)];

      // Find K maximally distant points (if possible)
      m_K = 0;
      do {
        m_Means[m_K] = furthestVal;
        m_K++;
        if (m_K >= K) {
          break;
        }
        double maxMinDist = smallestDistance(values[0]);
        furthestVal = values[0];
        for (int i = 1; i < values.length; i++) {
          double minDist = smallestDistance(values[i]);
          if (minDist > maxMinDist) {
            maxMinDist = minDist;
            furthestVal = values[i];
          }
        }
        if (maxMinDist <= 0) {
          break;
        }
      } while (true);

      // Shrink array of means if necessary
      if (m_K < K) {
        double[] tempMeans = new double[m_K];
        System.arraycopy(m_Means, 0, tempMeans, 0, m_K);
        m_Means = tempMeans;
      }

      // Establish initial cluster assignments
      double[][] probs = new double[m_K][values.length];
      for (int i = 0; i < values.length; i++) {
        probs[nearestMean(values[i])][i] = 1.0;
      }

      // Compute initial parameters
      m_StdDevs = new double[m_K];
      m_LogPriors = new double[m_K];
      estimateParameters(values, weights, probs);
    }

    /**
     * Estimate parameters.
     */
    protected void estimateParameters(double[] values, double[] weights, double[][] probs) {

      double totalSumOfWeights = 0;
      for (int j = 0; j < m_K; j++) {
        double sum = 0;
        double sumWeights = 0;
        for (int i = 0; i < values.length; i++) {
          double weight = probs[j][i] * weights[i];
          sum += weight * values[i];
          sumWeights += weight;
        }
        if (sumWeights <= 0) {
          m_Means[j] = 0;
        } else {
          m_Means[j] = sum / sumWeights;
        }
        totalSumOfWeights += sumWeights;
      }

      for (int j = 0; j < m_K; j++) {
        double sum = 0;
        double sumWeights = 0;
        for (int i = 0; i < values.length; i++) {
          double weight = probs[j][i] * weights[i];
          double diff = values[i] - m_Means[j];
          sum += weight * diff * diff;
          sumWeights += weight;
        }
        if ((sum <= 0) || (sumWeights <= 0)) {
          m_StdDevs[j] = 1.0e-6; // Hack to prevent unpleasantness
        } else {
          m_StdDevs[j] = Math.sqrt(sum / sumWeights);
          if (m_StdDevs[j] < 1.0e-6) {
            m_StdDevs[j] = 1.0e-6;
          }
        }
        if (sumWeights <= 0) {
          m_LogPriors[j] = -Double.MAX_VALUE;
        } else {
          m_LogPriors[j] = Math.log(sumWeights / totalSumOfWeights);
        }
      }
    }

    /**
     * Computes loglikelihood of current model.
     */
    public double loglikelihood(double[] values, double[] weights) {

      double sum = 0;
      double sumOfWeights = 0;
      for (int i = 0; i < values.length; i++) {
        sum += weights[i] * logDensity(values[i]);
        sumOfWeights += weights[i];
      }
      return sum / sumOfWeights;
    }

    /**
     * Returns average of squared errors for current model.
     */
    public double MSE() {

      double mse = 0;
      for (int i = 0; i < m_K; i++) {
        mse += m_StdDevs[i] * m_StdDevs[i] * Math.exp(m_LogPriors[i]);
      }
      return mse;
    }  

    /**
     * Density function of normal distribution.
     */
    protected double logNormalDens(double x, double mean, double stdDev) {

      double diff = x - mean;
      return -(diff * diff / (2 * stdDev * stdDev)) - m_normConst - Math.log(stdDev);
    }

    /**
     * Joint densities per cluster.
     */
    protected double[] logJointDensities(double value) {

      double[] a = new double[m_K];
      for (int i = 0; i < m_K; i++) {
        a[i] = m_LogPriors[i] + logNormalDens(value, m_Means[i], m_StdDevs[i]);
      }
      return a;
    }

    /**
     * Computes log of density for given value.
     */
    public double logDensity(double value) {

      double[] a = logJointDensities(value);
      double max = a[Utils.maxIndex(a)];
      double sum = 0.0;
      for(int i = 0; i < a.length; i++) {
        sum += Math.exp(a[i] - max);
      }

      return max + Math.log(sum);
    }

    /**
     * Returns the interval for the given confidence value. 
     * 
     * @param conf the confidence value in the interval [0, 1]
     * @return the interval
     */
    public double[][] predictIntervals(double conf) {

      // Compute minimum and maximum value, and delta
      double val = Statistics.normalInverse(1.0 - (1.0 - conf) / 2);
      double min = Double.MAX_VALUE;
      double max = -Double.MAX_VALUE;
      for (int i = 0; i < m_Means.length; i++) {
        double l = m_Means[i] - val * m_StdDevs[i];
        if (l < min) {
          min = l;
        }
        double r = m_Means[i] + val * m_StdDevs[i];
        if (r > max) {
          max = r;
        }
      }
      double delta = (max - min) / m_NumIntervals;

      // Create array with estimated probabilities
      double[] probabilities = new double[m_NumIntervals];
      double leftVal = Math.exp(logDensity(min));
      for (int i = 0; i < m_NumIntervals; i++) {
        double rightVal = Math.exp(logDensity(min + (i + 1) * delta));
        probabilities[i] = 0.5 * (leftVal + rightVal) * delta;
        leftVal = rightVal;
      }

      // Sort array based on area of bin estimates
      int[] sortedIndices = Utils.sort(probabilities);

      // Mark the intervals to use
      double sum = 0;
      boolean[] toUse = new boolean[probabilities.length];
      int k = 0;
      while ((sum < conf) && (k < toUse.length)) {
        toUse[sortedIndices[toUse.length - (k + 1)]] = true;
        sum += probabilities[sortedIndices[toUse.length - (k + 1)]];
        k++;
      }

      // Don't need probabilities anymore
      probabilities = null;

      // Create final list of intervals
      ArrayList intervals = new ArrayList();

      // The current interval
      double[] interval = null;

      // Calculate actual intervals
      boolean haveStartedInterval = false;
      for (int i = 0; i < m_NumIntervals; i++) {

        // Should the current bin be used?
        if (toUse[i]) {

          // Do we need to create a new interval?
          if (haveStartedInterval == false) {
            haveStartedInterval = true;
            interval = new double[2];
            interval[0] = min + i * delta;
          }

          // Regardless, we should update the upper boundary
          interval[1] = min + (i + 1) * delta;
        } else {

          // We need to finalize and store the last interval
          // if necessary.
          if (haveStartedInterval) {
            haveStartedInterval = false;
            intervals.add(interval);
          }
        }
      }

      // Add last interval if there is one
      if (haveStartedInterval) {
        intervals.add(interval);
      }

      return intervals.toArray(new double[0][0]);
    }

    /**
     * Returns the quantile for the given percentage.
     * 
     * @param percentage the percentage
     * @return the quantile
     */
    public double predictQuantile(double percentage) {

      // Compute minimum and maximum value, and delta
      double valRight = Statistics.normalInverse(percentage);
      double valLeft = Statistics.normalInverse(0.001);
      double min = Double.MAX_VALUE;
      double max = -Double.MAX_VALUE;
      for (int i = 0; i < m_Means.length; i++) {
        double l = m_Means[i] - valLeft * m_StdDevs[i];
        if (l < min) {
          min = l;
        }
        double r = m_Means[i] + valRight * m_StdDevs[i];
        if (r > max) {
          max = r;
        }
      }
      double delta = (max - min) / m_NumIntervals;

      double sum = 0;
      double leftVal = Math.exp(logDensity(min));
      for (int i = 0; i < m_NumIntervals; i++) {
        if (sum >= percentage) {
          return min + i * delta;
        }
        double rightVal = Math.exp(logDensity(min + (i + 1) * delta));
        sum += 0.5 * (leftVal + rightVal) * delta;
        leftVal = rightVal;
      }
      return max;
    }
  }

  /** For serialization */
  private static final long serialVersionUID = -2035274930137353656L;

  /** The values used for this estimator */
  protected double[] m_Values = new double[1000];

  /** The weights used for this estimator */
  protected double[] m_Weights = new double[1000];

  /** The number of values that have been seen */
  protected int m_NumValues;

  /** The current mixture model */
  protected MM m_MixtureModel;

  /** The number of components to use (default is -1)*/
  protected int m_NumComponents = -1; 

  /** The maximum number of components to use (default is 5) */
  protected int m_MaxNumComponents = 5;

  /** The random number seed to use (default is 1*/
  protected int m_Seed = 1;

  /** The number of Bootstrap runs to use to select the number of components (default is 10) */
  protected int m_NumBootstrapRuns = 10;

  /** The number of intervals used to approximate prediction interval. */
  protected int m_NumIntervals = 1000;

  /** Whether to use normalized entropy instance of bootstrap. */
  protected boolean m_UseNormalizedEntropy = false;

  /** Whether to output debug info. */
  protected boolean m_Debug = false;

  /** The random number generator. */
  protected Random m_Random = new Random(m_Seed);

  /**
   * Returns a string describing the estimator.
   */
  public String globalInfo() {
    return "Estimates a univariate mixture model.";
  }

  /**
   * @return whether normalized entropy is used
   */
  public boolean getUseNormalizedEntropy() {
    return m_UseNormalizedEntropy;
  }

  /**
   * @param useNormalizedEntropy whether to use normalized entropy
   */
  public void setUseNormalizedEntropy(boolean useNormalizedEntropy) {
    m_UseNormalizedEntropy = useNormalizedEntropy;
  }

  /**
   * The tool tip for this property.
   */
  public String numBootstrapRunsToolTipText() {
    return "The number of Bootstrap runs to choose the number of components.";
  }

  /**
   * Returns the number of Bootstrap runs.
   * 
   * @return the number of Bootstrap runs
   */
  public int getNumBootstrapRuns() {
    return m_NumBootstrapRuns;
  }

  /**
   * Sets the number of Bootstrap runs.
   * 
   * @param mnumBootstrapRuns the number of Bootstrap runs
   */
  public void setNumBootstrapRuns(int numBootstrapRuns) {
    m_NumBootstrapRuns = numBootstrapRuns;
  }

  /**
   * The tool tip for this property.
   */
  public String numComponentsToolTipText() {
    return "The number of mixture components to use.";
  }

  /**
   * Returns the number of components to use.
   * 
   * @return the m_NumComponents
   */
  public int getNumComponents() {
    return m_NumComponents;
  }

  /**
   * Sets the number of components to use.
   * 
   * @param m_NumComponents the m_NumComponents to set
   */
  public void setNumComponents(int numComponents) {
    this.m_NumComponents = numComponents;
  }

  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
  public String seedTipText() {
    return "The random number seed to be used.";
  }

  /**
   * Set the seed for random number generation.
   *
   * @param seed the seed
   */
  public void setSeed(int seed) {

    m_Seed = seed;
    m_Random = new Random(seed);
  }

  /**
   * Gets the seed for the random number generations
   *
   * @return the seed for the random number generation
   */
  public int getSeed() {

    return m_Seed;
  } 
  /**
   * The tool tip for this property.
   */
  public String maxNumComponentsToolTipText() {
    return "The maximum number of mixture components to use.";
  }

  /**
   * Returns the number of components to use.
   * 
   * @return the maximum number of components to use
   */
  public int getMaxNumComponents() {
    return m_MaxNumComponents;
  }

  /**
   * Sets the number of components to use.
   * 
   * @param maxNumComponents the maximum number of components to evaluate
   */
  public void setMaxNumComponents(int maxNumComponents) {
    m_MaxNumComponents = maxNumComponents;
  }

  /**
   * Adds a value to the density estimator.
   *
   * @param value the value to add
   * @param weight the weight of the value
   */
  public void addValue(double value, double weight) {

    // Do we need to add value at all?
    if (!Utils.eq(weight, 0)) {

      // Invalidate current model
      m_MixtureModel = null;

      // Do we need to expand the arrays?
      if (m_NumValues == m_Values.length) {
        double[] newWeights = new double[2 * m_NumValues];
        double[] newValues = new double[2 * m_NumValues];
        System.arraycopy(m_Values, 0, newValues, 0, m_NumValues);
        System.arraycopy(m_Weights, 0, newWeights, 0, m_NumValues);
        m_Values = newValues;
        m_Weights = newWeights;
      }

      // Add values
      m_Values[m_NumValues] = value;
      m_Weights[m_NumValues] = weight;
      m_NumValues++;
    }
  }

  /**
   * Build mixture model. Assumes K >= 1, values.length >= 1,
   * and values.length = weights.length.
   */
  public MM buildModel(int K, double[] values, double[] weights) {

    // Initialize model using k-means
    MM model = null;
    double bestMSE = Double.MAX_VALUE;
    int numAttempts = 0;
    while (numAttempts < 5) {

      // Initialize model
      MM tempModel = new UnivariateMixtureEstimator().new MM();
      tempModel.initializeModel(K, values, weights, m_Random);

      // Run k-means until MSE converges
      double oldMSE = Double.MAX_VALUE;
      double MSE = tempModel.MSE();

      if (m_Debug) {
        System.err.println("MSE: " + MSE);
      }

      double[][] probs = new double[tempModel.m_K][values.length];
      while (Utils.sm(MSE, oldMSE)){

        // Compute memberships
        for (int j = 0; j < probs.length; j++) {
          Arrays.fill(probs[j], 0);
        }
        for (int i = 0; i < values.length; i++) {
          probs[tempModel.nearestMean(values[i])][i] = 1.0;
        }

        // Estimate parameters
        tempModel.estimateParameters(values, weights, probs);

        // Compute MSE for updated model
        oldMSE = MSE;
        MSE = tempModel.MSE();

        if (m_Debug) {
          System.err.println("MSE: " + MSE);
        }
      }
      if (MSE < bestMSE) {
        bestMSE = MSE;
        model = tempModel;
      }

      if (m_Debug) {
        System.err.println("Best MSE: " + bestMSE);
      }

      numAttempts++;
    }

    // Run until likelihood converges
    double oldLogLikelihood = -Double.MAX_VALUE;
    double loglikelihood = model.loglikelihood(values, weights);
    double[][] probs = new double[model.m_K][values.length];
    while (Utils.gr(loglikelihood, oldLogLikelihood)){

      // Establish membership probabilities
      for (int i = 0; i < values.length; i++) {
        double[] p = Utils.logs2probs(model.logJointDensities(values[i]));
        for (int j = 0; j < p.length; j++) {
          probs[j][i] = p[j];
        }
      }

      // Estimate parameters
      model.estimateParameters(values, weights, probs);

      // Compute loglikelihood for updated model
      oldLogLikelihood = loglikelihood;
      loglikelihood = model.loglikelihood(values, weights);
    }

    return model;
  }

  /**
   * Creates a new dataset of the same size using random sampling with
   * replacement according to the given weight vector. The weights of the
   * instances in the new dataset are set to one. 
   */
  public double[][] resampleWithWeights(Random random, boolean[] sampled) {

    // Walker's method, see pp. 232 of "Stochastic Simulation" by B.D. Ripley
    double[] P = new double[m_Weights.length];
    System.arraycopy(m_Weights, 0, P, 0, m_Weights.length);
    Utils.normalize(P);
    double[] Q = new double[m_Weights.length];
    int[] A = new int[m_Weights.length];
    int[] W = new int[m_Weights.length];
    int M = m_Weights.length;
    int NN = -1;
    int NP = M;
    for (int I = 0; I < M; I++) {
      if (P[I] < 0) {
        throw new IllegalArgumentException("Weights have to be positive.");
      }
      Q[I] = M * P[I];
      if (Q[I] < 1.0) {
        W[++NN] = I;
      } else {
        W[--NP] = I;
      }
    }
    if (NN > -1 && NP < M) {
      for (int S = 0; S < M - 1; S++) {
        int I = W[S];
        int J = W[NP];
        A[I] = J;
        Q[J] += Q[I] - 1.0;
        if (Q[J] < 1.0) {
          NP++;
        }
        if (NP >= M) {
          break;
        }
      }
      // A[W[M]] = W[M];
    }

    for (int I = 0; I < M; I++) {
      Q[I] += I;
    }

    // Do we need to keep track of how many copies to use?
    int[] counts = new int[M];

    int count = 0;
    for (int i = 0; i < m_Weights.length; i++) {
      int ALRV;
      double U = M * random.nextDouble();
      int I = (int) U;
      if (U < Q[I]) {
        ALRV = I;
      } else {
        ALRV = A[I];
      }
      counts[ALRV]++;
      if (!sampled[ALRV]) {
        sampled[ALRV] = true;
        count++;
      }
    }

    // Generate output
    double[][] output = new double[2][count];
    int index = 0;
    for (int i = 0; i < M; i++) {
      if (counts[i] > 0) {
        output[0][index] = m_Values[i];
        output[1][index] = counts[i];
        index++;
      }
    }

    return output;
  }

  /**
   * Selects the number of components using leave-one-out Bootstrap, estimating loglikelihood.
   *
   * @return the number of components to use
   */
  protected int findNumComponentsUsingBootStrap() {

    if (m_NumComponents > 0) {
      return m_NumComponents;
    }
    if (m_MaxNumComponents <= 1) {
      return 1;
    }

    double bestLogLikelihood = -Double.MAX_VALUE;
    int bestNumComponents = 1;  
    for (int i = 1; i <= m_MaxNumComponents; i++) {
      double logLikelihood = 0;
      for (int k = 0; k < m_NumBootstrapRuns; k++) {
        boolean[] inBag = new boolean[m_NumValues];
        double[][] output = resampleWithWeights(m_Random, inBag);
        MM mixtureModel = buildModel(i, output[0], output[1]);
        double locLogLikelihood = 0;
        double totalWeight = 0;
        for (int j = 0; j < m_NumValues; j++) {
          if (!inBag[j]) {
            double weight = m_Weights[j];
            locLogLikelihood += weight * mixtureModel.logDensity(m_Values[j]);
            totalWeight += weight;
          }
        }
        locLogLikelihood /= totalWeight;
        logLikelihood += locLogLikelihood;
      }
      logLikelihood /= (double)m_NumBootstrapRuns;
      if (m_Debug) {
        System.err.println("Loglikelihood: " + logLikelihood + "\tNumber of components: " + i);
      }
      if (logLikelihood > bestLogLikelihood) {
        bestNumComponents = i;
        bestLogLikelihood = logLikelihood;
      }
    }

    return bestNumComponents;
  }

  /**
   * Calculates entrpy for given model and data.
   */
  protected double entropy(MM mixtureModel) {

    double entropy = 0;
    for (int j = 0; j < m_NumValues; j++) {
      entropy += m_Weights[j] * 
        ContingencyTables.entropy(Utils.logs2probs(mixtureModel.logJointDensities(m_Values[j])));
    }
    entropy *= Utils.log2; // Need natural logarithm, not base-2 logarithm

    return entropy / (double)m_NumValues;
  }

  /**
   * Selects the number of components using normalized entropy.
   *
   * @return the model to use
   */
  protected MM findModelUsingNormalizedEntropy() {

    if (m_NumComponents > 0) {
      return buildModel(m_NumComponents, m_Values, m_Weights);
    }
    if (m_MaxNumComponents <= 1) {
      return buildModel(1, m_Values, m_Weights);
    }

    //Loglikelihood for one cluster
    MM bestMixtureModel = buildModel(1, m_Values, m_Weights);
    double loglikelihoodForOneCluster = bestMixtureModel.loglikelihood(m_Values, m_Weights);
    double bestNormalizedEntropy = 1;
    for (int i = 2; i <= m_MaxNumComponents; i++) {
      MM mixtureModel = buildModel(i, m_Values, m_Weights);

      double loglikelihood = mixtureModel.loglikelihood(m_Values, m_Weights);
      if (loglikelihood < loglikelihoodForOneCluster) {
        // This appears to happen in practice, hopefully not because of a bug...
        if (m_Debug) {
          System.err.println("Likelihood for one cluster greater than for " + i + " clusters.");
        }
        continue;
      }     
      double entropy = entropy(mixtureModel);
      double normalizedEntropy = entropy / (loglikelihood - loglikelihoodForOneCluster);

      if (m_Debug) {
        System.err.println("Entropy: " + entropy + "\tLogLikelihood: " + loglikelihood +
          "\tLoglikelihood for one cluster: " + loglikelihoodForOneCluster + "\tNormalized entropy: " + normalizedEntropy + "\tNumber of components: " + i);
      }
      if (normalizedEntropy < bestNormalizedEntropy) {
        bestMixtureModel = mixtureModel;
        bestNormalizedEntropy = normalizedEntropy;
      }
    }

    return bestMixtureModel;
  }

  /**
   * Updates the model based on the current data.
   * Uses the leave-one-out Bootstrap to choose the number of components.
   */
  protected void updateModel() {

    if (m_MixtureModel != null) {
      return;
    } else if (m_NumValues > 0) {

      // Shrink arrays if necessary
      if (m_Values.length > m_NumValues) {
        double[] values = new double[m_NumValues];
        double[] weights = new double[m_NumValues];
        System.arraycopy(m_Values,  0,  values,  0,  m_NumValues);
        System.arraycopy(m_Weights,  0,  weights,  0,  m_NumValues);
        m_Values = values;
        m_Weights = weights;
      }

      if (m_UseNormalizedEntropy) {
        m_MixtureModel = findModelUsingNormalizedEntropy();
      } else {
        m_MixtureModel = buildModel(findNumComponentsUsingBootStrap(), m_Values, m_Weights);
      }
    }
  }

  /**
   * Returns the interval for the given confidence value. 
   * 
   * @param conf the confidence value in the interval [0, 1]
   * @return the interval
   */
  public double[][] predictIntervals(double conf) {

    updateModel();

    return m_MixtureModel.predictIntervals(conf);
  }

  /**
   * Returns the quantile for the given percentage.
   * 
   * @param percentage the percentage
   * @return the quantile
   */
  public double predictQuantile(double percentage) {

    updateModel();

    return m_MixtureModel.predictQuantile(percentage);
  }


  /**
   * Returns the natural logarithm of the density estimate at the given
   * point.
   *
   * @param value the value at which to evaluate
   * @return the natural logarithm of the density estimate at the given
   * value
   */
  public double logDensity(double value) {

    updateModel();
    if (m_MixtureModel == null) {
      return Math.log(Double.MIN_VALUE);
    }
    return m_MixtureModel.logDensity(value);
  }

  /**
   * Returns textual description of this estimator.
   */
  public String toString() {

    updateModel();
    if (m_MixtureModel == null) {
      return "";
    }
    return m_MixtureModel.toString();
  }

  /**
   * Returns an enumeration that lists the command-line options that are available
   * 
   * @return the list of options as an enumeration
   */
  @Override
  public Enumeration listOptions() {

    Vector options = new Vector();
    options.addElement(new Option("\tNumber of components to use (default: -1).", "N", 1, "-N"));
    options.addElement(new Option("\tMaximum number of components to use (default: 5).", "M", 1, "-M"));
    options.addElement(new Option("\tSeed for the random number generator (default: 1).", "S", 1, "-S"));
    options.addElement(new Option("\tThe number of bootstrap runs to use (default: 10).", "B", 1, "-B"));
    options.addElement(new Option("\tUse normalized entropy instead of bootstrap.", "E", 1, "-E"));
    return options.elements();
  }

  /**
   * Sets options based on the given array of strings.
   * 
   * @param options the list of options to parse
   */
  @Override
  public void setOptions(String[] options) throws Exception {

    String optionString = Utils.getOption("N", options);
    if (optionString.length() > 0) {
      setNumComponents(Integer.parseInt(optionString));    
    } else {
      setNumComponents(-1);
    }
    optionString = Utils.getOption("M", options);
    if (optionString.length() > 0) {
      setMaxNumComponents(Integer.parseInt(optionString));    
    } else {
      setMaxNumComponents(5);
    }
    optionString = Utils.getOption("S", options);
    if (optionString.length() > 0) {
      setSeed(Integer.parseInt(optionString));    
    } else {
      setSeed(1);
    }
    optionString = Utils.getOption("B", options);
    if (optionString.length() > 0) {
      setNumBootstrapRuns(Integer.parseInt(optionString));    
    } else {
      setNumBootstrapRuns(10);
    }
    m_UseNormalizedEntropy = Utils.getFlag("E", options);
    Utils.checkForRemainingOptions(options);
  }

  /**
   * Returns the current set of options.
   * 
   * @return the current set of options as a string
   */
  @Override
  public String[] getOptions() {
    Vector options = new Vector();

    options.add("-N");
    options.add("" + getNumComponents());

    options.add("-M");
    options.add("" + getMaxNumComponents());

    options.add("-S");
    options.add("" + getSeed());

    options.add("-B");
    options.add("" + getNumBootstrapRuns());

    if (m_UseNormalizedEntropy) {
      options.add("-E");
    }

    return options.toArray(new String[0]);
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 10971 $");
  }

  /**
   * Main method, used for testing this class.
   */
  public static void main(String[] args) throws Exception {

    // Get random number generator initialized by system
    Random r = new Random();

    // Create density estimator
    UnivariateMixtureEstimator e = new UnivariateMixtureEstimator();
    e.setOptions(Arrays.copyOf(args, args.length));

    // Output the density estimator
    System.out.println(e);

    // Monte Carlo integration
    double sum = 0;
    for (int i = 0; i < 100000; i++) {
      sum += Math.exp(e.logDensity(r.nextDouble() * 10.0 - 5.0));
    }
    System.out.println("Approximate integral: " + 10.0 * sum / 100000);

    // Add Gaussian values into it
    for (int i = 0; i < 100000; i++) {
      e.addValue(r.nextGaussian() * 0.5 - 1, 1);
      e.addValue(r.nextGaussian() * 0.5 + 1, 3);
    }

    // Output the density estimator
    System.out.println(e);

    // Monte Carlo integration
    sum = 0;
    for (int i = 0; i < 100000; i++) {
      sum += Math.exp(e.logDensity(r.nextDouble() * 10.0 - 5.0));
    }
    System.out.println("Approximate integral: " + 10.0 * sum / 100000);

    // Create density estimator
    e = new UnivariateMixtureEstimator();
    e.setOptions(Arrays.copyOf(args, args.length));

    // Add Gaussian values into it
    for (int i = 0; i < 100000; i++) {
      e.addValue(r.nextGaussian() * 0.5 - 1, 1);
      e.addValue(r.nextGaussian() * 0.5 + 1, 1);
      e.addValue(r.nextGaussian() * 0.5 + 1, 1);
      e.addValue(r.nextGaussian() * 0.5 + 1, 1);
    }

    // Output the density estimator
    System.out.println(e);

    // Monte Carlo integration
    sum = 0;
    for (int i = 0; i < 100000; i++) {
      sum += Math.exp(e.logDensity(r.nextDouble() * 10.0 - 5.0));
    }
    System.out.println("Approximate integral: " + 10.0 * sum / 100000);

    // Create density estimator
    e = new UnivariateMixtureEstimator();
    e.setOptions(Arrays.copyOf(args, args.length));

    // Add Gaussian values into it
    for (int i = 0; i < 100000; i++) {
      e.addValue(r.nextGaussian() * 5.0 + 3.0 , 1);
    }

    // Output the density estimator
    System.out.println(e);

    // Check interval estimates
    double[][] intervals = e.predictIntervals(0.95);
    System.out.println("Lower: " + intervals[0][0] + " Upper: " + intervals[0][1]);
    double covered = 0;
    for (int i = 0; i < 100000; i++) {
      double val = r.nextGaussian() * 5.0 + 3.0;
      if (val >= intervals[0][0] && val <= intervals[0][1]) {
        covered++;
      }
    }
    System.out.println("Coverage: " + covered / 100000);

    intervals = e.predictIntervals(0.8);
    System.out.println("Lower: " + intervals[0][0] + " Upper: " + intervals[0][1]);
    covered = 0;
    for (int i = 0; i < 100000; i++) {
      double val = r.nextGaussian() * 5.0 + 3.0;
      if (val >= intervals[0][0] && val <= intervals[0][1]) {
        covered++;
      }
    }
    System.out.println("Coverage: " + covered / 100000);

    // Output quantile
    System.out.println("95% quantile: " + e.predictQuantile(0.95));
  }
}