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The Waikato Environment for Knowledge Analysis (WEKA), a machine learning workbench. This version represents the developer version, the "bleeding edge" of development, you could say. New functionality gets added to this version.
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/*
 *   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 .
 */

/**
 *    KStarNumericAttribute.java
 *    Copyright (C) 1995-2012 Univeristy of Waikato
 *    Java port to Weka by Abdelaziz Mahoui ([email protected]).
 *
 */

package weka.classifiers.lazy.kstar;

import weka.core.Attribute;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.RevisionHandler;
import weka.core.RevisionUtils;

/**
 * A custom class which provides the environment for computing the
 * transformation probability of a specified test instance numeric attribute to
 * a specified train instance numeric attribute.
 * 
 * @author Len Trigg ([email protected])
 * @author Abdelaziz Mahoui ([email protected])
 * @version $Revision 1.0 $
 */
public class KStarNumericAttribute implements KStarConstants, RevisionHandler {

  /** The training instances used for classification. */
  protected Instances m_TrainSet;

  /** The test instance */
  protected Instance m_Test;

  /** The train instance */
  protected Instance m_Train;

  /** The index of the attribute in the test and train instances */
  protected int m_AttrIndex;

  /** The scale parameter */
  protected double m_Scale = 1.0;

  /**
   * Probability of test attribute transforming into train attribute with
   * missing value
   */
  protected double m_MissingProb = 1.0;

  /**
   * Average probability of test attribute transforming into train attribute
   */
  protected double m_AverageProb = 1.0;

  /**
   * Smallest probability of test attribute transforming into train attribute
   */
  protected double m_SmallestProb = 1.0;

  /**
   * The set of disctances from the test attribute to the set of train
   * attributes
   */
  protected double[] m_Distances;

  /**
   * Set of colomns: each colomn representing a randomised version of the train
   * dataset class colomn
   */
  protected int[][] m_RandClassCols;

  /** The number of train instances with no missing attribute values */
  protected int m_ActualCount = 0;

  /**
   * A cache for storing attribute values and their corresponding scale
   * parameters
   */
  protected KStarCache m_Cache;

  /** The number of instances in the dataset */
  protected int m_NumInstances;

  /** The number of class values */
  protected int m_NumClasses;

  /** The number of attributes */
  protected int m_NumAttributes;

  /** The class attribute type */
  protected int m_ClassType;

  /** missing value treatment */
  protected int m_MissingMode = M_AVERAGE;

  /** 0 = use specified blend, 1 = entropic blend setting */
  protected int m_BlendMethod = B_SPHERE;

  /** default sphere of influence blend setting */
  protected int m_BlendFactor = 20;

  /**
   * Constructor
   */
  public KStarNumericAttribute(Instance test, Instance train, int attrIndex,
    Instances trainSet, int[][] randClassCols, KStarCache cache) {
    m_Test = test;
    m_Train = train;
    m_AttrIndex = attrIndex;
    m_TrainSet = trainSet;
    m_RandClassCols = randClassCols;
    m_Cache = cache;
    init();
  }

  /**
   * Initializes the m_Attributes of the class.
   */
  private void init() {
    try {
      m_NumInstances = m_TrainSet.numInstances();
      m_NumClasses = m_TrainSet.numClasses();
      m_NumAttributes = m_TrainSet.numAttributes();
      m_ClassType = m_TrainSet.classAttribute().type();
    } catch (Exception e) {
      e.printStackTrace();
    }
  }

  /**
   * Calculates the transformation probability of the attribute indexed
   * "m_AttrIndex" in test instance "m_Test" to the same attribute in the train
   * instance "m_Train".
   * 
   * @return the probability value
   */
  public double transProb() {
    double transProb, distance;
    // check if the attribute value has been encountred before
    // in which case it should be in the numeric cache
    if (m_Cache.containsKey(m_Test.value(m_AttrIndex))) {
      KStarCache.TableEntry te = m_Cache.getCacheValues(m_Test
        .value(m_AttrIndex));
      m_Scale = te.value;
      m_MissingProb = te.pmiss;
    } else {
      if (m_BlendMethod == B_ENTROPY) {
        m_Scale = scaleFactorUsingEntropy();
      } else { // default is B_SPHERE
        m_Scale = scaleFactorUsingBlend();
      }
      m_Cache.store(m_Test.value(m_AttrIndex), m_Scale, m_MissingProb);
    }
    // now what???
    if (m_Train.isMissing(m_AttrIndex)) {
      transProb = m_MissingProb;
    } else {
      distance = Math.abs(m_Test.value(m_AttrIndex)
        - m_Train.value(m_AttrIndex));
      transProb = PStar(distance, m_Scale);
    }
    return transProb;
  }

  /**
   * Calculates the scale factor for the attribute indexed "m_AttrIndex" in test
   * instance "m_Test" using a global blending factor (default value is 20%).
   * 
   * @return the scale factor value
   */
  private double scaleFactorUsingBlend() {
    int i, j, lowestcount = 0;
    double lowest = -1.0, nextlowest = -1.0;
    double root, broot, up, bot;
    double aimfor, min_val = 9e300, scale = 1.0;
    double avgprob = 0.0, minprob = 0.0, min_pos = 0.0;

    KStarWrapper botvals = new KStarWrapper();
    KStarWrapper upvals = new KStarWrapper();
    KStarWrapper vals = new KStarWrapper();

    m_Distances = new double[m_NumInstances];

    for (j = 0; j < m_NumInstances; j++) {
      if (m_TrainSet.instance(j).isMissing(m_AttrIndex)) {
        // mark the train instance with a missing value by setting
        // the distance to -1.0
        m_Distances[j] = -1.0;
      } else {
        m_Distances[j] = Math.abs(m_TrainSet.instance(j).value(m_AttrIndex)
          - m_Test.value(m_AttrIndex));
        if ((m_Distances[j] + 1e-5) < nextlowest || nextlowest == -1.0) {
          if ((m_Distances[j] + 1e-5) < lowest || lowest == -1.0) {
            nextlowest = lowest;
            lowest = m_Distances[j];
            lowestcount = 1;
          } else if (Math.abs(m_Distances[j] - lowest) < 1e-5) {
            // record the number training instances (number n0) at
            // the smallest distance from test instance
            lowestcount++;
          } else {
            nextlowest = m_Distances[j];
          }
        }
        // records the actual number of instances with no missing value
        m_ActualCount++;
      }
    }

    if (nextlowest == -1 || lowest == -1) { // Data values are all the same
      scale = 1.0;
      m_SmallestProb = m_AverageProb = 1.0;
      return scale;
    } else {
      // starting point for root
      root = 1.0 / (nextlowest - lowest);
      i = 0;
      // given the expression: n0 <= E(scale) <= N
      // E(scale) = (N - n0) * b + n0 with blending factor: 0 <= b <= 1
      // aimfor = (N - n0) * b + n0
      aimfor = (m_ActualCount - lowestcount) * (double) m_BlendFactor / 100.0
        + lowestcount;
      if (m_BlendFactor == 0) {
        aimfor += 1.0;
      }
      // root is bracketed in interval [bot,up]
      bot = 0.0 + ROOT_FINDER_ACCURACY / 2.0;
      up = root * 16; // This is bodgy
      // E(bot)
      calculateSphereSize(bot, botvals);
      botvals.sphere -= aimfor;
      // E(up)
      calculateSphereSize(up, upvals);
      upvals.sphere -= aimfor;

      if (botvals.sphere < 0) { // Couldn't include that many
        // instances - going for max possible
        min_pos = bot;
        avgprob = botvals.avgProb;
        minprob = botvals.minProb;
      } else if (upvals.sphere > 0) { // Couldn't include that few,
        // going for min possible
        min_pos = up;
        avgprob = upvals.avgProb;
        minprob = upvals.minProb;
      } else {
        // Root finding Algorithm starts here !
        for (;;) {
          calculateSphereSize(root, vals);
          vals.sphere -= aimfor;
          if (Math.abs(vals.sphere) < min_val) {
            min_val = Math.abs(vals.sphere);
            min_pos = root;
            avgprob = vals.avgProb;
            minprob = vals.minProb;
          }
          if (Math.abs(vals.sphere) <= ROOT_FINDER_ACCURACY) {
            break; // converged to a solution, done!
          }
          if (vals.sphere > 0.0) {
            broot = (root + up) / 2.0;
            bot = root;
            root = broot;
          } else {
            broot = (root + bot) / 2.0;
            up = root;
            root = broot;
          }
          i++;
          if (i > ROOT_FINDER_MAX_ITER) {
            // System.err.println("Warning: "+debug+"
            // ROOT_FINDER_MAX_ITER exceeded");
            root = min_pos;
            break;
          }
        }
      }

      m_SmallestProb = minprob;
      m_AverageProb = avgprob;
      // Set the probability of transforming to a missing value
      switch (m_MissingMode) {
      case M_DELETE:
        m_MissingProb = 0.0;
        break;
      case M_NORMAL:
        m_MissingProb = 1.0;
        break;
      case M_MAXDIFF:
        m_MissingProb = m_SmallestProb;
        break;
      case M_AVERAGE:
        m_MissingProb = m_AverageProb;
        break;
      }
      // set the scale factor value
      scale = min_pos;
      return scale;
    }
  }

  /**
   * Calculates the size of the "sphere of influence" defined as: sphere =
   * sum(P)^2/sum(P^2) where P(i) = root*exp(-2*i*root). Since there are n
   * different training instances we multiply P(i) by 1/n.
   */
  private void calculateSphereSize(double scale, KStarWrapper params) {
    int i;
    double sphereSize, minprob = 1.0;
    double pstar; // P*(b|a)
    double pstarSum = 0.0; // sum(P*)
    double pstarSquareSum = 0.0; // sum(P*^2)
    double inc;
    for (i = 0; i < m_NumInstances; i++) {
      if (m_Distances[i] < 0) {
        // instance with missing value
        continue;
      } else {
        pstar = PStar(m_Distances[i], scale);
        if (minprob > pstar) {
          minprob = pstar;
        }
        inc = pstar / m_ActualCount;
        pstarSum += inc;
        pstarSquareSum += inc * inc;
      }
    }
    sphereSize = (pstarSquareSum == 0 ? 0 : pstarSum * pstarSum
      / pstarSquareSum);
    // return the values
    params.sphere = sphereSize;
    params.avgProb = pstarSum;
    params.minProb = minprob;
  }

  /**
   * Calculates the scale factor using entropy.
   * 
   * @return the scale factor value
   */
  private double scaleFactorUsingEntropy() {
    String debug = "(KStarNumericAttribute.scaleFactorUsingEntropy)";
    if (m_ClassType != Attribute.NOMINAL) {
      System.err.println("Error: " + debug
        + " attribute class must be nominal!");
      System.exit(1);
    }
    int j, itcount;
    double lowest = -1.0, nextlowest = -1.0;
    double root, up, bot, stepsize, delta;
    double randscale;
    double bestdiff, bestroot, currentdiff, lastdiff;
    double bestpsum, bestminprob, scale = 1.0;

    KStarWrapper botvals = new KStarWrapper();
    KStarWrapper upvals = new KStarWrapper();
    KStarWrapper vals = new KStarWrapper();

    m_Distances = new double[m_NumInstances];

    for (j = 0; j < m_NumInstances; j++) {
      if (m_TrainSet.instance(j).isMissing(m_AttrIndex)) {
        // mark the train instance with a missing value by setting
        // the distance to -1.0
        m_Distances[j] = -1.0;
      } else {
        m_Distances[j] = Math.abs(m_TrainSet.instance(j).value(m_AttrIndex)
          - m_Test.value(m_AttrIndex));

        if ((m_Distances[j] + 1e-5) < nextlowest || nextlowest == -1.0) {
          if ((m_Distances[j] + 1e-5) < lowest || lowest == -1.0) {
            nextlowest = lowest;
            lowest = m_Distances[j];
          } else if (Math.abs(m_Distances[j] - lowest) < 1e-5) {
          } else {
            nextlowest = m_Distances[j];
          }
        }
        // records the actual number of instances with no missing value
        m_ActualCount++;
      }
    } // for

    if (nextlowest == -1 || lowest == -1) { // Data values are all the same
      scale = 1.0;
      m_SmallestProb = m_AverageProb = 1.0;
      return scale;
    } else {
      // starting point for root
      root = 1.0 / (nextlowest - lowest);
      // root is bracketed in interval [bot,up]
      bot = 0.0 + ROOT_FINDER_ACCURACY / 2;
      up = root * 8; // This is bodgy
      // Find (approx) entropy ranges
      calculateEntropy(up, upvals);
      calculateEntropy(bot, botvals);
      randscale = botvals.randEntropy - upvals.randEntropy;
      // Optimise the scale factor
      bestroot = root = bot;
      bestdiff = currentdiff = FLOOR1;
      bestpsum = botvals.avgProb;
      bestminprob = botvals.minProb;
      stepsize = (up - bot) / 20.0;
      itcount = 0;
      // Root finding algorithm starts here!
      while (true) {
        itcount++;
        lastdiff = currentdiff;
        root += Math.log(root + 1.0) * stepsize;
        if (root <= bot) {
          root = bot;
          currentdiff = 0.0;
          delta = -1.0;
        } else if (root >= up) {
          root = up;
          currentdiff = 0.0;
          delta = -1.0;
        } else {
          calculateEntropy(root, vals);
          // Normalise entropies
          vals.randEntropy = (vals.randEntropy - upvals.randEntropy)
            / randscale;
          vals.actEntropy = (vals.actEntropy - upvals.actEntropy) / randscale;
          currentdiff = vals.randEntropy - vals.actEntropy;

          if (currentdiff < FLOOR1) {
            currentdiff = FLOOR1;
            if (stepsize < 0) {
              // If we've hit the end and turned around we can't
              // have found any peaks
              bestdiff = currentdiff;
              bestroot = bot;
              bestpsum = botvals.avgProb;
              bestminprob = botvals.minProb;
              break;
            }
          }
          delta = currentdiff - lastdiff;
        }
        if (currentdiff > bestdiff) {
          bestdiff = currentdiff;
          bestroot = root;
          bestminprob = vals.minProb;
          bestpsum = vals.avgProb;
        }
        if (delta < 0) {
          if (Math.abs(stepsize) < ROOT_FINDER_ACCURACY) {
            break;
          } else {
            stepsize /= -4.0;
          }
        }
        if (itcount > ROOT_FINDER_MAX_ITER) {
          // System.err.println("Warning: "+debug+" ROOT_FINDER_MAX_ITER
          // exceeded");
          break;
        }
      } // while

      m_SmallestProb = bestminprob;
      m_AverageProb = bestpsum;
      // Set the probability of transforming to a missing value
      switch (m_MissingMode) {
      case M_DELETE:
        m_MissingProb = 0.0;
        break;
      case M_NORMAL:
        m_MissingProb = 1.0;
        break;
      case M_MAXDIFF:
        m_MissingProb = m_SmallestProb;
        break;
      case M_AVERAGE:
        m_MissingProb = m_AverageProb;
        break;
      }
      // set scale factor
      scale = bestroot;
    } // else
    return scale;
  }

  /**
   * Calculates several parameters aside from the entropy: for a specified scale
   * factor, calculates the actual entropy, a random entropy using a randomized
   * set of class value colomns, and records the average and smallest
   * probabilities (for use in missing value case).
   */
  private void calculateEntropy(double scale, KStarWrapper params) {
    int i, j, k;
    double actent = 0.0, randent = 0.0;
    double pstar, tprob, avgprob = 0.0, minprob = 1.0;
    double actClassProb, randClassProb;
    double[][] pseudoClassProbs = new double[NUM_RAND_COLS + 1][m_NumClasses];
    // init
    for (j = 0; j <= NUM_RAND_COLS; j++) {
      for (i = 0; i < m_NumClasses; i++) {
        pseudoClassProbs[j][i] = 0.0;
      }
    }
    for (i = 0; i < m_NumInstances; i++) {
      if (m_Distances[i] < 0) {
        // train instance has mising value
        continue;
      } else {
        pstar = PStar(m_Distances[i], scale);
        tprob = pstar / m_ActualCount;
        avgprob += tprob;
        if (pstar < minprob) {
          minprob = pstar;
        }
        // filter instances with same class value
        for (k = 0; k <= NUM_RAND_COLS; k++) {
          // instance i is assigned a random class value in colomn k;
          // colomn k = NUM_RAND_COLS contains the original mapping:
          // instance -> class vlaue
          pseudoClassProbs[k][m_RandClassCols[k][i]] += tprob;
        }
      }
    }
    // compute the actual entropy using the class probabilities
    // with the original class value mapping (colomn NUM_RAND_COLS)
    for (j = m_NumClasses - 1; j >= 0; j--) {
      actClassProb = pseudoClassProbs[NUM_RAND_COLS][j] / avgprob;
      if (actClassProb > 0) {
        actent -= actClassProb * Math.log(actClassProb) / LOG2;
      }
    }
    // compute a random entropy using the pseudo class probs
    // excluding the colomn NUM_RAND_COLS
    for (k = 0; k < NUM_RAND_COLS; k++) {
      for (i = m_NumClasses - 1; i >= 0; i--) {
        randClassProb = pseudoClassProbs[k][i] / avgprob;
        if (randClassProb > 0) {
          randent -= randClassProb * Math.log(randClassProb) / LOG2;
        }
      }
    }
    randent /= NUM_RAND_COLS;
    // return the values
    params.actEntropy = actent;
    params.randEntropy = randent;
    params.avgProb = avgprob;
    params.minProb = minprob;
  }

  /**
   * Calculates the value of P for a given value x using the expression: P(x) =
   * scale * exp( -2.0 * x * scale )
   * 
   * @param x input value
   * @param scale the scale factor
   * @return output of the function P(x)
   */
  private double PStar(double x, double scale) {
    return scale * Math.exp(-2.0 * x * scale);
  }

  /**
   * Set options.
   * 
   * @param missingmode the missing value treatment to use
   * @param blendmethod the blending method to use
   * @param blendfactor the level of blending to use
   */
  public void setOptions(int missingmode, int blendmethod, int blendfactor) {
    m_MissingMode = missingmode;
    m_BlendMethod = blendmethod;
    m_BlendFactor = blendfactor;
  }

  /**
   * Set the missing value mode.
   * 
   * @param mode the type of missing value treatment to use
   */
  public void setMissingMode(int mode) {
    m_MissingMode = mode;
  }

  /**
   * Set the blending method
   * 
   * @param method the blending method to use
   */
  public void setBlendMethod(int method) {
    m_BlendMethod = method;
  }

  /**
   * Set the blending factor
   * 
   * @param factor the level of blending to use
   */
  public void setBlendFactor(int factor) {
    m_BlendFactor = factor;
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 10153 $");
  }
} // class