Exemplo n.º 1
0
  /** Computes average class values for each attribute and value */
  private void computeAverageClassValues() {

    double totalCounts, sum;
    Instance instance;
    double[] counts;

    double[][] avgClassValues = new double[getInputFormat().numAttributes()][0];
    m_Indices = new int[getInputFormat().numAttributes()][0];
    for (int j = 0; j < getInputFormat().numAttributes(); j++) {
      Attribute att = getInputFormat().attribute(j);
      if (att.isNominal()) {
        avgClassValues[j] = new double[att.numValues()];
        counts = new double[att.numValues()];
        for (int i = 0; i < getInputFormat().numInstances(); i++) {
          instance = getInputFormat().instance(i);
          if (!instance.classIsMissing() && (!instance.isMissing(j))) {
            counts[(int) instance.value(j)] += instance.weight();
            avgClassValues[j][(int) instance.value(j)] += instance.weight() * instance.classValue();
          }
        }
        sum = Utils.sum(avgClassValues[j]);
        totalCounts = Utils.sum(counts);
        if (Utils.gr(totalCounts, 0)) {
          for (int k = 0; k < att.numValues(); k++) {
            if (Utils.gr(counts[k], 0)) {
              avgClassValues[j][k] /= counts[k];
            } else {
              avgClassValues[j][k] = sum / totalCounts;
            }
          }
        }
        m_Indices[j] = Utils.sort(avgClassValues[j]);
      }
    }
  }
  /**
   * Normalizes branch sizes so they contain frequencies (stored in "props") instead of counts
   * (stored in "dist").
   *
   * <p>Overwrites the supplied "props"!
   *
   * <p>props.length must be == dist.length.
   */
  protected static void countsToFreqs(double[][] dist, double[] props) {

    for (int k = 0; k < props.length; k++) {
      props[k] = Utils.sum(dist[k]);
    }
    if (Utils.eq(Utils.sum(props), 0)) {
      for (int k = 0; k < props.length; k++) {
        props[k] = 1.0 / (double) props.length;
      }
    } else {
      FastRfUtils.normalize(props);
    }
  }
  /**
   * Normalizes branch sizes so they contain frequencies (stored in "props") instead of counts
   * (stored in "dist"). Creates a new double[] which it returns.
   */
  protected static double[] countsToFreqs(double[][] dist) {

    double[] props = new double[dist.length];

    for (int k = 0; k < props.length; k++) {
      props[k] = Utils.sum(dist[k]);
    }
    if (Utils.eq(Utils.sum(props), 0)) {
      for (int k = 0; k < props.length; k++) {
        props[k] = 1.0 / (double) props.length;
      }
    } else {
      FastRfUtils.normalize(props);
    }
    return props;
  }
Exemplo n.º 4
0
 /**
  * Normalize the instance
  *
  * @param inst instance to be normalized
  * @return a new Instance with normalized values
  */
 private Instance normalizeInstance(Instance inst) {
   double[] vals = inst.toDoubleArray();
   double sum = Utils.sum(vals);
   for (int i = 0; i < vals.length; i++) {
     vals[i] /= sum;
   }
   return new DenseInstance(inst.weight(), vals);
 }
Exemplo n.º 5
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  /**
   * Calculates the class membership probabilities for the given test instance.
   *
   * @param instance the instance to be classified
   * @return predicted class probability distribution
   * @throws Exception if an error occurred during the prediction
   */
  public double[] distributionForInstance(Instance instance) throws Exception {

    String debug = "(KStar.distributionForInstance) ";
    double transProb = 0.0, temp = 0.0;
    double[] classProbability = new double[m_NumClasses];
    double[] predictedValue = new double[1];

    // initialization ...
    for (int i = 0; i < classProbability.length; i++) {
      classProbability[i] = 0.0;
    }
    predictedValue[0] = 0.0;
    if (m_InitFlag == ON) {
      // need to compute them only once and will be used for all instances.
      // We are doing this because the evaluation module controls the calls.
      if (m_BlendMethod == B_ENTROPY) {
        generateRandomClassColomns();
      }
      m_Cache = new KStarCache[m_NumAttributes];
      for (int i = 0; i < m_NumAttributes; i++) {
        m_Cache[i] = new KStarCache();
      }
      m_InitFlag = OFF;
      //      System.out.println("Computing...");
    }
    // init done.
    Instance trainInstance;
    Enumeration enu = m_Train.enumerateInstances();
    while (enu.hasMoreElements()) {
      trainInstance = (Instance) enu.nextElement();
      transProb = instanceTransformationProbability(instance, trainInstance);
      switch (m_ClassType) {
        case Attribute.NOMINAL:
          classProbability[(int) trainInstance.classValue()] += transProb;
          break;
        case Attribute.NUMERIC:
          predictedValue[0] += transProb * trainInstance.classValue();
          temp += transProb;
          break;
      }
    }
    if (m_ClassType == Attribute.NOMINAL) {
      double sum = Utils.sum(classProbability);
      if (sum <= 0.0)
        for (int i = 0; i < classProbability.length; i++)
          classProbability[i] = (double) 1 / (double) m_NumClasses;
      else Utils.normalize(classProbability, sum);
      return classProbability;
    } else {
      predictedValue[0] = (temp != 0) ? predictedValue[0] / temp : 0.0;
      return predictedValue;
    }
  }
Exemplo n.º 6
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 private Matrix getTransposedNormedMatrix(Instances data) {
   Matrix matrix = new Matrix(data.numAttributes(), data.numInstances());
   for (int i = 0; i < data.numInstances(); i++) {
     double[] vals = data.instance(i).toDoubleArray();
     double sum = Utils.sum(vals);
     for (int v = 0; v < vals.length; v++) {
       vals[v] /= sum;
       matrix.set(v, i, vals[v]);
     }
   }
   return matrix;
 }
Exemplo n.º 7
0
  /**
   * Classifies a given instance. Either this or distributionForInstance() needs to be implemented
   * by subclasses.
   *
   * @param instance the instance to be assigned to a cluster
   * @return the number of the assigned cluster as an integer
   * @exception Exception if instance could not be clustered successfully
   */
  @Override
  public int clusterInstance(Instance instance) throws Exception {

    double[] dist = distributionForInstance(instance);

    if (dist == null) {
      throw new Exception("Null distribution predicted");
    }

    if (Utils.sum(dist) <= 0) {
      throw new Exception("Unable to cluster instance");
    }
    return Utils.maxIndex(dist);
  }
Exemplo n.º 8
0
  /**
   * Calculates the class membership probabilities for the given test instance
   *
   * @param instance the instance to be classified
   * @return predicted class probability distribution
   * @throws Exception if there is a problem generating the prediction
   */
  public double[] distributionForInstance(Instance instance) throws Exception {

    // default model?
    if (m_ZeroR != null) {
      return m_ZeroR.distributionForInstance(instance);
    }

    // Definition of local variables
    double[] probs = new double[m_NumClasses];
    double prob;
    double mutualInfoSum;

    // store instance's att values in an int array
    int[] attIndex = new int[m_NumAttributes];
    for (int att = 0; att < m_NumAttributes; att++) {
      if (att == m_ClassIndex) attIndex[att] = -1;
      else attIndex[att] = m_StartAttIndex[att] + (int) instance.value(att);
    }

    // calculate probabilities for each possible class value
    for (int classVal = 0; classVal < m_NumClasses; classVal++) {
      probs[classVal] = 0;
      prob = 1;
      mutualInfoSum = 0.0;
      for (int parent = 0; parent < m_NumAttributes; parent++) {
        if (attIndex[parent] == -1) continue;
        prob =
            (m_ClassAttAttCounts[classVal][attIndex[parent]][attIndex[parent]]
                    + 1.0 / (m_NumClasses * m_NumAttValues[parent]))
                / (m_NumInstances + 1.0);
        for (int son = 0; son < m_NumAttributes; son++) {
          if (attIndex[son] == -1 || son == parent) continue;
          prob *=
              (m_ClassAttAttCounts[classVal][attIndex[parent]][attIndex[son]]
                      + 1.0 / m_NumAttValues[son])
                  / (m_ClassAttAttCounts[classVal][attIndex[parent]][attIndex[parent]] + 1.0);
        }
        mutualInfoSum += m_mutualInformation[parent];
        probs[classVal] += m_mutualInformation[parent] * prob;
      }
      probs[classVal] /= mutualInfoSum;
    }
    if (!Double.isNaN(Utils.sum(probs))) Utils.normalize(probs);
    return probs;
  }
Exemplo n.º 9
0
  /**
   * Calculates the class membership probabilities for the given test instance.
   *
   * @param instance the instance to be classified
   * @return predicted class probability distribution
   * @exception Exception if distribution can't be computed successfully
   */
  public double[] distributionForInstance(Instance instance) throws Exception {
    if (instance.classAttribute().isNumeric()) {
      throw new UnsupportedClassTypeException("Decorate can't handle a numeric class!");
    }
    double[] sums = new double[instance.numClasses()], newProbs;
    Classifier curr;

    for (int i = 0; i < m_Committee.size(); i++) {
      curr = (Classifier) m_Committee.get(i);
      newProbs = curr.distributionForInstance(instance);
      for (int j = 0; j < newProbs.length; j++) sums[j] += newProbs[j];
    }
    if (Utils.eq(Utils.sum(sums), 0)) {
      return sums;
    } else {
      Utils.normalize(sums);
      return sums;
    }
  }
Exemplo n.º 10
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 /**
  * Compute the JS divergence between an instance and a cluster, used for test data
  *
  * @param inst instance to be clustered
  * @param t index of the cluster
  * @param pi1
  * @param pi2
  * @return the JS divergence
  */
 private double JS(Instance inst, int t, double pi1, double pi2) {
   if (Math.min(pi1, pi2) <= 0) {
     System.out.format(
         "Warning: zero or negative weights in JS calculation! (pi1 %s, pi2 %s)\n", pi1, pi2);
     return 0;
   }
   double sum = Utils.sum(inst.toDoubleArray());
   double kl1 = 0.0, kl2 = 0.0, tmp = 0.0;
   for (int i = 0; i < inst.numValues(); i++) {
     tmp = inst.valueSparse(i) / sum;
     if (tmp != 0) {
       kl1 += tmp * Math.log(tmp / (tmp * pi1 + pi2 * bestT.Py_t.get(inst.index(i), t)));
     }
   }
   for (int i = 0; i < m_numAttributes; i++) {
     if ((tmp = bestT.Py_t.get(i, t)) != 0) {
       kl2 += tmp * Math.log(tmp / (inst.value(i) * pi1 / sum + pi2 * tmp));
     }
   }
   return pi1 * kl1 + pi2 * kl2;
 }
Exemplo n.º 11
0
  /**
   * Test using Kononenko's MDL criterion.
   *
   * @param priorCounts
   * @param bestCounts
   * @param numInstances
   * @param numCutPoints
   * @return true if the split is acceptable
   */
  private boolean KononenkosMDL(
      double[] priorCounts, double[][] bestCounts, double numInstances, int numCutPoints) {

    double distPrior, instPrior, distAfter = 0, sum, instAfter = 0;
    double before, after;
    int numClassesTotal;

    // Number of classes occuring in the set
    numClassesTotal = 0;
    for (double priorCount : priorCounts) {
      if (priorCount > 0) {
        numClassesTotal++;
      }
    }

    // Encode distribution prior to split
    distPrior =
        SpecialFunctions.log2Binomial(numInstances + numClassesTotal - 1, numClassesTotal - 1);

    // Encode instances prior to split.
    instPrior = SpecialFunctions.log2Multinomial(numInstances, priorCounts);

    before = instPrior + distPrior;

    // Encode distributions and instances after split.
    for (double[] bestCount : bestCounts) {
      sum = Utils.sum(bestCount);
      distAfter += SpecialFunctions.log2Binomial(sum + numClassesTotal - 1, numClassesTotal - 1);
      instAfter += SpecialFunctions.log2Multinomial(sum, bestCount);
    }

    // Coding cost after split
    after = Utils.log2(numCutPoints) + distAfter + instAfter;

    // Check if split is to be accepted
    return (before > after);
  }
Exemplo n.º 12
0
  /**
   * Compute the entropy score based on an array of probabilities
   *
   * @param probs array of non-negative and normalized probabilities
   * @return the entropy value
   */
  private double Entropy(double[] probs) {
    for (double prob : probs) {
      if (prob <= 0) {
        if (m_verbose) {
          System.out.println("Warning: Negative probability.");
        }
        return Double.NaN;
      }
    }
    // could be unormalized, when normalization is not specified
    if (Math.abs(Utils.sum(probs) - 1) >= 1e-6) {
      if (m_verbose) {
        System.out.println("Warning: Not normalized.");
      }
      return Double.NaN;
    }

    double mi = 0.0;
    for (double prob : probs) {
      mi += prob * Math.log(prob);
    }
    mi = -mi;
    return mi;
  }
Exemplo n.º 13
0
  /**
   * Generates the classifier.
   *
   * @param instances set of instances serving as training data
   * @exception Exception if the classifier has not been generated successfully
   */
  @Override
  public void buildClassifier(Instances instances) throws Exception {

    int attIndex = 0;
    double sum;

    // can classifier handle the data?
    getCapabilities().testWithFail(instances);

    // remove instances with missing class
    instances = new Instances(instances);
    instances.deleteWithMissingClass();

    m_Instances = new Instances(instances, 0);

    // Reserve space
    m_Counts = new double[instances.numClasses()][instances.numAttributes() - 1][0];
    m_Means = new double[instances.numClasses()][instances.numAttributes() - 1];
    m_Devs = new double[instances.numClasses()][instances.numAttributes() - 1];
    m_Priors = new double[instances.numClasses()];
    Enumeration<Attribute> enu = instances.enumerateAttributes();
    while (enu.hasMoreElements()) {
      Attribute attribute = enu.nextElement();
      if (attribute.isNominal()) {
        for (int j = 0; j < instances.numClasses(); j++) {
          m_Counts[j][attIndex] = new double[attribute.numValues()];
        }
      } else {
        for (int j = 0; j < instances.numClasses(); j++) {
          m_Counts[j][attIndex] = new double[1];
        }
      }
      attIndex++;
    }

    // Compute counts and sums
    Enumeration<Instance> enumInsts = instances.enumerateInstances();
    while (enumInsts.hasMoreElements()) {
      Instance instance = enumInsts.nextElement();
      if (!instance.classIsMissing()) {
        Enumeration<Attribute> enumAtts = instances.enumerateAttributes();
        attIndex = 0;
        while (enumAtts.hasMoreElements()) {
          Attribute attribute = enumAtts.nextElement();
          if (!instance.isMissing(attribute)) {
            if (attribute.isNominal()) {
              m_Counts[(int) instance.classValue()][attIndex][(int) instance.value(attribute)]++;
            } else {
              m_Means[(int) instance.classValue()][attIndex] += instance.value(attribute);
              m_Counts[(int) instance.classValue()][attIndex][0]++;
            }
          }
          attIndex++;
        }
        m_Priors[(int) instance.classValue()]++;
      }
    }

    // Compute means
    Enumeration<Attribute> enumAtts = instances.enumerateAttributes();
    attIndex = 0;
    while (enumAtts.hasMoreElements()) {
      Attribute attribute = enumAtts.nextElement();
      if (attribute.isNumeric()) {
        for (int j = 0; j < instances.numClasses(); j++) {
          if (m_Counts[j][attIndex][0] < 2) {
            throw new Exception(
                "attribute "
                    + attribute.name()
                    + ": less than two values for class "
                    + instances.classAttribute().value(j));
          }
          m_Means[j][attIndex] /= m_Counts[j][attIndex][0];
        }
      }
      attIndex++;
    }

    // Compute standard deviations
    enumInsts = instances.enumerateInstances();
    while (enumInsts.hasMoreElements()) {
      Instance instance = enumInsts.nextElement();
      if (!instance.classIsMissing()) {
        enumAtts = instances.enumerateAttributes();
        attIndex = 0;
        while (enumAtts.hasMoreElements()) {
          Attribute attribute = enumAtts.nextElement();
          if (!instance.isMissing(attribute)) {
            if (attribute.isNumeric()) {
              m_Devs[(int) instance.classValue()][attIndex] +=
                  (m_Means[(int) instance.classValue()][attIndex] - instance.value(attribute))
                      * (m_Means[(int) instance.classValue()][attIndex]
                          - instance.value(attribute));
            }
          }
          attIndex++;
        }
      }
    }
    enumAtts = instances.enumerateAttributes();
    attIndex = 0;
    while (enumAtts.hasMoreElements()) {
      Attribute attribute = enumAtts.nextElement();
      if (attribute.isNumeric()) {
        for (int j = 0; j < instances.numClasses(); j++) {
          if (m_Devs[j][attIndex] <= 0) {
            throw new Exception(
                "attribute "
                    + attribute.name()
                    + ": standard deviation is 0 for class "
                    + instances.classAttribute().value(j));
          } else {
            m_Devs[j][attIndex] /= m_Counts[j][attIndex][0] - 1;
            m_Devs[j][attIndex] = Math.sqrt(m_Devs[j][attIndex]);
          }
        }
      }
      attIndex++;
    }

    // Normalize counts
    enumAtts = instances.enumerateAttributes();
    attIndex = 0;
    while (enumAtts.hasMoreElements()) {
      Attribute attribute = enumAtts.nextElement();
      if (attribute.isNominal()) {
        for (int j = 0; j < instances.numClasses(); j++) {
          sum = Utils.sum(m_Counts[j][attIndex]);
          for (int i = 0; i < attribute.numValues(); i++) {
            m_Counts[j][attIndex][i] =
                (m_Counts[j][attIndex][i] + 1) / (sum + attribute.numValues());
          }
        }
      }
      attIndex++;
    }

    // Normalize priors
    sum = Utils.sum(m_Priors);
    for (int j = 0; j < instances.numClasses(); j++) {
      m_Priors[j] = (m_Priors[j] + 1) / (sum + instances.numClasses());
    }
  }
Exemplo n.º 14
0
  /**
   * Classifies the given test instance.
   *
   * @param instance the instance to be classified
   * @return the predicted class for the instance
   * @throws Exception if the instance can't be classified
   */
  public double[] distributionForInstance(Instance instance) throws Exception {
    double[] dist = new double[m_NumClasses];
    double[] temp = new double[m_NumClasses];
    double weight = 1.0;

    for (int i = 0; i < instance.numAttributes(); i++) {
      if (i != m_ClassIndex && !instance.isMissing(i)) {
        double val = instance.value(i);
        boolean ok = false;
        if (instance.attribute(i).isNumeric()) {
          int k;
          for (k = m_intervalBounds[i].length - 1; k >= 0; k--) {
            if (val > m_intervalBounds[i][k]) {
              for (int j = 0; j < m_NumClasses; j++) {
                if (m_globalCounts[j] > 0) {
                  temp[j] = ((m_counts[i][k][j] + TINY) / (m_globalCounts[j] + TINY));
                }
              }
              ok = true;
              break;
            } else if (val == m_intervalBounds[i][k]) {
              for (int j = 0; j < m_NumClasses; j++) {
                if (m_globalCounts[j] > 0) {
                  temp[j] = ((m_counts[i][k][j] + m_counts[i][k - 1][j]) / 2.0) + TINY;
                  temp[j] /= (m_globalCounts[j] + TINY);
                }
              }
              ok = true;
              break;
            }
          }
          if (!ok) {
            throw new Exception("This shouldn't happen");
          }
        } else { // nominal attribute
          ok = true;
          for (int j = 0; j < m_NumClasses; j++) {
            if (m_globalCounts[j] > 0) {
              temp[j] = ((m_counts[i][(int) val][j] + TINY) / (m_globalCounts[j] + TINY));
            }
          }
        }

        double sum = Utils.sum(temp);
        if (sum <= 0) {
          for (int j = 0; j < temp.length; j++) {
            temp[j] = 1.0 / (double) temp.length;
          }
        } else {
          Utils.normalize(temp, sum);
        }

        if (m_weightByConfidence) {
          weight = weka.core.ContingencyTables.entropy(temp);
          weight = Math.pow(weight, m_bias);
          if (weight < 1.0) {
            weight = 1.0;
          }
        }

        for (int j = 0; j < m_NumClasses; j++) {
          dist[j] += (temp[j] * weight);
        }
      }
    }

    double sum = Utils.sum(dist);
    if (sum <= 0) {
      for (int j = 0; j < dist.length; j++) {
        dist[j] = 1.0 / (double) dist.length;
      }
      return dist;
    } else {
      Utils.normalize(dist, sum);
      return dist;
    }
  }
  private double[] calculateRegionProbs(int j, int i) throws Exception {
    double[] sumOfProbsForRegion = new double[m_trainingData.classAttribute().numValues()];

    for (int u = 0; u < m_numOfSamplesPerRegion; u++) {

      double[] sumOfProbsForLocation = new double[m_trainingData.classAttribute().numValues()];

      m_weightingAttsValues[m_xAttribute] = getRandomX(j);
      m_weightingAttsValues[m_yAttribute] = getRandomY(m_panelHeight - i - 1);

      m_dataGenerator.setWeightingValues(m_weightingAttsValues);

      double[] weights = m_dataGenerator.getWeights();
      double sumOfWeights = Utils.sum(weights);
      int[] indices = Utils.sort(weights);

      // Prune 1% of weight mass
      int[] newIndices = new int[indices.length];
      double sumSoFar = 0;
      double criticalMass = 0.99 * sumOfWeights;
      int index = weights.length - 1;
      int counter = 0;
      for (int z = weights.length - 1; z >= 0; z--) {
        newIndices[index--] = indices[z];
        sumSoFar += weights[indices[z]];
        counter++;
        if (sumSoFar > criticalMass) {
          break;
        }
      }
      indices = new int[counter];
      System.arraycopy(newIndices, index + 1, indices, 0, counter);

      for (int z = 0; z < m_numOfSamplesPerGenerator; z++) {

        m_dataGenerator.setWeightingValues(m_weightingAttsValues);
        double[][] values = m_dataGenerator.generateInstances(indices);

        for (int q = 0; q < values.length; q++) {
          if (values[q] != null) {
            System.arraycopy(values[q], 0, m_vals, 0, m_vals.length);
            m_vals[m_xAttribute] = m_weightingAttsValues[m_xAttribute];
            m_vals[m_yAttribute] = m_weightingAttsValues[m_yAttribute];

            // classify the instance
            m_dist = m_classifier.distributionForInstance(m_predInst);

            for (int k = 0; k < sumOfProbsForLocation.length; k++) {
              sumOfProbsForLocation[k] += (m_dist[k] * weights[q]);
            }
          }
        }
      }

      for (int k = 0; k < sumOfProbsForRegion.length; k++) {
        sumOfProbsForRegion[k] += (sumOfProbsForLocation[k] * sumOfWeights);
      }
    }

    // average
    Utils.normalize(sumOfProbsForRegion);

    // cache
    double[] tempDist = new double[sumOfProbsForRegion.length];
    System.arraycopy(sumOfProbsForRegion, 0, tempDist, 0, sumOfProbsForRegion.length);

    return tempDist;
  }
  /**
   * Recursively generates a tree. A derivative of the buildTree function from the
   * "weka.classifiers.trees.RandomTree" class, with the following changes made:
   *
   * <ul>
   *   <li>m_ClassProbs are now remembered only in leaves, not in every node of the tree
   *   <li>m_Distribution has been removed
   *   <li>members of dists, splits, props and vals arrays which are not used are dereferenced prior
   *       to recursion to reduce memory requirements
   *   <li>a check for "branch with no training instances" is now (FastRF 0.98) made before
   *       recursion; with the current implementation of splitData(), empty branches can appear only
   *       with nominal attributes with more than two categories
   *   <li>each new 'tree' (i.e. node or leaf) is passed a reference to its 'mother forest',
   *       necessary to look up parameters such as maxDepth and K
   *   <li>pre-split entropy is not recalculated unnecessarily
   *   <li>uses DataCache instead of weka.core.Instances, the reference to the DataCache is stored
   *       as a field in FastRandomTree class and not passed recursively down new buildTree() calls
   *   <li>similarly, a reference to the random number generator is stored in a field of the
   *       DataCache
   *   <li>m_ClassProbs are now normalized by dividing with number of instances in leaf, instead of
   *       forcing the sum of class probabilities to 1.0; this has a large effect when
   *       class/instance weights are set by user
   *   <li>a little imprecision is allowed in checking whether there was a decrease in entropy after
   *       splitting
   *   <li>0.99: the temporary arrays splits, props, vals now are not wide as the full number of
   *       attributes in the dataset (of which only "k" columns of randomly chosen attributes get
   *       filled). Now, it's just a single array which gets replaced as the k features are
   *       evaluated sequentially, but it gets replaced only if a next feature is better than a
   *       previous one.
   *   <li>0.99: the SortedIndices are now not cut up into smaller arrays on every split, but rather
   *       re-sorted within the same array in the splitDataNew(), and passed down to buildTree() as
   *       the original large matrix, but with start and end points explicitly specified
   * </ul>
   *
   * @param sortedIndices the indices of the instances of the whole bootstrap replicate
   * @param startAt First index of the instance to consider in this split; inclusive.
   * @param endAt Last index of the instance to consider; inclusive.
   * @param classProbs the class distribution
   * @param debug whether debugging is on
   * @param attIndicesWindow the attribute window to choose attributes from
   * @param depth the current depth
   */
  protected void buildTree(
      int[][] sortedIndices,
      int startAt,
      int endAt,
      double[] classProbs,
      boolean debug,
      int[] attIndicesWindow,
      int depth) {

    m_Debug = debug;
    int sortedIndicesLength = endAt - startAt + 1;

    // Check if node doesn't contain enough instances or is pure
    // or maximum depth reached, make leaf.
    if ((sortedIndicesLength < Math.max(2, getMinNum())) // small
        || Utils.eq(classProbs[Utils.maxIndex(classProbs)], Utils.sum(classProbs)) // pure
        || ((getMaxDepth() > 0) && (depth >= getMaxDepth())) // deep
    ) {
      m_Attribute = -1; // indicates leaf (no useful attribute to split on)

      // normalize by dividing with the number of instances (as of ver. 0.97)
      // unless leaf is empty - this can happen with splits on nominal
      // attributes with more than two categories
      if (sortedIndicesLength != 0)
        for (int c = 0; c < classProbs.length; c++) {
          classProbs[c] /= sortedIndicesLength;
        }
      m_ClassProbs = classProbs;
      this.data = null;
      return;
    } // (leaf making)

    // new 0.99: all the following are for the best attribute only! they're updated while
    // sequentially through the attributes
    double val = Double.NaN; // value of splitting criterion
    double[][] dist =
        new double[2]
            [data.numClasses]; // class distributions (contingency table), indexed first by branch,
                               // then by class
    double[] prop = new double[2]; // the branch sizes (as fraction)
    double split = Double.NaN; // split point

    // Investigate K random attributes
    int attIndex = 0;
    int windowSize = attIndicesWindow.length;
    int k = getKValue();
    boolean sensibleSplitFound = false;
    double prior = Double.NaN;
    double bestNegPosterior = -Double.MAX_VALUE;
    int bestAttIdx = -1;

    while ((windowSize > 0) && (k-- > 0 || !sensibleSplitFound)) {

      int chosenIndex = data.reusableRandomGenerator.nextInt(windowSize);
      attIndex = attIndicesWindow[chosenIndex];

      // shift chosen attIndex out of window
      attIndicesWindow[chosenIndex] = attIndicesWindow[windowSize - 1];
      attIndicesWindow[windowSize - 1] = attIndex;
      windowSize--;

      // new: 0.99
      double candidateSplit =
          distributionSequentialAtt(
              prop, dist, bestNegPosterior, attIndex, sortedIndices[attIndex], startAt, endAt);

      if (Double.isNaN(candidateSplit)) {
        continue; // we did not improve over a previous attribute! "dist" is unchanged from before
      }
      // by this point we know we have an improvement, so we keep the new split point
      split = candidateSplit;
      bestAttIdx = attIndex;

      if (Double.isNaN(
          prior)) { // needs to be computed only once per branch - is same for all attributes (even
                    // regardless of missing values)
        prior = SplitCriteria.entropyOverColumns(dist);
      }

      double negPosterior =
          -SplitCriteria.entropyConditionedOnRows(dist); // this is an updated dist
      if (negPosterior > bestNegPosterior) {
        bestNegPosterior = negPosterior;
      } else {
        throw new IllegalArgumentException("Very strange!");
      }

      val = prior - (-negPosterior); // we want the greatest reduction in entropy
      if (val > 1e-2) { // we allow some leeway here to compensate
        sensibleSplitFound = true; // for imprecision in entropy computation
      }
    } // feature by feature in window

    if (sensibleSplitFound) {

      m_Attribute = bestAttIdx; // find best attribute
      m_SplitPoint = split;
      m_Prop = prop;
      prop = null; // can be GC'ed

      // int[][][] subsetIndices =
      //        new int[dist.length][data.numAttributes][];
      // splitData( subsetIndices, m_Attribute,
      //        m_SplitPoint, sortedIndices );
      // int numInstancesBeforeSplit = sortedIndices[0].length;

      int belowTheSplitStartsAt =
          splitDataNew(m_Attribute, m_SplitPoint, sortedIndices, startAt, endAt);

      m_Successors = new FastRandomTree[dist.length]; // dist.length now always == 2
      for (int i = 0; i < dist.length; i++) {
        m_Successors[i] = new FastRandomTree();
        m_Successors[i].m_MotherForest = this.m_MotherForest;
        m_Successors[i].data = this.data;
        // new in 0.99 - used in distributionSequentialAtt()
        m_Successors[i].tempDists = this.tempDists;
        m_Successors[i].tempDistsOther = this.tempDistsOther;
        m_Successors[i].tempProps = this.tempProps;

        // check if we're about to make an empty branch - this can happen with
        // nominal attributes with more than two categories (as of ver. 0.98)
        if (belowTheSplitStartsAt - startAt == 0) {
          // in this case, modify the chosenAttDists[i] so that it contains
          // the current, before-split class probabilities, properly normalized
          // by the number of instances (as we won't be able to normalize
          // after the split)
          for (int j = 0; j < dist[i].length; j++) dist[i][j] = classProbs[j] / sortedIndicesLength;
        }

        if (i == 0) { // before split
          m_Successors[i].buildTree(
              sortedIndices,
              startAt,
              belowTheSplitStartsAt - 1,
              dist[i],
              m_Debug,
              attIndicesWindow,
              depth + 1);
        } else { // after split
          m_Successors[i].buildTree(
              sortedIndices,
              belowTheSplitStartsAt,
              endAt,
              dist[i],
              m_Debug,
              attIndicesWindow,
              depth + 1);
        }

        dist[i] = null;
      }
      sortedIndices = null;

    } else { // ------ make leaf --------

      m_Attribute = -1;

      // normalize by dividing with the number of instances (as of ver. 0.97)
      // unless leaf is empty - this can happen with splits on nominal attributes
      if (sortedIndicesLength != 0)
        for (int c = 0; c < classProbs.length; c++) {
          classProbs[c] /= sortedIndicesLength;
        }

      m_ClassProbs = classProbs;
    }

    this.data = null; // dereference all pointers so data can be GC'd after tree is built
  }