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• MDD.java

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weka.classifiers.mi.MDD 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 .
 */

/*
 * MDD.java
 * Copyright (C) 2005 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.classifiers.mi;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Enumeration;
import java.util.Vector;

import weka.classifiers.AbstractClassifier;
import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.MultiInstanceCapabilitiesHandler;
import weka.core.Optimization;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.SelectedTag;
import weka.core.Tag;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
import weka.filters.Filter;
import weka.filters.unsupervised.attribute.Normalize;
import weka.filters.unsupervised.attribute.ReplaceMissingValues;
import weka.filters.unsupervised.attribute.Standardize;

/**
 *  Modified Diverse Density algorithm, with collective
 * assumption.

 * 

 * More information about DD:

 * 

 * Oded Maron (1998). Learning from ambiguity.

 * 

 * O. Maron, T. Lozano-Perez (1998). A Framework for Multiple Instance Learning.
 * Neural Information Processing Systems. 10.
 * 

 * 
 * 
 *  BibTeX:
 * 
 * 
 * @phdthesis{Maron1998,
 *    author = {Oded Maron},
 *    school = {Massachusetts Institute of Technology},
 *    title = {Learning from ambiguity},
 *    year = {1998}
 * }
 * 
 * @article{Maron1998,
 *    author = {O. Maron and T. Lozano-Perez},
 *    journal = {Neural Information Processing Systems},
 *    title = {A Framework for Multiple Instance Learning},
 *    volume = {10},
 *    year = {1998}
 * }
 * 
 * 

 * 
 * 
 *  Valid options are:
 * 

 * 
 * 
 * -D
 *  Turn on debugging output.
 * 
 * 
 * 
 * -N <num>
 *  Whether to 0=normalize/1=standardize/2=neither.
 *  (default 1=standardize)
 * 
 * 
 * 
 * 
 * @author Eibe Frank ([email protected])
 * @author Xin Xu ([email protected])
 * @version $Revision: 10369 $
 */
public class MDD extends AbstractClassifier implements OptionHandler,
  MultiInstanceCapabilitiesHandler, TechnicalInformationHandler {

  /** for serialization */
  static final long serialVersionUID = -7273119490545290581L;

  /** The index of the class attribute */
  protected int m_ClassIndex;

  protected double[] m_Par;

  /** The number of the class labels */
  protected int m_NumClasses;

  /** Class labels for each bag */
  protected int[] m_Classes;

  /** MI data */
  protected double[][][] m_Data;

  /** All attribute names */
  protected Instances m_Attributes;

  /** The filter used to standardize/normalize all values. */
  protected Filter m_Filter = null;

  /** Whether to normalize/standardize/neither, default:standardize */
  protected int m_filterType = FILTER_STANDARDIZE;

  /** Normalize training data */
  public static final int FILTER_NORMALIZE = 0;
  /** Standardize training data */
  public static final int FILTER_STANDARDIZE = 1;
  /** No normalization/standardization */
  public static final int FILTER_NONE = 2;
  /** The filter to apply to the training data */
  public static final Tag[] TAGS_FILTER = {
    new Tag(FILTER_NORMALIZE, "Normalize training data"),
    new Tag(FILTER_STANDARDIZE, "Standardize training data"),
    new Tag(FILTER_NONE, "No normalization/standardization"), };

  /** The filter used to get rid of missing values. */
  protected ReplaceMissingValues m_Missing = new ReplaceMissingValues();

  /**
   * Returns a string describing this filter
   * 
   * @return a description of the filter suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String globalInfo() {
    return "Modified Diverse Density algorithm, with collective assumption.\n\n"
      + "More information about DD:\n\n" + getTechnicalInformation().toString();
  }

  /**
   * Returns an instance of a TechnicalInformation object, containing detailed
   * information about the technical background of this class, e.g., paper
   * reference or book this class is based on.
   * 
   * @return the technical information about this class
   */
  @Override
  public TechnicalInformation getTechnicalInformation() {
    TechnicalInformation result;
    TechnicalInformation additional;

    result = new TechnicalInformation(Type.PHDTHESIS);
    result.setValue(Field.AUTHOR, "Oded Maron");
    result.setValue(Field.YEAR, "1998");
    result.setValue(Field.TITLE, "Learning from ambiguity");
    result.setValue(Field.SCHOOL, "Massachusetts Institute of Technology");

    additional = result.add(Type.ARTICLE);
    additional.setValue(Field.AUTHOR, "O. Maron and T. Lozano-Perez");
    additional.setValue(Field.YEAR, "1998");
    additional.setValue(Field.TITLE,
      "A Framework for Multiple Instance Learning");
    additional.setValue(Field.JOURNAL, "Neural Information Processing Systems");
    additional.setValue(Field.VOLUME, "10");

    return result;
  }

  /**
   * Returns an enumeration describing the available options
   * 
   * @return an enumeration of all the available options
   */
  @Override
  public Enumeration listOptions() {

    Vector result = new Vector();

    result.addElement(new Option("\tTurn on debugging output.", "D", 0, "-D"));

    result.addElement(new Option(
      "\tWhether to 0=normalize/1=standardize/2=neither.\n"
        + "\t(default 1=standardize)", "N", 1, "-N "));

    result.addAll(Collections.list(super.listOptions()));

    return result.elements();
  }

  /**
   * Parses a given list of options.
   * 
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
  @Override
  public void setOptions(String[] options) throws Exception {
    setDebug(Utils.getFlag('D', options));

    String nString = Utils.getOption('N', options);
    if (nString.length() != 0) {
      setFilterType(new SelectedTag(Integer.parseInt(nString), TAGS_FILTER));
    } else {
      setFilterType(new SelectedTag(FILTER_STANDARDIZE, TAGS_FILTER));
    }

    super.setOptions(options);

    Utils.checkForRemainingOptions(options);
  }

  /**
   * Gets the current settings of the classifier.
   * 
   * @return an array of strings suitable for passing to setOptions
   */
  @Override
  public String[] getOptions() {

    Vector result = new Vector();

    if (getDebug()) {
      result.add("-D");
    }

    result.add("-N");
    result.add("" + m_filterType);

    Collections.addAll(result, super.getOptions());

    return result.toArray(new String[result.size()]);
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String filterTypeTipText() {
    return "The filter type for transforming the training data.";
  }

  /**
   * Gets how the training data will be transformed. Will be one of
   * FILTER_NORMALIZE, FILTER_STANDARDIZE, FILTER_NONE.
   * 
   * @return the filtering mode
   */
  public SelectedTag getFilterType() {
    return new SelectedTag(m_filterType, TAGS_FILTER);
  }

  /**
   * Sets how the training data will be transformed. Should be one of
   * FILTER_NORMALIZE, FILTER_STANDARDIZE, FILTER_NONE.
   * 
   * @param newType the new filtering mode
   */
  public void setFilterType(SelectedTag newType) {

    if (newType.getTags() == TAGS_FILTER) {
      m_filterType = newType.getSelectedTag().getID();
    }
  }

  private class OptEng extends Optimization {

    /**
     * Evaluate objective function
     * 
     * @param x the current values of variables
     * @return the value of the objective function
     */
    @Override
    protected double objectiveFunction(double[] x) {
      double nll = 0; // -LogLikelihood
      for (int i = 0; i < m_Classes.length; i++) { // ith bag
        int nI = m_Data[i][0].length; // numInstances in ith bag
        double bag = 0; // NLL of each bag

        for (int j = 0; j < nI; j++) {
          double ins = 0.0;
          for (int k = 0; k < m_Data[i].length; k++) {
            ins += (m_Data[i][k][j] - x[k * 2]) * (m_Data[i][k][j] - x[k * 2])
              / (x[k * 2 + 1] * x[k * 2 + 1]);
          }
          ins = Math.exp(-ins);

          if (m_Classes[i] == 1) {
            bag += ins / nI;
          } else {
            bag += (1.0 - ins) / nI;
          }
        }
        if (bag <= m_Zero) {
          bag = m_Zero;
        }
        nll -= Math.log(bag);
      }

      return nll;
    }

    /**
     * Evaluate Jacobian vector
     * 
     * @param x the current values of variables
     * @return the gradient vector
     */
    @Override
    protected double[] evaluateGradient(double[] x) {
      double[] grad = new double[x.length];
      for (int i = 0; i < m_Classes.length; i++) { // ith bag
        int nI = m_Data[i][0].length; // numInstances in ith bag

        double denom = 0.0;
        double[] numrt = new double[x.length];

        for (int j = 0; j < nI; j++) {
          double exp = 0.0;
          for (int k = 0; k < m_Data[i].length; k++) {
            exp += (m_Data[i][k][j] - x[k * 2]) * (m_Data[i][k][j] - x[k * 2])
              / (x[k * 2 + 1] * x[k * 2 + 1]);
          }
          exp = Math.exp(-exp);
          if (m_Classes[i] == 1) {
            denom += exp;
          } else {
            denom += (1.0 - exp);
          }

          // Instance-wise update
          for (int p = 0; p < m_Data[i].length; p++) { // pth variable
            numrt[2 * p] += exp * 2.0 * (x[2 * p] - m_Data[i][p][j])
              / (x[2 * p + 1] * x[2 * p + 1]);
            numrt[2 * p + 1] += exp * (x[2 * p] - m_Data[i][p][j])
              * (x[2 * p] - m_Data[i][p][j])
              / (x[2 * p + 1] * x[2 * p + 1] * x[2 * p + 1]);
          }
        }

        if (denom <= m_Zero) {
          denom = m_Zero;
        }

        // Bag-wise update
        for (int q = 0; q < m_Data[i].length; q++) {
          if (m_Classes[i] == 1) {
            grad[2 * q] += numrt[2 * q] / denom;
            grad[2 * q + 1] -= numrt[2 * q + 1] / denom;
          } else {
            grad[2 * q] -= numrt[2 * q] / denom;
            grad[2 * q + 1] += numrt[2 * q + 1] / denom;
          }
        }
      }

      return grad;
    }

    /**
     * Returns the revision string.
     * 
     * @return the revision
     */
    @Override
    public String getRevision() {
      return RevisionUtils.extract("$Revision: 10369 $");
    }
  }

  /**
   * Returns default capabilities of the classifier.
   * 
   * @return the capabilities of this classifier
   */
  @Override
  public Capabilities getCapabilities() {
    Capabilities result = super.getCapabilities();
    result.disableAll();

    // attributes
    result.enable(Capability.NOMINAL_ATTRIBUTES);
    result.enable(Capability.RELATIONAL_ATTRIBUTES);

    // class
    result.enable(Capability.BINARY_CLASS);
    result.enable(Capability.MISSING_CLASS_VALUES);

    // other
    result.enable(Capability.ONLY_MULTIINSTANCE);

    return result;
  }

  /**
   * Returns the capabilities of this multi-instance classifier for the
   * relational data.
   * 
   * @return the capabilities of this object
   * @see Capabilities
   */
  @Override
  public Capabilities getMultiInstanceCapabilities() {
    Capabilities result = super.getCapabilities();
    result.disableAll();

    // attributes
    result.enable(Capability.NOMINAL_ATTRIBUTES);
    result.enable(Capability.NUMERIC_ATTRIBUTES);
    result.enable(Capability.DATE_ATTRIBUTES);
    result.enable(Capability.MISSING_VALUES);

    // class
    result.disableAllClasses();
    result.enable(Capability.NO_CLASS);

    return result;
  }

  /**
   * Builds the classifier
   * 
   * @param train the training data to be used for generating the boosted
   *          classifier.
   * @throws Exception if the classifier could not be built successfully
   */
  @Override
  public void buildClassifier(Instances train) throws Exception {
    // can classifier handle the data?
    getCapabilities().testWithFail(train);

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

    m_ClassIndex = train.classIndex();
    m_NumClasses = train.numClasses();

    int nR = train.attribute(1).relation().numAttributes();
    int nC = train.numInstances();
    int[] bagSize = new int[nC];
    Instances datasets = new Instances(train.attribute(1).relation(), 0);

    m_Data = new double[nC][nR][]; // Data values
    m_Classes = new int[nC]; // Class values
    m_Attributes = datasets.stringFreeStructure();
    // double sY1=0, sY0=0; // Number of classes NOT USED

    if (m_Debug) {
      System.out.println("Extracting data...");
    }
    ArrayList maxSzIdx = new ArrayList();
    int maxSz = 0;

    for (int h = 0; h < nC; h++) {
      Instance current = train.instance(h);
      m_Classes[h] = (int) current.classValue(); // Class value starts from 0
      Instances currInsts = current.relationalValue(1);
      int nI = currInsts.numInstances();
      bagSize[h] = nI;

      for (int i = 0; i < nI; i++) {
        Instance inst = currInsts.instance(i);
        datasets.add(inst);
      }

      if (m_Classes[h] == 1) {
        if (nI > maxSz) {
          maxSz = nI;
          maxSzIdx = new ArrayList(1);
          maxSzIdx.add(new Integer(h));
        } else if (nI == maxSz) {
          maxSzIdx.add(new Integer(h));
        }
      }
    }

    /* filter the training data */
    if (m_filterType == FILTER_STANDARDIZE) {
      m_Filter = new Standardize();
    } else if (m_filterType == FILTER_NORMALIZE) {
      m_Filter = new Normalize();
    } else {
      m_Filter = null;
    }

    if (m_Filter != null) {
      m_Filter.setInputFormat(datasets);
      datasets = Filter.useFilter(datasets, m_Filter);
    }

    m_Missing.setInputFormat(datasets);
    datasets = Filter.useFilter(datasets, m_Missing);

    int instIndex = 0;
    int start = 0;
    for (int h = 0; h < nC; h++) {
      for (int i = 0; i < datasets.numAttributes(); i++) {
        // initialize m_data[][][]
        m_Data[h][i] = new double[bagSize[h]];
        instIndex = start;
        for (int k = 0; k < bagSize[h]; k++) {
          m_Data[h][i][k] = datasets.instance(instIndex).value(i);
          instIndex++;
        }
      }
      start = instIndex;

      // Class count NOT USED
      /*
       * if (m_Classes[h] == 1) sY1++; else sY0++;
       */
    }

    if (m_Debug) {
      System.out.println("\nIteration History...");
    }

    double[] x = new double[nR * 2], tmp = new double[x.length];
    double[][] b = new double[2][x.length];

    OptEng opt;
    double nll, bestnll = Double.MAX_VALUE;
    for (int t = 0; t < x.length; t++) {
      b[0][t] = Double.NaN;
      b[1][t] = Double.NaN;
    }

    // Largest positive exemplar
    for (int s = 0; s < maxSzIdx.size(); s++) {
      int exIdx = maxSzIdx.get(s).intValue();
      for (int p = 0; p < m_Data[exIdx][0].length; p++) {
        for (int q = 0; q < nR; q++) {
          x[2 * q] = m_Data[exIdx][q][p]; // pick one instance
          x[2 * q + 1] = 1.0;
        }

        opt = new OptEng();
        tmp = opt.findArgmin(x, b);
        while (tmp == null) {
          tmp = opt.getVarbValues();
          if (m_Debug) {
            System.out.println("200 iterations finished, not enough!");
          }
          tmp = opt.findArgmin(tmp, b);
        }
        nll = opt.getMinFunction();

        if (nll < bestnll) {
          bestnll = nll;
          m_Par = tmp;
          if (m_Debug) {
            System.out.println("!!!!!!!!!!!!!!!!Smaller NLL found: " + nll);
          }
        }
        if (m_Debug) {
          System.out.println(exIdx
            + ":  ---------------------------");
        }
      }
    }
  }

  /**
   * Computes the distribution for a given exemplar
   * 
   * @param exmp the exemplar for which distribution is computed
   * @return the distribution
   * @throws Exception if the distribution can't be computed successfully
   */
  @Override
  public double[] distributionForInstance(Instance exmp) throws Exception {

    // Extract the data
    Instances ins = exmp.relationalValue(1);
    if (m_Filter != null) {
      ins = Filter.useFilter(ins, m_Filter);
    }

    ins = Filter.useFilter(ins, m_Missing);

    int nI = ins.numInstances(), nA = ins.numAttributes();
    double[][] dat = new double[nI][nA];
    for (int j = 0; j < nI; j++) {
      for (int k = 0; k < nA; k++) {
        dat[j][k] = ins.instance(j).value(k);
      }
    }

    // Compute the probability of the bag
    double[] distribution = new double[2];
    distribution[1] = 0.0; // Prob. for class 1

    for (int i = 0; i < nI; i++) {
      double exp = 0.0;
      for (int r = 0; r < nA; r++) {
        exp += (m_Par[r * 2] - dat[i][r]) * (m_Par[r * 2] - dat[i][r])
          / ((m_Par[r * 2 + 1]) * (m_Par[r * 2 + 1]));
      }
      exp = Math.exp(-exp);

      // Prob. updated for one instance
      distribution[1] += exp / nI;
      distribution[0] += (1.0 - exp) / nI;
    }

    return distribution;
  }

  /**
   * Gets a string describing the classifier.
   * 
   * @return a string describing the classifer built.
   */
  @Override
  public String toString() {

    String result = "Modified Logistic Regression";
    if (m_Par == null) {
      return result + ": No model built yet.";
    }

    result += "\nCoefficients...\n" + "Variable      Coeff.\n";
    for (int j = 0, idx = 0; j < m_Par.length / 2; j++, idx++) {

      result += m_Attributes.attribute(idx).name();
      result += " " + Utils.doubleToString(m_Par[j * 2], 12, 4);
      result += " " + Utils.doubleToString(m_Par[j * 2 + 1], 12, 4) + "\n";
    }

    return result;
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 10369 $");
  }

  /**
   * Main method for testing this class.
   * 
   * @param argv should contain the command line arguments to the scheme (see
   *          Evaluation)
   */
  public static void main(String[] argv) {
    runClassifier(new MDD(), argv);
  }
}