source: branches/MetisMQI/src/main/java/weka/classifiers/meta/Dagging.java @ 38

/*
 *    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 2 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, write to the Free Software
 *    Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

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

package weka.classifiers.meta;

import weka.classifiers.Classifier;
import weka.classifiers.AbstractClassifier;
import weka.classifiers.RandomizableSingleClassifierEnhancer;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.RevisionUtils;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;

import java.util.Enumeration;
import java.util.Vector;

/**
 <!-- globalinfo-start -->
 * This meta classifier creates a number of disjoint, stratified folds out of the data and feeds each chunk of data to a copy of the supplied base classifier. Predictions are made via majority vote, since all the generated base classifiers are put into the Vote meta classifier. <br/>
 * Useful for base classifiers that are quadratic or worse in time behavior, regarding number of instances in the training data. <br/>
 * <br/>
 * For more information, see: <br/>
 * Ting, K. M., Witten, I. H.: Stacking Bagged and Dagged Models. In: Fourteenth international Conference on Machine Learning, San Francisco, CA, 367-375, 1997.
 * <p/>
 <!-- globalinfo-end -->
 * 
 <!-- technical-bibtex-start -->
 * BibTeX:
 * <pre>
 * &#64;inproceedings{Ting1997,
 *    address = {San Francisco, CA},
 *    author = {Ting, K. M. and Witten, I. H.},
 *    booktitle = {Fourteenth international Conference on Machine Learning},
 *    editor = {D. H. Fisher},
 *    pages = {367-375},
 *    publisher = {Morgan Kaufmann Publishers},
 *    title = {Stacking Bagged and Dagged Models},
 *    year = {1997}
 * }
 * </pre>
 * <p/>
 <!-- technical-bibtex-end -->
 *
 <!-- options-start -->
 * Valid options are: <p/>
 * 
 * <pre> -F &lt;folds&gt;
 *  The number of folds for splitting the training set into
 *  smaller chunks for the base classifier.
 *  (default 10)</pre>
 * 
 * <pre> -verbose
 *  Whether to print some more information during building the
 *  classifier.
 *  (default is off)</pre>
 * 
 * <pre> -S &lt;num&gt;
 *  Random number seed.
 *  (default 1)</pre>
 * 
 * <pre> -D
 *  If set, classifier is run in debug mode and
 *  may output additional info to the console</pre>
 * 
 * <pre> -W
 *  Full name of base classifier.
 *  (default: weka.classifiers.functions.SMO)</pre>
 * 
 * <pre> 
 * Options specific to classifier weka.classifiers.functions.SMO:
 * </pre>
 * 
 * <pre> -D
 *  If set, classifier is run in debug mode and
 *  may output additional info to the console</pre>
 * 
 * <pre> -no-checks
 *  Turns off all checks - use with caution!
 *  Turning them off assumes that data is purely numeric, doesn't
 *  contain any missing values, and has a nominal class. Turning them
 *  off also means that no header information will be stored if the
 *  machine is linear. Finally, it also assumes that no instance has
 *  a weight equal to 0.
 *  (default: checks on)</pre>
 * 
 * <pre> -C &lt;double&gt;
 *  The complexity constant C. (default 1)</pre>
 * 
 * <pre> -N
 *  Whether to 0=normalize/1=standardize/2=neither. (default 0=normalize)</pre>
 * 
 * <pre> -L &lt;double&gt;
 *  The tolerance parameter. (default 1.0e-3)</pre>
 * 
 * <pre> -P &lt;double&gt;
 *  The epsilon for round-off error. (default 1.0e-12)</pre>
 * 
 * <pre> -M
 *  Fit logistic models to SVM outputs. </pre>
 * 
 * <pre> -V &lt;double&gt;
 *  The number of folds for the internal
 *  cross-validation. (default -1, use training data)</pre>
 * 
 * <pre> -W &lt;double&gt;
 *  The random number seed. (default 1)</pre>
 * 
 * <pre> -K &lt;classname and parameters&gt;
 *  The Kernel to use.
 *  (default: weka.classifiers.functions.supportVector.PolyKernel)</pre>
 * 
 * <pre> 
 * Options specific to kernel weka.classifiers.functions.supportVector.PolyKernel:
 * </pre>
 * 
 * <pre> -D
 *  Enables debugging output (if available) to be printed.
 *  (default: off)</pre>
 * 
 * <pre> -no-checks
 *  Turns off all checks - use with caution!
 *  (default: checks on)</pre>
 * 
 * <pre> -C &lt;num&gt;
 *  The size of the cache (a prime number), 0 for full cache and 
 *  -1 to turn it off.
 *  (default: 250007)</pre>
 * 
 * <pre> -E &lt;num&gt;
 *  The Exponent to use.
 *  (default: 1.0)</pre>
 * 
 * <pre> -L
 *  Use lower-order terms.
 *  (default: no)</pre>
 * 
 <!-- options-end -->
 *
 * Options after -- are passed to the designated classifier.<p/>
 *
 * @author Bernhard Pfahringer (bernhard at cs dot waikato dot ac dot nz)
 * @author FracPete (fracpete at waikato dot ac dot nz)
 * @version $Revision: 5928 $
 * @see       Vote
 */
public class Dagging
  extends RandomizableSingleClassifierEnhancer
  implements TechnicalInformationHandler {
  
  /** for serialization */
  static final long serialVersionUID = 4560165876570074309L;

  /** the number of folds to use to split the training data */
  protected int m_NumFolds = 10;

  /** the classifier used for voting */
  protected Vote m_Vote = null;

  /** whether to output some progress information during building */
  protected boolean m_Verbose = false;
    
  /**
   * Returns a string describing classifier
   * @return a description suitable for
   * displaying in the explorer/experimenter gui
   */
  public String globalInfo() {
    return 
     "This meta classifier creates a number of disjoint, stratified folds out "
     + "of the data and feeds each chunk of data to a copy of the supplied "
     + "base classifier. Predictions are made via averaging, since all the "
     + "generated base classifiers are put into the Vote meta classifier. \n"
     + "Useful for base classifiers that are quadratic or worse in time "
     + "behavior, regarding number of instances in the training data. \n"
     + "\n"
     + "For more information, see: \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
   */
  public TechnicalInformation getTechnicalInformation() {
    TechnicalInformation        result;
    
    result = new TechnicalInformation(Type.INPROCEEDINGS);
    result.setValue(Field.AUTHOR, "Ting, K. M. and Witten, I. H.");
    result.setValue(Field.TITLE, "Stacking Bagged and Dagged Models");
    result.setValue(Field.BOOKTITLE, "Fourteenth international Conference on Machine Learning");
    result.setValue(Field.EDITOR, "D. H. Fisher");
    result.setValue(Field.YEAR, "1997");
    result.setValue(Field.PAGES, "367-375");
    result.setValue(Field.PUBLISHER, "Morgan Kaufmann Publishers");
    result.setValue(Field.ADDRESS, "San Francisco, CA");
    
    return result;
  }
    
  /**
   * Constructor.
   */
  public Dagging() {
    m_Classifier = new weka.classifiers.functions.SMO();
  }

  /**
   * String describing default classifier.
   * 
   * @return the default classifier classname
   */
  protected String defaultClassifierString() {
    return weka.classifiers.functions.SMO.class.getName();
  }

  /**
   * Returns an enumeration describing the available options.
   *
   * @return an enumeration of all the available options.
   */
  public Enumeration listOptions() {
    Vector result = new Vector();
    
    result.addElement(new Option(
        "\tThe number of folds for splitting the training set into\n"
        + "\tsmaller chunks for the base classifier.\n"
        + "\t(default 10)",
        "F", 1, "-F <folds>"));
    
    result.addElement(new Option(
        "\tWhether to print some more information during building the\n"
        + "\tclassifier.\n"
        + "\t(default is off)",
        "verbose", 0, "-verbose"));
    
    Enumeration en = super.listOptions();
    while (en.hasMoreElements())
      result.addElement(en.nextElement());
      
    return result.elements();
  }


  /**
   * Parses a given list of options. <p/>
   *
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <pre> -F &lt;folds&gt;
   *  The number of folds for splitting the training set into
   *  smaller chunks for the base classifier.
   *  (default 10)</pre>
   * 
   * <pre> -verbose
   *  Whether to print some more information during building the
   *  classifier.
   *  (default is off)</pre>
   * 
   * <pre> -S &lt;num&gt;
   *  Random number seed.
   *  (default 1)</pre>
   * 
   * <pre> -D
   *  If set, classifier is run in debug mode and
   *  may output additional info to the console</pre>
   * 
   * <pre> -W
   *  Full name of base classifier.
   *  (default: weka.classifiers.functions.SMO)</pre>
   * 
   * <pre> 
   * Options specific to classifier weka.classifiers.functions.SMO:
   * </pre>
   * 
   * <pre> -D
   *  If set, classifier is run in debug mode and
   *  may output additional info to the console</pre>
   * 
   * <pre> -no-checks
   *  Turns off all checks - use with caution!
   *  Turning them off assumes that data is purely numeric, doesn't
   *  contain any missing values, and has a nominal class. Turning them
   *  off also means that no header information will be stored if the
   *  machine is linear. Finally, it also assumes that no instance has
   *  a weight equal to 0.
   *  (default: checks on)</pre>
   * 
   * <pre> -C &lt;double&gt;
   *  The complexity constant C. (default 1)</pre>
   * 
   * <pre> -N
   *  Whether to 0=normalize/1=standardize/2=neither. (default 0=normalize)</pre>
   * 
   * <pre> -L &lt;double&gt;
   *  The tolerance parameter. (default 1.0e-3)</pre>
   * 
   * <pre> -P &lt;double&gt;
   *  The epsilon for round-off error. (default 1.0e-12)</pre>
   * 
   * <pre> -M
   *  Fit logistic models to SVM outputs. </pre>
   * 
   * <pre> -V &lt;double&gt;
   *  The number of folds for the internal
   *  cross-validation. (default -1, use training data)</pre>
   * 
   * <pre> -W &lt;double&gt;
   *  The random number seed. (default 1)</pre>
   * 
   * <pre> -K &lt;classname and parameters&gt;
   *  The Kernel to use.
   *  (default: weka.classifiers.functions.supportVector.PolyKernel)</pre>
   * 
   * <pre> 
   * Options specific to kernel weka.classifiers.functions.supportVector.PolyKernel:
   * </pre>
   * 
   * <pre> -D
   *  Enables debugging output (if available) to be printed.
   *  (default: off)</pre>
   * 
   * <pre> -no-checks
   *  Turns off all checks - use with caution!
   *  (default: checks on)</pre>
   * 
   * <pre> -C &lt;num&gt;
   *  The size of the cache (a prime number), 0 for full cache and 
   *  -1 to turn it off.
   *  (default: 250007)</pre>
   * 
   * <pre> -E &lt;num&gt;
   *  The Exponent to use.
   *  (default: 1.0)</pre>
   * 
   * <pre> -L
   *  Use lower-order terms.
   *  (default: no)</pre>
   * 
   <!-- options-end -->
   *
   * Options after -- are passed to the designated classifier.<p>
   *
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
  public void setOptions(String[] options) throws Exception {
    String        tmpStr;

    tmpStr = Utils.getOption('F', options);
    if (tmpStr.length() != 0)
      setNumFolds(Integer.parseInt(tmpStr));
    else
      setNumFolds(10);
    
    setVerbose(Utils.getFlag("verbose", options));
    
    super.setOptions(options);
  }

  /**
   * Gets the current settings of the Classifier.
   *
   * @return an array of strings suitable for passing to setOptions
   */
  public String[] getOptions() {
    Vector        result;
    String[]      options;
    int           i;
    
    result  = new Vector();

    result.add("-F");
    result.add("" + getNumFolds());
    
    if (getVerbose())
      result.add("-verbose");
    
    options = super.getOptions();
    for (i = 0; i < options.length; i++)
      result.add(options[i]);
    
    return (String[]) result.toArray(new String[result.size()]);
  }

  /**
   * Gets the number of folds to use for splitting the training set.
   *
   * @return the number of folds
   */
  public int getNumFolds() {
    return m_NumFolds;
  }
  
  /**
   * Sets the number of folds to use for splitting the training set.
   *
   * @param value     the new number of folds
   */
  public void setNumFolds(int value) {
    if (value > 0)
      m_NumFolds = value;
    else
      System.out.println(
          "At least 1 fold is necessary (provided: " + value + ")!");
  }

  /**
   * Returns the tip text for this property
   *
   * @return tip text for this property suitable for
   *         displaying in the explorer/experimenter gui
   */
  public String numFoldsTipText() {
    return "The number of folds to use for splitting the training set into smaller chunks for the base classifier.";
  }
  
  /**
   * Set the verbose state.
   *
   * @param value the verbose state
   */
  public void setVerbose(boolean value) {
    m_Verbose = value;
  }
  
  /**
   * Gets the verbose state
   *
   * @return the verbose state
   */
  public boolean getVerbose() {
    return m_Verbose;
  }
  
  /**
   * Returns the tip text for this property
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
  public String verboseTipText() {
    return "Whether to ouput some additional information during building.";
  }

  /**
   * Bagging method.
   *
   * @param data the training data to be used for generating the
   * bagged classifier.
   * @throws Exception if the classifier could not be built successfully
   */
  public void buildClassifier(Instances data) throws Exception {
    Classifier[]        base;
    int                 i;
    int                 n;
    int                 fromIndex;
    int                 toIndex;
    Instances           train;
    double              chunkSize;
    
    // can classifier handle the data?
    getCapabilities().testWithFail(data);

    // remove instances with missing class
    data = new Instances(data);
    data.deleteWithMissingClass();
    
    m_Vote    = new Vote();
    base      = new Classifier[getNumFolds()];
    chunkSize = (double) data.numInstances() / (double) getNumFolds();
    
    // stratify data
    if (getNumFolds() > 1) {
      data.randomize(data.getRandomNumberGenerator(getSeed()));
      data.stratify(getNumFolds());
    }

    // generate <folds> classifiers
    for (i = 0; i < getNumFolds(); i++) {
      base[i] = makeCopy(getClassifier());

      // generate training data
      if (getNumFolds() > 1) {
        // some progress information
        if (getVerbose())
          System.out.print(".");
        
        train     = data.testCV(getNumFolds(), i);
      }
      else {
        train = data;
      }

      // train classifier
      base[i].buildClassifier(train);
    }
    
    // init vote
    m_Vote.setClassifiers(base);
    
    if (getVerbose())
      System.out.println();
  }

  /**
   * Calculates the class membership probabilities for the given test
   * instance.
   *
   * @param instance the instance to be classified
   * @return preedicted class probability distribution
   * @throws Exception if distribution can't be computed successfully 
   */
  public double[] distributionForInstance(Instance instance) throws Exception {
    return m_Vote.distributionForInstance(instance);
  }

  /**
   * Returns description of the classifier.
   *
   * @return description of the classifier as a string
   */
  public String toString() {
    if (m_Vote == null)
      return this.getClass().getName().replaceAll(".*\\.", "") 
             + ": No model built yet.";
    else
      return m_Vote.toString();
  }
  
  /**
   * Returns the revision string.
   * 
   * @return            the revision
   */
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 5928 $");
  }

  /**
   * Main method for testing this class.
   *
   * @param args the options
   */
  public static void main(String[] args) {
    runClassifier(new Dagging(), args);
  }
}