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weka.classifiers.functions.supportVector.RBFKernel 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 .
 */

/*
 *    RBFKernel.java
 *    Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
 *    Copyright (C) 2005 J. Lindgren
 *
 */

package weka.classifiers.functions.supportVector;

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

import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.RevisionUtils;
import weka.core.Utils;

/**
 *  The RBF kernel. K(x, y) = e^-(gamma * <x-y,
 * x-y>^2)
 * 

 * 
 * 
 *  Valid options are:
 * 

 * 
 * 
 * -D
 *  Enables debugging output (if available) to be printed.
 *  (default: off)
 * 
 * 
 * 
 * -no-checks
 *  Turns off all checks - use with caution!
 *  (default: checks on)
 * 
 * 
 * 
 * -C <num>
 *  The size of the cache (a prime number), 0 for full cache and 
 *  -1 to turn it off.
 *  (default: 250007)
 * 
 * 
 * 
 * -G <num>
 *  The Gamma parameter.
 *  (default: 0.01)
 * 
 * 
 * 
 * 
 * @author Eibe Frank ([email protected])
 * @author Shane Legg ([email protected]) (sparse vector code)
 * @author Stuart Inglis ([email protected]) (sparse vector code)
 * @author J. Lindgren (jtlindgr{at}cs.helsinki.fi) (RBF kernel)
 * @version $Revision: 10169 $
 */
public class RBFKernel extends CachedKernel {

  /** for serialization */
  static final long serialVersionUID = 5247117544316387852L;

  /** The precalculated dotproducts of <inst_i,inst_i> */
  protected double m_kernelPrecalc[];

  /** Gamma for the RBF kernel. */
  protected double m_gamma = 0.01;

  /**
   * default constructor - does nothing.
   */
  public RBFKernel() {
    super();
  }

  /**
   * Constructor. Initializes m_kernelPrecalc[].
   * 
   * @param data the data to use
   * @param cacheSize the size of the cache
   * @param gamma the bandwidth
   * @throws Exception if something goes wrong
   */
  public RBFKernel(Instances data, int cacheSize, double gamma) throws Exception {

    super();

    setCacheSize(cacheSize);
    setGamma(gamma);

    buildKernel(data);
  }

  /**
   * Returns a string describing the kernel
   * 
   * @return a description suitable for displaying in the explorer/experimenter
   *         gui
   */
  @Override
  public String globalInfo() {
    return "The RBF kernel. K(x, y) = e^-(gamma * ^2)";
  }

  /**
   * 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("\tThe Gamma parameter.\n"
      + "\t(default: 0.01)", "G", 1, "-G "));

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

    return result.elements();
  }

  /**
   * Parses a given list of options.
   * 

   * 
   *  Valid options are:
   * 

   * 
   * 
   * -D
   *  Enables debugging output (if available) to be printed.
   *  (default: off)
   * 
   * 
   * 
   * -no-checks
   *  Turns off all checks - use with caution!
   *  (default: checks on)
   * 
   * 
   * 
   * -C <num>
   *  The size of the cache (a prime number), 0 for full cache and 
   *  -1 to turn it off.
   *  (default: 250007)
   * 
   * 
   * 
   * -G <num>
   *  The Gamma parameter.
   *  (default: 0.01)
   * 
   * 
   * 
   * 
   * @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 {
    String tmpStr;

    tmpStr = Utils.getOption('G', options);
    if (tmpStr.length() != 0) {
      setGamma(Double.parseDouble(tmpStr));
    } else {
      setGamma(0.01);
    }

    super.setOptions(options);
  }

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

    Vector result = new Vector();

    result.add("-G");
    result.add("" + getGamma());

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

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

  /**
   * 
   * @param id1 the index of instance 1
   * @param id2 the index of instance 2
   * @param inst1 the instance 1 object
   * @return the dot product
   * @throws Exception if something goes wrong
   */
  @Override
  protected double evaluate(int id1, int id2, Instance inst1) throws Exception {

    if (id1 == id2) {
      return 1.0;
    } else {
      double precalc1;
      if (id1 == -1) {
        precalc1 = dotProd(inst1, inst1);
      } else {
        precalc1 = m_kernelPrecalc[id1];
      }
      Instance inst2 = m_data.instance(id2);
      double result = Math.exp(m_gamma
        * (2. * dotProd(inst1, inst2) - precalc1 - m_kernelPrecalc[id2]));

      return result;
    }
  }

  /**
   * Sets the gamma value.
   * 
   * @param value the gamma value
   */
  public void setGamma(double value) {
    m_gamma = value;
  }

  /**
   * Gets the gamma value.
   * 
   * @return the gamma value
   */
  public double getGamma() {
    return m_gamma;
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String gammaTipText() {
    return "The Gamma value.";
  }

  /**
   * initializes variables etc.
   * 
   * @param data the data to use
   */
  @Override
  protected void initVars(Instances data) {
    super.initVars(data);

    m_kernelPrecalc = new double[data.numInstances()];
  }

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

    result.enable(Capability.NUMERIC_ATTRIBUTES);
    result.enableAllClasses();
    result.enable(Capability.MISSING_CLASS_VALUES);

    return result;
  }

  /**
   * builds the kernel with the given data. Initializes the kernel cache. The
   * actual size of the cache in bytes is (64 * cacheSize).
   * 
   * @param data the data to base the kernel on
   * @throws Exception if something goes wrong
   */
  @Override
  public void buildKernel(Instances data) throws Exception {
    // does kernel handle the data?
    if (!getChecksTurnedOff()) {
      getCapabilities().testWithFail(data);
    }

    initVars(data);

    for (int i = 0; i < data.numInstances(); i++) {
      m_kernelPrecalc[i] = dotProd(data.instance(i), data.instance(i));
    }
  }

  /**
   * returns a string representation for the Kernel
   * 
   * @return a string representaiton of the kernel
   */
  @Override
  public String toString() {
    return "RBF kernel: K(x,y) = e^-(" + getGamma() + "* ^2)";
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 10169 $");
  }
}