/*
* 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.
*/
/*
* CostSensitiveClassifier.java
* Copyright (C) 2002 University of Waikato, Hamilton, New Zealand
*
*/
package weka.classifiers.meta;
import weka.classifiers.Classifier;
import weka.classifiers.CostMatrix;
import weka.classifiers.RandomizableSingleClassifierEnhancer;
import weka.core.Capabilities;
import weka.core.Drawable;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.SelectedTag;
import weka.core.Tag;
import weka.core.Utils;
import weka.core.WeightedInstancesHandler;
import weka.core.Capabilities.Capability;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.StringReader;
import java.io.StringWriter;
import java.util.Enumeration;
import java.util.Random;
import java.util.Vector;
/**
<!-- globalinfo-start -->
* A metaclassifier that makes its base classifier cost-sensitive. Two methods can be used to introduce cost-sensitivity: reweighting training instances according to the total cost assigned to each class; or predicting the class with minimum expected misclassification cost (rather than the most likely class). Performance can often be improved by using a Bagged classifier to improve the probability estimates of the base classifier.
* <p/>
<!-- globalinfo-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -M
* Minimize expected misclassification cost. Default is to
* reweight training instances according to costs per class</pre>
*
* <pre> -C <cost file name>
* File name of a cost matrix to use. If this is not supplied,
* a cost matrix will be loaded on demand. The name of the
* on-demand file is the relation name of the training data
* plus ".cost", and the path to the on-demand file is
* specified with the -N option.</pre>
*
* <pre> -N <directory>
* Name of a directory to search for cost files when loading
* costs on demand (default current directory).</pre>
*
* <pre> -cost-matrix <matrix>
* The cost matrix in Matlab single line format.</pre>
*
* <pre> -S <num>
* 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.rules.ZeroR)</pre>
*
* <pre>
* Options specific to classifier weka.classifiers.rules.ZeroR:
* </pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
<!-- options-end -->
*
* Options after -- are passed to the designated classifier.<p>
*
* @author Len Trigg (len@reeltwo.com)
* @version $Revision: 1.29 $
*/
public class CostSensitiveClassifier
extends RandomizableSingleClassifierEnhancer
implements OptionHandler, Drawable {
/** for serialization */
static final long serialVersionUID = -720658209263002404L;
/** load cost matrix on demand */
public static final int MATRIX_ON_DEMAND = 1;
/** use explicit cost matrix */
public static final int MATRIX_SUPPLIED = 2;
/** Specify possible sources of the cost matrix */
public static final Tag [] TAGS_MATRIX_SOURCE = {
new Tag(MATRIX_ON_DEMAND, "Load cost matrix on demand"),
new Tag(MATRIX_SUPPLIED, "Use explicit cost matrix")
};
/** Indicates the current cost matrix source */
protected int m_MatrixSource = MATRIX_ON_DEMAND;
/**
* The directory used when loading cost files on demand, null indicates
* current directory
*/
protected File m_OnDemandDirectory = new File(System.getProperty("user.dir"));
/** The name of the cost file, for command line options */
protected String m_CostFile;
/** The cost matrix */
protected CostMatrix m_CostMatrix = new CostMatrix(1);
/**
* True if the costs should be used by selecting the minimum expected
* cost (false means weight training data by the costs)
*/
protected boolean m_MinimizeExpectedCost;
/**
* String describing default classifier.
*
* @return the default classifier classname
*/
protected String defaultClassifierString() {
return "weka.classifiers.rules.ZeroR";
}
/**
* Default constructor.
*/
public CostSensitiveClassifier() {
m_Classifier = new weka.classifiers.rules.ZeroR();
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector newVector = new Vector(5);
newVector.addElement(new Option(
"\tMinimize expected misclassification cost. Default is to\n"
+"\treweight training instances according to costs per class",
"M", 0, "-M"));
newVector.addElement(new Option(
"\tFile name of a cost matrix to use. If this is not supplied,\n"
+"\ta cost matrix will be loaded on demand. The name of the\n"
+"\ton-demand file is the relation name of the training data\n"
+"\tplus \".cost\", and the path to the on-demand file is\n"
+"\tspecified with the -N option.",
"C", 1, "-C <cost file name>"));
newVector.addElement(new Option(
"\tName of a directory to search for cost files when loading\n"
+"\tcosts on demand (default current directory).",
"N", 1, "-N <directory>"));
newVector.addElement(new Option(
"\tThe cost matrix in Matlab single line format.",
"cost-matrix", 1, "-cost-matrix <matrix>"));
Enumeration enu = super.listOptions();
while (enu.hasMoreElements()) {
newVector.addElement(enu.nextElement());
}
return newVector.elements();
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -M
* Minimize expected misclassification cost. Default is to
* reweight training instances according to costs per class</pre>
*
* <pre> -C <cost file name>
* File name of a cost matrix to use. If this is not supplied,
* a cost matrix will be loaded on demand. The name of the
* on-demand file is the relation name of the training data
* plus ".cost", and the path to the on-demand file is
* specified with the -N option.</pre>
*
* <pre> -N <directory>
* Name of a directory to search for cost files when loading
* costs on demand (default current directory).</pre>
*
* <pre> -cost-matrix <matrix>
* The cost matrix in Matlab single line format.</pre>
*
* <pre> -S <num>
* 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.rules.ZeroR)</pre>
*
* <pre>
* Options specific to classifier weka.classifiers.rules.ZeroR:
* </pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</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 {
setMinimizeExpectedCost(Utils.getFlag('M', options));
String costFile = Utils.getOption('C', options);
if (costFile.length() != 0) {
try {
setCostMatrix(new CostMatrix(new BufferedReader(
new FileReader(costFile))));
} catch (Exception ex) {
// now flag as possible old format cost matrix. Delay cost matrix
// loading until buildClassifer is called
setCostMatrix(null);
}
setCostMatrixSource(new SelectedTag(MATRIX_SUPPLIED,
TAGS_MATRIX_SOURCE));
m_CostFile = costFile;
} else {
setCostMatrixSource(new SelectedTag(MATRIX_ON_DEMAND,
TAGS_MATRIX_SOURCE));
}
String demandDir = Utils.getOption('N', options);
if (demandDir.length() != 0) {
setOnDemandDirectory(new File(demandDir));
}
String cost_matrix = Utils.getOption("cost-matrix", options);
if (cost_matrix.length() != 0) {
StringWriter writer = new StringWriter();
CostMatrix.parseMatlab(cost_matrix).write(writer);
setCostMatrix(new CostMatrix(new StringReader(writer.toString())));
setCostMatrixSource(new SelectedTag(MATRIX_SUPPLIED,
TAGS_MATRIX_SOURCE));
}
super.setOptions(options);
}
/**
* Gets the current settings of the Classifier.
*
* @return an array of strings suitable for passing to setOptions
*/
public String [] getOptions() {
String [] superOptions = super.getOptions();
String [] options = new String [superOptions.length + 7];
int current = 0;
if (m_MatrixSource == MATRIX_SUPPLIED) {
if (m_CostFile != null) {
options[current++] = "-C";
options[current++] = "" + m_CostFile;
}
else {
options[current++] = "-cost-matrix";
options[current++] = getCostMatrix().toMatlab();
}
} else {
options[current++] = "-N";
options[current++] = "" + getOnDemandDirectory();
}
if (getMinimizeExpectedCost()) {
options[current++] = "-M";
}
System.arraycopy(superOptions, 0, options, current,
superOptions.length);
while (current < options.length) {
if (options[current] == null) {
options[current] = "";
}
current++;
}
return options;
}
/**
* @return a description of the classifier suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return "A metaclassifier that makes its base classifier cost-sensitive. "
+ "Two methods can be used to introduce cost-sensitivity: reweighting "
+ "training instances according to the total cost assigned to each "
+ "class; or predicting the class with minimum expected "
+ "misclassification cost (rather than the most likely class). "
+ "Performance can often be "
+ "improved by using a Bagged classifier to improve the probability "
+ "estimates of the base classifier.";
}
/**
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String costMatrixSourceTipText() {
return "Sets where to get the cost matrix. The two options are"
+ "to use the supplied explicit cost matrix (the setting of the "
+ "costMatrix property), or to load a cost matrix from a file when "
+ "required (this file will be loaded from the directory set by the "
+ "onDemandDirectory property and will be named relation_name"
+ CostMatrix.FILE_EXTENSION + ").";
}
/**
* Gets the source location method of the cost matrix. Will be one of
* MATRIX_ON_DEMAND or MATRIX_SUPPLIED.
*
* @return the cost matrix source.
*/
public SelectedTag getCostMatrixSource() {
return new SelectedTag(m_MatrixSource, TAGS_MATRIX_SOURCE);
}
/**
* Sets the source location of the cost matrix. Values other than
* MATRIX_ON_DEMAND or MATRIX_SUPPLIED will be ignored.
*
* @param newMethod the cost matrix location method.
*/
public void setCostMatrixSource(SelectedTag newMethod) {
if (newMethod.getTags() == TAGS_MATRIX_SOURCE) {
m_MatrixSource = newMethod.getSelectedTag().getID();
}
}
/**
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String onDemandDirectoryTipText() {
return "Sets the directory where cost files are loaded from. This option "
+ "is used when the costMatrixSource is set to \"On Demand\".";
}
/**
* Returns the directory that will be searched for cost files when
* loading on demand.
*
* @return The cost file search directory.
*/
public File getOnDemandDirectory() {
return m_OnDemandDirectory;
}
/**
* Sets the directory that will be searched for cost files when
* loading on demand.
*
* @param newDir The cost file search directory.
*/
public void setOnDemandDirectory(File newDir) {
if (newDir.isDirectory()) {
m_OnDemandDirectory = newDir;
} else {
m_OnDemandDirectory = new File(newDir.getParent());
}
m_MatrixSource = MATRIX_ON_DEMAND;
}
/**
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String minimizeExpectedCostTipText() {
return "Sets whether the minimum expected cost criteria will be used. If "
+ "this is false, the training data will be reweighted according to the "
+ "costs assigned to each class. If true, the minimum expected cost "
+ "criteria will be used.";
}
/**
* Gets the value of MinimizeExpectedCost.
*
* @return Value of MinimizeExpectedCost.
*/
public boolean getMinimizeExpectedCost() {
return m_MinimizeExpectedCost;
}
/**
* Set the value of MinimizeExpectedCost.
*
* @param newMinimizeExpectedCost Value to assign to MinimizeExpectedCost.
*/
public void setMinimizeExpectedCost(boolean newMinimizeExpectedCost) {
m_MinimizeExpectedCost = newMinimizeExpectedCost;
}
/**
* Gets the classifier specification string, which contains the class name of
* the classifier and any options to the classifier
*
* @return the classifier string.
*/
protected String getClassifierSpec() {
Classifier c = getClassifier();
if (c instanceof OptionHandler) {
return c.getClass().getName() + " "
+ Utils.joinOptions(((OptionHandler)c).getOptions());
}
return c.getClass().getName();
}
/**
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String costMatrixTipText() {
return "Sets the cost matrix explicitly. This matrix is used if the "
+ "costMatrixSource property is set to \"Supplied\".";
}
/**
* Gets the misclassification cost matrix.
*
* @return the cost matrix
*/
public CostMatrix getCostMatrix() {
return m_CostMatrix;
}
/**
* Sets the misclassification cost matrix.
*
* @param newCostMatrix the cost matrix
*/
public void setCostMatrix(CostMatrix newCostMatrix) {
m_CostMatrix = newCostMatrix;
m_MatrixSource = MATRIX_SUPPLIED;
}
/**
* Returns default capabilities of the classifier.
*
* @return the capabilities of this classifier
*/
public Capabilities getCapabilities() {
Capabilities result = super.getCapabilities();
// class
result.disableAllClasses();
result.disableAllClassDependencies();
result.enable(Capability.NOMINAL_CLASS);
return result;
}
/**
* Builds the model of the base learner.
*
* @param data the training data
* @throws Exception if the classifier could not be built successfully
*/
public void buildClassifier(Instances data) throws Exception {
// can classifier handle the data?
getCapabilities().testWithFail(data);
// remove instances with missing class
data = new Instances(data);
data.deleteWithMissingClass();
if (m_Classifier == null) {
throw new Exception("No base classifier has been set!");
}
if (m_MatrixSource == MATRIX_ON_DEMAND) {
String costName = data.relationName() + CostMatrix.FILE_EXTENSION;
File costFile = new File(getOnDemandDirectory(), costName);
if (!costFile.exists()) {
throw new Exception("On-demand cost file doesn't exist: " + costFile);
}
setCostMatrix(new CostMatrix(new BufferedReader(
new FileReader(costFile))));
} else if (m_CostMatrix == null) {
// try loading an old format cost file
m_CostMatrix = new CostMatrix(data.numClasses());
m_CostMatrix.readOldFormat(new BufferedReader(
new FileReader(m_CostFile)));
}
if (!m_MinimizeExpectedCost) {
Random random = null;
if (!(m_Classifier instanceof WeightedInstancesHandler)) {
random = new Random(m_Seed);
}
data = m_CostMatrix.applyCostMatrix(data, random);
}
m_Classifier.buildClassifier(data);
}
/**
* Returns class probabilities. When minimum expected cost approach is chosen,
* returns probability one for class with the minimum expected misclassification
* cost. Otherwise it returns the probability distribution returned by
* the base classifier.
*
* @param instance the instance to be classified
* @return the computed distribution for the given instance
* @throws Exception if instance could not be classified
* successfully */
public double[] distributionForInstance(Instance instance) throws Exception {
if (!m_MinimizeExpectedCost) {
return m_Classifier.distributionForInstance(instance);
}
double [] pred = m_Classifier.distributionForInstance(instance);
double [] costs = m_CostMatrix.expectedCosts(pred, instance);
/*
for (int i = 0; i < pred.length; i++) {
System.out.print(pred[i] + " ");
}
System.out.println();
for (int i = 0; i < costs.length; i++) {
System.out.print(costs[i] + " ");
}
System.out.println("\n");
*/
// This is probably not ideal
int classIndex = Utils.minIndex(costs);
for (int i = 0; i < pred.length; i++) {
if (i == classIndex) {
pred[i] = 1.0;
} else {
pred[i] = 0.0;
}
}
return pred;
}
/**
* Returns the type of graph this classifier
* represents.
*
* @return the type of graph this classifier represents
*/
public int graphType() {
if (m_Classifier instanceof Drawable)
return ((Drawable)m_Classifier).graphType();
else
return Drawable.NOT_DRAWABLE;
}
/**
* Returns graph describing the classifier (if possible).
*
* @return the graph of the classifier in dotty format
* @throws Exception if the classifier cannot be graphed
*/
public String graph() throws Exception {
if (m_Classifier instanceof Drawable)
return ((Drawable)m_Classifier).graph();
else throw new Exception("Classifier: " + getClassifierSpec()
+ " cannot be graphed");
}
/**
* Output a representation of this classifier
*
* @return a string representation of the classifier
*/
public String toString() {
if (m_Classifier == null) {
return "CostSensitiveClassifier: No model built yet.";
}
String result = "CostSensitiveClassifier using ";
if (m_MinimizeExpectedCost) {
result += "minimized expected misclasification cost\n";
} else {
result += "reweighted training instances\n";
}
result += "\n" + getClassifierSpec()
+ "\n\nClassifier Model\n"
+ m_Classifier.toString()
+ "\n\nCost Matrix\n"
+ m_CostMatrix.toString();
return result;
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.29 $");
}
/**
* Main method for testing this class.
*
* @param argv should contain the following arguments:
* -t training file [-T test file] [-c class index]
*/
public static void main(String [] argv) {
runClassifier(new CostSensitiveClassifier(), argv);
}
}