/*
* 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 <http://www.gnu.org/licenses/>.
*/
/*
* Stacking.java
* Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
*
*/
package weka.classifiers.meta;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Random;
import java.util.Vector;
import weka.classifiers.AbstractClassifier;
import weka.classifiers.Classifier;
import weka.classifiers.RandomizableParallelMultipleClassifiersCombiner;
import weka.classifiers.rules.ZeroR;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.DenseInstance;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
/**
<!-- globalinfo-start -->
* Combines several classifiers using the stacking method. Can do classification or regression.<br/>
* <br/>
* For more information, see<br/>
* <br/>
* David H. Wolpert (1992). Stacked generalization. Neural Networks. 5:241-259.
* <p/>
<!-- globalinfo-end -->
*
<!-- technical-bibtex-start -->
* BibTeX:
* <pre>
* @article{Wolpert1992,
* author = {David H. Wolpert},
* journal = {Neural Networks},
* pages = {241-259},
* publisher = {Pergamon Press},
* title = {Stacked generalization},
* volume = {5},
* year = {1992}
* }
* </pre>
* <p/>
<!-- technical-bibtex-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -M <scheme specification>
* Full name of meta classifier, followed by options.
* (default: "weka.classifiers.rules.Zero")</pre>
*
* <pre> -X <number of folds>
* Sets the number of cross-validation folds.</pre>
*
* <pre> -S <num>
* Random number seed.
* (default 1)</pre>
*
* <pre> -B <classifier specification>
* Full class name of classifier to include, followed
* by scheme options. May be specified multiple times.
* (default: "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 -->
*
* @author Eibe Frank (eibe@cs.waikato.ac.nz)
* @version $Revision: 8034 $
*/
public class Stacking
extends RandomizableParallelMultipleClassifiersCombiner
implements TechnicalInformationHandler {
/** for serialization */
static final long serialVersionUID = 5134738557155845452L;
/** The meta classifier */
protected Classifier m_MetaClassifier = new ZeroR();
/** Format for meta data */
protected Instances m_MetaFormat = null;
/** Format for base data */
protected Instances m_BaseFormat = null;
/** Set the number of folds for the cross-validation */
protected int m_NumFolds = 10;
/**
* Returns a string describing classifier
* @return a description suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return "Combines several classifiers using the stacking method. "
+ "Can do classification or regression.\n\n"
+ "For more information, see\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
*/
public TechnicalInformation getTechnicalInformation() {
TechnicalInformation result;
result = new TechnicalInformation(Type.ARTICLE);
result.setValue(Field.AUTHOR, "David H. Wolpert");
result.setValue(Field.YEAR, "1992");
result.setValue(Field.TITLE, "Stacked generalization");
result.setValue(Field.JOURNAL, "Neural Networks");
result.setValue(Field.VOLUME, "5");
result.setValue(Field.PAGES, "241-259");
result.setValue(Field.PUBLISHER, "Pergamon Press");
return result;
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector newVector = new Vector(2);
newVector.addElement(new Option(
metaOption(),
"M", 0, "-M <scheme specification>"));
newVector.addElement(new Option(
"\tSets the number of cross-validation folds.",
"X", 1, "-X <number of folds>"));
Enumeration enu = super.listOptions();
while (enu.hasMoreElements()) {
newVector.addElement(enu.nextElement());
}
return newVector.elements();
}
/**
* String describing option for setting meta classifier
*
* @return the string describing the option
*/
protected String metaOption() {
return "\tFull name of meta classifier, followed by options.\n" +
"\t(default: \"weka.classifiers.rules.Zero\")";
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -M <scheme specification>
* Full name of meta classifier, followed by options.
* (default: "weka.classifiers.rules.Zero")</pre>
*
* <pre> -X <number of folds>
* Sets the number of cross-validation folds.</pre>
*
* <pre> -S <num>
* Random number seed.
* (default 1)</pre>
*
* <pre> -B <classifier specification>
* Full class name of classifier to include, followed
* by scheme options. May be specified multiple times.
* (default: "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 -->
*
* @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 numFoldsString = Utils.getOption('X', options);
if (numFoldsString.length() != 0) {
setNumFolds(Integer.parseInt(numFoldsString));
} else {
setNumFolds(10);
}
processMetaOptions(options);
super.setOptions(options);
}
/**
* Process options setting meta classifier.
*
* @param options the options to parse
* @throws Exception if the parsing fails
*/
protected void processMetaOptions(String[] options) throws Exception {
String classifierString = Utils.getOption('M', options);
String [] classifierSpec = Utils.splitOptions(classifierString);
String classifierName;
if (classifierSpec.length == 0) {
classifierName = "weka.classifiers.rules.ZeroR";
} else {
classifierName = classifierSpec[0];
classifierSpec[0] = "";
}
setMetaClassifier(AbstractClassifier.forName(classifierName, classifierSpec));
}
/**
* 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 + 4];
int current = 0;
options[current++] = "-X"; options[current++] = "" + getNumFolds();
options[current++] = "-M";
options[current++] = getMetaClassifier().getClass().getName() + " "
+ Utils.joinOptions(((OptionHandler)getMetaClassifier()).getOptions());
System.arraycopy(superOptions, 0, options, current,
superOptions.length);
return options;
}
/**
* 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 used for cross-validation.";
}
/**
* Gets the number of folds for the cross-validation.
*
* @return the number of folds for the cross-validation
*/
public int getNumFolds() {
return m_NumFolds;
}
/**
* Sets the number of folds for the cross-validation.
*
* @param numFolds the number of folds for the cross-validation
* @throws Exception if parameter illegal
*/
public void setNumFolds(int numFolds) throws Exception {
if (numFolds < 0) {
throw new IllegalArgumentException("Stacking: Number of cross-validation " +
"folds must be positive.");
}
m_NumFolds = numFolds;
}
/**
* Returns the tip text for this property
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String metaClassifierTipText() {
return "The meta classifiers to be used.";
}
/**
* Adds meta classifier
*
* @param classifier the classifier with all options set.
*/
public void setMetaClassifier(Classifier classifier) {
m_MetaClassifier = classifier;
}
/**
* Gets the meta classifier.
*
* @return the meta classifier
*/
public Classifier getMetaClassifier() {
return m_MetaClassifier;
}
/**
* Returns combined capabilities of the base classifiers, i.e., the
* capabilities all of them have in common.
*
* @return the capabilities of the base classifiers
*/
public Capabilities getCapabilities() {
Capabilities result;
result = super.getCapabilities();
result.setMinimumNumberInstances(getNumFolds());
return result;
}
/**
* Buildclassifier selects a classifier from the set of classifiers
* by minimising error on the training data.
*
* @param data the training data to be used for generating the
* boosted classifier.
* @throws Exception if the classifier could not be built successfully
*/
public void buildClassifier(Instances data) throws Exception {
if (m_MetaClassifier == null) {
throw new IllegalArgumentException("No meta classifier has been set");
}
// can classifier handle the data?
getCapabilities().testWithFail(data);
// remove instances with missing class
Instances newData = new Instances(data);
m_BaseFormat = new Instances(data, 0);
newData.deleteWithMissingClass();
Random random = new Random(m_Seed);
newData.randomize(random);
if (newData.classAttribute().isNominal()) {
newData.stratify(m_NumFolds);
}
// Create meta level
generateMetaLevel(newData, random);
// restart the executor pool because at the end of processing
// a set of classifiers it gets shutdown to prevent the program
// executing as a server
super.buildClassifier(newData);
// Rebuild all the base classifiers on the full training data
buildClassifiers(newData);
}
/**
* Generates the meta data
*
* @param newData the data to work on
* @param random the random number generator to use for cross-validation
* @throws Exception if generation fails
*/
protected void generateMetaLevel(Instances newData, Random random)
throws Exception {
Instances metaData = metaFormat(newData);
m_MetaFormat = new Instances(metaData, 0);
for (int j = 0; j < m_NumFolds; j++) {
Instances train = newData.trainCV(m_NumFolds, j, random);
// start the executor pool (if necessary)
// has to be done after each set of classifiers as the
// executor pool gets shut down in order to prevent the
// program executing as a server (and not returning to
// the command prompt when run from the command line
super.buildClassifier(train);
// construct the actual classifiers
buildClassifiers(train);
// Classify test instances and add to meta data
Instances test = newData.testCV(m_NumFolds, j);
for (int i = 0; i < test.numInstances(); i++) {
metaData.add(metaInstance(test.instance(i)));
}
}
m_MetaClassifier.buildClassifier(metaData);
}
/**
* Returns class probabilities.
*
* @param instance the instance to be classified
* @return the distribution
* @throws Exception if instance could not be classified
* successfully
*/
public double[] distributionForInstance(Instance instance) throws Exception {
return m_MetaClassifier.distributionForInstance(metaInstance(instance));
}
/**
* Output a representation of this classifier
*
* @return a string representation of the classifier
*/
public String toString() {
if (m_Classifiers.length == 0) {
return "Stacking: No base schemes entered.";
}
if (m_MetaClassifier == null) {
return "Stacking: No meta scheme selected.";
}
if (m_MetaFormat == null) {
return "Stacking: No model built yet.";
}
String result = "Stacking\n\nBase classifiers\n\n";
for (int i = 0; i < m_Classifiers.length; i++) {
result += getClassifier(i).toString() +"\n\n";
}
result += "\n\nMeta classifier\n\n";
result += m_MetaClassifier.toString();
return result;
}
/**
* Makes the format for the level-1 data.
*
* @param instances the level-0 format
* @return the format for the meta data
* @throws Exception if the format generation fails
*/
protected Instances metaFormat(Instances instances) throws Exception {
ArrayList<Attribute> attributes = new ArrayList<Attribute>();
Instances metaFormat;
for (int k = 0; k < m_Classifiers.length; k++) {
Classifier classifier = (Classifier) getClassifier(k);
String name = classifier.getClass().getName() + "-" + (k+1);
if (m_BaseFormat.classAttribute().isNumeric()) {
attributes.add(new Attribute(name));
} else {
for (int j = 0; j < m_BaseFormat.classAttribute().numValues(); j++) {
attributes.add(
new Attribute(
name + ":" + m_BaseFormat.classAttribute().value(j)));
}
}
}
attributes.add((Attribute) m_BaseFormat.classAttribute().copy());
metaFormat = new Instances("Meta format", attributes, 0);
metaFormat.setClassIndex(metaFormat.numAttributes() - 1);
return metaFormat;
}
/**
* Makes a level-1 instance from the given instance.
*
* @param instance the instance to be transformed
* @return the level-1 instance
* @throws Exception if the instance generation fails
*/
protected Instance metaInstance(Instance instance) throws Exception {
double[] values = new double[m_MetaFormat.numAttributes()];
Instance metaInstance;
int i = 0;
for (int k = 0; k < m_Classifiers.length; k++) {
Classifier classifier = getClassifier(k);
if (m_BaseFormat.classAttribute().isNumeric()) {
values[i++] = classifier.classifyInstance(instance);
} else {
double[] dist = classifier.distributionForInstance(instance);
for (int j = 0; j < dist.length; j++) {
values[i++] = dist[j];
}
}
}
values[i] = instance.classValue();
metaInstance = new DenseInstance(1, values);
metaInstance.setDataset(m_MetaFormat);
return metaInstance;
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 8034 $");
}
/**
* 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 Stacking(), argv);
}
}