/*
* 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.
*/
/*
* WAODE.java
* Copyright 2006 Liangxiao Jiang
*/
package weka.classifiers.bayes;
import weka.classifiers.Classifier;
import weka.core.Capabilities;
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.Capabilities.Capability;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import java.util.Enumeration;
import java.util.Vector;
import weka.classifiers.AbstractClassifier;
/**
<!-- globalinfo-start -->
* WAODE contructs the model called Weightily Averaged One-Dependence Estimators.<br/>
* <br/>
* For more information, see<br/>
* <br/>
* L. Jiang, H. Zhang: Weightily Averaged One-Dependence Estimators. In: Proceedings of the 9th Biennial Pacific Rim International Conference on Artificial Intelligence, PRICAI 2006, 970-974, 2006.
* <p/>
<!-- globalinfo-end -->
*
<!-- technical-bibtex-start -->
* BibTeX:
* <pre>
* @inproceedings{Jiang2006,
* author = {L. Jiang and H. Zhang},
* booktitle = {Proceedings of the 9th Biennial Pacific Rim International Conference on Artificial Intelligence, PRICAI 2006},
* pages = {970-974},
* series = {LNAI},
* title = {Weightily Averaged One-Dependence Estimators},
* volume = {4099},
* year = {2006}
* }
* </pre>
* <p/>
<!-- technical-bibtex-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
* <pre> -I
* Whether to print some more internals.
* (default: no)</pre>
*
<!-- options-end -->
*
* @author Liangxiao Jiang (ljiang@cug.edu.cn)
* @author H. Zhang (hzhang@unb.ca)
* @version $Revision: 5516 $
*/
public class WAODE
extends AbstractClassifier implements TechnicalInformationHandler {
/** for serialization */
private static final long serialVersionUID = 2170978824284697882L;
/** The number of each class value occurs in the dataset */
private double[] m_ClassCounts;
/** The number of each attribute value occurs in the dataset */
private double[] m_AttCounts;
/** The number of two attributes values occurs in the dataset */
private double[][] m_AttAttCounts;
/** The number of class and two attributes values occurs in the dataset */
private double[][][] m_ClassAttAttCounts;
/** The number of values for each attribute in the dataset */
private int[] m_NumAttValues;
/** The number of values for all attributes in the dataset */
private int m_TotalAttValues;
/** The number of classes in the dataset */
private int m_NumClasses;
/** The number of attributes including class in the dataset */
private int m_NumAttributes;
/** The number of instances in the dataset */
private int m_NumInstances;
/** The index of the class attribute in the dataset */
private int m_ClassIndex;
/** The starting index of each attribute in the dataset */
private int[] m_StartAttIndex;
/** The array of mutual information between each attribute and class */
private double[] m_mutualInformation;
/** the header information of the training data */
private Instances m_Header = null;
/** whether to print more internals in the toString method
* @see #toString() */
private boolean m_Internals = false;
/** a ZeroR model in case no model can be built from the data */
private Classifier m_ZeroR;
/**
* Returns a string describing this classifier
*
* @return a description of the classifier suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return
"WAODE contructs the model called Weightily Averaged One-Dependence "
+ "Estimators.\n\n"
+ "For more information, see\n\n"
+ getTechnicalInformation().toString();
}
/**
* Gets an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector result = new Vector();
Enumeration enm = super.listOptions();
while (enm.hasMoreElements())
result.add(enm.nextElement());
result.addElement(new Option(
"\tWhether to print some more internals.\n"
+ "\t(default: no)",
"I", 0, "-I"));
return result.elements();
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
* <pre> -I
* Whether to print some more internals.
* (default: no)</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 {
super.setOptions(options);
setInternals(Utils.getFlag('I', options));
}
/**
* Gets the current settings of the filter.
*
* @return an array of strings suitable for passing to setOptions
*/
public String[] getOptions() {
Vector result;
String[] options;
int i;
result = new Vector();
options = super.getOptions();
for (i = 0; i < options.length; i++)
result.add(options[i]);
if (getInternals())
result.add("-I");
return (String[]) 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 internalsTipText() {
return "Prints more internals of the classifier.";
}
/**
* Sets whether internals about classifier are printed via toString().
*
* @param value if internals should be printed
* @see #toString()
*/
public void setInternals(boolean value) {
m_Internals = value;
}
/**
* Gets whether more internals of the classifier are printed.
*
* @return true if more internals are printed
*/
public boolean getInternals() {
return m_Internals;
}
/**
* 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, "L. Jiang and H. Zhang");
result.setValue(Field.TITLE, "Weightily Averaged One-Dependence Estimators");
result.setValue(Field.BOOKTITLE, "Proceedings of the 9th Biennial Pacific Rim International Conference on Artificial Intelligence, PRICAI 2006");
result.setValue(Field.YEAR, "2006");
result.setValue(Field.PAGES, "970-974");
result.setValue(Field.SERIES, "LNAI");
result.setValue(Field.VOLUME, "4099");
return result;
}
/**
* Returns default capabilities of the classifier.
*
* @return the capabilities of this classifier
*/
public Capabilities getCapabilities() {
Capabilities result = super.getCapabilities();
result.disableAll();
// attributes
result.enable(Capability.NOMINAL_ATTRIBUTES);
// class
result.enable(Capability.NOMINAL_CLASS);
return result;
}
/**
* Generates the classifier.
*
* @param instances set of instances serving as training data
* @throws Exception if the classifier has not been generated successfully
*/
public void buildClassifier(Instances instances) throws Exception {
// can classifier handle the data?
getCapabilities().testWithFail(instances);
// only class? -> build ZeroR model
if (instances.numAttributes() == 1) {
System.err.println(
"Cannot build model (only class attribute present in data!), "
+ "using ZeroR model instead!");
m_ZeroR = new weka.classifiers.rules.ZeroR();
m_ZeroR.buildClassifier(instances);
return;
}
else {
m_ZeroR = null;
}
// reset variable
m_NumClasses = instances.numClasses();
m_ClassIndex = instances.classIndex();
m_NumAttributes = instances.numAttributes();
m_NumInstances = instances.numInstances();
m_TotalAttValues = 0;
// allocate space for attribute reference arrays
m_StartAttIndex = new int[m_NumAttributes];
m_NumAttValues = new int[m_NumAttributes];
// set the starting index of each attribute and the number of values for
// each attribute and the total number of values for all attributes (not including class).
for (int i = 0; i < m_NumAttributes; i++) {
if (i != m_ClassIndex) {
m_StartAttIndex[i] = m_TotalAttValues;
m_NumAttValues[i] = instances.attribute(i).numValues();
m_TotalAttValues += m_NumAttValues[i];
}
else {
m_StartAttIndex[i] = -1;
m_NumAttValues[i] = m_NumClasses;
}
}
// allocate space for counts and frequencies
m_ClassCounts = new double[m_NumClasses];
m_AttCounts = new double[m_TotalAttValues];
m_AttAttCounts = new double[m_TotalAttValues][m_TotalAttValues];
m_ClassAttAttCounts = new double[m_NumClasses][m_TotalAttValues][m_TotalAttValues];
m_Header = new Instances(instances, 0);
// Calculate the counts
for (int k = 0; k < m_NumInstances; k++) {
int classVal=(int)instances.instance(k).classValue();
m_ClassCounts[classVal] ++;
int[] attIndex = new int[m_NumAttributes];
for (int i = 0; i < m_NumAttributes; i++) {
if (i == m_ClassIndex){
attIndex[i] = -1;
}
else{
attIndex[i] = m_StartAttIndex[i] + (int)instances.instance(k).value(i);
m_AttCounts[attIndex[i]]++;
}
}
for (int Att1 = 0; Att1 < m_NumAttributes; Att1++) {
if (attIndex[Att1] == -1) continue;
for (int Att2 = 0; Att2 < m_NumAttributes; Att2++) {
if ((attIndex[Att2] != -1)) {
m_AttAttCounts[attIndex[Att1]][attIndex[Att2]] ++;
m_ClassAttAttCounts[classVal][attIndex[Att1]][attIndex[Att2]] ++;
}
}
}
}
//compute mutual information between each attribute and class
m_mutualInformation=new double[m_NumAttributes];
for (int att=0;att<m_NumAttributes;att++){
if (att == m_ClassIndex) continue;
m_mutualInformation[att]=mutualInfo(att);
}
}
/**
* Computes mutual information between each attribute and class attribute.
*
* @param att is the attribute
* @return the conditional mutual information between son and parent given class
*/
private double mutualInfo(int att) {
double mutualInfo=0;
int attIndex=m_StartAttIndex[att];
double[] PriorsClass = new double[m_NumClasses];
double[] PriorsAttribute = new double[m_NumAttValues[att]];
double[][] PriorsClassAttribute=new double[m_NumClasses][m_NumAttValues[att]];
for (int i=0;i<m_NumClasses;i++){
PriorsClass[i]=m_ClassCounts[i]/m_NumInstances;
}
for (int j=0;j<m_NumAttValues[att];j++){
PriorsAttribute[j]=m_AttCounts[attIndex+j]/m_NumInstances;
}
for (int i=0;i<m_NumClasses;i++){
for (int j=0;j<m_NumAttValues[att];j++){
PriorsClassAttribute[i][j]=m_ClassAttAttCounts[i][attIndex+j][attIndex+j]/m_NumInstances;
}
}
for (int i=0;i<m_NumClasses;i++){
for (int j=0;j<m_NumAttValues[att];j++){
mutualInfo+=PriorsClassAttribute[i][j]*log2(PriorsClassAttribute[i][j],PriorsClass[i]*PriorsAttribute[j]);
}
}
return mutualInfo;
}
/**
* compute the logarithm whose base is 2.
*
* @param x numerator of the fraction.
* @param y denominator of the fraction.
* @return the natual logarithm of this fraction.
*/
private double log2(double x,double y){
if (x < Utils.SMALL || y < Utils.SMALL)
return 0.0;
else
return Math.log(x/y)/Math.log(2);
}
/**
* Calculates the class membership probabilities for the given test instance
*
* @param instance the instance to be classified
* @return predicted class probability distribution
* @throws Exception if there is a problem generating the prediction
*/
public double[] distributionForInstance(Instance instance) throws Exception {
// default model?
if (m_ZeroR != null) {
return m_ZeroR.distributionForInstance(instance);
}
//Definition of local variables
double[] probs = new double[m_NumClasses];
double prob;
double mutualInfoSum;
// store instance's att values in an int array
int[] attIndex = new int[m_NumAttributes];
for (int att = 0; att < m_NumAttributes; att++) {
if (att == m_ClassIndex)
attIndex[att] = -1;
else
attIndex[att] = m_StartAttIndex[att] + (int)instance.value(att);
}
// calculate probabilities for each possible class value
for (int classVal = 0; classVal < m_NumClasses; classVal++) {
probs[classVal] = 0;
prob=1;
mutualInfoSum=0.0;
for (int parent = 0; parent < m_NumAttributes; parent++) {
if (attIndex[parent]==-1) continue;
prob=(m_ClassAttAttCounts[classVal][attIndex[parent]][attIndex[parent]] + 1.0/(m_NumClasses*m_NumAttValues[parent]))/(m_NumInstances + 1.0);
for (int son = 0; son < m_NumAttributes; son++) {
if (attIndex[son]==-1 || son == parent) continue;
prob*=(m_ClassAttAttCounts[classVal][attIndex[parent]][attIndex[son]] + 1.0/m_NumAttValues[son])/(m_ClassAttAttCounts[classVal][attIndex[parent]][attIndex[parent]] + 1.0);
}
mutualInfoSum+=m_mutualInformation[parent];
probs[classVal]+=m_mutualInformation[parent]*prob;
}
probs[classVal]/=mutualInfoSum;
}
if (!Double.isNaN(Utils.sum(probs)))
Utils.normalize(probs);
return probs;
}
/**
* returns a string representation of the classifier
*
* @return string representation of the classifier
*/
public String toString() {
StringBuffer result;
String classname;
int i;
// only ZeroR model?
if (m_ZeroR != null) {
result = new StringBuffer();
result.append(this.getClass().getName().replaceAll(".*\\.", "") + "\n");
result.append(this.getClass().getName().replaceAll(".*\\.", "").replaceAll(".", "=") + "\n\n");
result.append("Warning: No model could be built, hence ZeroR model is used:\n\n");
result.append(m_ZeroR.toString());
}
else {
classname = this.getClass().getName().replaceAll(".*\\.", "");
result = new StringBuffer();
result.append(classname + "\n");
result.append(classname.replaceAll(".", "=") + "\n\n");
if (m_Header == null) {
result.append("No Model built yet.\n");
}
else {
if (getInternals()) {
result.append("Mutual information of attributes with class attribute:\n");
for (i = 0; i < m_Header.numAttributes(); i++) {
// skip class
if (i == m_Header.classIndex())
continue;
result.append(
(i+1) + ". " + m_Header.attribute(i).name() + ": "
+ Utils.doubleToString(m_mutualInformation[i], 6) + "\n");
}
}
else {
result.append("Model built successfully.\n");
}
}
}
return result.toString();
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 5516 $");
}
/**
* Main method for testing this class.
*
* @param argv the commandline options, use -h to list all options
*/
public static void main(String[] argv) {
runClassifier(new WAODE(), argv);
}
}