/*
* 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/>.
*/
/*
* TAN.java
* Copyright (C) 2004-2012 University of Waikato, Hamilton, New Zealand
*
*/
package weka.classifiers.bayes.net.search.local;
import java.util.Enumeration;
import weka.classifiers.bayes.BayesNet;
import weka.core.Instances;
import weka.core.RevisionUtils;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import weka.core.TechnicalInformationHandler;
/**
<!-- globalinfo-start -->
* This Bayes Network learning algorithm determines the maximum weight spanning tree and returns a Naive Bayes network augmented with a tree.<br/>
* <br/>
* For more information see:<br/>
* <br/>
* N. Friedman, D. Geiger, M. Goldszmidt (1997). Bayesian network classifiers. Machine Learning. 29(2-3):131-163.
* <p/>
<!-- globalinfo-end -->
*
<!-- technical-bibtex-start -->
* BibTeX:
* <pre>
* @article{Friedman1997,
* author = {N. Friedman and D. Geiger and M. Goldszmidt},
* journal = {Machine Learning},
* number = {2-3},
* pages = {131-163},
* title = {Bayesian network classifiers},
* volume = {29},
* year = {1997}
* }
* </pre>
* <p/>
<!-- technical-bibtex-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -mbc
* Applies a Markov Blanket correction to the network structure,
* after a network structure is learned. This ensures that all
* nodes in the network are part of the Markov blanket of the
* classifier node.</pre>
*
* <pre> -S [BAYES|MDL|ENTROPY|AIC|CROSS_CLASSIC|CROSS_BAYES]
* Score type (BAYES, BDeu, MDL, ENTROPY and AIC)</pre>
*
<!-- options-end -->
*
* @author Remco Bouckaert
* @version $Revision: 8034 $
*/
public class TAN
extends LocalScoreSearchAlgorithm
implements TechnicalInformationHandler {
/** for serialization */
static final long serialVersionUID = 965182127977228690L;
/**
* 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, "N. Friedman and D. Geiger and M. Goldszmidt");
result.setValue(Field.YEAR, "1997");
result.setValue(Field.TITLE, "Bayesian network classifiers");
result.setValue(Field.JOURNAL, "Machine Learning");
result.setValue(Field.VOLUME, "29");
result.setValue(Field.NUMBER, "2-3");
result.setValue(Field.PAGES, "131-163");
return result;
}
/**
* buildStructure determines the network structure/graph of the network
* using the maximimum weight spanning tree algorithm of Chow and Liu
*
* @param bayesNet the network
* @param instances the data to use
* @throws Exception if something goes wrong
*/
public void buildStructure(BayesNet bayesNet, Instances instances) throws Exception {
m_bInitAsNaiveBayes = true;
m_nMaxNrOfParents = 2;
super.buildStructure(bayesNet, instances);
int nNrOfAtts = instances.numAttributes();
if (nNrOfAtts <= 2) {
return;
}
// determine base scores
double[] fBaseScores = new double[instances.numAttributes()];
for (int iAttribute = 0; iAttribute < nNrOfAtts; iAttribute++) {
fBaseScores[iAttribute] = calcNodeScore(iAttribute);
}
// // cache scores & whether adding an arc makes sense
double[][] fScore = new double[nNrOfAtts][nNrOfAtts];
for (int iAttributeHead = 0; iAttributeHead < nNrOfAtts; iAttributeHead++) {
for (int iAttributeTail = 0; iAttributeTail < nNrOfAtts; iAttributeTail++) {
if (iAttributeHead != iAttributeTail) {
fScore[iAttributeHead][iAttributeTail] = calcScoreWithExtraParent(iAttributeHead, iAttributeTail);
}
}
}
// TAN greedy search (not restricted by ordering like K2)
// 1. find strongest link
// 2. find remaining links by adding strongest link to already
// connected nodes
// 3. assign direction to links
int nClassNode = instances.classIndex();
int [] link1 = new int [nNrOfAtts - 1];
int [] link2 = new int [nNrOfAtts - 1];
boolean [] linked = new boolean [nNrOfAtts];
// 1. find strongest link
int nBestLinkNode1 = -1;
int nBestLinkNode2 = -1;
double fBestDeltaScore = 0.0;
int iLinkNode1;
for (iLinkNode1 = 0; iLinkNode1 < nNrOfAtts; iLinkNode1++) {
if (iLinkNode1 != nClassNode) {
for (int iLinkNode2 = 0; iLinkNode2 < nNrOfAtts; iLinkNode2++) {
if ((iLinkNode1 != iLinkNode2) &&
(iLinkNode2 != nClassNode) && (
(nBestLinkNode1 == -1) || (fScore[iLinkNode1][iLinkNode2] - fBaseScores[iLinkNode1] > fBestDeltaScore)
)) {
fBestDeltaScore = fScore[iLinkNode1][iLinkNode2] - fBaseScores[iLinkNode1];
nBestLinkNode1 = iLinkNode2;
nBestLinkNode2 = iLinkNode1;
}
}
}
}
link1[0] = nBestLinkNode1;
link2[0] = nBestLinkNode2;
linked[nBestLinkNode1] = true;
linked[nBestLinkNode2] = true;
// 2. find remaining links by adding strongest link to already
// connected nodes
for (int iLink = 1; iLink < nNrOfAtts - 2; iLink++) {
nBestLinkNode1 = -1;
for (iLinkNode1 = 0; iLinkNode1 < nNrOfAtts; iLinkNode1++) {
if (iLinkNode1 != nClassNode) {
for (int iLinkNode2 = 0; iLinkNode2 < nNrOfAtts; iLinkNode2++) {
if ((iLinkNode1 != iLinkNode2) &&
(iLinkNode2 != nClassNode) &&
(linked[iLinkNode1] || linked[iLinkNode2]) &&
(!linked[iLinkNode1] || !linked[iLinkNode2]) &&
(
(nBestLinkNode1 == -1) || (fScore[iLinkNode1][iLinkNode2] - fBaseScores[iLinkNode1] > fBestDeltaScore)
)) {
fBestDeltaScore = fScore[iLinkNode1][iLinkNode2] - fBaseScores[iLinkNode1];
nBestLinkNode1 = iLinkNode2;
nBestLinkNode2 = iLinkNode1;
}
}
}
}
link1[iLink] = nBestLinkNode1;
link2[iLink] = nBestLinkNode2;
linked[nBestLinkNode1] = true;
linked[nBestLinkNode2] = true;
}
// 3. assign direction to links
boolean [] hasParent = new boolean [nNrOfAtts];
for (int iLink = 0; iLink < nNrOfAtts - 2; iLink++) {
if (!hasParent[link1[iLink]]) {
bayesNet.getParentSet(link1[iLink]).addParent(link2[iLink], instances);
hasParent[link1[iLink]] = true;
} else {
if (hasParent[link2[iLink]]) {
throw new Exception("Bug condition found: too many arrows");
}
bayesNet.getParentSet(link2[iLink]).addParent(link1[iLink], instances);
hasParent[link2[iLink]] = true;
}
}
} // buildStructure
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
return super.listOptions();
} // listOption
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -mbc
* Applies a Markov Blanket correction to the network structure,
* after a network structure is learned. This ensures that all
* nodes in the network are part of the Markov blanket of the
* classifier node.</pre>
*
* <pre> -S [BAYES|MDL|ENTROPY|AIC|CROSS_CLASSIC|CROSS_BAYES]
* Score type (BAYES, BDeu, MDL, ENTROPY and AIC)</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);
} // setOptions
/**
* Gets the current settings of the Classifier.
*
* @return an array of strings suitable for passing to setOptions
*/
public String [] getOptions() {
return super.getOptions();
} // getOptions
/**
* This will return a string describing the classifier.
* @return The string.
*/
public String globalInfo() {
return
"This Bayes Network learning algorithm determines the maximum weight spanning tree "
+ " and returns a Naive Bayes network augmented with a tree.\n\n"
+ "For more information see:\n\n"
+ getTechnicalInformation().toString();
} // globalInfo
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 8034 $");
}
} // TAN