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The Waikato Environment for Knowledge Analysis (WEKA), a machine learning workbench. This version represents the developer version, the "bleeding edge" of development, you could say. New functionality gets added to this version.

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/*
 *   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 .
 */

/*
 * BIFReader.java
 * Copyright (C) 2003-2012 University of Waikato, Hamilton, New Zealand
 * 
 */

package weka.classifiers.bayes.net;

import java.io.File;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.StringTokenizer;

import javax.xml.parsers.DocumentBuilderFactory;

import org.w3c.dom.CharacterData;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;

import weka.classifiers.bayes.BayesNet;
import weka.classifiers.bayes.net.estimate.DiscreteEstimatorBayes;
import weka.core.Attribute;
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;
import weka.estimators.Estimator;

/**
 *  Builds a description of a Bayes Net classifier
 * stored in XML BIF 0.3 format.
*
* For more details on XML BIF see:
*
* Fabio Cozman, Marek Druzdzel, Daniel Garcia (1998). XML BIF version 0.3. URL * http://www-2.cs.cmu.edu/~fgcozman/Research/InterchangeFormat/. *

* * * BibTeX: * *

 * @misc{Cozman1998,
 *    author = {Fabio Cozman and Marek Druzdzel and Daniel Garcia},
 *    title = {XML BIF version 0.3},
 *    year = {1998},
 *    URL = {http://www-2.cs.cmu.edu/\~fgcozman/Research/InterchangeFormat/}
 * }
 * 
*

* * * Valid options are: *

* *

 * -D
 *  Do not use ADTree data structure
 * 
* *
 * -B <BIF file>
 *  BIF file to compare with
 * 
* *
 * -Q weka.classifiers.bayes.net.search.SearchAlgorithm
 *  Search algorithm
 * 
* *
 * -E weka.classifiers.bayes.net.estimate.SimpleEstimator
 *  Estimator algorithm
 * 
* * * * @author Remco Bouckaert ([email protected]) * @version $Revision: 10153 $ */ public class BIFReader extends BayesNet implements TechnicalInformationHandler { protected int[] m_nPositionX; protected int[] m_nPositionY; private int[] m_order; /** for serialization */ static final long serialVersionUID = -8358864680379881429L; /** * This will return a string describing the classifier. * * @return The string. */ @Override public String globalInfo() { return "Builds a description of a Bayes Net classifier stored in XML " + "BIF 0.3 format.\n\n" + "For more details on XML BIF see:\n\n" + getTechnicalInformation().toString(); } /** * processFile reads a BIFXML file and initializes a Bayes Net * * @param sFile name of the file to parse * @return the BIFReader * @throws Exception if processing fails */ public BIFReader processFile(String sFile) throws Exception { m_sFile = sFile; DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(true); Document doc = factory.newDocumentBuilder().parse(new File(sFile)); doc.normalize(); buildInstances(doc, sFile); buildStructure(doc); return this; } // processFile public BIFReader processString(String sStr) throws Exception { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(true); Document doc = factory.newDocumentBuilder().parse( new org.xml.sax.InputSource(new StringReader(sStr))); doc.normalize(); buildInstances(doc, "from-string"); buildStructure(doc); return this; } // processString /** the current filename */ String m_sFile; /** * returns the current filename * * @return the current filename */ public String getFileName() { return m_sFile; } /** * 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 */ @Override public TechnicalInformation getTechnicalInformation() { TechnicalInformation result; result = new TechnicalInformation(Type.MISC); result.setValue(Field.AUTHOR, "Fabio Cozman and Marek Druzdzel and Daniel Garcia"); result.setValue(Field.YEAR, "1998"); result.setValue(Field.TITLE, "XML BIF version 0.3"); result.setValue(Field.URL, "http://www-2.cs.cmu.edu/~fgcozman/Research/InterchangeFormat/"); return result; } /** * buildStructure parses the BIF document in the DOM tree contained in the doc * parameter and specifies the the network structure and probability tables. * It assumes that buildInstances has been called before * * @param doc DOM document containing BIF document in DOM tree * @throws Exception if building of structure fails */ void buildStructure(Document doc) throws Exception { // Get the name of the network // initialize conditional distribution tables m_Distributions = new Estimator[m_Instances.numAttributes()][]; for (int iNode = 0; iNode < m_Instances.numAttributes(); iNode++) { // find definition that goes with this node String sName = m_Instances.attribute(iNode).name(); Element definition = getDefinition(doc, sName); /* * if (nodelist.getLength() == 0) { throw new * Exception("No definition found for node " + sName); } if * (nodelist.getLength() > 1) { * System.err.println("More than one definition found for node " + sName + * ". Using first definition."); } Element definition = (Element) * nodelist.item(0); */ // get the parents for this node // resolve structure ArrayList nodelist = getParentNodes(definition); for (int iParent = 0; iParent < nodelist.size(); iParent++) { Node parentName = nodelist.get(iParent).getFirstChild(); String sParentName = ((CharacterData) (parentName)).getData(); int nParent = getNode(sParentName); m_ParentSets[iNode].addParent(nParent, m_Instances); } // resolve conditional probability table int nCardinality = m_ParentSets[iNode].getCardinalityOfParents(); int nValues = m_Instances.attribute(iNode).numValues(); m_Distributions[iNode] = new Estimator[nCardinality]; for (int i = 0; i < nCardinality; i++) { m_Distributions[iNode][i] = new DiscreteEstimatorBayes(nValues, 0.0f); } /* * StringBuffer sTable = new StringBuffer(); for (int iText = 0; iText < * nodelist.getLength(); iText++) { sTable.append(((CharacterData) * (nodelist.item(iText))).getData()); sTable.append(' '); } * StringTokenizer st = new StringTokenizer(sTable.toString()); */ String sTable = getTable(definition); StringTokenizer st = new StringTokenizer(sTable.toString()); for (int i = 0; i < nCardinality; i++) { DiscreteEstimatorBayes d = (DiscreteEstimatorBayes) m_Distributions[iNode][i]; for (int iValue = 0; iValue < nValues; iValue++) { String sWeight = st.nextToken(); d.addValue(iValue, new Double(sWeight).doubleValue()); } } } } // buildStructure /** * synchronizes the node ordering of this Bayes network with those in the * other network (if possible). * * @param other Bayes network to synchronize with * @throws Exception if nr of attributes differs or not all of the variables * have the same name. */ public void Sync(BayesNet other) throws Exception { int nAtts = m_Instances.numAttributes(); if (nAtts != other.m_Instances.numAttributes()) { throw new Exception( "Cannot synchronize networks: different number of attributes."); } m_order = new int[nAtts]; for (int iNode = 0; iNode < nAtts; iNode++) { String sName = other.getNodeName(iNode); m_order[getNode(sName)] = iNode; } } // Sync /** * Returns all TEXT children of the given node in one string. Between the node * values new lines are inserted. * * @param node the node to return the content for * @return the content of the node */ public String getContent(Element node) { NodeList list; Node item; int i; String result; result = ""; list = node.getChildNodes(); for (i = 0; i < list.getLength(); i++) { item = list.item(i); if (item.getNodeType() == Node.TEXT_NODE) { result += "\n" + item.getNodeValue(); } } return result; } /** * buildInstances parses the BIF document and creates a Bayes Net with its * nodes specified, but leaves the network structure and probability tables * empty. * * @param doc DOM document containing BIF document in DOM tree * @param sName default name to give to the Bayes Net. Will be overridden if * specified in the BIF document. * @throws Exception if building fails */ void buildInstances(Document doc, String sName) throws Exception { NodeList nodelist; // Get the name of the network nodelist = selectAllNames(doc); if (nodelist.getLength() > 0) { sName = ((CharacterData) (nodelist.item(0).getFirstChild())).getData(); } // Process variables nodelist = selectAllVariables(doc); int nNodes = nodelist.getLength(); // initialize structure ArrayList attInfo = new ArrayList(nNodes); // Initialize m_nPositionX = new int[nodelist.getLength()]; m_nPositionY = new int[nodelist.getLength()]; // Process variables for (int iNode = 0; iNode < nodelist.getLength(); iNode++) { // Get element ArrayList valueslist; // Get the name of the network valueslist = selectOutCome(nodelist.item(iNode)); int nValues = valueslist.size(); // generate value strings ArrayList nomStrings = new ArrayList(nValues + 1); for (int iValue = 0; iValue < nValues; iValue++) { Node node = valueslist.get(iValue).getFirstChild(); String sValue = ((CharacterData) (node)).getData(); if (sValue == null) { sValue = "Value" + (iValue + 1); } nomStrings.add(sValue); } ArrayList nodelist2; // Get the name of the network nodelist2 = selectName(nodelist.item(iNode)); if (nodelist2.size() == 0) { throw new Exception("No name specified for variable"); } String sNodeName = ((CharacterData) (nodelist2.get(0).getFirstChild())) .getData(); weka.core.Attribute att = new weka.core.Attribute(sNodeName, nomStrings); attInfo.add(att); valueslist = selectProperty(nodelist.item(iNode)); nValues = valueslist.size(); // generate value strings for (int iValue = 0; iValue < nValues; iValue++) { // parsing for strings of the form "position = (73, 165)" Node node = valueslist.get(iValue).getFirstChild(); String sValue = ((CharacterData) (node)).getData(); if (sValue.startsWith("position")) { int i0 = sValue.indexOf('('); int i1 = sValue.indexOf(','); int i2 = sValue.indexOf(')'); String sX = sValue.substring(i0 + 1, i1).trim(); String sY = sValue.substring(i1 + 1, i2).trim(); try { m_nPositionX[iNode] = Integer.parseInt(sX); m_nPositionY[iNode] = Integer.parseInt(sY); } catch (NumberFormatException e) { System.err.println("Wrong number format in position :(" + sX + "," + sY + ")"); m_nPositionX[iNode] = 0; m_nPositionY[iNode] = 0; } } } } m_Instances = new Instances(sName, attInfo, 100); m_Instances.setClassIndex(nNodes - 1); setUseADTree(false); initStructure(); } // buildInstances // /** selectNodeList selects list of nodes from document specified in XPath // expression // * @param doc : document (or node) to query // * @param sXPath : XPath expression // * @return list of nodes conforming to XPath expression in doc // * @throws Exception // */ // private NodeList selectNodeList(Node doc, String sXPath) throws Exception { // NodeList nodelist = org.apache.xpath.XPathAPI.selectNodeList(doc, sXPath); // return nodelist; // } // selectNodeList NodeList selectAllNames(Document doc) throws Exception { // NodeList nodelist = selectNodeList(doc, "//NAME"); NodeList nodelist = doc.getElementsByTagName("NAME"); return nodelist; } // selectAllNames NodeList selectAllVariables(Document doc) throws Exception { // NodeList nodelist = selectNodeList(doc, "//VARIABLE"); NodeList nodelist = doc.getElementsByTagName("VARIABLE"); return nodelist; } // selectAllVariables Element getDefinition(Document doc, String sName) throws Exception { // NodeList nodelist = selectNodeList(doc, // "//DEFINITION[normalize-space(FOR/text())=\"" + sName + "\"]"); NodeList nodelist = doc.getElementsByTagName("DEFINITION"); for (int iNode = 0; iNode < nodelist.getLength(); iNode++) { Node node = nodelist.item(iNode); ArrayList list = selectElements(node, "FOR"); if (list.size() > 0) { Node forNode = list.get(0); if (getContent((Element) forNode).trim().equals(sName)) { return (Element) node; } } } throw new Exception("Could not find definition for ((" + sName + "))"); } // getDefinition ArrayList getParentNodes(Node definition) throws Exception { // NodeList nodelist = selectNodeList(definition, "GIVEN"); ArrayList nodelist = selectElements(definition, "GIVEN"); return nodelist; } // getParentNodes String getTable(Node definition) throws Exception { // NodeList nodelist = selectNodeList(definition, "TABLE/text()"); ArrayList nodelist = selectElements(definition, "TABLE"); String sTable = getContent((Element) nodelist.get(0)); sTable = sTable.replaceAll("\\n", " "); return sTable; } // getTable ArrayList selectOutCome(Node item) throws Exception { // NodeList nodelist = selectNodeList(item, "OUTCOME"); ArrayList nodelist = selectElements(item, "OUTCOME"); return nodelist; } // selectOutCome ArrayList selectName(Node item) throws Exception { // NodeList nodelist = selectNodeList(item, "NAME"); ArrayList nodelist = selectElements(item, "NAME"); return nodelist; } // selectName ArrayList selectProperty(Node item) throws Exception { // NodeList nodelist = selectNodeList(item, "PROPERTY"); ArrayList nodelist = selectElements(item, "PROPERTY"); return nodelist; } // selectProperty ArrayList selectElements(Node item, String sElement) throws Exception { NodeList children = item.getChildNodes(); ArrayList nodelist = new ArrayList(); for (int iNode = 0; iNode < children.getLength(); iNode++) { Node node = children.item(iNode); if ((node.getNodeType() == Node.ELEMENT_NODE) && node.getNodeName().equals(sElement)) { nodelist.add(node); } } return nodelist; } // selectElements /** * Count nr of arcs missing from other network compared to current network * Note that an arc is not 'missing' if it is reversed. * * @param other network to compare with * @return nr of missing arcs */ public int missingArcs(BayesNet other) { try { Sync(other); int nMissing = 0; for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) { for (int iParent = 0; iParent < m_ParentSets[iAttribute] .getNrOfParents(); iParent++) { int nParent = m_ParentSets[iAttribute].getParent(iParent); if (!other.getParentSet(m_order[iAttribute]).contains( m_order[nParent]) && !other.getParentSet(m_order[nParent]).contains( m_order[iAttribute])) { nMissing++; } } } return nMissing; } catch (Exception e) { System.err.println(e.getMessage()); return 0; } } // missingArcs /** * Count nr of exta arcs from other network compared to current network Note * that an arc is not 'extra' if it is reversed. * * @param other network to compare with * @return nr of missing arcs */ public int extraArcs(BayesNet other) { try { Sync(other); int nExtra = 0; for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) { for (int iParent = 0; iParent < other.getParentSet(m_order[iAttribute]) .getNrOfParents(); iParent++) { int nParent = m_order[other.getParentSet(m_order[iAttribute]) .getParent(iParent)]; if (!m_ParentSets[iAttribute].contains(nParent) && !m_ParentSets[nParent].contains(iAttribute)) { nExtra++; } } } return nExtra; } catch (Exception e) { System.err.println(e.getMessage()); return 0; } } // extraArcs /** * calculates the divergence between the probability distribution represented * by this network and that of another, that is, \sum_{x\in X} P(x)log * P(x)/Q(x) where X is the set of values the nodes in the network can take, * P(x) the probability of this network for configuration x Q(x) the * probability of the other network for configuration x * * @param other network to compare with * @return divergence between this and other Bayes Network */ public double divergence(BayesNet other) { try { Sync(other); // D: divergence double D = 0.0; int nNodes = m_Instances.numAttributes(); int[] nCard = new int[nNodes]; for (int iNode = 0; iNode < nNodes; iNode++) { nCard[iNode] = m_Instances.attribute(iNode).numValues(); } // x: holds current configuration of nodes int[] x = new int[nNodes]; // simply sum over all configurations to calc divergence D int i = 0; while (i < nNodes) { // update configuration x[i]++; while (i < nNodes && x[i] == m_Instances.attribute(i).numValues()) { x[i] = 0; i++; if (i < nNodes) { x[i]++; } } if (i < nNodes) { i = 0; // calc P(x) and Q(x) double P = 1.0; for (int iNode = 0; iNode < nNodes; iNode++) { int iCPT = 0; for (int iParent = 0; iParent < m_ParentSets[iNode] .getNrOfParents(); iParent++) { int nParent = m_ParentSets[iNode].getParent(iParent); iCPT = iCPT * nCard[nParent] + x[nParent]; } P = P * m_Distributions[iNode][iCPT].getProbability(x[iNode]); } double Q = 1.0; for (int iNode = 0; iNode < nNodes; iNode++) { int iCPT = 0; for (int iParent = 0; iParent < other.getParentSet(m_order[iNode]) .getNrOfParents(); iParent++) { int nParent = m_order[other.getParentSet(m_order[iNode]) .getParent(iParent)]; iCPT = iCPT * nCard[nParent] + x[nParent]; } Q = Q * other.m_Distributions[m_order[iNode]][iCPT] .getProbability(x[iNode]); } // update divergence if probabilities are positive if (P > 0.0 && Q > 0.0) { D = D + P * Math.log(Q / P); } } } return D; } catch (Exception e) { System.err.println(e.getMessage()); return 0; } } // divergence /** * Count nr of reversed arcs from other network compared to current network * * @param other network to compare with * @return nr of missing arcs */ public int reversedArcs(BayesNet other) { try { Sync(other); int nReversed = 0; for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) { for (int iParent = 0; iParent < m_ParentSets[iAttribute] .getNrOfParents(); iParent++) { int nParent = m_ParentSets[iAttribute].getParent(iParent); if (!other.getParentSet(m_order[iAttribute]).contains( m_order[nParent]) && other.getParentSet(m_order[nParent]).contains( m_order[iAttribute])) { nReversed++; } } } return nReversed; } catch (Exception e) { System.err.println(e.getMessage()); return 0; } } // reversedArcs /** * getNode finds the index of the node with name sNodeName and throws an * exception if no such node can be found. * * @param sNodeName name of the node to get the index from * @return index of the node with name sNodeName * @throws Exception if node cannot be found */ public int getNode(String sNodeName) throws Exception { int iNode = 0; while (iNode < m_Instances.numAttributes()) { if (m_Instances.attribute(iNode).name().equals(sNodeName)) { return iNode; } iNode++; } throw new Exception("Could not find node [[" + sNodeName + "]]"); } // getNode /** * the default constructor */ public BIFReader() { } /** * Returns the revision string. * * @return the revision */ @Override public String getRevision() { return RevisionUtils.extract("$Revision: 10153 $"); } /** * Loads the file specified as first parameter and prints it to stdout. * * @param args the command line parameters */ public static void main(String[] args) { try { BIFReader br = new BIFReader(); br.processFile(args[0]); System.out.println(br.toString()); } catch (Throwable t) { t.printStackTrace(); } } // main } // class BIFReader




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