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Java Source Code / Java Documentation » Science » weka » weka.classifiers.bayes.net

Source Cross Reference

Class Diagram

Java Document (Java Doc)

weka.classifiers.bayes .BayesNet

weka.classifiers.bayes.net .BIFReader

BIFReader

public class BIFReader extends BayesNet implements TechnicalInformationHandler(Code)

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 (rrb@xm.co.nz)
version:
$Revision: 1.11 $

Field Summary
String	m_sFile
final static long	serialVersionUID

Constructor Summary
public	BIFReader()

Method Summary
public void	Sync(BayesNet other) synchronizes the node ordering of this Bayes network with those in the other network (if possible).
void	buildInstances(Document doc, String sName) buildInstances parses the BIF document and creates a Bayes Net with its nodes specified, but leaves the network structure and probability tables empty. Parameters: doc - DOM document containing BIF document in DOM tree Parameters: sName - default name to give to the Bayes Net.
void	buildStructure(Document doc) buildStructure parses the BIF document in the DOM tree contained in the doc parameter and specifies the the network structure and probability tables.
public double	divergence(BayesNet other)
public int	extraArcs(BayesNet other) Count nr of exta arcs from other network compared to current network Note that an arc is not 'extra' if it is reversed.
public String	getContent(Element node) Returns all TEXT children of the given node in one string.
Element	getDefinition(Document doc, String sName)
public String	getFileName()
public int	getNode(String sNodeName) getNode finds the index of the node with name sNodeName and throws an exception if no such node can be found.
FastVector	getParentNodes(Node definition)
String	getTable(Node definition)
public TechnicalInformation	getTechnicalInformation() 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.
public String	globalInfo() This will return a string describing the classifier.
public static void	main(String[] args) Loads the file specified as first parameter and prints it to stdout.
public int	missingArcs(BayesNet other) Count nr of arcs missing from other network compared to current network Note that an arc is not 'missing' if it is reversed.
public BIFReader	processFile(String sFile)
public int	reversedArcs(BayesNet other)
NodeList	selectAllNames(Document doc)
NodeList	selectAllVariables(Document doc)
FastVector	selectElements(Node item, String sElement)
FastVector	selectName(Node item)
FastVector	selectOutCome(Node item)
FastVector	selectProperty(Node item)

Field Detail

m_sFile
String m_sFile(Code)
	the current filename

serialVersionUID
final static long serialVersionUID(Code)
	for serialization

Constructor Detail

BIFReader
public BIFReader()(Code)
	the default constructor

Method Detail

Sync
public void Sync(BayesNet other) throws Exception(Code)
	synchronizes the node ordering of this Bayes network with those in the other network (if possible). Parameters: other - Bayes network to synchronize with throws: Exception - if nr of attributes differs or not all of the variables have the same name.

buildInstances
void buildInstances(Document doc, String sName) throws Exception(Code)
	buildInstances parses the BIF document and creates a Bayes Net with its nodes specified, but leaves the network structure and probability tables empty. Parameters: doc - DOM document containing BIF document in DOM tree Parameters: sName - default name to give to the Bayes Net. Will be overridden if specified in the BIF document. throws: Exception - if building fails

buildStructure
void buildStructure(Document doc) throws Exception(Code)
	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 Parameters: doc - DOM document containing BIF document in DOM tree throws: Exception - if building of structure fails

divergence
public double divergence(BayesNet other)(Code)
	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 Parameters: other - network to compare with divergence between this and other Bayes Network

extraArcs
public int extraArcs(BayesNet other)(Code)
	Count nr of exta arcs from other network compared to current network Note that an arc is not 'extra' if it is reversed. Parameters: other - network to compare with nr of missing arcs

getContent
public String getContent(Element node)(Code)
	Returns all TEXT children of the given node in one string. Between the node values new lines are inserted. Parameters: node - the node to return the content for the content of the node

getDefinition
Element getDefinition(Document doc, String sName) throws Exception(Code)

getFileName
public String getFileName()(Code)
	returns the current filename the current filename

getNode
public int getNode(String sNodeName) throws Exception(Code)
	getNode finds the index of the node with name sNodeName and throws an exception if no such node can be found. Parameters: sNodeName - name of the node to get the index from index of the node with name sNodeName throws: Exception - if node cannot be found

getParentNodes
FastVector getParentNodes(Node definition) throws Exception(Code)

getTable
String getTable(Node definition) throws Exception(Code)

getTechnicalInformation
public TechnicalInformation getTechnicalInformation()(Code)
	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. the technical information about this class

globalInfo
public String globalInfo()(Code)
	This will return a string describing the classifier. The string.

main
public static void main(String[] args)(Code)
	Loads the file specified as first parameter and prints it to stdout. Parameters: args - the command line parameters

missingArcs
public int missingArcs(BayesNet other)(Code)
	Count nr of arcs missing from other network compared to current network Note that an arc is not 'missing' if it is reversed. Parameters: other - network to compare with nr of missing arcs

processFile
public BIFReader processFile(String sFile) throws Exception(Code)
	processFile reads a BIFXML file and initializes a Bayes Net Parameters: sFile - name of the file to parse the BIFReader throws: Exception - if processing fails

reversedArcs
public int reversedArcs(BayesNet other)(Code)
	Count nr of reversed arcs from other network compared to current network Parameters: other - network to compare with nr of missing arcs

selectAllNames
NodeList selectAllNames(Document doc) throws Exception(Code)

selectAllVariables
NodeList selectAllVariables(Document doc) throws Exception(Code)

selectElements
FastVector selectElements(Node item, String sElement) throws Exception(Code)

selectName
FastVector selectName(Node item) throws Exception(Code)

selectOutCome
FastVector selectOutCome(Node item) throws Exception(Code)

selectProperty
FastVector selectProperty(Node item) throws Exception(Code)

Fields inherited from weka.classifiers.bayes.BayesNet

public Estimator[][] m_Distributions(Code)(Java Doc)
public Instances m_Instances(Code)(Java Doc)
protected int m_NumClasses(Code)(Java Doc)
protected ParentSet[] m_ParentSets(Code)(Java Doc)
protected BIFReader m_otherBayesNet(Code)(Java Doc)

Methods inherited from weka.classifiers.bayes.BayesNet

public String BIFFileTipText()(Code)(Java Doc)
public void buildClassifier(Instances instances) throws Exception(Code)(Java Doc)
public void buildStructure() throws Exception(Code)(Java Doc)
public double[] countsForInstance(Instance instance) throws Exception(Code)(Java Doc)
public double[] distributionForInstance(Instance instance) throws Exception(Code)(Java Doc)
public Enumeration enumerateMeasures()(Code)(Java Doc)
public void estimateCPTs() throws Exception(Code)(Java Doc)
public String estimatorTipText()(Code)(Java Doc)
public ADNode getADTree()(Code)(Java Doc)
public String getBIFFile()(Code)(Java Doc)
public Capabilities getCapabilities()(Code)(Java Doc)
public int getCardinality(int iNode)(Code)(Java Doc)
public Estimator[][] getDistributions()(Code)(Java Doc)
public BayesNetEstimator getEstimator()(Code)(Java Doc)
public double getMeasure(String measureName)(Code)(Java Doc)
public String getName()(Code)(Java Doc)
public String getNodeName(int iNode)(Code)(Java Doc)
public String getNodeValue(int iNode, int iValue)(Code)(Java Doc)
public int getNrOfNodes()(Code)(Java Doc)
public int getNrOfParents(int iNode)(Code)(Java Doc)
public String[] getOptions()(Code)(Java Doc)
public int getParent(int iNode, int iParent)(Code)(Java Doc)
public int getParentCardinality(int iNode)(Code)(Java Doc)
public ParentSet getParentSet(int iNode)(Code)(Java Doc)
public ParentSet[] getParentSets()(Code)(Java Doc)
public double getProbability(int iNode, int iParent, int iValue)(Code)(Java Doc)
public SearchAlgorithm getSearchAlgorithm()(Code)(Java Doc)
public boolean getUseADTree()(Code)(Java Doc)
public String globalInfo()(Code)(Java Doc)
public String graph() throws Exception(Code)(Java Doc)
public int graphType()(Code)(Java Doc)
public void initCPTs() throws Exception(Code)(Java Doc)
public void initStructure() throws Exception(Code)(Java Doc)
public Enumeration listOptions()(Code)(Java Doc)
public static void main(String[] argv)(Code)(Java Doc)
public double measureAICScore()(Code)(Java Doc)
public double measureBDeuScore()(Code)(Java Doc)
public double measureBayesScore()(Code)(Java Doc)
public double measureDivergence()(Code)(Java Doc)
public double measureEntropyScore()(Code)(Java Doc)
public double measureExtraArcs()(Code)(Java Doc)
public double measureMDLScore()(Code)(Java Doc)
public double measureMissingArcs()(Code)(Java Doc)
public double measureReversedArcs()(Code)(Java Doc)
public static String[] partitionOptions(String[] options)(Code)(Java Doc)
public String searchAlgorithmTipText()(Code)(Java Doc)
public void setBIFFile(String sBIFFile)(Code)(Java Doc)
public void setEstimator(BayesNetEstimator newBayesNetEstimator)(Code)(Java Doc)
public void setOptions(String[] options) throws Exception(Code)(Java Doc)
public void setSearchAlgorithm(SearchAlgorithm newSearchAlgorithm)(Code)(Java Doc)
public void setUseADTree(boolean bUseADTree)(Code)(Java Doc)
public String toString()(Code)(Java Doc)
public String toXMLBIF03()(Code)(Java Doc)
public void updateClassifier(Instance instance) throws Exception(Code)(Java Doc)
public String useADTreeTipText()(Code)(Java Doc)

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