weka.classifiers.bayes.net

Class BIFReader

java.lang.Object

weka.classifiers.Classifier

weka.classifiers.bayes.BayesNet

weka.classifiers.bayes.net.BIFReader

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, AdditionalMeasureProducer, CapabilitiesHandler, Drawable, OptionHandler, RevisionHandler, TechnicalInformationHandler, WeightedInstancesHandler

public class BIFReader
extends BayesNet
implements TechnicalInformationHandler

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
 

Version:

$Revision: 1.15 $

Author:

Remco Bouckaert (rrb@xm.co.nz)

See Also:

Serialized Form

Field Summary

Fields inherited from class weka.classifiers.bayes.BayesNet

m_Distributions, m_Instances

Fields inherited from interface weka.core.Drawable

BayesNet, Newick, NOT_DRAWABLE, TREE

Constructor Summary

Constructors

Constructor and Description
BIFReader() the default constructor

Method Summary

Modifier and Type	Method and Description
double	divergence(BayesNet other) 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
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.
java.lang.String	getContent(org.w3c.dom.Element node) Returns all TEXT children of the given node in one string.
java.lang.String	getFileName() returns the current filename
int	getNode(java.lang.String sNodeName) getNode finds the index of the node with name sNodeName and throws an exception if no such node can be found.
java.lang.String	getRevision() Returns the revision string.
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.
java.lang.String	globalInfo() This will return a string describing the classifier.
static void	main(java.lang.String[] args) Loads the file specified as first parameter and prints it to stdout.
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.
BIFReader	processFile(java.lang.String sFile) processFile reads a BIFXML file and initializes a Bayes Net
BIFReader	processString(java.lang.String sStr)
int	reversedArcs(BayesNet other) Count nr of reversed arcs from other network compared to current network
void	Sync(BayesNet other) synchronizes the node ordering of this Bayes network with those in the other network (if possible).

Methods inherited from class weka.classifiers.bayes.BayesNet

BIFFileTipText, buildClassifier, buildStructure, countsForInstance, distributionForInstance, enumerateMeasures, estimateCPTs, estimatorTipText, getADTree, getBIFFile, getBIFHeader, getCapabilities, getCardinality, getDistributions, getEstimator, getMeasure, getName, getNodeName, getNodeValue, getNrOfNodes, getNrOfParents, getOptions, getParent, getParentCardinality, getParentSet, getParentSets, getProbability, getSearchAlgorithm, getUseADTree, graph, graphType, initCPTs, initStructure, listOptions, measureAICScore, measureBayesScore, measureBDeuScore, measureDivergence, measureEntropyScore, measureExtraArcs, measureMDLScore, measureMissingArcs, measureReversedArcs, partitionOptions, searchAlgorithmTipText, setBIFFile, setEstimator, setOptions, setSearchAlgorithm, setUseADTree, toString, toXMLBIF03, updateClassifier, useADTreeTipText

Methods inherited from class weka.classifiers.Classifier

classifyInstance, debugTipText, forName, getDebug, makeCopies, makeCopy, setDebug

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

BIFReader

public BIFReader()

the default constructor

Method Detail

globalInfo

public java.lang.String globalInfo()

This will return a string describing the classifier.

Overrides:

globalInfo in class BayesNet

Returns:

The string.

processFile

public BIFReader processFile(java.lang.String sFile)
                      throws java.lang.Exception

processFile reads a BIFXML file and initializes a Bayes Net

Parameters:

sFile - name of the file to parse

Returns:

the BIFReader

Throws:

java.lang.Exception - if processing fails

processString

public BIFReader processString(java.lang.String sStr)
                        throws java.lang.Exception

Throws:

java.lang.Exception

getFileName

public java.lang.String getFileName()

returns the current filename

Returns:

the current filename

getTechnicalInformation

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.

Specified by:

getTechnicalInformation in interface TechnicalInformationHandler

Returns:

the technical information about this class

Sync

public void Sync(BayesNet other)
          throws java.lang.Exception

synchronizes the node ordering of this Bayes network with those in the other network (if possible).

Parameters:

other - Bayes network to synchronize with

Throws:

java.lang.Exception - if nr of attributes differs or not all of the variables have the same name.

getContent

public java.lang.String getContent(org.w3c.dom.Element node)

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

Returns:

the content of the node

missingArcs

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.

Parameters:

other - network to compare with

Returns:

nr of missing arcs

extraArcs

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.

Parameters:

other - network to compare with

Returns:

nr of missing arcs

divergence

public double divergence(BayesNet other)

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

Returns:

divergence between this and other Bayes Network

reversedArcs

public int reversedArcs(BayesNet other)

Count nr of reversed arcs from other network compared to current network

Parameters:

other - network to compare with

Returns:

nr of missing arcs

getNode

public int getNode(java.lang.String sNodeName)
            throws java.lang.Exception

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

Returns:

index of the node with name sNodeName

Throws:

java.lang.Exception - if node cannot be found

getRevision

public java.lang.String getRevision()

Returns the revision string.

Specified by:

getRevision in interface RevisionHandler

Overrides:

getRevision in class BayesNet

Returns:

the revision

main

public static void main(java.lang.String[] args)

Loads the file specified as first parameter and prints it to stdout.

Parameters:

args - the command line parameters