de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures
Class BTMutualInformation

java.lang.Object
  de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure
      de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Cloneable

public class BTMutualInformation
extends Measure

Structure learning Measure that computes a maximum spanning tree based on mutual information and uses the resulting tree structure as structure of a Bayesian tree (special case of a Bayesian network) in a BayesianNetworkDiffSM .

Author:

Jan Grau

Nested Class Summary

static class	BTMutualInformation.BTMutualInformationParameterSet Class for the parameters of a BTMutualInformation structure Measure.
static class	BTMutualInformation.DataSource Enum defining the possible sources of data to compute the mutual information.

Nested classes/interfaces inherited from class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure

Measure.MeasureParameterSet

Field Summary

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure

parameters

Constructor Summary

BTMutualInformation(BTMutualInformation.BTMutualInformationParameterSet parameters)
Creates a new BTMutualInformation from the corresponding InstanceParameterSet parameters.

BTMutualInformation(BTMutualInformation.DataSource clazz, double[] ess)
Creates a new mutual information Bayesian tree Measure.

BTMutualInformation(StringBuffer buf)
The standard constructor for the interface Storable.

Method Summary

String	getInstanceName() Returns the name of the Measure and possibly some additional information about the current instance.
int[][]	getParents(DataSet fg, DataSet bg, double[] weightsFg, double[] weightsBg, int length) Returns the optimal parents for the given data and weights.
String	getXMLTag() Returns the XML-tag for storing this measure

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure

clone, fillTensor, fillTensor, getCMI, getCMI, getCurrentParameterSet, getEAR, getEAR, getMI, getMI, getStatistics, getStatisticsOrderTwo, isShiftable, sum, toParents, toXML, union

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BTMutualInformation

public BTMutualInformation(StringBuffer buf)
                    throws NonParsableException

The standard constructor for the interface Storable. Recreates a BTMutualInformation from is XML representation as returned by Measure.toXML().

Parameters:

buf - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

BTMutualInformation

public BTMutualInformation(BTMutualInformation.DataSource clazz,
                           double[] ess)
                    throws CloneNotSupportedException,
                           Exception

Creates a new mutual information Bayesian tree Measure.

Parameters:

clazz - the classes used for computation of mutual information, as defined by BTMutualInformation.DataSource

ess - the equivalent sample sizes for both classes

Throws:

CloneNotSupportedException - if the parameters could not be created

Exception - if the parameters could not be created for the ess

BTMutualInformation

public BTMutualInformation(BTMutualInformation.BTMutualInformationParameterSet parameters)
                    throws CloneNotSupportedException

Creates a new BTMutualInformation from the corresponding InstanceParameterSet parameters.

Parameters:

parameters - the corresponding parameters

Throws:

CloneNotSupportedException - if the parameters could not be cloned

Method Detail

getInstanceName

public String getInstanceName()

Description copied from class: Measure

Returns the name of the Measure and possibly some additional information about the current instance.

Specified by:

getInstanceName in class Measure

Returns:

the name of the Measure

getParents

public int[][] getParents(DataSet fg,
                          DataSet bg,
                          double[] weightsFg,
                          double[] weightsBg,
                          int length)
                   throws Exception

Description copied from class: Measure

Returns the optimal parents for the given data and weights. The returned array of parents p at each position i is build as follows:

• p[i][p.length - 1] contains the index i itself
• p[i][p.length - 2] contains the "most important" parent
• ...
• p[i][0] contains the "least important" parent

Specified by:

getParents in class Measure

Parameters:

fg - the data of the current (foreground) class

bg - the data of the negative (background) class

weightsFg - the weights for the sequences of fg

weightsBg - the weights for the sequences of bg

length - the length of the model, must be equal to the length of the sequences

Returns:

the the array p with the optimal parents

Throws:

Exception - if the lengths do not match or other problems concerning the data occur

getXMLTag

public String getXMLTag()

Description copied from class: Measure

Returns the XML-tag for storing this measure

Specified by:

getXMLTag in class Measure

Returns:

the tag