de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures
Class PMMMutualInformation

java.lang.Object
  de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure
      de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Cloneable

public class PMMMutualInformation
extends Measure

Class for the network structure of a BayesianNetworkDiffSM that is a permuted Markov model based on mutual information.

Author:

Jan Grau

Nested Class Summary

static class

PMMMutualInformation.PMMMutualInformationParameterSet Class for the parameters of a PMMMutualInformation structure Measure.

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

PMMMutualInformation(byte order, BTMutualInformation.DataSource clazz, double[] ess)
Creates a new PMMMutualInformation of order order.

PMMMutualInformation(PMMMutualInformation.PMMMutualInformationParameterSet parameters)
Creates a new PMMMutualInformation from the corresponding InstanceParameterSet parameters.

PMMMutualInformation(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

PMMMutualInformation

public PMMMutualInformation(byte order,
                            BTMutualInformation.DataSource clazz,
                            double[] ess)
                     throws Exception

Creates a new PMMMutualInformation of order order.

Parameters:

order - the order, may be 1 or 2.

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

ess - the equivalent sample sizes of both classes

Throws:

Exception - if the order is not 1 or 2

PMMMutualInformation

public PMMMutualInformation(PMMMutualInformation.PMMMutualInformationParameterSet parameters)
                     throws Exception

Creates a new PMMMutualInformation from the corresponding InstanceParameterSet parameters.

Parameters:

parameters - the corresponding parameters

Throws:

Exception - if the order is not 1 or 2

PMMMutualInformation

public PMMMutualInformation(StringBuffer buf)
                     throws NonParsableException

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

Parameters:

buf - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

Method Detail

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

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