de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
Class PMMMutualInformation

java.lang.Object
  de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure
      de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.PMMMutualInformation

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Cloneable

public class PMMMutualInformation
extends Measure

Class for the network structure of a BayesianNetworkScoringFunction 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.

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/code>.

PMMMutualInformation(StringBuffer buf)
Re-creates a PMMMutualInformation from its XML-representation as returned by toXML().

Method Summary

PMMMutualInformation	clone()
InstanceParameterSet	getCurrentParameterSet() Returns the InstanceParameterSet that has been used to instantiate the current instance of the implementing class.
String	getInstanceName() Returns the name of the Measure and possibly some additional information about the current instance.
int[][]	getParents(Sample fg, Sample bg, double[] weightsFg, double[] weightsBg, int length) Returns the optimal parents for the given data and weights.
StringBuffer	toXML() This method returns an XML-representation of an instance of the implementing class.

Methods inherited from class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure

fillTensor, fillTensor, getCMI, getCMI, getEAR, getEAR, getMI, getMI, getStatistics, getStatisticsOrderTwo, isShiftable, sum, toParents, 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 size for both classes

Throws:

Exception - is thrown 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/code>.

Parameters:

parameters - the parameters

Throws:

Exception - is thrown if the order is not 1 or 2

PMMMutualInformation

public PMMMutualInformation(StringBuffer buf)
                     throws NonParsableException

Re-creates a PMMMutualInformation from its XML-representation as returned by toXML().

Parameters:

buf - the XML-representation

Throws:

NonParsableException - is thrown if the XML-code could not be parsed

Method Detail

clone

public PMMMutualInformation clone()
                           throws CloneNotSupportedException

Overrides:

clone in class Measure

Throws:

CloneNotSupportedException

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

getParents

public int[][] getParents(Sample fg,
                          Sample 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 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 parents

Throws:

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

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML-representation of an instance of the implementing class.

Returns:

the XML-representation

getCurrentParameterSet

public InstanceParameterSet getCurrentParameterSet()
                                            throws Exception

Description copied from interface: InstantiableFromParameterSet

Returns the InstanceParameterSet that has been used to instantiate the current instance of the implementing class. If the current instance was not created using a InstanceParameterSet, an equivalent InstanceParameterSet should be returned, such that an instance created using this InstanceParameterSet would be in principle equal to the current instance.

Returns:

the current InstanceParameterSet

Throws:

Exception - is thrown if the InstanceParameterSet could not be returned