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

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

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Cloneable

public class PMMExplainingAwayResidual
extends Measure

Class for the network structure of a BayesianNetworkScoringFunction that is a permuted Markov model based on the explaining away residual.

Author:

Jan Grau

Nested Class Summary

static class

PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet Class for the parameters of a PMMExplainingAwayResidual structure Measure.

Constructor Summary

PMMExplainingAwayResidual(byte order, double[] ess)
Creates a new PMMExplainingAwayResidual of order order.

PMMExplainingAwayResidual(PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet parameters)
Creates a new PMMExplainingAwayResidual from the corresponding InstanceParameterSet parameters/code>.

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

Method Summary

PMMExplainingAwayResidual	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 as StringBuffer 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

PMMExplainingAwayResidual

public PMMExplainingAwayResidual(StringBuffer buf)
                          throws NonParsableException

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

Parameters:

buf - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

PMMExplainingAwayResidual

public PMMExplainingAwayResidual(byte order,
                                 double[] ess)
                          throws Exception

Creates a new PMMExplainingAwayResidual of order order.

Parameters:

order - the order, may be 1 or 2

ess - the equivalent sample sizes of both classes

Throws:

Exception - if the order is not 1 or 2

PMMExplainingAwayResidual

public PMMExplainingAwayResidual(PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet parameters)
                          throws Exception

Creates a new PMMExplainingAwayResidual from the corresponding InstanceParameterSet parameters/code>.

Parameters:

parameters - the corresponding parameters

Throws:

Exception - if the order is not 1 or 2

Method Detail

clone

public PMMExplainingAwayResidual 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 of the Measure

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 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

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer 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 an InstanceParameterSet, an equivalent InstanceParameterSet should be returned, so that an instance created using this InstanceParameterSet would be in principle equal to the current instance.

Returns:

the current InstanceParameterSet

Throws:

Exception - if the InstanceParameterSet could not be returned