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

Class BTExplainingAwayResidual

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure

de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Cloneable

public class BTExplainingAwayResidual
extends Measure

Structure learning Measure that computes a maximum spanning tree based on the explaining away residual 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

Nested Classes

Modifier and Type	Class and Description
static class	BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet Class for the parameters of a BTExplainingAwayResidual 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

Constructors

Constructor and Description
BTExplainingAwayResidual(BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet parameters) Creates a new BTExplainingAwayResidual from the corresponding InstanceParameterSet parameters.
BTExplainingAwayResidual(double[] ess) Creates a new explaining away residual Bayesian tree Measure.
BTExplainingAwayResidual(StringBuffer buf) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
double[][]	getEAR(DataSet fg, DataSet bg, double[] weightsFg, double[] weightsBg, int length) Returns the explaining away residual (EAR) between all pairs of positions as a matrix.
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, fromXML, getCMI, getCMI, getCurrentParameterSet, getEAR, getEAR, getMatrixForKruskal, getMI, getMI, getStatistics, getStatisticsOrderTwo, isShiftable, reStructure, sum, toParents, toXML, union

Methods inherited from class java.lang.Object

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

Constructor Detail

BTExplainingAwayResidual

public BTExplainingAwayResidual(double[] ess)
                         throws Exception

Creates a new explaining away residual Bayesian tree Measure.

Parameters:

ess - the equivalent sample sizes (ess) for the classes

Throws:

Exception - if the parameters could bot be created for the

BTExplainingAwayResidual

public BTExplainingAwayResidual(BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet parameters)
                         throws CloneNotSupportedException

Creates a new BTExplainingAwayResidual from the corresponding InstanceParameterSet parameters.

Parameters:

parameters - the corresponding parameters

Throws:

CloneNotSupportedException - if the parameters could not be cloned

BTExplainingAwayResidual

public BTExplainingAwayResidual(StringBuffer buf)
                         throws NonParsableException

The standard constructor for the interface Storable. Recreates a BTExplainingAwayResidual 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

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

getEAR

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

Returns the explaining away residual (EAR) between all pairs of positions as a matrix.

Parameters:

fg - the foreground data

bg - the background data

weightsFg - the weights associated with the foreground data

weightsBg - the weights associated with the background data

length - the length of the sequences

Returns:

the pairwise EAR

Throws:

Exception - if the specified length does not match the length of the sequences in the data

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