de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels
Class BNDiffSMParameter

java.lang.Object
  de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter

All Implemented Interfaces:

Storable, Cloneable

public class BNDiffSMParameter
extends Object
implements Storable, Cloneable

Class for the parameters of a BayesianNetworkDiffSM. Each parameter holds its current value, the symbol and position it is responsible for and the context of the current symbol. A parameter can either be free or determined by other parameters (on the same simplex).

Author:

Jan Grau

Field Summary

protected int[][]	context The context of this parameter.
protected double	count The counts for this parameter.
protected int	position The position of symbol this parameter is responsible for.
protected double	pseudoCount The pseudocount for this parameter.
protected byte	symbol The symbol (out of some Alphabet) this parameter is responsible for.

Constructor Summary

BNDiffSMParameter(int index, byte symbol, int position, double pseudoCount, boolean free)
Creates a new BNDiffSMParameter, that is BNDiffSMParameter no index in the list of BNDiffSMParameters of the BayesianNetworkDiffSM and responsible for symbol at position position and pseudo count pseudoCount.

BNDiffSMParameter(int index, byte symbol, int position, int[][] context, double pseudoCount, boolean free)
Creates a new BNDiffSMParameter, that is BNDiffSMParameter no index in the list of BNDiffSMParameters of the BayesianNetworkDiffSM and responsible for symbol at position position having context context and pseudocount pseudoCount.

BNDiffSMParameter(StringBuffer representation)
The standard constructor for the interface Storable.

Method Summary

void	addCount(double count2) Adds count2 to the counts of this parameter.
BNDiffSMParameter	clone()
double	doesApplyFor(Sequence seq) Indicates if the Sequence seq fulfills all requirements defined in the context.
double	getCounts() Returns the current counts for this parameter.
int	getDepth() Returns the depth of the tree, i.e. the number of parents of this parameter.
double	getExpValue() Returns Math.exp(getValue()), which is pre-computed.
int	getIndex() Returns the index of this parameter as defined in the constructor.
double	getLogPartialNormalizer() Returns the partial derivative of the normalization constant with respect to this parameter.
double	getLogT() Returns the part of the normalization constant of parameters before this parameter in the structure of the network.
double	getLogZ() Returns the part of the normalization constant of parameters after this parameter in the structure of the network.
int	getPosition() Returns the position of the symbol this parameter is responsible for as defined in the constructor.
double	getPseudoCount() Returns the pseudocount as given in the constructor.
double	getValue() Returns the current value of this parameter.
void	invalidateNormalizers() Resets all internal normalization constants to null.
boolean	isFree() Indicates if this parameter is free.
void	print() Prints the counts and the value of this parameter to System.out.
void	reset() Resets the counts to the pseudocounts and the value to 0.
void	setValue(double value) Sets the current value of this parameter.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class java.lang.Object

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

Field Detail

symbol

protected byte symbol

The symbol (out of some Alphabet) this parameter is responsible for.

position

protected int position

The position of symbol this parameter is responsible for.

context

protected int[][] context

The context of this parameter. The length context.length is equal to the number of parents, context[i] holds the information for parent no i, context[i][0] holds the position of parent i, context[i][1] ,... hold the possible configurations of parent i in the context. Normally, only context[i][1] exists, i.e. only one configuration is allowed in the context.

count

protected double count

The counts for this parameter. Used for determination of plug-in parameters.

pseudoCount

protected double pseudoCount

The pseudocount for this parameter. Used for determination of plug-in parameters.

Constructor Detail

BNDiffSMParameter

public BNDiffSMParameter(int index,
                         byte symbol,
                         int position,
                         double pseudoCount,
                         boolean free)

Creates a new BNDiffSMParameter, that is BNDiffSMParameter no index in the list of BNDiffSMParameters of the BayesianNetworkDiffSM and responsible for symbol at position position and pseudo count pseudoCount.

Parameters:

index - the index in the list of all parameters

symbol - the symbol this parameter is responsible for

position - the position of the symbol

pseudoCount - the pseudocount

free - indicates if this parameter is a free parameter

BNDiffSMParameter

public BNDiffSMParameter(int index,
                         byte symbol,
                         int position,
                         int[][] context,
                         double pseudoCount,
                         boolean free)

Creates a new BNDiffSMParameter, that is BNDiffSMParameter no index in the list of BNDiffSMParameters of the BayesianNetworkDiffSM and responsible for symbol at position position having context context and pseudocount pseudoCount.

Parameters:

index - the index in the list of all parameters

symbol - the symbol this parameter is responsible for

position - the position of the symbol

context - the context of this parameter

pseudoCount - the pseudocount

free - indicates if this parameter is a free parameter

BNDiffSMParameter

public BNDiffSMParameter(StringBuffer representation)
                  throws NonParsableException

The standard constructor for the interface Storable. Re-creates a parameter from its XML-representation as returned by the method toXML().

Parameters:

representation - the XML code as StringBuffer

Throws:

NonParsableException - if the StringBuffer representation could not be parsed

Method Detail

clone

public BNDiffSMParameter clone()
                        throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

getPseudoCount

public double getPseudoCount()

Returns the pseudocount as given in the constructor.

Returns:

the pseudocount

See Also:

BNDiffSMParameter(int, byte, int, double, boolean), BNDiffSMParameter(int, byte, int, int[][], double, boolean)

reset

public void reset()

Resets the counts to the pseudocounts and the value to 0.

getDepth

public int getDepth()

Returns the depth of the tree, i.e. the number of parents of this parameter.

Returns:

the depth of the tree

print

public void print()

Prints the counts and the value of this parameter to System.out.

doesApplyFor

public double doesApplyFor(Sequence seq)

Indicates if the Sequence seq fulfills all requirements defined in the context.

Parameters:

seq - the sequence

Returns:

true if this parameter is responsible for seq, false otherwise

getValue

public double getValue()

Returns the current value of this parameter.

Returns:

the current value

setValue

public void setValue(double value)

Sets the current value of this parameter.

Parameters:

value - the new value to be set

getExpValue

public double getExpValue()

Returns Math.exp(getValue()), which is pre-computed.

Returns:

the exponential value of this parameter

toXML

public StringBuffer toXML()

Description copied from interface: Storable

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

Specified by:

toXML in interface Storable

Returns:

the XML representation

invalidateNormalizers

public void invalidateNormalizers()

Resets all internal normalization constants to null.

getLogPartialNormalizer

public double getLogPartialNormalizer()
                               throws Exception

Returns the partial derivative of the normalization constant with respect to this parameter.

Returns:

the partial derivative

Throws:

Exception - if no normalization constants have been pre-computed

getCounts

public double getCounts()

Returns the current counts for this parameter.

Returns:

the current counts

addCount

public void addCount(double count2)

Adds count2 to the counts of this parameter.

Parameters:

count2 - the counts to be added

isFree

public boolean isFree()

Indicates if this parameter is free.

Returns:

true if the parameter is free, false otherwise

getPosition

public int getPosition()

Returns the position of the symbol this parameter is responsible for as defined in the constructor.

Returns:

the position of this parameter this parameter is responsible for

See Also:

BNDiffSMParameter(int, byte, int, double, boolean), BNDiffSMParameter(int, byte, int, int[][], double, boolean)

getIndex

public int getIndex()

Returns the index of this parameter as defined in the constructor.

Returns:

the index of this parameter in the list of all parameters

See Also:

BNDiffSMParameter(int, byte, int, double, boolean), BNDiffSMParameter(int, byte, int, int[][], double, boolean)

getLogZ

public double getLogZ()

Returns the part of the normalization constant of parameters after this parameter in the structure of the network.

Returns:

the normalization constant

getLogT

public double getLogT()

Returns the part of the normalization constant of parameters before this parameter in the structure of the network.

Returns:

the normalization constant