de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

Class BNDiffSMParameterTree

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree

All Implemented Interfaces:

Storable, Cloneable

public class BNDiffSMParameterTree
extends Object
implements Cloneable, Storable

Class for the tree that represents the context of a BNDiffSMParameter in a BayesianNetworkDiffSM.

Author:

Jan Grau

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	BNDiffSMParameterTree.TreeElement Class for the nodes of a BNDiffSMParameterTree

Constructor Summary

Constructors

Constructor and Description
BNDiffSMParameterTree(int pos, int[] contextPoss, AlphabetContainer alphabet, int firstParent, int[] firstChildren) Creates a new BNDiffSMParameterTree for the parameters at position pos using the parent positions in contextPoss.
BNDiffSMParameterTree(StringBuffer source) Recreates a BNDiffSMParameterTree from its XML representation as returned by toXML().

Method Summary

Modifier and Type	Method and Description
void	addCount(Sequence seq, int start, double count) Adds count to the parameter as returned by getParameterFor(Sequence, int).
void	backward(BNDiffSMParameterTree[] trees, int[][] order) Computes the backward-part of the normalization constant starting from this BNDiffSMParameterTree.
BNDiffSMParameterTree	clone()
Double	computeGammaNorm() Computes the Gamma-normalization for the prior.
void	copy(BNDiffSMParameterTree parameterTree) Copies the values of the parameters from another BNDiffSMParameterTree.
void	divideByUnfree() Divides each of the normalized parameters on a simplex by the last BNDiffSMParameter, which is defined not to be free.
void	drawKLDivergences(double[] kls, double[] weights, double[][][][] contrast, double samples) Draws KL-divergences between the distributions given by contrast[i] each weighted by weights[i] kls.length distributions drawn from a Dirichlet density centered around contrast, i.e.
void	drawKLDivergences(double weight, double[] kls, int startIdx, int endIdx, double[][][] contrast, double samples) Draws KL-divergences between the distribution given by contrast and endIdx-startIdx distributions drawn from a Dirichlet density centered around contrast, i.e.
void	fill(double[] weight, double[][][][] distribution) Fills all parameters with the probabilities given in distribution.
double	forward(BNDiffSMParameterTree[] trees) Computes the forward-part of the normalization constant starting from this BNDiffSMParameterTree.
int	getFirstParent() Returns the first parent of the random variable of this BNDiffSMParameterTree in the topological ordering of the network structure of the enclosing BayesianNetworkDiffSM.
double	getKLDivergence(double[][][] ds) Returns the KL-divergence of the distribution of this BNDiffSMParameterTree and the distribution given by ds.
double	getKLDivergence(double[] weight, double[][][][] distribution) Returns the KL-divergence of the distribution of this BNDiffSMParameterTree and a number of distribution given by ds and weighted by weight
double	getLocalScoreFor(Sequence seq, int i) Returns the score for the symbol at this BNDiffSMParameterTree starting from offset i
byte	getMaximalMarkovOrder() Returns the maximal Markov order of this tree.
double	getMaximumScore() Returns the maximum score in this tree.
int	getNumberOfParents() Returns the number of parents for the random variable of this BNDiffSMParameterTree in the network structure of the enclosing BayesianNetworkDiffSM.
BNDiffSMParameter	getParameterFor(int[] seq, int start) Returns the BNDiffSMParameter that is responsible for the suffix of sequence seq starting at position start.
BNDiffSMParameter	getParameterFor(Sequence seq, int start) Returns the BNDiffSMParameter that is responsible for the suffix of sequence seq starting at position start.
int[]	getParameterIndexesForSamplingStep(int step, int offset) Returns the indexes of the parameters, incremented by offset, that shall be sampled in step step of a grouped sampling process.
double	getProbFor(Sequence sequence) Returns the probability of Sequence sequence in this BNDiffSMParameterTree.
void	initializeRandomly(double ess) Initializes the parameters of this BNDiffSMParameterTree randomly.
void	insertProbs(double[] probs) Computes the probabilities for a PWM, i.e.
void	invalidateNormalizers() Resets all pre-computed normalization constants.
boolean	isLeaf() Indicates if the random variable of this BNDiffSMParameterTree is a leaf, i.e.
LinkedList<BNDiffSMParameter>	linearizeParameters() Extracts the BNDiffSMParameters from the leaves of this tree in left-to-right order (as specified by the order of the alphabet) and returns them as a LinkedList.
void	normalizeParameters() Normalizes the parameter values to the corresponding log-probabilities.
void	normalizePlugInParameters() Starts the normalization of the plug-in parameters to the logarithm of the MAP-estimates.
void	print() Prints the structure of this tree.
void	setParameterFor(int symbol, int[][] context, BNDiffSMParameter par) Sets the instance of the BNDiffSMParameter for symbol symbol and context context to BNDiffSMParameter par.
String	toHtml(NumberFormat nf) Returns an HTML representation of this tree.
String	toString(NumberFormat nf) Returns a string representation of this tree using the provided NumberFormat.
StringBuffer	toXML() Works as defined in Storable.

Methods inherited from class java.lang.Object

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

Constructor Detail

BNDiffSMParameterTree

public BNDiffSMParameterTree(int pos,
                             int[] contextPoss,
                             AlphabetContainer alphabet,
                             int firstParent,
                             int[] firstChildren)

Creates a new BNDiffSMParameterTree for the parameters at position pos using the parent positions in contextPoss. These are used to extract the correct alphabet out of alphabet for every context position. The first parent is the first parent of the random variable at pos as given by the topological ordering of the network structure of the enclosing BayesianNetworkDiffSM. The first children are the children the random variable at pos is the first parent for.

Parameters:

pos - the position of the random variable of the parameters in the tree

contextPoss - the positions of the context

alphabet - the alphabet of the enclosing BayesianNetworkDiffSM

firstParent - the first parent of this random variable, or -1 if the random variable has no parent

firstChildren - the first children of this random variable

BNDiffSMParameterTree

public BNDiffSMParameterTree(StringBuffer source)
                      throws NonParsableException

Recreates a BNDiffSMParameterTree from its XML representation as returned by toXML(). BNDiffSMParameterTree does not implement the Storable interface to recycle the AlphabetContainer of the enclosing BayesianNetworkDiffSM, but besides the different constructor works like any implementation of Storable.

Parameters:

source - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

Method Detail

clone

public BNDiffSMParameterTree clone()
                            throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

toString

public String toString(NumberFormat nf)

Returns a string representation of this tree using the provided NumberFormat.

Parameters:

nf - the number format

Returns:

the string representation

insertProbs

public void insertProbs(double[] probs)
                 throws Exception

Computes the probabilities for a PWM, i.e. the parameters in the tree have an empty context, and inserts them into probs. Used by BayesianNetworkDiffSM.getPWM().

Parameters:

probs - the array to store the probabilities for a PWM

Throws:

Exception - if the tree structure does have a non-empty context

linearizeParameters

public LinkedList<BNDiffSMParameter> linearizeParameters()

Extracts the BNDiffSMParameters from the leaves of this tree in left-to-right order (as specified by the order of the alphabet) and returns them as a LinkedList.

Returns:

the BNDiffSMParameters from the leaves in linear order

isLeaf

public boolean isLeaf()

Indicates if the random variable of this BNDiffSMParameterTree is a leaf, i.e. it has no children in the network structure of the enclosing BayesianNetworkDiffSM.

Returns:

true if this tree is a leaf, false otherwise

getNumberOfParents

public int getNumberOfParents()

Returns the number of parents for the random variable of this BNDiffSMParameterTree in the network structure of the enclosing BayesianNetworkDiffSM. This corresponds to the length of the context or the depth of the tree.

Returns:

the number of parents

print

public void print()

Prints the structure of this tree.

getParameterFor

public BNDiffSMParameter getParameterFor(Sequence seq,
                                         int start)

Returns the BNDiffSMParameter that is responsible for the suffix of sequence seq starting at position start.

Parameters:

seq - the Sequence

start - the first position in the suffix

Returns:

the BNDiffSMParameter that is responsible for the suffix

getParameterFor

public BNDiffSMParameter getParameterFor(int[] seq,
                                         int start)

Returns the BNDiffSMParameter that is responsible for the suffix of sequence seq starting at position start.

Parameters:

seq - the sequence encoded as int array

start - the first position in the suffix

Returns:

the BNDiffSMParameter that is responsible for the suffix

setParameterFor

public void setParameterFor(int symbol,
                            int[][] context,
                            BNDiffSMParameter par)

Sets the instance of the BNDiffSMParameter for symbol symbol and context context to BNDiffSMParameter par.

Parameters:

symbol - the symbol

context - the context

par - the new BNDiffSMParameter instance

invalidateNormalizers

public void invalidateNormalizers()

Resets all pre-computed normalization constants.

forward

public double forward(BNDiffSMParameterTree[] trees)
               throws RuntimeException

Computes the forward-part of the normalization constant starting from this BNDiffSMParameterTree. This is only possible for roots, i.e. BNDiffSMParameterTrees that do not have parents in the network structure of the enclosing BayesianNetworkDiffSM.

Parameters:

trees - the array of all trees as from the enclosing BayesianNetworkDiffSM

Returns:

the forward-part of the normalization constant

Throws:

RuntimeException - if this BNDiffSMParameterTree is not a root

backward

public void backward(BNDiffSMParameterTree[] trees,
                     int[][] order)
              throws RuntimeException

Computes the backward-part of the normalization constant starting from this BNDiffSMParameterTree. This is only possible for leaves, i.e. BNDiffSMParameterTrees that do not have children in the network structure of the enclosing BayesianNetworkDiffSM.

Parameters:

trees - the array of all trees as from the enclosing BayesianNetworkDiffSM

order - the topological ordering as returned by TopSort.getTopologicalOrder(int[][])

Throws:

RuntimeException - if this BNDiffSMParameterTree is not a leaf

addCount

public void addCount(Sequence seq,
                     int start,
                     double count)

Adds count to the parameter as returned by getParameterFor(Sequence, int).

Parameters:

seq - the sequence

start - the first position of the suffix of seq

count - the added count

normalizePlugInParameters

public void normalizePlugInParameters()

Starts the normalization of the plug-in parameters to the logarithm of the MAP-estimates.

normalizeParameters

public void normalizeParameters()

Normalizes the parameter values to the corresponding log-probabilities. After this step, BayesianNetworkDiffSM.getLogNormalizationConstant() should return 0.

divideByUnfree

public void divideByUnfree()

Divides each of the normalized parameters on a simplex by the last BNDiffSMParameter, which is defined not to be free. In the log-space this amounts to subtracting the value of the last BNDiffSMParameter from all BNDiffSMParameters on the simplex.

toXML

public StringBuffer toXML()

Works as defined in Storable. Returns an XML representation of this BNDiffSMParameterTree.

Specified by:

toXML in interface Storable

Returns:

the XML representation of this BNDiffSMParameterTree

See Also:

Storable.toXML()

getFirstParent

public int getFirstParent()

Returns the first parent of the random variable of this BNDiffSMParameterTree in the topological ordering of the network structure of the enclosing BayesianNetworkDiffSM.

Returns:

the first parent

drawKLDivergences

public void drawKLDivergences(double weight,
                              double[] kls,
                              int startIdx,
                              int endIdx,
                              double[][][] contrast,
                              double samples)

Draws KL-divergences between the distribution given by contrast and endIdx-startIdx distributions drawn from a Dirichlet density centered around contrast, i.e. the hyper-parameters of the Dirichlet density are the probabilities of contrast weighted by samples. The drawn KL-divergences are stored into kls between startIndex and endIndex (exclusive).

Parameters:

weight - a weight on the KL-divergences

kls - the array of KL-divergences which is filled

startIdx - the first index

endIdx - the index after the last index

contrast - the distribution to check against

samples - number of sequences + equivalent sample size

getKLDivergence

public double getKLDivergence(double[][][] ds)

Returns the KL-divergence of the distribution of this BNDiffSMParameterTree and the distribution given by ds.

Parameters:

ds - the distribution

Returns:

the KL-divergence

getKLDivergence

public double getKLDivergence(double[] weight,
                              double[][][][] distribution)

Returns the KL-divergence of the distribution of this BNDiffSMParameterTree and a number of distribution given by ds and weighted by weight

Parameters:

distribution - the distribution

weight - the weights on the distributions

Returns:

the KL-divergence

drawKLDivergences

public void drawKLDivergences(double[] kls,
                              double[] weights,
                              double[][][][] contrast,
                              double samples)

Draws KL-divergences between the distributions given by contrast[i] each weighted by weights[i] kls.length distributions drawn from a Dirichlet density centered around contrast, i.e. the hyper-parameters of the Dirichlet density are the probabilities of contrast weighted by samples. The drawn KL-divergences are added to the entries of kls.

Parameters:

kls - the array of KL-divergences which is filled

weights - the weights on the distributions in contrast

contrast - the distribution to check against

samples - number of sequences + equivalent sample size

fill

public void fill(double[] weight,
                 double[][][][] distribution)

Fills all parameters with the probabilities given in distribution.

Parameters:

distribution - the distribution

weight - the weights on the distributions

copy

public void copy(BNDiffSMParameterTree parameterTree)

Copies the values of the parameters from another BNDiffSMParameterTree.

Parameters:

parameterTree - the template

initializeRandomly

public void initializeRandomly(double ess)

Initializes the parameters of this BNDiffSMParameterTree randomly.

Parameters:

ess - the equivalent sample size

computeGammaNorm

public Double computeGammaNorm()

Computes the Gamma-normalization for the prior.

Returns:

the Gamma-normalization

getProbFor

public double getProbFor(Sequence sequence)

Returns the probability of Sequence sequence in this BNDiffSMParameterTree.

Parameters:

sequence - the sequence

Returns:

the probability

getParameterIndexesForSamplingStep

public int[] getParameterIndexesForSamplingStep(int step,
                                                int offset)

Returns the indexes of the parameters, incremented by offset, that shall be sampled in step step of a grouped sampling process.

Parameters:

step - the step

offset - the offset on the parameter indexes

Returns:

the indexes of the group of parameters

getMaximalMarkovOrder

public byte getMaximalMarkovOrder()

Returns the maximal Markov order of this tree.

Returns:

the order

getMaximumScore

public double getMaximumScore()

Returns the maximum score in this tree.

Returns:

the score

toHtml

public String toHtml(NumberFormat nf)

Returns an HTML representation of this tree.

Parameters:

nf - the number format

Returns:

the HTML representation

getLocalScoreFor

public double getLocalScoreFor(Sequence seq,
                               int i)

Returns the score for the symbol at this BNDiffSMParameterTree starting from offset i

Parameters:

seq - the sequence

i - the offset

Returns:

the score