de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
Class DAGTrainSM

java.lang.Object
  de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel
      de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM
          de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhomogeneousDGTrainSM
              de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.DAGTrainSM

All Implemented Interfaces:

InstantiableFromParameterSet, SequenceScore, StatisticalModel, TrainableStatisticalModel, Storable, Cloneable

Direct Known Subclasses:

BayesianNetworkTrainSM, FSDAGTrainSM

public abstract class DAGTrainSM
extends InhomogeneousDGTrainSM

The abstract class for directed acyclic graphical models (DAGTrainSM).

Author:

Jens Keilwagen

Field Summary

protected InhCondProb[]

constraints The constraints for the model.

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhomogeneousDGTrainSM

DEFAULT_STREAM, sostream

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM

params, trained

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel

alphabets, length

Constructor Summary

protected	DAGTrainSM(IDGTrainSMParameterSet params) This is the main constructor.
protected	DAGTrainSM(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

protected static boolean	checkAcyclic(int length, int[][] graph) This method checks whether a given graph is acyclic.
DAGTrainSM	clone() Follows the conventions of Object's clone()-method.
protected void	createConstraints(int[][] structure) This method creates the constraints for a given structure.
protected void	drawParameters(DataSet data, double[] weights) This method draws the parameter of the model from the likelihood or the posterior, respectively.
DataSet	emitDataSet(int n, int... lengths) This method returns a DataSet object containing artificial sequence(s).
protected void	estimateParameters(DataSet data, double[] weights) This method estimates the parameter of the model from the likelihood or the posterior, respectively.
protected StringBuffer	getFurtherModelInfos() Returns further model information as a StringBuffer.
double	getLogPriorTerm() Returns a value that is proportional to the log of the prior.
double	getLogProbFor(Sequence sequence, int startpos, int endpos) Returns the logarithm of the probability of (a part of) the given sequence given the model.
NumericalResultSet	getNumericalCharacteristics() Returns the subset of numerical values that are also returned by SequenceScore.getCharacteristics().
String	getStructure() Returns a String representation of the underlying graph.
protected void	setFurtherModelInfos(StringBuffer xml) This method replaces the internal model information with those from a StringBuffer.
String	toString(NumberFormat nf) This method returns a String representation of the instance.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhomogeneousDGTrainSM

check, set, setOutputStream

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DiscreteGraphicalTrainSM

fromXML, getCurrentParameterSet, getDescription, getESS, getXMLTag, isInitialized, toXML

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel

getAlphabetContainer, getCharacteristics, getLength, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getMaximalMarkovOrder, toString, train

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel

train

Methods inherited from interface de.jstacs.sequenceScores.SequenceScore

getInstanceName

Field Detail

constraints

protected InhCondProb[] constraints

The constraints for the model.

Constructor Detail

DAGTrainSM

protected DAGTrainSM(IDGTrainSMParameterSet params)
              throws CloneNotSupportedException,
                     IllegalArgumentException,
                     NonParsableException

This is the main constructor. It creates a new DAGTrainSM from the given IDGTrainSMParameterSet.

Parameters:

params - the given parameter set

Throws:

CloneNotSupportedException - if the parameter set could not be cloned

IllegalArgumentException - if the parameter set is not instantiated

NonParsableException - if the parameter set is not parsable

See Also:

InhomogeneousDGTrainSM.InhomogeneousDGTrainSM(IDGTrainSMParameterSet)

DAGTrainSM

protected DAGTrainSM(StringBuffer xml)
              throws NonParsableException

The standard constructor for the interface Storable. Creates a new DAGTrainSM out of its XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the DAGTrainSM could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)

See Also:

Storable, InhomogeneousDGTrainSM.InhomogeneousDGTrainSM(StringBuffer)

Method Detail

clone

public DAGTrainSM clone()
                 throws CloneNotSupportedException

Description copied from class: AbstractTrainableStatisticalModel

Follows the conventions of Object's clone()-method.

Specified by:

clone in interface SequenceScore

Specified by:

clone in interface TrainableStatisticalModel

Overrides:

clone in class InhomogeneousDGTrainSM

Returns:

an object, that is a copy of the current AbstractTrainableStatisticalModel (the member-AlphabetContainer isn't deeply cloned since it is assumed to be immutable). The type of the returned object is defined by the class X directly inherited from AbstractTrainableStatisticalModel. Hence X's clone()-method should work as:
1. Object o = (X)super.clone();
2. all additional member variables of o defined by X that are not of simple data-types like int, double, ... have to be deeply copied
3. return o

Throws:

CloneNotSupportedException - if something went wrong while cloning

emitDataSet

public DataSet emitDataSet(int n,
                           int... lengths)
                    throws NotTrainedException,
                           Exception

Description copied from interface: StatisticalModel

This method returns a DataSet object containing artificial sequence(s).

There are two different possibilities to create a data set for a model with length 0 (homogeneous models).

1. emitDataSet( int n, int l ) should return a data set with n sequences of length l.
2. emitDataSet( int n, int[] l ) should return a data set with n sequences which have a sequence length corresponding to the entry in the given array l.

There are two different possibilities to create a data set for a model with length greater than 0 (inhomogeneous models).
emitDataSet( int n ) and emitDataSet( int n, null ) should return a data set with n sequences of length of the model ( SequenceScore.getLength()).

The standard implementation throws an Exception.

Specified by:

emitDataSet in interface StatisticalModel

Overrides:

emitDataSet in class AbstractTrainableStatisticalModel

Parameters:

n - the number of sequences that should be contained in the returned data set

lengths - the length of the sequences for a homogeneous model; for an inhomogeneous model this parameter should be null or an array of size 0.

Returns:

a DataSet containing the artificial sequence(s)

Throws:

NotTrainedException - if the model is not trained yet

Exception - if the emission did not succeed

See Also:

DataSet

getLogPriorTerm

public double getLogPriorTerm()
                       throws Exception

Description copied from interface: StatisticalModel

Returns a value that is proportional to the log of the prior. For maximum likelihood (ML) 0 should be returned.

Returns:

a value that is proportional to the log of the prior

Throws:

Exception - if something went wrong

getLogProbFor

public double getLogProbFor(Sequence sequence,
                            int startpos,
                            int endpos)
                     throws NotTrainedException,
                            Exception

Description copied from interface: StatisticalModel

Returns the logarithm of the probability of (a part of) the given sequence given the model. If at least one random variable is continuous the value of density function is returned.

It extends the possibility given by the method StatisticalModel.getLogProbFor(Sequence, int) by the fact, that the model could be e.g. homogeneous and therefore the length of the sequences, whose probability should be returned, is not fixed. Additionally, the end position of the part of the given sequence is given and the probability of the part from position startpos to endpos (inclusive) should be returned.
The length and the alphabets define the type of data that can be modeled and therefore both has to be checked.

Parameters:

sequence - the given sequence

startpos - the start position within the given sequence

endpos - the last position to be taken into account

Returns:

the logarithm of the probability or the value of the density function of (the part of) the given sequence given the model

Throws:

NotTrainedException - if the model is not trained yet

Exception - if the sequence could not be handled (e.g. startpos > , endpos > sequence.length, ...) by the model

getNumericalCharacteristics

public NumericalResultSet getNumericalCharacteristics()

Description copied from interface: SequenceScore

Returns the subset of numerical values that are also returned by SequenceScore.getCharacteristics().

Returns:

the numerical characteristics of the current instance

getStructure

public String getStructure()
                    throws NotTrainedException

Description copied from class: InhomogeneousDGTrainSM

Returns a String representation of the underlying graph.

Specified by:

getStructure in class InhomogeneousDGTrainSM

Returns:

a String representation of the underlying graph

Throws:

NotTrainedException - if the structure is not set, this can only be the case if the model is not trained

toString

public String toString(NumberFormat nf)

Description copied from interface: SequenceScore

This method returns a String representation of the instance.

Specified by:

toString in interface SequenceScore

Overrides:

toString in class DiscreteGraphicalTrainSM

Parameters:

nf - the NumberFormat for the String representation of parameters or probabilities

Returns:

a String representation of the instance

checkAcyclic

protected static boolean checkAcyclic(int length,
                                      int[][] graph)

This method checks whether a given graph is acyclic.

Parameters:

length - the sequence length (which corresponds to the number of nodes in the graph)

graph - the specified graph

Returns:

true if the given graph is acyclic, false otherwise

createConstraints

protected void createConstraints(int[][] structure)

This method creates the constraints for a given structure.

Parameters:

structure - the specified structure

drawParameters

protected void drawParameters(DataSet data,
                              double[] weights)
                       throws Exception

This method draws the parameter of the model from the likelihood or the posterior, respectively.

Parameters:

data - the given data

weights - the weights for the sequences in the data

Throws:

Exception - if something went wrong while counting or drawing

See Also:

ConstraintManager.countInhomogeneous(de.jstacs.data.AlphabetContainer, int, DataSet, double[], boolean, de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint...), ConstraintManager.drawFreqs(double, InhCondProb...)

estimateParameters

protected void estimateParameters(DataSet data,
                                  double[] weights)
                           throws Exception

This method estimates the parameter of the model from the likelihood or the posterior, respectively.

Parameters:

data - the data

weights - the weights for the sequences in the data

Throws:

Exception - if something went wrong while counting or estimating

See Also:

drawParameters(DataSet, double[])

getFurtherModelInfos

protected StringBuffer getFurtherModelInfos()

Description copied from class: DiscreteGraphicalTrainSM

Returns further model information as a StringBuffer.

Specified by:

getFurtherModelInfos in class DiscreteGraphicalTrainSM

Returns:

further model information like parameters of the distribution etc. in XML format

See Also:

DiscreteGraphicalTrainSM.toXML()

setFurtherModelInfos

protected void setFurtherModelInfos(StringBuffer xml)
                             throws NonParsableException

Description copied from class: DiscreteGraphicalTrainSM

This method replaces the internal model information with those from a StringBuffer.

Specified by:

setFurtherModelInfos in class DiscreteGraphicalTrainSM

Parameters:

xml - contains the model information like parameters of the distribution etc. in XML format

Throws:

NonParsableException - if the StringBuffer could not be parsed

See Also:

DiscreteGraphicalTrainSM.fromXML(StringBuffer)