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public interface VariableLengthDiffSM
This is an interface for all DifferentiableStatisticalModel
s that allow to score
subsequences of arbitrary length. This DifferentiableStatisticalModel
should be the
super class for non-motif DifferentiableStatisticalModel
s like homogeneous Markov
models, cyclic Markov models, ... etc.
Field Summary |
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Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore |
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UNKNOWN |
Method Summary | |
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double |
getLogNormalizationConstant(int length)
This method returns the logarithm of the normalization constant for a given sequence length. |
double |
getLogPartialNormalizationConstant(int parameterIndex,
int length)
This method returns the logarithm of the partial normalization constant for a given parameter index and a sequence length. |
double |
getLogScoreAndPartialDerivation(Sequence seq,
int startpos,
int endpos,
IntList indices,
DoubleList partialDer)
Returns the logarithmic score for a Sequence beginning at
position start in the Sequence and fills lists with
the indices and the partial derivations. |
double |
getLogScoreFor(Sequence seq,
int startpos,
int endpos)
Returns the logarithmic score for the Sequence seq
beginning at position start in the Sequence . |
void |
setStatisticForHyperparameters(int[] length,
double[] weight)
This method sets the hyperparameters for the model parameters by evaluating the given statistic. |
Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel |
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addGradientOfLogPriorTerm, getESS, getLogNormalizationConstant, getLogPartialNormalizationConstant, getLogPriorTerm, getSizeOfEventSpaceForRandomVariablesOfParameter, isNormalized |
Methods inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore |
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clone, getCurrentParameterValues, getInitialClassParam, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getNumberOfParameters, getNumberOfRecommendedStarts, initializeFunction, initializeFunctionRandomly, setParameters |
Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.StatisticalModel |
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emitDataSet, getLogProbFor, getLogProbFor, getLogProbFor, getMaximalMarkovOrder |
Methods inherited from interface de.jstacs.sequenceScores.SequenceScore |
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getAlphabetContainer, getCharacteristics, getInstanceName, getLength, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getNumericalCharacteristics, isInitialized |
Methods inherited from interface de.jstacs.Storable |
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toXML |
Method Detail |
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double getLogNormalizationConstant(int length)
length
- the sequence length
DifferentiableStatisticalModel.getLogNormalizationConstant()
double getLogPartialNormalizationConstant(int parameterIndex, int length) throws Exception
parameterIndex
- the index of the parameterlength
- the sequence length
Exception
- if something went wrongDifferentiableStatisticalModel.getLogPartialNormalizationConstant(int)
double getLogScoreFor(Sequence seq, int startpos, int endpos)
SequenceScore
Sequence
seq
beginning at position start
in the Sequence
.
getLogScoreFor
in interface SequenceScore
seq
- the Sequence
startpos
- the start position in the Sequence
endpos
- the end position (inclusive) in the Sequence
Sequence
double getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer)
DifferentiableSequenceScore
Sequence
beginning at
position start
in the Sequence
and fills lists with
the indices and the partial derivations.
getLogScoreAndPartialDerivation
in interface DifferentiableSequenceScore
seq
- the Sequence
startpos
- the start position in the Sequence
endpos
- the end position (inclusive) in the Sequence
indices
- an IntList
of indices, after method invocation the
list should contain the indices i where
partialDer
- a DoubleList
of partial derivations, after method
invocation the list should contain the corresponding
Sequence
void setStatisticForHyperparameters(int[] length, double[] weight) throws Exception
length
) and how often (
weight
) they have been seen.
length
- the non-negative lengths of the sequencesweight
- the non-negative weight for the corresponding sequence
Exception
- if something went wrongMutable
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