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java.lang.Objectde.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.MappingDiffSM
public final class MappingDiffSM
This class implements a DifferentiableStatisticalModel
that works on
mapped Sequence
s. For instance this can be useful for protein
sequences to reduce the alphabet of size 20 to a smaller alphabet using for
instance some chemical properties of the amino acids.
Be careful with references to Sequence
s in the internal
DifferentiableStatisticalModel
, since the Sequence
s might be
unexpectedly mutable.
MappedDiscreteSequence
,
DiscreteAlphabetMapping
Nested Class Summary |
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Nested classes/interfaces inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer |
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MotifDiscoverer.KindOfProfile |
Field Summary |
---|
Fields inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore |
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alphabets, length, r |
Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore |
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UNKNOWN |
Constructor Summary | |
---|---|
MappingDiffSM(AlphabetContainer originalAlphabetContainer,
DifferentiableStatisticalModel nsf,
DiscreteAlphabetMapping... mapping)
The main constructor creating a MappingDiffSM . |
|
MappingDiffSM(StringBuffer xml)
This is the constructor for Storable . |
Method Summary | |
---|---|
void |
addGradientOfLogPriorTerm(double[] grad,
int start)
This method computes the gradient of DifferentiableStatisticalModel.getLogPriorTerm() for each
parameter of this model. |
void |
adjustHiddenParameters(int index,
DataSet[] data,
double[][] weights)
Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters. |
MappingDiffSM |
clone()
Creates a clone (deep copy) of the current DifferentiableSequenceScore
instance. |
protected void |
fromXML(StringBuffer xml)
This method is called in the constructor for the Storable
interface to create a scoring function from a StringBuffer . |
double[] |
getCurrentParameterValues()
Returns a double array of dimension
DifferentiableSequenceScore.getNumberOfParameters() containing the current parameter values. |
double |
getESS()
Returns the equivalent sample size (ess) of this model, i.e. the equivalent sample size for the class or component that is represented by this model. |
DifferentiableStatisticalModel |
getFunction()
This method return the internal function. |
int |
getGlobalIndexOfMotifInComponent(int component,
int motif)
Returns the global index of the motif used in
component . |
int |
getIndexOfMaximalComponentFor(Sequence sequence)
Returns the index of the component with the maximal score for the sequence sequence . |
String |
getInstanceName()
Should return a short instance name such as iMM(0), BN(2), ... |
double |
getLogNormalizationConstant()
Returns the logarithm of the sum of the scores over all sequences of the event space. |
double |
getLogPartialNormalizationConstant(int parameterIndex)
Returns the logarithm of the partial normalization constant for the parameter with index parameterIndex . |
double |
getLogPriorTerm()
This method computes a value that is proportional to
where prior is the prior for the parameters of this model. |
double |
getLogScoreAndPartialDerivation(Sequence seq,
int start,
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 start)
Returns the logarithmic score for the Sequence seq
beginning at position start in the Sequence . |
int |
getMotifLength(int motif)
This method returns the length of the motif with index motif
. |
int |
getNumberOfComponents()
Returns the number of components in this MotifDiscoverer . |
int |
getNumberOfMotifs()
Returns the number of motifs for this MotifDiscoverer . |
int |
getNumberOfMotifsInComponent(int component)
Returns the number of motifs that are used in the component component of this MotifDiscoverer . |
int |
getNumberOfParameters()
Returns the number of parameters in this DifferentiableSequenceScore . |
double[] |
getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind)
Returns the profile of the scores for component component
and motif motif at all possible start positions of the motif
in the sequence sequence beginning at startpos . |
int |
getSizeOfEventSpaceForRandomVariablesOfParameter(int index)
Returns the size of the event space of the random variables that are affected by parameter no. |
double[] |
getStrandProbabilitiesFor(int component,
int motif,
Sequence sequence,
int startpos)
This method returns the probabilities of the strand orientations for a given subsequence if it is considered as site of the motif model in a specific component. |
void |
initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
This method creates the underlying structure of the DifferentiableSequenceScore . |
void |
initializeFunctionRandomly(boolean freeParams)
This method initializes the DifferentiableSequenceScore randomly. |
void |
initializeMotif(int motifIndex,
DataSet data,
double[] weights)
This method allows to initialize the model of a motif manually using a weighted sample. |
void |
initializeMotifRandomly(int motif)
This method initializes the motif with index motif randomly using for instance DifferentiableSequenceScore.initializeFunctionRandomly(boolean) . |
boolean |
isInitialized()
This method can be used to determine whether the instance is initialized. |
boolean |
modify(int offsetLeft,
int offsetRight)
Manually modifies the model. |
boolean |
modifyMotif(int motifIndex,
int offsetLeft,
int offsetRight)
Manually modifies the motif model with index motifIndex . |
void |
setParameters(double[] params,
int start)
This method sets the internal parameters to the values of params between start and
start + |
String |
toString()
|
StringBuffer |
toXML()
This method returns an XML representation as StringBuffer of an
instance of the implementing class. |
Methods inherited from class de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel |
---|
emitDataSet, getInitialClassParam, getLogProbFor, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getMaximalMarkovOrder, isNormalized, isNormalized |
Methods inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore |
---|
getAlphabetContainer, getCharacteristics, getLength, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreFor, getLogScoreFor, getNumberOfRecommendedStarts, getNumberOfStarts, getNumericalCharacteristics |
Methods inherited from class java.lang.Object |
---|
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore |
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getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getNumberOfRecommendedStarts |
Methods inherited from interface de.jstacs.sequenceScores.SequenceScore |
---|
getAlphabetContainer, getCharacteristics, getLength, getLogScoreFor, getLogScoreFor, getNumericalCharacteristics |
Constructor Detail |
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public MappingDiffSM(AlphabetContainer originalAlphabetContainer, DifferentiableStatisticalModel nsf, DiscreteAlphabetMapping... mapping) throws WrongAlphabetException, CloneNotSupportedException
MappingDiffSM
.
originalAlphabetContainer
- the original AlphabetContainer
nsf
- the internally used DifferentiableStatisticalModel
mapping
- the DiscreteAlphabetMapping
s defining the
transformation from the original AlphabetContainer
to
the AlphabetContainer
of the
DifferentiableStatisticalModel
nsf
WrongAlphabetException
- if there is a problem with the mapping of the
Alphabet
s
CloneNotSupportedException
- if the DifferentiableStatisticalModel
could not be
clonedpublic MappingDiffSM(StringBuffer xml) throws NonParsableException
Storable
. Creates a new
MappingDiffSM
out of a StringBuffer
.
xml
- the XML representation as StringBuffer
NonParsableException
- if the XML representation could not be parsedMethod Detail |
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public MappingDiffSM clone() throws CloneNotSupportedException
DifferentiableSequenceScore
DifferentiableSequenceScore
instance.
clone
in interface MotifDiscoverer
clone
in interface DifferentiableSequenceScore
clone
in interface SequenceScore
clone
in class AbstractDifferentiableStatisticalModel
DifferentiableSequenceScore
CloneNotSupportedException
- if something went wrong while cloning the
DifferentiableSequenceScore
Cloneable
public StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.
toXML
in interface Storable
protected void fromXML(StringBuffer xml) throws NonParsableException
AbstractDifferentiableSequenceScore
Storable
interface to create a scoring function from a StringBuffer
.
fromXML
in class AbstractDifferentiableSequenceScore
xml
- the XML representation as StringBuffer
NonParsableException
- if the StringBuffer
could not be parsedAbstractDifferentiableSequenceScore.AbstractDifferentiableSequenceScore(StringBuffer)
public void addGradientOfLogPriorTerm(double[] grad, int start) throws Exception
DifferentiableStatisticalModel
DifferentiableStatisticalModel.getLogPriorTerm()
for each
parameter of this model. The results are added to the array
grad
beginning at index start
.
addGradientOfLogPriorTerm
in interface DifferentiableStatisticalModel
grad
- the array of gradientsstart
- the start index in the grad
array, where the
partial derivations for the parameters of this models shall be
entered
Exception
- if something went wrong with the computing of the gradientsDifferentiableStatisticalModel.getLogPriorTerm()
public double getESS()
DifferentiableStatisticalModel
getESS
in interface DifferentiableStatisticalModel
public double getLogNormalizationConstant()
DifferentiableStatisticalModel
getLogNormalizationConstant
in interface DifferentiableStatisticalModel
public double getLogPartialNormalizationConstant(int parameterIndex) throws Exception
DifferentiableStatisticalModel
parameterIndex
. This is the logarithm of the partial derivation of the
normalization constant for the parameter with index
parameterIndex
,
getLogPartialNormalizationConstant
in interface DifferentiableStatisticalModel
parameterIndex
- the index of the parameter
Exception
- if something went wrong with the normalizationDifferentiableStatisticalModel.getLogNormalizationConstant()
public double getLogPriorTerm()
DifferentiableStatisticalModel
DifferentiableStatisticalModel.getESS()
* DifferentiableStatisticalModel.getLogNormalizationConstant()
+ Math.log( prior )
prior
is the prior for the parameters of this model.
getLogPriorTerm
in interface DifferentiableStatisticalModel
getLogPriorTerm
in interface StatisticalModel
DifferentiableStatisticalModel.getESS()
* DifferentiableStatisticalModel.getLogNormalizationConstant()
+ Math.log( prior ).
DifferentiableStatisticalModel.getESS()
,
DifferentiableStatisticalModel.getLogNormalizationConstant()
public int getSizeOfEventSpaceForRandomVariablesOfParameter(int index)
DifferentiableStatisticalModel
index
, i.e. the product of the
sizes of the alphabets at the position of each random variable affected
by parameter index
. For DNA alphabets this corresponds to 4
for a PWM, 16 for a WAM except position 0, ...
getSizeOfEventSpaceForRandomVariablesOfParameter
in interface DifferentiableStatisticalModel
index
- the index of the parameter
public double[] getCurrentParameterValues() throws Exception
DifferentiableSequenceScore
double
array of dimension
DifferentiableSequenceScore.getNumberOfParameters()
containing the current parameter values.
If one likes to use these parameters to start an optimization it is
highly recommended to invoke
DifferentiableSequenceScore.initializeFunction(int, boolean, DataSet[], double[][])
before.
After an optimization this method can be used to get the current
parameter values.
getCurrentParameterValues
in interface DifferentiableSequenceScore
Exception
- if no parameters exist (yet)public String getInstanceName()
SequenceScore
getInstanceName
in interface SequenceScore
public double getLogScoreFor(Sequence seq, int start)
SequenceScore
Sequence
seq
beginning at position start
in the Sequence
.
getLogScoreFor
in interface SequenceScore
seq
- the Sequence
start
- the start position in the Sequence
Sequence
public double getLogScoreAndPartialDerivation(Sequence seq, int start, 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
start
- the start position 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
public int getNumberOfParameters()
DifferentiableSequenceScore
DifferentiableSequenceScore
. If the
number of parameters is not known yet, the method returns
DifferentiableSequenceScore.UNKNOWN
.
getNumberOfParameters
in interface DifferentiableSequenceScore
DifferentiableSequenceScore
DifferentiableSequenceScore.UNKNOWN
public void initializeFunction(int index, boolean freeParams, DataSet[] data, double[][] weights) throws Exception
DifferentiableSequenceScore
DifferentiableSequenceScore
.
initializeFunction
in interface DifferentiableSequenceScore
index
- the index of the class the DifferentiableSequenceScore
modelsfreeParams
- indicates whether the (reduced) parameterization is useddata
- the samplesweights
- the weights of the sequences in the samples
Exception
- if something went wrongpublic void initializeFunctionRandomly(boolean freeParams) throws Exception
DifferentiableSequenceScore
DifferentiableSequenceScore
randomly. It has to
create the underlying structure of the DifferentiableSequenceScore
.
initializeFunctionRandomly
in interface DifferentiableSequenceScore
freeParams
- indicates whether the (reduced) parameterization is used
Exception
- if something went wrongpublic boolean isInitialized()
SequenceScore
SequenceScore.getLogScoreFor(Sequence)
.
isInitialized
in interface SequenceScore
true
if the instance is initialized, false
otherwisepublic void setParameters(double[] params, int start)
DifferentiableSequenceScore
params
between start
and
start + DifferentiableSequenceScore.getNumberOfParameters()
- 1
setParameters
in interface DifferentiableSequenceScore
params
- the new parametersstart
- the start index in params
public String toString()
toString
in class Object
public DifferentiableStatisticalModel getFunction() throws CloneNotSupportedException
DifferentiableStatisticalModel
that is internally used
CloneNotSupportedException
- if the DifferentiableStatisticalModel
could not be
clonedpublic int getNumberOfMotifs()
MotifDiscoverer
MotifDiscoverer
.
getNumberOfMotifs
in interface MotifDiscoverer
public void adjustHiddenParameters(int index, DataSet[] data, double[][] weights) throws Exception
MutableMotifDiscoverer
adjustHiddenParameters
in interface MutableMotifDiscoverer
index
- the index of the class of this MutableMotifDiscoverer
data
- the array of data for all classesweights
- the weights for all sequences in data
Exception
- thrown if the hidden parameters could not be adjustedpublic void initializeMotif(int motifIndex, DataSet data, double[] weights) throws Exception
MutableMotifDiscoverer
initializeMotif
in interface MutableMotifDiscoverer
motifIndex
- the index of the motif in the motif discovererdata
- the sample of sequencesweights
- either null
or an array of length data.getNumberofElements()
with non-negative weights.
Exception
- if initialize was not possiblepublic void initializeMotifRandomly(int motif) throws Exception
MutableMotifDiscoverer
motif
randomly using for instance DifferentiableSequenceScore.initializeFunctionRandomly(boolean)
.
Furthermore, if available, it also initializes the positional distribution.
initializeMotifRandomly
in interface MutableMotifDiscoverer
motif
- the index of the motif
Exception
- either if the index is wrong or if it is thrown by the method DifferentiableSequenceScore.initializeFunctionRandomly(boolean)
public boolean modifyMotif(int motifIndex, int offsetLeft, int offsetRight) throws Exception
MutableMotifDiscoverer
motifIndex
. The two offsets offsetLeft
and offsetRight
define how many positions the left or right border positions shall be moved. Negative numbers indicate moves to the left while positive
numbers correspond to moves to the right. The distribution for sequences to the left and right side of the motif shall be computed internally.
modifyMotif
in interface MutableMotifDiscoverer
motifIndex
- the index of the motif in the motif discovereroffsetLeft
- the offset on the left sideoffsetRight
- the offset on the right side
true
if the motif model was modified otherwise false
Exception
- if some unexpected error occurred during the modificationMutableMotifDiscoverer.modifyMotif(int, int, int)
,
Mutable.modify(int, int)
public int getGlobalIndexOfMotifInComponent(int component, int motif)
MotifDiscoverer
motif
used in
component
. The index returned must be at least 0 and less
than MotifDiscoverer.getNumberOfMotifs()
.
getGlobalIndexOfMotifInComponent
in interface MotifDiscoverer
component
- the component indexmotif
- the motif index in the component
motif in component
getIndexOfMaximalComponentFor
public int getIndexOfMaximalComponentFor(Sequence sequence)
throws Exception
- Description copied from interface:
MotifDiscoverer
- Returns the index of the component with the maximal score for the
sequence
sequence
.
- Specified by:
getIndexOfMaximalComponentFor
in interface MotifDiscoverer
- Parameters:
sequence
- the given sequence
- Returns:
- the index of the component with the maximal score for the given
sequence
- Throws:
Exception
- if the index could not be computed for any reasons
getMotifLength
public int getMotifLength(int motif)
- Description copied from interface:
MotifDiscoverer
- This method returns the length of the motif with index
motif
.
- Specified by:
getMotifLength
in interface MotifDiscoverer
- Parameters:
motif
- the index of the motif
- Returns:
- the length of the motif with index
motif
getNumberOfComponents
public int getNumberOfComponents()
- Description copied from interface:
MotifDiscoverer
- Returns the number of components in this
MotifDiscoverer
.
- Specified by:
getNumberOfComponents
in interface MotifDiscoverer
- Returns:
- the number of components
getNumberOfMotifsInComponent
public int getNumberOfMotifsInComponent(int component)
- Description copied from interface:
MotifDiscoverer
- Returns the number of motifs that are used in the component
component
of this MotifDiscoverer
.
- Specified by:
getNumberOfMotifsInComponent
in interface MotifDiscoverer
- Parameters:
component
- the component of the MotifDiscoverer
- Returns:
- the number of motifs
getProfileOfScoresFor
public double[] getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind)
throws Exception
- Description copied from interface:
MotifDiscoverer
- Returns the profile of the scores for component
component
and motif motif
at all possible start positions of the motif
in the sequence sequence
beginning at startpos
.
This array should be of length
sequence.length() - startpos - motifs[motif].length() + 1
.
A high score should encode for a probable start position.
- Specified by:
getProfileOfScoresFor
in interface MotifDiscoverer
- Parameters:
component
- the component indexmotif
- the index of the motif in the componentsequence
- the given sequencestartpos
- the start position in the sequencekind
- indicates the kind of profile
- Returns:
- the profile of scores
- Throws:
Exception
- if the score could not be computed for any reasons
getStrandProbabilitiesFor
public double[] getStrandProbabilitiesFor(int component,
int motif,
Sequence sequence,
int startpos)
throws Exception
- Description copied from interface:
MotifDiscoverer
- This method returns the probabilities of the strand orientations for a given subsequence if it is
considered as site of the motif model in a specific component.
- Specified by:
getStrandProbabilitiesFor
in interface MotifDiscoverer
- Parameters:
component
- the component indexmotif
- the index of the motif in the componentsequence
- the given sequencestartpos
- the start position in the sequence
- Returns:
- the probabilities of the strand orientations
- Throws:
Exception
- if the strand could not be computed for any reasons
modify
public boolean modify(int offsetLeft,
int offsetRight)
- Description copied from interface:
Mutable
- Manually modifies the model. The two offsets
offsetLeft
and offsetRight
define how many positions the left or
right border positions shall be moved. Negative numbers indicate moves to
the left while positive numbers correspond to moves to the right.
- Specified by:
modify
in interface Mutable
- Parameters:
offsetLeft
- the offset on the left sideoffsetRight
- the offset on the right side
- Returns:
true
if the motif model was modified otherwise
false
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