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## de.jstacs.scoringFunctions.homogeneous
Class HMMScoringFunction

    java.lang.Object
      de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
          de.jstacs.scoringFunctions.VariableLengthScoringFunction
              de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction
                  de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction

All Implemented Interfaces:
  NormalizableScoringFunction, ScoringFunction, Storable, Cloneable

    public class HMMScoringFunction

extends HomogeneousScoringFunction

This scoring function implements a homogeneous Markov model of arbitrary order for any sequence length. The scoring function uses the parameterization of Meila if one uses the free parameters, which yields in a non-concave log conditional likelihood.

Author:
  Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
`alphabets, length, r`

Fields inherited from interface de.jstacs.scoringFunctions.ScoringFunction
`UNKNOWN`

Constructor Summary
`HMMScoringFunction(AlphabetContainer alphabets, int order, double classEss, double[] sumOfHyperParams, boolean plugIn, boolean optimize, int starts)` This is the main constructor that creates an instance of a homogeneous Markov model of arbitrary order.
`HMMScoringFunction(StringBuffer xml)` This is the constructor for `Storable`.

Method Summary
`void` | `addGradientOfLogPriorTerm(double[] grad, int start)` This method computes the gradient of `NormalizableScoringFunction.getLogPriorTerm()` for each parameter of this model.
`HMMScoringFunction` | `clone()` Creates a clone (deep copy) of the current `ScoringFunction` instance.
`Sample` | `emit(int numberOfSequences, int... seqLength)` This method returns a `Sample` object containing artificial sequence(s).
`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[][][]` | `getAllConditionalStationaryDistributions()` This method returns the stationary conditional distributions.
`double[]` | `getCurrentParameterValues()` Returns a `double` array of dimension `ScoringFunction.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.
`String` | `getInstanceName()` Returns a short instance name.
`double` | `getLogPriorTerm()` This method computes a value that is proportional to `NormalizableScoringFunction.getEss()` `* Math.log( `NormalizableScoringFunction.getNormalizationConstant()` ) + Math.log( prior ).`
`double` | `getLogScore(Sequence seq, int start, int length)` This method computes the logarithm of the score for a given subsequence.
`double` | `getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)` This method computes the logarithm of the score and the partial derivations for a given subsequence.
`int` | `getMaximalMarkovOrder()` Returns the maximal used markov oder.
`double` | `getNormalizationConstant(int length)` This method returns the normalization constant for a given sequence length.
`int` | `getNumberOfParameters()` Returns the number of parameters in this `ScoringFunction`.
`int` | `getNumberOfRecommendedStarts()` This method returns the number of recommended optimization starts.
`double` | `getPartialNormalizationConstant(int parameterIndex, int length)` This method returns the partial normalization constant for a given parameter index and a sequence length.
`int` | `getSizeOfEventSpaceForRandomVariablesOfParameter(int index)` Returns the size of the event space of the random variables that are affected by parameter no.
`void` | `initializeFunction(int index, boolean freeParams, Sample[] data, double[][] weights)` This method creates the underlying structure of the `ScoringFunction`.
`void` | `initializeFunctionRandomly(boolean freeParams)` This method initializes the `ScoringFunction` randomly.
`void` | `initializeUniformly(boolean freeParams)` This method allows to initialize the instance with an uniform distribution.
`boolean` | `isInitialized()` This method can be used to determine whether the model is initialized.
`boolean` | `isNormalized()` This method indicates whether the implemented score is already normalized to 1 or not.
`void` | `setParameterOptimization(boolean optimize)` This method allows the user to specify whether the parameters should be optimized or not.
`void` | `setParameters(double[] params, int start)` This method sets the internal parameters to the values of `params` between `start` and `start + `ScoringFunction.getNumberOfParameters()` - 1`
`void` | `setStatisticForHyperparameters(int[] length, double[] weight)` This method sets the hyperparameters for the model parameters by evaluating the given statistic.
`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.scoringFunctions.VariableLengthScoringFunction
`getLogScore, getLogScoreAndPartialDerivation, getNormalizationConstant, getPartialNormalizationConstant`

Methods inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
`getAlphabetContainer, getInitialClassParam, getLength, getLogScore, getLogScoreAndPartialDerivation, isNormalized`

Methods inherited from class java.lang.Object
`equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Constructor Detail

### HMMScoringFunction

    public HMMScoringFunction(AlphabetContainer alphabets,
                              int order,
                              double classEss,
                              double[] sumOfHyperParams,
                              boolean plugIn,
                              boolean optimize,
                              int starts)

  This is the main constructor that creates an instance of a homogeneous Markov model of arbitrary order.

  Parameters:
    `alphabets` - the `AlphabetContainer`
    `order` - the oder of the model (has to be non-negative)
    `classEss` - the equivalent sample size (ess) of the class
    `sumOfHyperParams` - the sum of the hyperparameters for each order (length has to be `order`, each entry has to be non-negative)
    `plugIn` - a switch which enables to use the MAP-parameters as plug-in parameters
    `optimize` - a switch which enables to optimize or fix the parameters
    `starts` - the number of recommended starts

### HMMScoringFunction

    public HMMScoringFunction(StringBuffer xml)
                       throws NonParsableException

  This is the constructor for `Storable`. Creates a new `HMMScoringFunction` out of its XML representation as returned by `fromXML(StringBuffer)`.

  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `StringBuffer` `representation` could not be parsed

Method Detail

### clone

    public HMMScoringFunction clone()
                             throws CloneNotSupportedException

  Description copied from interface: `ScoringFunction`
  Creates a clone (deep copy) of the current `ScoringFunction` instance.

  Specified by:
    `clone` in interface `ScoringFunction`
  Overrides:
    `clone` in class `AbstractNormalizableScoringFunction`
  Returns:
    the cloned instance of the current `ScoringFunction`
  Throws:
    `CloneNotSupportedException` - if something went wrong while cloning the `ScoringFunction`

### getInstanceName

    public String getInstanceName()

  Description copied from interface: `ScoringFunction`
  Returns a short instance name.

  Returns:
    a short instance name

### getLogScore

    public double getLogScore(Sequence seq,
                              int start,
                              int length)

  Description copied from class: `VariableLengthScoringFunction`
  This method computes the logarithm of the score for a given subsequence.

  Specified by:
    `getLogScore` in class `VariableLengthScoringFunction`
  Parameters:
    `seq` - the `Sequence`
    `start` - the start index in the `Sequence`
    `length` - the length of the `Sequence` beginning at `start`
  Returns:
    the logarithm of the score for the subsequence
  See Also:
    `ScoringFunction.getLogScore(Sequence, int)`

### getLogScoreAndPartialDerivation

    public double getLogScoreAndPartialDerivation(Sequence seq,
                                                  int start,
                                                  int length,
                                                  IntList indices,
                                                  DoubleList dList)

  Description copied from class: `VariableLengthScoringFunction`
  This method computes the logarithm of the score and the partial derivations for a given subsequence.

  Specified by:
    `getLogScoreAndPartialDerivation` in class `VariableLengthScoringFunction`
  Parameters:
    `seq` - the `Sequence`
    `start` - the start index in the `Sequence`
    `length` - the end index in the `Sequence`
    `indices` - an `IntList` of indices, after method invocation the list should contain the indices i where `\frac{\partial \log score(seq,start,length)}{\partial \lambda_i}` is not zero
    `dList` - a `DoubleList` of partial derivations, after method invocation the list should contain the corresponding `\frac{\partial \log score(seq,start,length)}{\partial \lambda_i}`
  Returns:
    the logarithm of the score
  See Also:
    `ScoringFunction.getLogScoreAndPartialDerivation(Sequence, int, IntList, DoubleList)`

### getNumberOfParameters

    public int getNumberOfParameters()

  Description copied from interface: `ScoringFunction`
  Returns the number of parameters in this `ScoringFunction`. If the number of parameters is not known yet, the method returns `ScoringFunction.UNKNOWN`.

  Returns:
    the number of parameters in this `ScoringFunction`
  See Also:
    `ScoringFunction.UNKNOWN`

### setParameters

    public void setParameters(double[] params,
                              int start)

  Description copied from interface: `ScoringFunction`
  This method sets the internal parameters to the values of `params` between `start` and `start + `ScoringFunction.getNumberOfParameters()` - 1`

  Parameters:
    `params` - the new parameters
    `start` - the start index in `params`

### toXML

    public StringBuffer toXML()

  Description copied from interface: `Storable`
  This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

  Returns:
    the XML representation

### getCurrentParameterValues

    public double[] getCurrentParameterValues()

  Description copied from interface: `ScoringFunction`
  Returns a `double` array of dimension `ScoringFunction.getNumberOfParameters()` containing the current parameter values. If one likes to use these parameters to start an optimization it is highly recommended to invoke `ScoringFunction.initializeFunction(int, boolean, Sample[], double[][])` before. After an optimization this method can be used to get the current parameter values.

  Returns:
    the current parameter values

### initializeFunction

    public void initializeFunction(int index,
                                   boolean freeParams,
                                   Sample[] data,
                                   double[][] weights)

  Description copied from interface: `ScoringFunction`
  This method creates the underlying structure of the `ScoringFunction`.

  Parameters:
    `index` - the index of the class the `ScoringFunction` models
    `freeParams` - indicates whether the (reduced) parameterization is used
    `data` - the samples
    `weights` - the weights of the sequences in the samples

### initializeFunctionRandomly

    public void initializeFunctionRandomly(boolean freeParams)

  Description copied from interface: `ScoringFunction`
  This method initializes the `ScoringFunction` randomly. It has to create the underlying structure of the `ScoringFunction`.

  Parameters:
    `freeParams` - indicates whether the (reduced) parameterization is used

### fromXML

    protected void fromXML(StringBuffer xml)
                    throws NonParsableException

  Description copied from class: `AbstractNormalizableScoringFunction`
  This method is called in the constructor for the `Storable` interface to create a scoring function from a `StringBuffer`.

  Specified by:
    `fromXML` in class `AbstractNormalizableScoringFunction`
  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `StringBuffer` could not be parsed
  See Also:
    `AbstractNormalizableScoringFunction.AbstractNormalizableScoringFunction(StringBuffer)`

### getSizeOfEventSpaceForRandomVariablesOfParameter

    public int getSizeOfEventSpaceForRandomVariablesOfParameter(int index)

  Description copied from interface: `NormalizableScoringFunction`
  Returns the size of the event space of the random variables that are affected by parameter no. `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, ...

  Parameters:
    `index` - the index of the parameter
  Returns:
    the size of the event space

### getNormalizationConstant

    public double getNormalizationConstant(int length)

  Description copied from class: `VariableLengthScoringFunction`
  This method returns the normalization constant for a given sequence length.

  Specified by:
    `getNormalizationConstant` in class `VariableLengthScoringFunction`
  Parameters:
    `length` - the sequence length
  Returns:
    the normalization constant
  See Also:
    `NormalizableScoringFunction.getNormalizationConstant()`

### getPartialNormalizationConstant

    public double getPartialNormalizationConstant(int parameterIndex,
                                                  int length)
                                           throws Exception

  Description copied from class: `VariableLengthScoringFunction`
  This method returns the partial normalization constant for a given parameter index and a sequence length.

  Specified by:
    `getPartialNormalizationConstant` in class `VariableLengthScoringFunction`
  Parameters:
    `parameterIndex` - the index of the parameter
    `length` - the sequence length
  Returns:
    the partial normalization constant
  Throws:
    `Exception` - if something went wrong
  See Also:
    `NormalizableScoringFunction.getPartialNormalizationConstant(int)`

### getEss

    public double getEss()

  Description copied from interface: `NormalizableScoringFunction`
  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.

  Returns:
    the equivalent sample size.

### toString

    public String toString()

  Overrides:
    `toString` in class `Object`

### getLogPriorTerm

    public double getLogPriorTerm()

  Description copied from interface: `NormalizableScoringFunction`
  This method computes a value that is proportional to

  `NormalizableScoringFunction.getEss()` `* Math.log( `NormalizableScoringFunction.getNormalizationConstant()` ) + Math.log( prior ).`

  where `prior` is the prior for the parameters of this model.

  Returns:
    a value that is proportional to `NormalizableScoringFunction.getEss()` `* Math.log( `NormalizableScoringFunction.getNormalizationConstant()` ) + Math.log( prior ).`
  See Also:
    `NormalizableScoringFunction.getEss()`, `NormalizableScoringFunction.getNormalizationConstant()`

### addGradientOfLogPriorTerm

    public void addGradientOfLogPriorTerm(double[] grad,
                                          int start)

  Description copied from interface: `NormalizableScoringFunction`
  This method computes the gradient of `NormalizableScoringFunction.getLogPriorTerm()` for each parameter of this model. The results are added to the array `grad` beginning at index `start`.

  Parameters:
    `grad` - the array of gradients
    `start` - the start index in the `grad` array, where the partial derivations for the parameters of this models shall be entered
  See Also:
    `NormalizableScoringFunction.getLogPriorTerm()`

### isNormalized

    public boolean isNormalized()

  Description copied from interface: `NormalizableScoringFunction`
  This method indicates whether the implemented score is already normalized to 1 or not. The standard implementation returns `false`.

  Specified by:
    `isNormalized` in interface `NormalizableScoringFunction`
  Overrides:
    `isNormalized` in class `AbstractNormalizableScoringFunction`
  Returns:
    `true` if the implemented score is already normalized to 1, `false` otherwise

### isInitialized

    public boolean isInitialized()

  Description copied from interface: `ScoringFunction`
  This method can be used to determine whether the model is initialized. If the model is not initialized you should invoke the method `ScoringFunction.initializeFunction(int, boolean, Sample[], double[][])`.

  Returns:
    `true` if the model is initialized, `false` otherwise

### getMaximalMarkovOrder

    public int getMaximalMarkovOrder()

  Description copied from class: `HomogeneousScoringFunction`
  Returns the maximal used markov oder.

  Specified by:
    `getMaximalMarkovOrder` in class `HomogeneousScoringFunction`
  Returns:
    the maximal used markov oder

### getNumberOfRecommendedStarts

    public int getNumberOfRecommendedStarts()

  Description copied from interface: `ScoringFunction`
  This method returns the number of recommended optimization starts. The standard implementation returns 1.

  Specified by:
    `getNumberOfRecommendedStarts` in interface `ScoringFunction`
  Overrides:
    `getNumberOfRecommendedStarts` in class `AbstractNormalizableScoringFunction`
  Returns:
    the number of recommended optimization starts

### setParameterOptimization

    public void setParameterOptimization(boolean optimize)

  This method allows the user to specify whether the parameters should be optimized or not.

  Parameters:
    `optimize` - indicates if the parameters should be optimized or not

### getAllConditionalStationaryDistributions

    public double[][][] getAllConditionalStationaryDistributions()

  Description copied from class: `VariableLengthScoringFunction`
  This method returns the stationary conditional distributions. The first dimension of the result is used for the order, the second is used for encoding the context, and the third is used for the different values of the random variable.
  For an homogeneous Markov model of order 2 it returns an array containing the stationary symbol distribution as first entry, the conditional stationary distribution of order 1 as second entry and the conditional distribution of order 2 as third entry.
  This method is used to determine the contrast for `Mutable.determineNotSignificantPositions(double, double[], double[], double[][][][], double[][][][], double)` .

  Specified by:
    `getAllConditionalStationaryDistributions` in class `VariableLengthScoringFunction`
  Returns:
    all conditional stationary distributions
  See Also:
    `Mutable`

### setStatisticForHyperparameters

    public void setStatisticForHyperparameters(int[] length,
                                               double[] weight)
                                        throws Exception

  Description copied from class: `VariableLengthScoringFunction`
  This method sets the hyperparameters for the model parameters by evaluating the given statistic. The statistic can be interpreted as follows: The model has seen a number of sequences. From these sequences it is only known how long (`length`) and how often ( `weight`) they have been seen.

  Specified by:
    `setStatisticForHyperparameters` in class `VariableLengthScoringFunction`
  Parameters:
    `length` - the non-negative lengths of the sequences
    `weight` - the non-negative weight for the corresponding sequence
  Throws:
    `Exception` - if something went wrong
  See Also:
    `Mutable`

### emit

    public Sample emit(int numberOfSequences,
                       int... seqLength)
                throws Exception

  This method returns a `Sample` object containing artificial sequence(s).
  There are 2 different possibilities to create a `Sample`:
  1. `emitSample( int n, int l )` returns a `Sample` with `n` sequences of length `l`.
  2. `emitSample( int n, int[] l )` should return a `Sample` with `n` sequences which have a sequence length corresponding to the entry in the array.

  Parameters:
    `numberOfSequences` - the number of sequences that should be contained in the returned `Sample`
    `seqLength` - the length of the sequences
  Returns:
    a `Sample` containing `numberOfSequences` artificial sequence(s)
  Throws:
    `Exception` - if the emission of the artificial `Sample` did not succeed
  See Also:
    `Sample`

### initializeUniformly

    public void initializeUniformly(boolean freeParams)

  Description copied from class: `HomogeneousScoringFunction`
  This method allows to initialize the instance with an uniform distribution.

  Specified by:
    `initializeUniformly` in class `HomogeneousScoringFunction`
  Parameters:
    `freeParams` - a switch whether to take only free parameters or to take all

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