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## de.jstacs.classifier.scoringFunctionBased.gendismix
Class LogGenDisMixFunction

    java.lang.Object
      de.jstacs.algorithms.optimization.DifferentiableFunction
          de.jstacs.classifier.scoringFunctionBased.OptimizableFunction
              de.jstacs.classifier.scoringFunctionBased.AbstractOptimizableFunction
                  de.jstacs.classifier.scoringFunctionBased.AbstractMultiThreadedOptimizableFunction
                      de.jstacs.classifier.scoringFunctionBased.SFBasedOptimizableFunction
                          de.jstacs.classifier.scoringFunctionBased.gendismix.LogGenDisMixFunction

All Implemented Interfaces:
  Function

Direct Known Subclasses:
  OneSampleLogGenDisMixFunction

    public class LogGenDisMixFunction

extends SFBasedOptimizableFunction

This class implements the the following function

The weights have to sum to 1. For special weights the optimization turns out to be well known

- if the weights are (0,1,0), one obtains maximum likelihood,
- if the weights are (0,0.5,0.5), one obtains maximum a posteriori,
- if the weights are (1,0,0), one obtains maximum conditional likelihood,
- if the weights are (0.5,0,0.5), one obtains maximum supervised posterior,
- if the =0, one obtains the generative-discriminative trade-off,
- if the =0.5, one obtains the penalized generative-discriminative trade-off.

Of course, there are also some very interesting cases with other weights.
It can be used to maximize the parameters.
This class enables the user to exploit all CPUs of the computer by using threads. The number of compute threads can be determined in the constructor.
It is very important for this class that the `ScoringFunction.clone()` method works correctly, since each thread works on its own clones.

Author:
  Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.classifier.scoringFunctionBased.OptimizableFunction
`OptimizableFunction.KindOfParameter`

Field Summary
`protected double[]` | `beta` The mixture parameters of the GenDisMix
`protected double[][]` | `cllGrad` Array for the gradient of the conditional log-likelihood
`protected double[][]` | `helpArray` General temporary array
`protected double[][]` | `llGrad` Array for the gradient of the log-likelihood
`protected double[]` | `prGrad` Array for the gradient of the prior

Fields inherited from class de.jstacs.classifier.scoringFunctionBased.SFBasedOptimizableFunction
`dList, iList, prior, score, shortcut`

Fields inherited from class de.jstacs.classifier.scoringFunctionBased.AbstractMultiThreadedOptimizableFunction
`params`

Fields inherited from class de.jstacs.classifier.scoringFunctionBased.AbstractOptimizableFunction
`cl, clazz, data, freeParams, logClazz, norm, sum, weights`

Constructor Summary
`LogGenDisMixFunction(int threads, ScoringFunction[] score, Sample[] data, double[][] weights, LogPrior prior, double[] beta, boolean norm, boolean freeParams)` The constructor for creating an instance that can be used in an `Optimizer`.

Method Summary
`protected void` | `evaluateFunction(int index, int startClass, int startSeq, int endClass, int endSeq)` This method evaluates the function for a part of the data.
`protected void` | `evaluateGradientOfFunction(int index, int startClass, int startSeq, int endClass, int endSeq)` This method evaluates the gradient of the function for a part of the data.
`protected double` | `joinFunction()` This method joins the partial results that have been computed using `AbstractMultiThreadedOptimizableFunction.evaluateFunction(int, int, int, int, int)`.
`protected double[]` | `joinGradients()` This method joins the gradients of each part that have been computed using `AbstractMultiThreadedOptimizableFunction.evaluateGradientOfFunction(int, int, int, int, int)`.
`void` | `reset(ScoringFunction[] funs)` This method allows to reset the internally used functions and the corresponding objects.

Methods inherited from class de.jstacs.classifier.scoringFunctionBased.SFBasedOptimizableFunction
`addTermToClassParameter, getClassParams, getDimensionOfScope, getParameters, reset, setParams, setThreadIndependentParameters`

Methods inherited from class de.jstacs.classifier.scoringFunctionBased.AbstractMultiThreadedOptimizableFunction
`evaluateFunction, evaluateGradientOfFunction, getNumberOfAvailableProcessors, getNumberOfThreads, setDataAndWeights, setParams, stopThreads`

Methods inherited from class de.jstacs.classifier.scoringFunctionBased.AbstractOptimizableFunction
`getData, getParameters, getSequenceWeights`

Methods inherited from class de.jstacs.algorithms.optimization.DifferentiableFunction
`findOneDimensionalMin`

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

Field Detail

### helpArray

    protected double[][] helpArray

  General temporary array

### llGrad

    protected double[][] llGrad

  Array for the gradient of the log-likelihood

### cllGrad

    protected double[][] cllGrad

  Array for the gradient of the conditional log-likelihood

### beta

    protected double[] beta

  The mixture parameters of the GenDisMix

### prGrad

    protected double[] prGrad

  Array for the gradient of the prior

Constructor Detail

### LogGenDisMixFunction

    public LogGenDisMixFunction(int threads,
                                ScoringFunction[] score,
                                Sample[] data,
                                double[][] weights,
                                LogPrior prior,
                                double[] beta,
                                boolean norm,
                                boolean freeParams)
                         throws IllegalArgumentException

  The constructor for creating an instance that can be used in an `Optimizer`.

  Parameters:
    `threads` - the number of threads used for evaluating the function and determining the gradient of the function
    `score` - an array containing the `ScoringFunction`s that are used for determining the sequences scores; if the weight `beta[LearningPrinciple.LIKELIHOOD_INDEX]` is positive all elements of `score` have to be `NormalizableScoringFunction`
    `data` - the array of `Sample`s containing the data that is needed to evaluate the function
    `weights` - the weights for each `Sequence` in each `Sample` of `data`
    `prior` - the prior that is used for learning the parameters
    `beta` - the beta-weights for the three terms of the learning principle
    `norm` - the switch for using the normalization (division by the number of sequences)
    `freeParams` - the switch for using only the free parameters
  Throws:
    `IllegalArgumentException` - if the number of threads is not positive, the number of classes or the dimension of the weights is not correct

Method Detail

### joinGradients

    protected double[] joinGradients()
                              throws EvaluationException

  Description copied from class: `AbstractMultiThreadedOptimizableFunction`
  This method joins the gradients of each part that have been computed using `AbstractMultiThreadedOptimizableFunction.evaluateGradientOfFunction(int, int, int, int, int)`.

  Specified by:
    `joinGradients` in class `AbstractMultiThreadedOptimizableFunction`
  Returns:
    the gradient
  Throws:
    `EvaluationException` - if the gradient could not be evaluated properly

### evaluateGradientOfFunction

    protected void evaluateGradientOfFunction(int index,
                                              int startClass,
                                              int startSeq,
                                              int endClass,
                                              int endSeq)

  Description copied from class: `AbstractMultiThreadedOptimizableFunction`
  This method evaluates the gradient of the function for a part of the data.

  Specified by:
    `evaluateGradientOfFunction` in class `AbstractMultiThreadedOptimizableFunction`
  Parameters:
    `index` - the index of the part
    `startClass` - the index of the start class
    `startSeq` - the index of the start sequence
    `endClass` - the index of the end class (inclusive)
    `endSeq` - the index of the end sequence (exclusive)

### joinFunction

    protected double joinFunction()
                           throws DimensionException,
                                  EvaluationException

  Description copied from class: `AbstractMultiThreadedOptimizableFunction`
  This method joins the partial results that have been computed using `AbstractMultiThreadedOptimizableFunction.evaluateFunction(int, int, int, int, int)`.

  Specified by:
    `joinFunction` in class `AbstractMultiThreadedOptimizableFunction`
  Returns:
    the value of the function
  Throws:
    `DimensionException` - if the parameters could not be set
    `EvaluationException` - if the gradient could not be evaluated properly

### evaluateFunction

    protected void evaluateFunction(int index,
                                    int startClass,
                                    int startSeq,
                                    int endClass,
                                    int endSeq)
                             throws EvaluationException

  Description copied from class: `AbstractMultiThreadedOptimizableFunction`
  This method evaluates the function for a part of the data.

  Specified by:
    `evaluateFunction` in class `AbstractMultiThreadedOptimizableFunction`
  Parameters:
    `index` - the index of the part
    `startClass` - the index of the start class
    `startSeq` - the index of the start sequence
    `endClass` - the index of the end class (inclusive)
    `endSeq` - the index of the end sequence (exclusive)
  Throws:
    `EvaluationException` - if the gradient could not be evaluated properly

### reset

    public void reset(ScoringFunction[] funs)
               throws Exception

  Description copied from class: `SFBasedOptimizableFunction`
  This method allows to reset the internally used functions and the corresponding objects.

  Specified by:
    `reset` in class `SFBasedOptimizableFunction`
  Parameters:
    `funs` - the new instances
  Throws:
    `Exception` - if something went wrong

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