LogisticDiffSS

java.lang.Object
- de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
- - de.jstacs.sequenceScores.differentiable.logistic.LogisticDiffSS

All Implemented Interfaces:

DifferentiableSequenceScore, SequenceScore, Storable, Cloneable
```
public class LogisticDiffSS
extends AbstractDifferentiableSequenceScore
```
This class implements a logistic function. The score is computed by the following formula
$s(\underline{x}) = \exp\left(\sum_i \lambda_{2i} \cdot (f_i(\underline{x})-\lambda_{2i+1})\right).$
The constraints $f_i(\underline{x})$ are defined by LogisticConstraints.

Author:

Jens Keilwagen

Field Summary

Fields
Modifier and Type Field and Description

protected double[] parameter
the parameters of the logistic regression
- Fields inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
  alphabets, length, r
- Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore
  UNKNOWN

Fields
Modifier and Type	Field and Description
`protected double[]`	`parameter` the parameters of the logistic regression

Constructor Summary

Constructors
Constructor and Description
`LogisticDiffSS(AlphabetContainer con, int length, LogisticConstraint... constraint)` This is the main constructor to create `LogisticDiffSS` instance.
`LogisticDiffSS(StringBuffer xml)` This is the constructor for `Storable`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`LogisticDiffSS`	`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.
`String`	`getInstanceName()` Should return a short instance name such as iMM(0), BN(2), ...
`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`	`getNumberOfParameters()` Returns the number of parameters in this `DifferentiableSequenceScore`.
`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.
`boolean`	`isInitialized()` This method can be used to determine whether the instance is initialized.
`void`	`setParameters(double[] params, int start)` This method sets the internal parameters to the values of `params` between `start` and `start + DifferentiableSequenceScore.getNumberOfParameters() - 1`
`String`	`toString(NumberFormat nf)` This method returns a `String` representation of the instance.
`StringBuffer`	`toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

Methods inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
getAlphabetContainer, getCharacteristics, getInitialClassParam, getLength, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getNumberOfRecommendedStarts, getNumberOfStarts, getNumericalCharacteristics, toString

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

- Field Detail
  - parameter
```
protected double[] parameter
```
    the parameters of the logistic regression
- Constructor Detail
  - LogisticDiffSS
```
public LogisticDiffSS(AlphabetContainer con,
                      int length,
                      LogisticConstraint... constraint)
               throws CloneNotSupportedException
```
    This is the main constructor to create LogisticDiffSS instance.
    
    Parameters:
    
    con - the AlphabetContainer of this instance
    
    length - the length of this instance, i.e. the length of the modeled sequences
    
    constraint - the constraints used in this instance
    
    Throws:
    
    CloneNotSupportedException - if the constraints could not be cloned
  - LogisticDiffSS
```
public LogisticDiffSS(StringBuffer xml)
               throws NonParsableException
```
    This is the constructor for Storable. Creates a new LogisticDiffSS out of a StringBuffer .
    
    Parameters:
    
    xml - the XML representation as StringBuffer
    
    Throws:
    
    NonParsableException - if the XML representation could not be parsed
- Method Detail
  - clone
```
public LogisticDiffSS clone()
                     throws CloneNotSupportedException
```
    Description copied from interface: DifferentiableSequenceScore
    
    Creates a clone (deep copy) of the current DifferentiableSequenceScore instance.
    
    Specified by:
    
    clone in interface DifferentiableSequenceScore
    
    Specified by:
    
    clone in interface SequenceScore
    
    Overrides:
    
    clone in class AbstractDifferentiableSequenceScore
    
    Returns:
    
    the cloned instance of the current DifferentiableSequenceScore
    
    Throws:
    
    CloneNotSupportedException - if something went wrong while cloning the DifferentiableSequenceScore
  - getCurrentParameterValues
```
public double[] getCurrentParameterValues()
                                   throws Exception
```
    Description copied from interface: DifferentiableSequenceScore
    
    Returns a 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.
    
    Returns:
    
    the current parameter values
    
    Throws:
    
    Exception - if no parameters exist (yet)
  - getInstanceName
```
public String getInstanceName()
```
    Description copied from interface: SequenceScore
    
    Should return a short instance name such as iMM(0), BN(2), ...
    
    Returns:
    
    a short instance name
  - getLogScoreFor
```
public double getLogScoreFor(Sequence seq,
                             int start)
```
    Description copied from interface: SequenceScore
    
    Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.
    
    Parameters:
    
    seq - the Sequence
    
    start - the start position in the Sequence
    
    Returns:
    
    the logarithmic score for the Sequence
  - getLogScoreAndPartialDerivation
```
public double getLogScoreAndPartialDerivation(Sequence seq,
                                              int start,
                                              IntList indices,
                                              DoubleList partialDer)
```
    Description copied from interface: DifferentiableSequenceScore
    
    Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.
    
    Parameters:
    
    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 $\frac{\partial \log score(seq)}{\partial \lambda_i}$ is not zero
    
    partialDer - a DoubleList of partial derivations, after method invocation the list should contain the corresponding $\frac{\partial \log score(seq)}{\partial \lambda_i}$ that are not zero
    
    Returns:
    
    the logarithmic score for the Sequence
  - getNumberOfParameters
```
public int getNumberOfParameters()
```
    Description copied from interface: DifferentiableSequenceScore
    
    Returns the number of parameters in this DifferentiableSequenceScore. If the number of parameters is not known yet, the method returns DifferentiableSequenceScore.UNKNOWN.
    
    Returns:
    
    the number of parameters in this DifferentiableSequenceScore
    
    See Also:
    
    DifferentiableSequenceScore.UNKNOWN
  - initializeFunction
```
public void initializeFunction(int index,
                               boolean freeParams,
                               DataSet[] data,
                               double[][] weights)
                        throws Exception
```
    Description copied from interface: DifferentiableSequenceScore
    
    This method creates the underlying structure of the DifferentiableSequenceScore.
    
    Parameters:
    
    index - the index of the class the DifferentiableSequenceScore models
    
    freeParams - indicates whether the (reduced) parameterization is used
    
    data - the data sets
    
    weights - the weights of the sequences in the data sets
    
    Throws:
    
    Exception - if something went wrong
  - initializeFunctionRandomly
```
public void initializeFunctionRandomly(boolean freeParams)
                                throws Exception
```
    Description copied from interface: DifferentiableSequenceScore
    
    This method initializes the DifferentiableSequenceScore randomly. It has to create the underlying structure of the DifferentiableSequenceScore.
    
    Parameters:
    
    freeParams - indicates whether the (reduced) parameterization is used
    
    Throws:
    
    Exception - if something went wrong
  - isInitialized
```
public boolean isInitialized()
```
    Description copied from interface: SequenceScore
    
    This method can be used to determine whether the instance is initialized. If the instance is initialized you should be able to invoke SequenceScore.getLogScoreFor(Sequence).
    
    Returns:
    
    true if the instance is initialized, false otherwise
  - setParameters
```
public void setParameters(double[] params,
                          int start)
```
    Description copied from interface: DifferentiableSequenceScore
    
    This method sets the internal parameters to the values of params between start and start + DifferentiableSequenceScore.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
  - fromXML
```
protected void fromXML(StringBuffer xml)
                throws NonParsableException
```
    Description copied from class: AbstractDifferentiableSequenceScore
    
    This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.
    
    Specified by:
    
    fromXML in class AbstractDifferentiableSequenceScore
    
    Parameters:
    
    xml - the XML representation as StringBuffer
    
    Throws:
    
    NonParsableException - if the StringBuffer could not be parsed
    
    See Also:
    
    AbstractDifferentiableSequenceScore.AbstractDifferentiableSequenceScore(StringBuffer)
  - toString
```
public String toString(NumberFormat nf)
```
    Description copied from interface: SequenceScore
    
    This method returns a String representation of the instance.
    
    Parameters:
    
    nf - the NumberFormat for the String representation of parameters or probabilities
    
    Returns:
    
    a String representation of the instance

Class LogisticDiffSS

Field Summary

Fields inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore

Constructor Summary

Method Summary

Methods inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

Methods inherited from class java.lang.Object

Field Detail

parameter

Constructor Detail

LogisticDiffSS

LogisticDiffSS

Method Detail

clone

getCurrentParameterValues

getInstanceName

getLogScoreFor

getLogScoreAndPartialDerivation

getNumberOfParameters

initializeFunction

initializeFunctionRandomly

isInitialized

setParameters

toXML

fromXML

toString