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public interface ScoringFunction
This interface is the main part of any ScoreClassifier.
Field Summary | |
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static int |
UNKNOWN
Indicates that the number of parameters of this ScoringFunction is not known (yet). |
Method Summary | |
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ScoringFunction |
clone()
Creates a clone (deep copy) of the current ScoringFunction instance. |
AlphabetContainer |
getAlphabetContainer()
Returns the AlphabetContainer for this ScoringFunction . |
double[] |
getCurrentParameterValues()
Returns a double array of dimension getNumberOfParameters() containing the current parameter
values. |
double |
getInitialClassParam(double classProb)
Returns the initial class parameter for the class this ScoringFunction is responsible for, based on the probability classProb . |
String |
getInstanceName()
Returns a short instance name. |
int |
getLength()
Returns the length of this ScoringFunction . i.e. the length of the Sequence s this ScoringFunction can handle. |
double |
getLogScore(Sequence seq)
Returns the log score for the sequence |
double |
getLogScore(Sequence seq,
int start)
Returns the log score for the sequence |
double |
getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
Returns the log score for the sequence and fills the list with the indices and the partial derivations. |
double |
getLogScoreAndPartialDerivation(Sequence seq,
IntList indices,
DoubleList partialDer)
Returns the log score for the sequence and fills the list with the indices and the partial derivations. |
int |
getNumberOfParameters()
The number of parameters in this scoring function. |
int |
getNumberOfRecommendedStarts()
This method return the number of recommended optimization starts. |
void |
initializeFunction(int index,
boolean freeParams,
Sample[] data,
double[][] weights)
This method creates the underlying structure of the scoring function. |
void |
initializeFunctionRandomly(boolean freeParams)
This method initializes the scoring function randomly. |
boolean |
isInitialized()
This method can be used to determine whether the model is initialized. |
void |
setParameters(double[] params,
int start)
This method sets the internal parameters to the values of params between start and
start + this.getNumberOfParameters() - 1 |
Methods inherited from interface de.jstacs.Storable |
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toXML |
Field Detail |
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static final int UNKNOWN
ScoringFunction
is not known (yet).
Method Detail |
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ScoringFunction clone() throws CloneNotSupportedException
ScoringFunction
instance.
CloneNotSupportedException
void initializeFunction(int index, boolean freeParams, Sample[] data, double[][] weights) throws Exception
index
- the index of the class the scoring function modelsfreeParams
- if true, the (reduced) parameterization is useddata
- the samplesweights
- the weights of the sequences in the samples
- Throws:
Exception
void initializeFunctionRandomly(boolean freeParams) throws Exception
freeParams
- if true, the (reduced) parameterization is used
Exception
AlphabetContainer getAlphabetContainer()
AlphabetContainer
for this ScoringFunction
.
Only Sequence
s with a comparable AlphabetContainer can be modeled.
String getInstanceName()
int getLength()
ScoringFunction
. i.e. the length of the Sequence
s this ScoringFunction
can handle. For homogeneous ScoringFunction
, i.e.
ScoringFunction
s that support Sequence
s of different lengths, should return 0
.
double getLogScore(Sequence seq)
seq
- the sequence
double getLogScore(Sequence seq, int start)
seq
- the sequencestart
- the startposition in the sequence
double getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)
seq
- the sequenceindices
- after method invocation the list should contain the indices i where \frac{\partial \log
score(seq)}{\partial \lambda_i} is not zeropartialDer
- after method invocation the list should contain the corresponding \frac{\partial \log
score(seq)}{\partial \lambda_i}
double getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
seq
- the sequencestart
- the startposition in the sequenceindices
- after method invocation the list should contain the indices i where \frac{\partial \log
score(seq)}{\partial \lambda_i} is not zeropartialDer
- after method invocation the list should contain the corresponding \frac{\partial \log
score(seq)}{\partial \lambda_i}
int getNumberOfParameters()
UNKNOWN
.
UNKNOWN
int getNumberOfRecommendedStarts()
double[] getCurrentParameterValues() throws Exception
getNumberOfParameters()
containing the current parameter
values. If on e likes to use these parameters to start an optimization it is highly recommended to invoke
initializeFunction(int, boolean, Sample[], double[][])
before. After an optimization
this method can be used to get the current parameter values.
Exception
- is thrown if no parameters exist, yetvoid setParameters(double[] params, int start)
params
between start
and
start + this.getNumberOfParameters() - 1
params
- the parametersstart
- the start indexboolean isInitialized()
initializeFunction(int, boolean, Sample[], double[][])
.
true
if the model is initializeddouble getInitialClassParam(double classProb)
ScoringFunction
is responsible for, based on the probability classProb
.
classProb
- the class probability
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