Package | Description |
---|---|
de.jstacs.sequenceScores.statisticalModels.trainable.hmm |
The package provides all interfaces and classes for a hidden Markov model (HMM).
|
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models |
The package provides different implementations of hidden Markov models based on
AbstractHMM . |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training |
The package provides all classes used to determine the training algorithm of a hidden Markov model.
|
Modifier and Type | Method and Description |
---|---|
static AbstractHMM |
HMMFactory.createProfileHMM(MaxHMMTrainingParameterSet trainingParameterSet,
double[][] initFromTo,
boolean likelihood,
int order,
int numLayers,
AlphabetContainer con,
double ess,
boolean conditionalMain,
boolean closeCircle,
double[][] conditionInitProbs,
boolean insertUniform)
Creates a new profile HMM for a given architecture and number of layers.
|
static AbstractHMM |
HMMFactory.createProfileHMM(MaxHMMTrainingParameterSet trainingParameterSet,
double[][] initFromTo,
boolean likelihood,
int order,
int numLayers,
AlphabetContainer con,
double ess,
boolean conditionalMain,
int joiningStates,
double[][] conditionInitProbs,
boolean insertUniform)
Creates a new profile HMM for a given architecture and number of layers.
|
static AbstractHMM |
HMMFactory.createProfileHMM(MaxHMMTrainingParameterSet trainingParameterSet,
HMMFactory.HMMType type,
boolean likelihood,
int order,
int numLayers,
AlphabetContainer con,
double ess,
boolean conditionalMain,
boolean closeCircle,
double[][] conditionInitProbs)
Creates a new profile HMM for a given architecture and number of layers.
|
Constructor and Description |
---|
DifferentiableHigherOrderHMM(MaxHMMTrainingParameterSet trainingParameterSet,
String[] name,
int[] emissionIdx,
boolean[] forward,
DifferentiableEmission[] emission,
boolean likelihood,
double ess,
TransitionElement... te)
This is the main constructor.
|
Modifier and Type | Class and Description |
---|---|
class |
BaumWelchParameterSet
This class implements an
HMMTrainingParameterSet for the Baum-Welch training of an AbstractHMM . |
class |
MultiThreadedTrainingParameterSet
This class is the super class for any
MaxHMMTrainingParameterSet that
is used for a multi-threaded maximizing training algorithm of a hidden Markov model. |
class |
NumericalHMMTrainingParameterSet
This class implements an
ParameterSet for numerical training of an AbstractHMM . |
class |
ViterbiParameterSet
This class implements an
ParameterSet for the viterbi training of an AbstractHMM . |