bpp-core  2.1.0
bpp::HmmLikelihood Class Reference

Basal interface for Hidden Markov Models likelihood computation. More...

#include <Bpp/Numeric/Hmm/HmmLikelihood.h>

+ Inheritance diagram for bpp::HmmLikelihood:
+ Collaboration diagram for bpp::HmmLikelihood:

List of all members.

Public Member Functions

virtual HmmLikelihoodclone () const =0
 Create a copy of this object and send a pointer to it.
virtual const HmmStateAlphabetgetHmmStateAlphabet () const =0
virtual HmmStateAlphabetgetHmmStateAlphabet ()=0
virtual const HmmTransitionMatrixgetHmmTransitionMatrix () const =0
virtual HmmTransitionMatrixgetHmmTransitionMatrix ()=0
virtual const
HmmEmissionProbabilities
getHmmEmissionProbabilities () const =0
virtual HmmEmissionProbabilitiesgetHmmEmissionProbabilities ()=0
virtual void getHiddenStatesPosteriorProbabilities (std::vector< std::vector< double > > &probs, bool append) const =0 throw (Exception)
virtual Vdouble getHiddenStatesPosteriorProbabilitiesForASite (size_t site) const =0
virtual double getLogLikelihood () const =0
virtual double getDLogLikelihood () const =0
virtual double getD2LogLikelihood () const =0
virtual double getLikelihoodForASite (size_t site) const =0
 Get the likelihood for a site.
virtual Vdouble getLikelihoodForEachSite () const =0
 Get the likelihood for each site.
virtual const std::vector
< size_t > & 
getBreakPoints () const =0
virtual void setBreakPoints (const std::vector< size_t > &breakPoints)=0
virtual void enableSecondOrderDerivatives (bool yn)=0
 Tell if derivatives must be computed.
virtual bool enableSecondOrderDerivatives () const =0
 Tell if derivatives must be computed.
virtual double getSecondOrderDerivative (const std::string &variable) const =0 throw (Exception)
 Get the second order derivative of the function at the current point.
virtual double getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const =0 throw (Exception)
 Get the value of the cross derivative of the function according to a given set of parameters.
virtual double d2f (const std::string &variable, const ParameterList &parameters) throw (Exception)
 Get the value of the second order derivative of the function according to a given set of parameters.
virtual double d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters) throw (Exception)
 Get the value of the cross derivative of the function according to a given set of parameters.
virtual void enableFirstOrderDerivatives (bool yn)=0
 Tell if derivatives must be computed.
virtual bool enableFirstOrderDerivatives () const =0
 Tell if derivatives must be computed.
virtual double getFirstOrderDerivative (const std::string &variable) const =0 throw (Exception)
 Get the derivative of the function at the current point.
virtual double df (const std::string &variable, const ParameterList &parameters) throw (Exception)
 Get the value of the first derivative of the function according to a given set of parameters.
virtual void setParameters (const ParameterList &parameters)=0 throw (ParameterNotFoundException, ConstraintException, Exception)
 Set the point where the function must be computed.
virtual double getValue () const =0 throw (Exception)
 Get the value of the function at the current point.
virtual double f (const ParameterList &parameters) throw (Exception)
 Get the value of the function according to a given set of parameters.
virtual bool hasParameter (const std::string &name) const =0
 Tell if there is a parameter with specified name.
virtual const ParameterListgetParameters () const =0
 Get all parameters available.
virtual const ParametergetParameter (const std::string &name) const =0 throw (ParameterNotFoundException)
 Get the parameter with specified name.
virtual double getParameterValue (const std::string &name) const =0 throw (ParameterNotFoundException)
 Get the value for parameter of name 'name'.
virtual void setAllParametersValues (const ParameterList &parameters)=0 throw (ParameterNotFoundException, ConstraintException)
 Set the parameters values to be equals to those of parameters.
virtual void setParameterValue (const std::string &name, double value)=0 throw (ParameterNotFoundException, ConstraintException)
 Set the value of parameter with name name to be equal to value.
virtual void setParametersValues (const ParameterList &parameters)=0 throw (ParameterNotFoundException, ConstraintException)
 Update the parameters from parameters.
virtual bool matchParametersValues (const ParameterList &parameters)=0 throw (ConstraintException)
 Update the parameters from parameters.
virtual size_t getNumberOfParameters () const =0
 Get the number of parameters.
virtual void setNamespace (const std::string &prefix)=0
 Set the namespace for the parameter names.
virtual std::string getNamespace () const =0
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
 Resolves a parameter name according to the current namespace.

Protected Member Functions

virtual void computeDLikelihood_ () const =0
virtual void computeD2Likelihood_ () const =0

Detailed Description

Basal interface for Hidden Markov Models likelihood computation.

HmmLikelihood classes compute the probability of data according to parameters (likelihood), using the so-called forward recursion:

  • Initialisation:

    \[ f_0({\cal A}_0), \ldots, f_0({\cal A}_n) \]

    The initial frequencies, set to the equilibrium frequencies of the chain.
  • Recursion (for i=1 to l, the length of the sequence data):

    \[ f_i({\cal A}_y) = e_y(D_i) \sum_{x=1}^n f_{i-1}({\cal A}_x) \cdot p_{x,y} \]

  • Termination:

    \[ \Pr(D) = \sum_{x=1}^n f_l({\cal A}_x) \]

    where $ {\cal A}_{1..n} $ denotes the hidden states of the alphabet, $ e_y(D_i) $ the probability of the data at position i conditioned on hidden state y (emission probabilities) and $ p_{x,y} $ is the probability of havving hidden state y at state i+1 knowing there is hidden state x at position i (transition probabilities). These essential elements are given respectively by the HmmEmissionProbabilities and HmmTransitionMatrix object associated to this class. Both objects have to share the same HmmStateAlphabet instance, which describes all allowed hidden states.

The HmmLikelihood interface provides essentially two major methods:

  • A method to retrieve the likelihood value (parameter estimation)
  • Two methods to retrieve the posterio probabilities of each state using the forward and backward conditionnal likelihoods (posterior decoding).

Definition at line 77 of file HmmLikelihood.h.


Member Function Documentation

virtual HmmLikelihood* bpp::HmmLikelihood::clone ( ) const [pure virtual]

Create a copy of this object and send a pointer to it.

Returns:
A pointer toward the copy object.

Implements bpp::DerivableSecondOrder.

Implemented in bpp::RescaledHmmLikelihood, bpp::LogsumHmmLikelihood, and bpp::LowMemoryRescaledHmmLikelihood.

virtual double bpp::DerivableSecondOrder::d2f ( const std::string &  variable,
const ParameterList parameters 
) throw (Exception) [inline, virtual, inherited]

Get the value of the second order derivative of the function according to a given set of parameters.

Parameters:
variableThe name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x^2} $.
parametersThe parameter set to pass to the function.
Returns:
The value of the function with the given parameter set.
Exceptions:
ExceptionIf an error occured.

Definition at line 236 of file Functions.h.

References bpp::DerivableSecondOrder::getSecondOrderDerivative(), and bpp::Function::setParameters().

virtual double bpp::DerivableSecondOrder::d2f ( const std::string &  variable1,
const std::string &  variable2,
const ParameterList parameters 
) throw (Exception) [inline, virtual, inherited]

Get the value of the cross derivative of the function according to a given set of parameters.

Parameters:
variable1The name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
variable2The name of the $ y $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
parametersThe parameter set to pass to the function.
Returns:
The value of the function with the given parameter set.
Exceptions:
ExceptionIf an error occured.

Definition at line 263 of file Functions.h.

References bpp::DerivableSecondOrder::getSecondOrderDerivative(), and bpp::Function::setParameters().

virtual double bpp::DerivableFirstOrder::df ( const std::string &  variable,
const ParameterList parameters 
) throw (Exception) [inline, virtual, inherited]

Get the value of the first derivative of the function according to a given set of parameters.

Parameters:
variableThe name of the $ x $ variable in $ \frac{df}{dx} $.
parametersThe parameter set to pass to the function.
Returns:
The value of the function with the given parameter set.
Exceptions:
ExceptionIf an error occured.

Definition at line 176 of file Functions.h.

References bpp::DerivableFirstOrder::getFirstOrderDerivative(), and bpp::Function::setParameters().

virtual bool bpp::DerivableFirstOrder::enableFirstOrderDerivatives ( ) const [pure virtual, inherited]
virtual void bpp::DerivableSecondOrder::enableSecondOrderDerivatives ( bool  yn) [pure virtual, inherited]
virtual bool bpp::DerivableSecondOrder::enableSecondOrderDerivatives ( ) const [pure virtual, inherited]
virtual const std::vector<size_t>& bpp::HmmLikelihood::getBreakPoints ( ) const [pure virtual]
virtual double bpp::HmmLikelihood::getD2LogLikelihood ( ) const [pure virtual]

Implemented in bpp::AbstractHmmLikelihood.

virtual double bpp::HmmLikelihood::getDLogLikelihood ( ) const [pure virtual]

Implemented in bpp::AbstractHmmLikelihood.

virtual double bpp::DerivableFirstOrder::getFirstOrderDerivative ( const std::string &  variable) const throw (Exception) [pure virtual, inherited]

Get the derivative of the function at the current point.

Parameters:
variableThe name of the $ x $ variable in $ \frac{df}{dx} $.
Returns:
The value of the function.
Exceptions:
ExceptionIf no point is specified or if an error occured.

Implemented in bpp::DerivableFirstOrderWrapper, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::AbstractHmmLikelihood, and bpp::AbstractNumericalDerivative.

Referenced by bpp::DerivableFirstOrder::df(), bpp::NewtonOneDimension::doStep(), bpp::AbstractNumericalDerivative::getFirstOrderDerivative(), bpp::ConjugateGradientMultiDimensions::getGradient(), and bpp::BfgsMultiDimensions::getGradient().

virtual void bpp::HmmLikelihood::getHiddenStatesPosteriorProbabilities ( std::vector< std::vector< double > > &  probs,
bool  append 
) const throw (Exception) [pure virtual]
virtual double bpp::HmmLikelihood::getLikelihoodForASite ( size_t  site) const [pure virtual]

Get the likelihood for a site.

Parameters:
siteThe site index to analyse.
Returns:
The likelihood for site site.

Implemented in bpp::RescaledHmmLikelihood, bpp::LogsumHmmLikelihood, and bpp::LowMemoryRescaledHmmLikelihood.

virtual Vdouble bpp::HmmLikelihood::getLikelihoodForEachSite ( ) const [pure virtual]

Get the likelihood for each site.

Returns:
A vector with all likelihoods for each site.

Implemented in bpp::RescaledHmmLikelihood, bpp::LogsumHmmLikelihood, and bpp::LowMemoryRescaledHmmLikelihood.

virtual std::string bpp::Parametrizable::getNamespace ( ) const [pure virtual, inherited]
Returns:
The current namespace used. This is an empty string if no namespace is currently defined.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getNamespace().

virtual size_t bpp::Parametrizable::getNumberOfParameters ( ) const [pure virtual, inherited]

Get the number of parameters.

See also:
getNumberOfIndependentParameters If some parameters are aliased.
Returns:
The number of parameters.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::AbstractParametrizable, and bpp::DirectionFunction.

Referenced by bpp::FunctionWrapper::getNumberOfParameters(), and bpp::BppODiscreteDistributionFormat::write().

virtual const Parameter& bpp::Parametrizable::getParameter ( const std::string &  name) const throw (ParameterNotFoundException) [pure virtual, inherited]

Get the parameter with specified name.

Parameters:
nameThe name of the parameter to look for.
Returns:
The parameter with given name.
Exceptions:
ParameterNotFoundExceptionif no parameter with this name is found.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameter().

virtual std::string bpp::Parametrizable::getParameterNameWithoutNamespace ( const std::string &  name) const [pure virtual, inherited]

Resolves a parameter name according to the current namespace.

Returns:
The parameter name without the namespace prefix, if any.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), bpp::BppODiscreteDistributionFormat::read(), and bpp::BppOParametrizableFormat::write().

virtual const ParameterList& bpp::Parametrizable::getParameters ( ) const [pure virtual, inherited]
virtual double bpp::Parametrizable::getParameterValue ( const std::string &  name) const throw (ParameterNotFoundException) [pure virtual, inherited]

Get the value for parameter of name 'name'.

Parameters:
nameThe name of the parameter.
Returns:
the value of parameter name.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameterValue(), and bpp::BppODiscreteDistributionFormat::read().

virtual double bpp::DerivableSecondOrder::getSecondOrderDerivative ( const std::string &  variable) const throw (Exception) [pure virtual, inherited]

Get the second order derivative of the function at the current point.

Parameters:
variableThe name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x^2} $.
Returns:
The value of the function.
Exceptions:
ExceptionIf no point is specified or if an error occured.

Implemented in bpp::DerivableSecondOrderWrapper, bpp::ReparametrizationDerivableSecondOrderWrapper, bpp::AbstractNumericalDerivative, bpp::AbstractHmmLikelihood, and bpp::TwoPointsNumericalDerivative.

Referenced by bpp::DerivableSecondOrder::d2f(), bpp::NewtonOneDimension::doStep(), and bpp::AbstractNumericalDerivative::getSecondOrderDerivative().

virtual double bpp::DerivableSecondOrder::getSecondOrderDerivative ( const std::string &  variable1,
const std::string &  variable2 
) const throw (Exception) [pure virtual, inherited]

Get the value of the cross derivative of the function according to a given set of parameters.

Parameters:
variable1The name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
variable2The name of the $ y $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
Returns:
The value of the function with the given parameter set.
Exceptions:
ExceptionIf an error occured.

Implemented in bpp::DerivableSecondOrderWrapper, bpp::ReparametrizationDerivableSecondOrderWrapper, bpp::AbstractNumericalDerivative, bpp::AbstractHmmLikelihood, bpp::FivePointsNumericalDerivative, and bpp::TwoPointsNumericalDerivative.

virtual bool bpp::Parametrizable::hasParameter ( const std::string &  name) const [pure virtual, inherited]

Tell if there is a parameter with specified name.

Parameters:
nameThe name of the parameter to look for.
Returns:
y/n.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::hasParameter().

virtual bool bpp::Parametrizable::matchParametersValues ( const ParameterList parameters) throw (ConstraintException) [pure virtual, inherited]

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters:
parametersA list of parameters.
Returns:
True if at least one parameter value has been changed.
Exceptions:
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

virtual void bpp::Parametrizable::setAllParametersValues ( const ParameterList parameters) throw (ParameterNotFoundException, ConstraintException) [pure virtual, inherited]

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters:
parametersA list with all parameters.
Exceptions:
ParameterNotFoundExceptionIf a some parameter in the list is not in params.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setAllParametersValues(), bpp::FunctionWrapper::setAllParametersValues(), and bpp::InfinityFunctionWrapper::setAllParametersValues().

virtual void bpp::HmmLikelihood::setBreakPoints ( const std::vector< size_t > &  breakPoints) [pure virtual]
virtual void bpp::Parametrizable::setNamespace ( const std::string &  prefix) [pure virtual, inherited]

Set the namespace for the parameter names.

Parameters:
prefixThe 'namespace', that is a prefix to add to all parameter names. If parameter names are already prefixed, the new prefix will be used instead.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, bpp::AbstractParametrizable, and bpp::InvariantMixedDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::setNamespace(), and bpp::FunctionWrapper::setNamespace().

virtual void bpp::Parametrizable::setParametersValues ( const ParameterList parameters) throw (ParameterNotFoundException, ConstraintException) [pure virtual, inherited]

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters:
parametersA list containing all parameters to update.
Exceptions:
ParameterNotFoundExceptionIf a some parameter in params is not in the list.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

virtual void bpp::Parametrizable::setParameterValue ( const std::string &  name,
double  value 
) throw (ParameterNotFoundException, ConstraintException) [pure virtual, inherited]

Set the value of parameter with name name to be equal to value.

Parameters:
namethe name of the parameter to set.
valueThe value of the parameter.
Exceptions:
ParameterNotFoundExceptionIf no parameter in the list has the name name.
ConstraintExceptionIf value does not match the constraint associated to parameter name.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setParameterValue(), bpp::FunctionWrapper::setParameterValue(), and bpp::InfinityFunctionWrapper::setParameterValue().


The documentation for this class was generated from the following file:
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