bpp::LegacyOptimizationTools Class Reference

Optimization methods for phylogenetic inference. More...

#include <Bpp/Phyl/Legacy/OptimizationTools.h>

Inheritance diagram for bpp::LegacyOptimizationTools:

Collaboration diagram for bpp::LegacyOptimizationTools:

Classes
class	ScaleFunction

Public Member Functions
	LegacyOptimizationTools ()
virtual	~LegacyOptimizationTools ()

Static Public Member Functions
static unsigned int	optimizeNumericalParameters (std::shared_ptr< DiscreteRatesAcrossSitesTreeLikelihoodInterface > tl, const ParameterList &parameters, std::shared_ptr< OptimizationListener > listener=nullptr, unsigned int nstep=1, double tolerance=0.000001, unsigned int tlEvalMax=1000000, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, bool reparametrization=false, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_NEWTON, const std::string &optMethodModel=OPTIMIZATION_BRENT)
	Optimize numerical parameters (branch length, substitution model & rate distribution) of a TreeLikelihood function. More...
static unsigned int	optimizeNumericalParameters2 (std::shared_ptr< DiscreteRatesAcrossSitesTreeLikelihoodInterface > tl, const ParameterList &parameters, std::shared_ptr< OptimizationListener > listener=nullptr, double tolerance=0.000001, unsigned int tlEvalMax=1000000, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, bool reparametrization=false, bool useClock=false, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_NEWTON)
	Optimize numerical parameters (branch length, substitution model & rate distribution) of a TreeLikelihood function. More...
static unsigned int	optimizeBranchLengthsParameters (std::shared_ptr< DiscreteRatesAcrossSitesTreeLikelihoodInterface > tl, const ParameterList &parameters, std::shared_ptr< OptimizationListener > listener=nullptr, double tolerance=0.000001, unsigned int tlEvalMax=1000000, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_NEWTON)
	Optimize branch lengths parameters of a TreeLikelihood function. More...
static unsigned int	optimizeTreeScale (std::shared_ptr< TreeLikelihoodInterface > tl, double tolerance=0.000001, unsigned int tlEvalMax=1000000, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, unsigned int verbose=1)
	Optimize the scale of a TreeLikelihood. More...
static std::shared_ptr< NNIHomogeneousTreeLikelihood >	optimizeTreeNNI (std::shared_ptr< NNIHomogeneousTreeLikelihood > tl, const ParameterList &parameters, bool optimizeNumFirst=true, double tolBefore=100, double tolDuring=100, unsigned int tlEvalMax=1000000, unsigned int numStep=1, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, bool reparametrization=false, unsigned int verbose=1, const std::string &optMethod=OptimizationTools::OPTIMIZATION_NEWTON, unsigned int nStep=1, const std::string &nniMethod=NNITopologySearch::PHYML)
	Optimize all parameters from a TreeLikelihood object, including tree topology using Nearest Neighbor Interchanges. More...
static std::shared_ptr< NNIHomogeneousTreeLikelihood >	optimizeTreeNNI2 (std::shared_ptr< NNIHomogeneousTreeLikelihood > tl, const ParameterList &parameters, bool optimizeNumFirst=true, double tolBefore=100, double tolDuring=100, unsigned int tlEvalMax=1000000, unsigned int numStep=1, std::shared_ptr< OutputStream > messageHandler=ApplicationTools::message, std::shared_ptr< OutputStream > profiler=ApplicationTools::message, bool reparametrization=false, unsigned int verbose=1, const std::string &optMethod=OptimizationTools::OPTIMIZATION_NEWTON, const std::string &nniMethod=NNITopologySearch::PHYML)
	Optimize all parameters from a TreeLikelihood object, including tree topology using Nearest Neighbor Interchanges. More...
static std::shared_ptr< DRTreeParsimonyScore >	optimizeTreeNNI (std::shared_ptr< DRTreeParsimonyScore > tp, unsigned int verbose=1)
	Optimize tree topology from a DRTreeParsimonyScore using Nearest Neighbor Interchanges. More...
static unsigned int	optimizeNumericalParameters (std::shared_ptr< PhyloLikelihoodInterface > lik, const OptimizationOptions &optopt)
	Optimize numerical parameters (branch length, substitution model & rate distribution) of a TreeLikelihood function. More...
static unsigned int	optimizeNumericalParameters2 (std::shared_ptr< PhyloLikelihoodInterface > lik, const OptimizationOptions &optopt)
	Optimize numerical parameters (branch length, substitution model & rate distribution) of a TreeLikelihood function. More...
static unsigned int	optimizeNumericalParameters2 (std::shared_ptr< SingleProcessPhyloLikelihood > lik, const OptimizationOptions &optopt)
static std::unique_ptr< DistanceMatrix >	estimateDistanceMatrix (DistanceEstimation &estimationMethod, const ParameterList &parametersToIgnore, const std::string &param=DISTANCEMETHOD_INIT, unsigned int verbose=0)
	Estimate a distance matrix using maximum likelihood. More...
static std::unique_ptr< TreeTemplate< Node > >	buildDistanceTree (DistanceEstimation &estimationMethod, AgglomerativeDistanceMethodInterface &reconstructionMethod, const std::string &param, OptimizationOptions &optopt)
	Build a tree using a distance method. More...

Static Public Attributes
static std::string	OPTIMIZATION_GRADIENT = "gradient"
static std::string	OPTIMIZATION_NEWTON = "newton"
static std::string	OPTIMIZATION_BRENT = "Brent"
static std::string	OPTIMIZATION_BFGS = "BFGS"
static std::string	DISTANCEMETHOD_INIT = "init"
static std::string	DISTANCEMETHOD_PAIRWISE = "pairwise"
static std::string	DISTANCEMETHOD_ITERATIONS = "iterations"

Detailed Description

Optimization methods for phylogenetic inference.

This class provides optimization methods for phylogenetics. Parameters of the optimization methods are set to work with TreeLikelihood object. Some non trivial parameters are left to the user choice (tolerance, maximum number of function evaluation, output streams).

Definition at line 221 of file OptimizationTools.h.

Constructor & Destructor Documentation

LegacyOptimizationTools()

LegacyOptimizationTools::LegacyOptimizationTools

(

)

Definition at line 29 of file OptimizationTools.cpp.

~LegacyOptimizationTools()

LegacyOptimizationTools::~LegacyOptimizationTools ( )

virtual

Definition at line 31 of file OptimizationTools.cpp.

Member Function Documentation

buildDistanceTree()

unique_ptr< TreeTemplate< Node > > OptimizationTools::buildDistanceTree ( DistanceEstimation &  estimationMethod, AgglomerativeDistanceMethodInterface &  reconstructionMethod, const std::string &  param, OptimizationOptions &  optopt  )

staticinherited

Build a tree using a distance method.

This method estimate a distance matrix using a DistanceEstimation object, and then builds the phylogenetic tree using a AgglomerativeDistanceMethod object. The main issue here is to estimate non-branch lengths parameters, as substitution model and rate distribution parameters. Three options are provideed here:

• DISTANCEMETHOD_INIT (default) keep parameters to there initial value,
• DISTANCEMETHOD_PAIRWISE estimated parameters in a pairwise manner, which is standard but not that satisfying...
• DISTANCEMETHOD_ITERATIONS uses Ninio et al's iterative algorithm, which uses Maximum Likelihood to estimate these parameters, and then update the distance matrix. Ninio M, Privman E, Pupko T, Friedman N. Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates. Bioinformatics. 2007 Jan 15;23(2):e136-41.

Parameters

estimationMethod	The distance estimation object to use.
reconstructionMethod	The tree reconstruction object to use.
param	Method of for distance calculation
optopt	Optimization Options

Definition at line 656 of file OptimizationTools.cpp.

References bpp::ParameterList::addParameters(), bpp::Node::addSon(), bpp::TreeTemplateTools::buildFromPhyloTree(), bpp::PhyloTreeTools::buildFromTreeTemplate(), bpp::SubstitutionProcessInterface::clone(), bpp::DistanceEstimation::computeMatrix(), bpp::DistanceMethodInterface::computeTree(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::OptimizationTools::DISTANCEMETHOD_ITERATIONS, bpp::OptimizationTools::DISTANCEMETHOD_PAIRWISE, bpp::ParameterList::getCommonParametersWith(), bpp::DistanceEstimation::getData(), bpp::DistanceEstimation::getMatrix(), bpp::SubstitutionProcessInterface::getRateDistributionParameters(), bpp::SubstitutionProcessInterface::getRootFrequenciesParameters(), bpp::SubstitutionProcessInterface::getSubstitutionModelParameters(), bpp::DistanceEstimation::getVerbose(), bpp::DistanceEstimation::matchParametersValues(), bpp::OptimizationTools::optimizeNumericalParameters(), bpp::OptimizationTools::OptimizationOptions::parameters, bpp::DistanceEstimation::process(), bpp::DistanceEstimation::resetAdditionalParameters(), bpp::TreeTools::robinsonFouldsDistance(), bpp::DistanceEstimation::setAdditionalParameters(), bpp::DistanceMethodInterface::setDistanceMatrix(), bpp::Node::setDistanceToFather(), bpp::DistanceEstimation::setVerbose(), bpp::TextTools::toString(), bpp::DistanceMethodInterface::tree(), and bpp::OptimizationTools::OptimizationOptions::verbose.

estimateDistanceMatrix()

unique_ptr< DistanceMatrix > OptimizationTools::estimateDistanceMatrix ( DistanceEstimation &  estimationMethod, const ParameterList &  parametersToIgnore, const std::string &  param = DISTANCEMETHOD_INIT, unsigned int  verbose = 0  )

staticinherited

Estimate a distance matrix using maximum likelihood.

This method estimate a distance matrix using a DistanceEstimation object. The main issue here is to estimate non-branch lengths parameters, as substitution model and rate distribution parameters. Twoe options are provideed here:

• DISTANCEMETHOD_INIT (default) keep parameters to there initial value,
• DISTANCEMETHOD_PAIRWISE estimated parameters in a pairwise manner, which is standard but not that satisfying...

Parameters

estimationMethod	The distance estimation object to use.
parametersToIgnore	A list of parameters to ignore while optimizing parameters.
param	String describing the type of optimization to use.
verbose	Verbose level.

See also

buildDistanceTree for a procedure to jointly estimate the distance matrix and underlying tree.

Definition at line 624 of file OptimizationTools.cpp.

References bpp::ParameterList::addParameters(), bpp::DistanceEstimation::computeMatrix(), bpp::ParameterList::deleteParameters(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::OptimizationTools::DISTANCEMETHOD_INIT, bpp::OptimizationTools::DISTANCEMETHOD_PAIRWISE, bpp::DistanceEstimation::getMatrix(), bpp::ParameterList::getParameterNames(), bpp::SubstitutionProcessInterface::getRateDistributionParameters(), bpp::SubstitutionProcessInterface::getRootFrequenciesParameters(), bpp::SubstitutionProcessInterface::getSubstitutionModelParameters(), bpp::DistanceEstimation::process(), bpp::DistanceEstimation::resetAdditionalParameters(), bpp::DistanceEstimation::setAdditionalParameters(), and bpp::DistanceEstimation::setVerbose().

optimizeBranchLengthsParameters()

unsigned int LegacyOptimizationTools::optimizeBranchLengthsParameters ( std::shared_ptr< DiscreteRatesAcrossSitesTreeLikelihoodInterface >  tl, const ParameterList &  parameters, std::shared_ptr< OptimizationListener >  listener = nullptr, double  tolerance = 0.000001, unsigned int  tlEvalMax = 1000000, std::shared_ptr< OutputStream >  messageHandler = ApplicationTools::message, std::shared_ptr< OutputStream >  profiler = ApplicationTools::message, unsigned int  verbose = 1, const std::string &  optMethodDeriv = OPTIMIZATION_NEWTON  )

static

Optimize branch lengths parameters of a TreeLikelihood function.

Uses Newton's method.

A condition over function values is used as a stop condition for the algorithm.

See also

NewtonBrentMetaOptimizer

Parameters

tl	A pointer toward the TreeLikelihood object to optimize.
parameters	The list of parameters to optimize. The intersection of branch length parameters and the input set will be used. Use tl->getBranchLengthsParameters() in order to estimate all branch length parameters.
listener	A pointer toward an optimization listener, if needed.
tolerance	The tolerance to use in the algorithm.
tlEvalMax	The maximum number of function evaluations.
messageHandler	The massage handler.
profiler	The profiler.
verbose	The verbose level.
optMethodDeriv	Optimization type for derivable parameters (first or second order derivatives).

See also

OPTIMIZATION_NEWTON, OPTIMIZATION_GRADIENT

Exceptions

Exception

any exception thrown by the Optimizer.

Definition at line 302 of file OptimizationTools.cpp.

References bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::ApplicationTools::displayMessage(), bpp::ParameterList::getCommonParametersWith(), bpp::OptimizationTools::OPTIMIZATION_BFGS, bpp::OptimizationTools::OPTIMIZATION_GRADIENT, and bpp::OptimizationTools::OPTIMIZATION_NEWTON.

optimizeNumericalParameters() [1/2]

unsigned int LegacyOptimizationTools::optimizeNumericalParameters ( std::shared_ptr< DiscreteRatesAcrossSitesTreeLikelihoodInterface >  tl, const ParameterList &  parameters, std::shared_ptr< OptimizationListener >  listener = nullptr, unsigned int  nstep = 1, double  tolerance = 0.000001, unsigned int  tlEvalMax = 1000000, std::shared_ptr< OutputStream >  messageHandler = ApplicationTools::message, std::shared_ptr< OutputStream >  profiler = ApplicationTools::message, bool  reparametrization = false, unsigned int  verbose = 1, const std::string &  optMethodDeriv = OPTIMIZATION_NEWTON, const std::string &  optMethodModel = OPTIMIZATION_BRENT  )

static

Optimize numerical parameters (branch length, substitution model & rate distribution) of a TreeLikelihood function.

Uses Newton's method for branch length and Brent or BFGS one dimensional method for other parameters.

A condition over function values is used as a stop condition for the algorithm.

See also

BrentOneDimension, BFGSMultiDimensions

Parameters

tl	A pointer toward the TreeLikelihood object to optimize.
parameters	The list of parameters to optimize. Use tl->getIndependentParameters() in order to estimate all parameters.
listener	A pointer toward an optimization listener, if needed.
nstep	The number of progressive steps to perform (see NewtonBrentMetaOptimizer). 1 means full precision from start.
tolerance	The tolerance to use in the algorithm.
tlEvalMax	The maximum number of function evaluations.
messageHandler	The massage handler.
profiler	The profiler.
reparametrization	Tell if parameters should be transformed in order to remove constraints. This can improve optimization, but is a bit slower.
verbose	The verbose level.
optMethodDeriv	Optimization type for derivable parameters (first or second order derivatives).

See also

OPTIMIZATION_NEWTON, OPTIMIZATION_GRADIENT

Parameters

optMethodModel

Optimization type for model parameters (Brent or BFGS).

See also

OPTIMIZATION_BRENT, OPTIMIZATION_BFGS

Exceptions

Exception

any exception thrown by the Optimizer.

Definition at line 106 of file OptimizationTools.cpp.

References bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::ParameterList::createSubList(), bpp::ApplicationTools::displayMessage(), bpp::ParameterList::getCommonParametersWith(), bpp::ParameterList::getParameterNames(), bpp::MetaOptimizerInfos::IT_TYPE_FULL, bpp::MetaOptimizerInfos::IT_TYPE_STEP, bpp::OptimizationTools::OPTIMIZATION_BFGS, bpp::OptimizationTools::OPTIMIZATION_BRENT, bpp::OptimizationTools::OPTIMIZATION_GRADIENT, bpp::OptimizationTools::OPTIMIZATION_NEWTON, and bpp::ParameterList::reset().

Referenced by bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters(), optimizeTreeNNI(), and bpp::NNITopologyListener::topologyChangeSuccessful().

optimizeNumericalParameters() [2/2]

unsigned int OptimizationTools::optimizeNumericalParameters ( std::shared_ptr< PhyloLikelihoodInterface >  lik, const OptimizationOptions &  optopt  )

staticinherited

Optimize numerical parameters (branch length, substitution model & rate distribution) of a TreeLikelihood function.

Uses Newton's method for branch length and Brent or BFGS one dimensional method for other parameters.

A condition over function values is used as a stop condition for the algorithm.

See also

BrentOneDimension, BFGSMultiDimensions

Parameters

lik	A pointer toward the PhyloLikelihood object to optimize.
optopt	Optimization Options

Definition at line 353 of file OptimizationTools.cpp.

References bpp::ParameterList::addParameters(), bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::ParameterList::createSubList(), bpp::ApplicationTools::displayMessage(), bpp::ParameterList::getCommonParametersWith(), bpp::ParameterList::getParameterNames(), bpp::MetaOptimizerInfos::IT_TYPE_FULL, bpp::MetaOptimizerInfos::IT_TYPE_STEP, bpp::OptimizationTools::OptimizationOptions::listener, bpp::OptimizationTools::OptimizationOptions::messenger, bpp::OptimizationTools::OptimizationOptions::nbEvalMax, bpp::OptimizationTools::OptimizationOptions::nstep, bpp::OptimizationTools::OPTIMIZATION_BFGS, bpp::OptimizationTools::OPTIMIZATION_BRENT, bpp::OptimizationTools::OPTIMIZATION_GRADIENT, bpp::OptimizationTools::OPTIMIZATION_NEWTON, bpp::OptimizationTools::OptimizationOptions::optMethodDeriv, bpp::OptimizationTools::OptimizationOptions::optMethodModel, bpp::OptimizationTools::OptimizationOptions::parameters, bpp::OptimizationTools::OptimizationOptions::profiler, bpp::OptimizationTools::OptimizationOptions::reparametrization, bpp::OptimizationTools::OptimizationOptions::tolerance, and bpp::OptimizationTools::OptimizationOptions::verbose.

Referenced by bpp::OptimizationTools::buildDistanceTree(), and bpp::PhylogeneticsApplicationTools::optimizeParameters().

optimizeNumericalParameters2() [1/3]

unsigned int LegacyOptimizationTools::optimizeNumericalParameters2 ( std::shared_ptr< DiscreteRatesAcrossSitesTreeLikelihoodInterface >  tl, const ParameterList &  parameters, std::shared_ptr< OptimizationListener >  listener = nullptr, double  tolerance = 0.000001, unsigned int  tlEvalMax = 1000000, std::shared_ptr< OutputStream >  messageHandler = ApplicationTools::message, std::shared_ptr< OutputStream >  profiler = ApplicationTools::message, bool  reparametrization = false, bool  useClock = false, unsigned int  verbose = 1, const std::string &  optMethodDeriv = OPTIMIZATION_NEWTON  )

static

Optimize numerical parameters (branch length, substitution model & rate distribution) of a TreeLikelihood function.

Uses Newton's method for all parameters, branch length derivatives are computed analytically, derivatives for other parameters numerically.

See also

PseudoNewtonOptimizer

Parameters

tl	A pointer toward the TreeLikelihood object to optimize.
parameters	The list of parameters to optimize. Use tl->getIndependentParameters() in order to estimate all parameters.
listener	A pointer toward an optimization listener, if needed.
tolerance	The tolerance to use in the algorithm.
tlEvalMax	The maximum number of function evaluations.
messageHandler	The massage handler.
profiler	The profiler.
reparametrization	Tell if parameters should be transformed in order to remove constraints. This can improve optimization, but is a bit slower.
useClock	Tell if branch lengths have to be optimized under a global molecular clock constraint.
verbose	The verbose level.
optMethodDeriv	Optimization type for derivable parameters (first or second order derivatives).

See also

OPTIMIZATION_NEWTON, OPTIMIZATION_GRADIENT

Exceptions

Exception

any exception thrown by the Optimizer.

Definition at line 208 of file OptimizationTools.cpp.

References bpp::ParameterList::addParameters(), bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::ParameterList::createSubList(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ParameterList::getCommonParametersWith(), bpp::ParameterList::getParameterNames(), bpp::OptimizationTools::OPTIMIZATION_BFGS, bpp::OptimizationTools::OPTIMIZATION_GRADIENT, bpp::OptimizationTools::OPTIMIZATION_NEWTON, and bpp::ParameterList::reset().

Referenced by bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters(), optimizeTreeNNI2(), and bpp::NNITopologyListener2::topologyChangeSuccessful().

optimizeNumericalParameters2() [2/3]

unsigned int OptimizationTools::optimizeNumericalParameters2 ( std::shared_ptr< PhyloLikelihoodInterface >  lik, const OptimizationOptions &  optopt  )

staticinherited

Optimize numerical parameters (branch length, substitution model & rate distribution) of a TreeLikelihood function.

Uses Newton's method for all parameters, branch length derivatives are computed analytically, derivatives for other parameters numerically.

See also

PseudoNewtonOptimizer

Parameters

lik	A pointer toward the PhyloLikelihood object to optimize.
optopt	Optimization Options

Exceptions

Exception

any exception thrown by the Optimizer.

Definition at line 451 of file OptimizationTools.cpp.

References bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::ParameterList::createSubList(), bpp::ApplicationTools::displayMessage(), bpp::ParameterList::getParameterNames(), bpp::OptimizationTools::OptimizationOptions::listener, bpp::OptimizationTools::OptimizationOptions::messenger, bpp::OptimizationTools::OptimizationOptions::nbEvalMax, bpp::OptimizationTools::OPTIMIZATION_BFGS, bpp::OptimizationTools::OPTIMIZATION_GRADIENT, bpp::OptimizationTools::OPTIMIZATION_NEWTON, bpp::OptimizationTools::OptimizationOptions::optMethodDeriv, bpp::OptimizationTools::OptimizationOptions::parameters, bpp::OptimizationTools::OptimizationOptions::profiler, bpp::OptimizationTools::OptimizationOptions::reparametrization, bpp::ParameterList::reset(), bpp::OptimizationTools::OptimizationOptions::tolerance, and bpp::OptimizationTools::OptimizationOptions::verbose.

Referenced by bpp::PhylogeneticsApplicationTools::optimizeParameters().

optimizeNumericalParameters2() [3/3]

unsigned int OptimizationTools::optimizeNumericalParameters2 ( std::shared_ptr< SingleProcessPhyloLikelihood >  lik, const OptimizationOptions &  optopt  )

staticinherited

Definition at line 542 of file OptimizationTools.cpp.

References bpp::AutoParameter::CONSTRAINTS_AUTO, bpp::ParameterList::createSubList(), bpp::ApplicationTools::displayMessage(), bpp::FivePoints, bpp::ParameterList::getParameterNames(), bpp::OptimizationTools::OptimizationOptions::listener, bpp::OptimizationTools::OptimizationOptions::messenger, bpp::OptimizationTools::OptimizationOptions::nbEvalMax, bpp::OptimizationTools::OPTIMIZATION_BFGS, bpp::OptimizationTools::OPTIMIZATION_GRADIENT, bpp::OptimizationTools::OPTIMIZATION_NEWTON, bpp::OptimizationTools::OptimizationOptions::optMethodDeriv, bpp::OptimizationTools::OptimizationOptions::parameters, bpp::OptimizationTools::OptimizationOptions::profiler, bpp::OptimizationTools::OptimizationOptions::reparametrization, bpp::ThreePoints, bpp::OptimizationTools::OptimizationOptions::tolerance, and bpp::OptimizationTools::OptimizationOptions::verbose.

optimizeTreeNNI() [1/2]

shared_ptr< DRTreeParsimonyScore > LegacyOptimizationTools::optimizeTreeNNI ( std::shared_ptr< DRTreeParsimonyScore >  tp, unsigned int  verbose = 1  )

static

Optimize tree topology from a DRTreeParsimonyScore using Nearest Neighbor Interchanges.

Parameters

tp	A pointer toward the DRTreeParsimonyScore object to optimize.
verbose	The verbose level.

Returns

A pointer toward the final parsimony score object. This pointer may be the same as passed in argument (tl), but in some cases the algorithm clone this object. We may change this behavior in the future... You hence should write something like

tp = OptimizationTools::optimizeTreeNNI(tp, ...);

Definition at line 449 of file OptimizationTools.cpp.

References bpp::NNITopologySearch::getSearchableObject(), bpp::NNITopologySearch::PHYML, and bpp::NNITopologySearch::search().

optimizeTreeNNI() [2/2]

shared_ptr< NNIHomogeneousTreeLikelihood > LegacyOptimizationTools::optimizeTreeNNI ( std::shared_ptr< NNIHomogeneousTreeLikelihood >  tl, const ParameterList &  parameters, bool  optimizeNumFirst = true, double  tolBefore = 100, double  tolDuring = 100, unsigned int  tlEvalMax = 1000000, unsigned int  numStep = 1, std::shared_ptr< OutputStream >  messageHandler = ApplicationTools::message, std::shared_ptr< OutputStream >  profiler = ApplicationTools::message, bool  reparametrization = false, unsigned int  verbose = 1, const std::string &  optMethod = OptimizationTools::OPTIMIZATION_NEWTON, unsigned int  nStep = 1, const std::string &  nniMethod = NNITopologySearch::PHYML  )

static

Optimize all parameters from a TreeLikelihood object, including tree topology using Nearest Neighbor Interchanges.

This function takes as input a TreeLikelihood object implementing the NNISearchable interface.

Details: A NNITopologySearch object is instantiated and is associated an additional TopologyListener. This listener is used to re-estimate numerical parameters after one or several topology change. By default, the PHYML option is used for the NNITopologySearch object, and numerical parameters are re-estimated every 4 NNI runs (as in the phyml software).

The optimizeNumericalParameters method is used for estimating numerical parameters. The tolerance passed to this function is specified as input parameters. They are generally very high to avoid local optima.

Parameters

tl	A pointer toward the TreeLikelihood object to optimize.
parameters	The list of parameters to optimize. Use tl->getIndependentParameters() in order to estimate all parameters.
optimizeNumFirst	Tell if we must optimize numerical parameters before searching topology.
tolBefore	The tolerance to use when estimating numerical parameters before topology search (if optimizeNumFirst is set to 'true').
tolDuring	The tolerance to use when estimating numerical parameters during the topology search.
tlEvalMax	The maximum number of function evaluations.
numStep	Number of NNI rounds before re-estimating numerical parameters.
messageHandler	The massage handler.
profiler	The profiler.
reparametrization	Tell if parameters should be transformed in order to remove constraints. This can improve optimization, but is a bit slower.
verbose	The verbose level.
optMethod	Option passed to optimizeNumericalParameters.
nStep	Option passed to optimizeNumericalParameters.
nniMethod	NNI algorithm to use.

Returns

A pointer toward the final likelihood object. This pointer may be the same as passed in argument (tl), but in some cases the algorithm clone this object. We may change this behavior in the future... You hence should write something like

tl = OptimizationTools::optimizeTreeNNI(tl, ...);

Exceptions

Exception

any exception thrown by the optimizer.

Definition at line 386 of file OptimizationTools.cpp.

References optimizeNumericalParameters().

Referenced by bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters().

optimizeTreeNNI2()

shared_ptr< NNIHomogeneousTreeLikelihood > LegacyOptimizationTools::optimizeTreeNNI2 ( std::shared_ptr< NNIHomogeneousTreeLikelihood >  tl, const ParameterList &  parameters, bool  optimizeNumFirst = true, double  tolBefore = 100, double  tolDuring = 100, unsigned int  tlEvalMax = 1000000, unsigned int  numStep = 1, std::shared_ptr< OutputStream >  messageHandler = ApplicationTools::message, std::shared_ptr< OutputStream >  profiler = ApplicationTools::message, bool  reparametrization = false, unsigned int  verbose = 1, const std::string &  optMethod = OptimizationTools::OPTIMIZATION_NEWTON, const std::string &  nniMethod = NNITopologySearch::PHYML  )

static

Optimize all parameters from a TreeLikelihood object, including tree topology using Nearest Neighbor Interchanges.

This function takes as input a TreeLikelihood object implementing the NNISearchable interface.

Details: A NNITopologySearch object is instantiated and is associated an additional TopologyListener. This listener is used to re-estimate numerical parameters after one or several topology change. By default, the PHYML option is used for the NNITopologySearch object, and numerical parameters are re-estimated every 4 NNI runs (as in the phyml software).

The optimizeNumericalParameters2 method is used for estimating numerical parameters. The tolerance passed to this function is specified as input parameters. They are generally very high to avoid local optima.

Parameters

tl	A pointer toward the TreeLikelihood object to optimize.
parameters	The list of parameters to optimize. Use tl->getIndependentParameters() in order to estimate all parameters.
optimizeNumFirst	Tell if we must optimize numerical parameters before searching topology.
tolBefore	The tolerance to use when estimating numerical parameters before topology search (if optimizeNumFirst is set to 'true').
tolDuring	The tolerance to use when estimating numerical parameters during the topology search.
tlEvalMax	The maximum number of function evaluations.
numStep	Number of NNI rounds before re-estimating numerical parameters.
messageHandler	The massage handler.
profiler	The profiler.
reparametrization	Tell if parameters should be transformed in order to remove constraints. This can improve optimization, but is a bit slower.
verbose	The verbose level.
optMethod	Option passed to optimizeNumericalParameters2.
nniMethod	NNI algorithm to use.

Returns

A pointer toward the final likelihood object. This pointer may be the same as passed in argument (tl), but in some cases the algorithm clone this object. We may change this behavior in the future... You hence should write something like

tl = OptimizationTools::optimizeTreeNNI2(tl, ...);

Exceptions

Exception

any exception thrown by the optimizer.

Definition at line 418 of file OptimizationTools.cpp.

References optimizeNumericalParameters2().

Referenced by bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters().

optimizeTreeScale()

unsigned int LegacyOptimizationTools::optimizeTreeScale ( std::shared_ptr< TreeLikelihoodInterface >  tl, double  tolerance = 0.000001, unsigned int  tlEvalMax = 1000000, std::shared_ptr< OutputStream >  messageHandler = ApplicationTools::message, std::shared_ptr< OutputStream >  profiler = ApplicationTools::message, unsigned int  verbose = 1  )

static

Optimize the scale of a TreeLikelihood.

This method only works on branch lengths parameters. It multiply all branch length by a factor 'x' which is optimized using Brent's algorithm in one dimension. This method may be useful for scaling a tree whose branch lengths come from the Neighbor-Joining algorithm for instance.

Practically, and contrarily to what one may expect, this does not speed up the optimization!

A condition over parameters is used as a stop condition for the algorithm.

Parameters

tl	A pointer toward the TreeLikelihood object to optimize.
tolerance	The tolerance to use in the algorithm.
tlEvalMax	The maximum number of function evaluations.
messageHandler	The massage handler.
profiler	The profiler.
verbose	The verbose level.

Exceptions

Exception

any exception thrown by the optimizer.

Definition at line 78 of file OptimizationTools.cpp.

References bpp::ParameterList::addParameter(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayTaskDone(), bpp::exp(), bpp::BrentOneDimension::getNumberOfEvaluations(), bpp::BrentOneDimension::init(), bpp::BrentOneDimension::optimize(), bpp::BrentOneDimension::setInitialInterval(), bpp::BrentOneDimension::setMaximumNumberOfEvaluations(), bpp::BrentOneDimension::setMessageHandler(), bpp::BrentOneDimension::setProfiler(), and bpp::BrentOneDimension::setStopCondition().

Referenced by bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters().

Member Data Documentation

DISTANCEMETHOD_INIT

std::string OptimizationTools::DISTANCEMETHOD_INIT = "init"

staticinherited

Definition at line 223 of file OptimizationTools.h.

Referenced by bpp::OptimizationTools::estimateDistanceMatrix().

DISTANCEMETHOD_ITERATIONS

std::string OptimizationTools::DISTANCEMETHOD_ITERATIONS = "iterations"

staticinherited

Definition at line 225 of file OptimizationTools.h.

Referenced by bpp::OptimizationTools::buildDistanceTree().

DISTANCEMETHOD_PAIRWISE

std::string OptimizationTools::DISTANCEMETHOD_PAIRWISE = "pairwise"

staticinherited

Definition at line 224 of file OptimizationTools.h.

Referenced by bpp::OptimizationTools::buildDistanceTree(), and bpp::OptimizationTools::estimateDistanceMatrix().

OPTIMIZATION_BFGS

std::string OptimizationTools::OPTIMIZATION_BFGS = "BFGS"

staticinherited

Definition at line 76 of file OptimizationTools.h.

Referenced by bpp::OptimizationTools::OptimizationOptions::OptimizationOptions(), optimizeBranchLengthsParameters(), optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters(), optimizeNumericalParameters2(), bpp::OptimizationTools::optimizeNumericalParameters2(), bpp::PhylogeneticsApplicationTools::optimizeParameters(), and bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters().

OPTIMIZATION_BRENT

std::string OptimizationTools::OPTIMIZATION_BRENT = "Brent"

staticinherited

Definition at line 75 of file OptimizationTools.h.

Referenced by bpp::OptimizationTools::OptimizationOptions::OptimizationOptions(), optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters(), bpp::PhylogeneticsApplicationTools::optimizeParameters(), and bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters().

OPTIMIZATION_GRADIENT

std::string OptimizationTools::OPTIMIZATION_GRADIENT = "gradient"

staticinherited

Definition at line 73 of file OptimizationTools.h.

Referenced by bpp::OptimizationTools::OptimizationOptions::OptimizationOptions(), optimizeBranchLengthsParameters(), optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters(), optimizeNumericalParameters2(), bpp::OptimizationTools::optimizeNumericalParameters2(), and bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters().

OPTIMIZATION_NEWTON

std::string OptimizationTools::OPTIMIZATION_NEWTON = "newton"

staticinherited

Definition at line 74 of file OptimizationTools.h.

Referenced by bpp::OptimizationTools::OptimizationOptions::OptimizationOptions(), optimizeBranchLengthsParameters(), optimizeNumericalParameters(), bpp::OptimizationTools::optimizeNumericalParameters(), optimizeNumericalParameters2(), bpp::OptimizationTools::optimizeNumericalParameters2(), bpp::PhylogeneticsApplicationTools::optimizeParameters(), and bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters().

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

• Bpp/Phyl/Legacy/OptimizationTools.h
• Bpp/Phyl/Legacy/OptimizationTools.cpp