Implementation of the EM-algorithm for statistical inference of assembling model parameters. Classic version described in (Murugan et al 2012) More...

#include <em_algorithm.h>

Inheritance diagram for ymir::EMAlgorithm:

Public Member Functions
virtual std::vector< prob_t >	statisticalInference (const ClonesetView &repertoire, ProbabilisticAssemblingModel &model, const AlgorithmParameters &algo_param=AlgorithmParameters().set("niter", 10).set("sample", 50000), ErrorMode error_mode=NO_ERRORS) const

Public Member Functions inherited from ymir::StatisticalInferenceAlgorithm
void	filterOut (const ClonesetView &rep_nonc, const MAAGRepertoire &maag_rep, vector< prob_t > &prob_vec, vector< bool > &good_clonotypes, size_t &removed, size_t &zero_prob, size_t &no_alignments) const

Protected Member Functions
bool	updateTempVec (MAAGForwardBackwardAlgorithm &fb, MAAG &maag, ModelParameterVector &new_param_vec, ErrorMode error_mode) const

void	updateModel (ProbabilisticAssemblingModel &model, ModelParameterVector &new_param_vec, MAAGRepertoire &maag_rep, vector< prob_t > &prob_vec, prob_t &prev_ll, size_t removed, ErrorMode error_mode) const

Detailed Description

Implementation of the EM-algorithm for statistical inference of assembling model parameters. Classic version described in (Murugan et al 2012)

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

Ymir/src/em_algorithm.h

Public Member Functions

Protected Member Functions

Detailed Description