1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
|
/***************************************************************************
* PHAST: PHylogenetic Analysis with Space/Time models
* Copyright (c) 2002-2005 University of California, 2006-2010 Cornell
* University. All rights reserved.
*
* This source code is distributed under a BSD-style license. See the
* file LICENSE.txt for details.
***************************************************************************/
/** @file em.h
Function for training an phylo-HMM via EM including its models.
@ingroup hmm
*/
#ifndef EM_H
#define EM_H
#include <hmm.h>
#include <tree_model.h>
//#define EM_CONVERGENCE_THRESHOLD 0.01
#define EM_CONVERGENCE_THRESHOLD 0.1 /* TEMPORARY! */
/** Train a Hidden Markov Model by using EM algorithm.
@param hmm Hidden Markov Model to train
@param models ???
@param data Training data (the ith training sample in data must be of length 'sample_lens[i]' )
@param nsamples Number of samples
@param sample_lens Lengths of each data sample
@param pseudocounts Pseudo counts of ???
@param compute_emissions (Optional) Function to compute emissions. If NULL simply not called
@param estimate_state_models (Optional) Function to estimate state models. If NULL fully general parameterization is assumed
@param estimate_transitions (Optional) Function to estimate transitional probabilities (M step). If NULL fully general is assumed
@param get_observation_index Function to get observation index
@param log_function Function to use for logging statistics
@param emissions_alloc (Optional) Used for emission probabilities (must be large enough for longest sample)
@param logf Log to save statistics to
@result Log likelihood of optimized model
@note HMM and models must be initialized appropriately
@note Must be one model for every state in the HMM
@note If sample size is 1, emissions can be pre-computed
@warning This function is experimental
*/
double hmm_train_by_em(HMM *hmm, void *models, void *data, int nsamples,
int *sample_lens, Matrix *pseudocounts,
void (*compute_emissions)(double**, void**, int, void*,
int, int),
void (*estimate_state_models)(TreeModel**, int, void*,
double**, int, FILE*),
void (*estimate_transitions)(HMM*, void*, double**),
int (*get_observation_index)(void*, int, int),
void (*log_function)(FILE*, double, HMM*, void*, int),
double **emissions_alloc, FILE *logf);
#endif
|
