baumWelch: Baum-Welch Algorithm
In tileHMM: Hidden Markov Models for ChIP-on-Chip Analysis

Description Usage Arguments Value Author(s) References See Also Examples

The Baum-Welch algorithm [Baum et al., 1970] is a well established method for estimating parameters of HMMs. It represents the EM algorithm [Dempster et al., 1977] for the specific case of HMMs. The formulation of the Baum-Welch algorithm used in this implementation is based on the description given by Rabiner [1989].

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## S4 method for signature 'hmm,list'
baumWelch(hmm, obs, max.iter=FALSE, eps=0.01, df=NULL, 
	trans.prior=NULL, init.prior=NULL, verbose=1)

`hmm`	An object of class `hmm` or one of its subclasses representing the hidden Markov model.
`obs`	A list of observation sequences.
`max.iter`	Maximum number of iterations. (optional)
`eps`	Minimum difference in log likelihood between iterations. Default: 0.01
`df`	If this is `NULL` the degrees of freedom for the t distributions are estimated from the data. Otherwise they are set to `df`.
`trans.prior`	Prior distribution of transition probabilities. A prior can be specified either by providing a matrix with transition probabilities or by setting `trans.prior=TRUE`. In the latter case the initial parameter estimates are used as prior. If `trans.prior` is `NULL` (the default) no prior is used.
`init.prior`	Prior distribution of initial state probabilities. A prior can be specified either by providing a vector with initial state probabilities or by setting `init.prior=TRUE`. In the latter case the initial parameter estimates are used as prior. If `init.prior` is `NULL` (the default) no prior is used.
`verbose`	Level of verbosity. Allows some control over the amount of output printed to the console.

Returns the HMM with optimised parameters.

Peter Humburg

Baum, L. E. and Petrie, T. and Soules, G. and Weiss, N. 1970 A maximization technique occuring in the statistical analysis of probabilistic functions of markov chains. The Annals of Mathematical Statistics, 41(1), 164–171.

Dempster, A. P. and Laird, N. M. and Rubin, D. B. 1977 Maximum likelihood for incomplete data via the EM algorithm. Journal of the Royal Statistical Society, Series B, 39(1).

Rabiner, L. R. 1989 A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE, 77(2), 257–286.

viterbiTraining, viterbiEM, getHMM, hmm.setup

## create two state HMM with t distributions
state.names <- c("one","two")
transition <- c(0.035, 0.01)
location <- c(1, 2)
scale <- c(1, 1)
df <- c(4, 6)
hmm1 <- getHMM(list(a=transition, mu=location, sigma=scale, nu=df), 
    state.names)

## generate observation sequences from model
obs.lst <- list()
for(i in 1:50) obs.lst[[i]] <- sampleSeq(hmm1, 100)

## fit an HMM to the data (with fixed degrees of freedom)
hmm2 <- hmm.setup(obs.lst, state=c("one","two"), df=5)
hmm2.fit <- baumWelch(hmm2, obs.lst, max.iter=20, df=5, verbose=1)

## fit an HMM to the data, this time estimating the degrees of freedom
hmm3.fit <- baumWelch(hmm2, obs.lst, max.iter=20, verbose=1)