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ToyHMM

A simple Hidden Markov Model implementation for educational purposes

Readme

ToyHMM.jl

A simple Hidden Markov Model implementation in Julia. Intended mostly for educational purposes. Only supports discrete emission probabilities

I am developing HMM.jl for a more general-purpose module.

Installation

Pkg.clone("https://github.com/ahwillia/ToyHMM.jl.git")

Simple Example

using ToyHMM

n_states = 2
n_outputs = 3
hmm = dHMM(n_states,n_outputs)

println(hmm.A) # state-transition matrix (randomly initialized, rows sum to 1)
println(hmm.B) # emmission matrix (randomly initialized, rows sum to 1)
println(hmm.p) # initial state probabilities (randomly initialized)

o = [1,1,2,1,1,2,1,2,1,3,3,3,3,2,2,3,3,3] # example observation sequence

ch = baum_welch!(hmm,o) # fit model using Expectation-Maximization

println(ch) # log-likelihood values, convergence history

println(hmm.A) # fitted values of the hmm model
println(hmm.B)
println(hmm.p)

println(viterbi(hmm,o)) # most likely state sequence given hmm params

(also see test/runtests.jl for some examples)

How fast is it?

using ToyHMM

n_states = 2
n_outputs = 3

# create a very long output sequence
true_model = dHMM(n_states,n_outputs)
(s,o) = generate(true_model,100_000)

# try to recover similar params by fitting new model
fit_model = dHMM(n_states,n_outputs)
@time ch = baum_welch!(fit_model,o)

elapsed time: 7.958006041 seconds (4140814448 bytes allocated, 26.85% gc time)

References and Acknowledgements:

Michael Hamilton's implementation (python): http://www.cs.colostate.edu/~hamiltom/code.html

Guy Zyskind's implementation (python): https://github.com/guyz/HMM

Rabiner, Lawrence R. "A tutorial on hidden Markov models and selected applications in speech recognition." Proceedings of the IEEE 77.2 (1989): 257-286.

To Do (Variational Bayes):

MacKay DJC (1997). Ensemble Learning for Hidden Markov Models Technical report, University of Cambridge

MacKay DJC (1998). Choice of Basis for Laplace Approximation. Machine Learning. 33(1), 77-86.

Beal MJ (2003). Variational Algorithms for Approximate Bayesian Inference. PhD Thesis, University College London

First Commit

04/12/2017

Last Touched

9 months ago

Commits

32 commits