Generating a Test Sequence

The following commands create the transition and emission matrices for the model described in the Introduction to Hidden Markov Models (HMM):

TRANS = [.9 .1; .05 .95];

EMIS = [1/6, 1/6, 1/6, 1/6, 1/6, 1/6;...
7/12, 1/12, 1/12, 1/12, 1/12, 1/12];

To generate a random sequence of states and emissions from the model, use hmmgenerate:

[seq,states] = hmmgenerate(1000,TRANS,EMIS);

The output seq is the sequence of emissions and the output states is the sequence of states.

hmmgenerate begins in state 1 at step 0, makes the transition to state i₁ at step 1, and returns i₁ as the first entry in states. To change the initial state, see Changing the Initial State Distribution.

Estimating the State Sequence

Given the transition and emission matrices TRANS and EMIS, the function hmmviterbi uses the Viterbi algorithm to compute the most likely sequence of states the model would go through to generate a given sequence seq of emissions:

likelystates = hmmviterbi(seq, TRANS, EMIS);

likelystates is a sequence the same length as seq.

To test the accuracy of hmmviterbi, compute the percentage of the actual sequence states that agrees with the sequence likelystates.

sum(states==likelystates)/1000
ans =
   0.8200

In this case, the most likely sequence of states agrees with the random sequence 82% of the time.

Estimating Transition and Emission Matrices

• Using hmmestimate

• Using hmmtrain

The functions hmmestimate and hmmtrain estimate the transition and emission matrices TRANS and EMIS given a sequence seq of emissions.

Using hmmestimate.  The function hmmestimate requires that you know the sequence of states states that the model went through to generate seq.

The following takes the emission and state sequences and returns estimates of the transition and emission matrices:

[TRANS_EST, EMIS_EST] = hmmestimate(seq, states)

TRANS_EST =
0.8989    0.1011
0.0585    0.9415

EMIS_EST =
0.1721    0.1721    0.1749    0.1612    0.1803    0.1393
0.5836    0.0741    0.0804    0.0789    0.0726    0.1104

You can compare the outputs with the original transition and emission matrices, TRANS and EMIS:

TRANS
TRANS =
0.9000    0.1000
0.0500    0.9500

EMIS
EMIS =
0.1667    0.1667    0.1667    0.1667    0.1667    0.1667
0.5833    0.0833    0.0833    0.0833    0.0833    0.0833

Using hmmtrain.  If you do not know the sequence of states states, but you have initial guesses for TRANS and EMIS, you can still estimate TRANS and EMIS using hmmtrain.

Suppose you have the following initial guesses for TRANS and EMIS.

TRANS_GUESS = [.85 .15; .1 .9];
EMIS_GUESS = [.17 .16 .17 .16 .17 .17;.6 .08 .08 .08 .08 08];

You estimate TRANS and EMIS as follows:

[TRANS_EST2, EMIS_EST2] = hmmtrain(seq, TRANS_GUESS, EMIS_GUESS)

TRANS_EST2 =
0.2286    0.7714
0.0032    0.9968

EMIS_EST2 =
0.1436    0.2348    0.1837    0.1963    0.2350    0.0066
0.4355    0.1089    0.1144    0.1082    0.1109    0.1220

hmmtrain uses an iterative algorithm that alters the matrices TRANS_GUESS and EMIS_GUESS so that at each step the adjusted matrices are more likely to generate the observed sequence, seq. The algorithm halts when the matrices in two successive iterations are within a small tolerance of each other.

If the algorithm fails to reach this tolerance within a maximum number of iterations, whose default value is 100, the algorithm halts. In this case, hmmtrain returns the last values of TRANS_EST and EMIS_EST and issues a warning that the tolerance was not reached.

If the algorithm fails to reach the desired tolerance, increase the default value of the maximum number of iterations with the command:

hmmtrain(seq,TRANS_GUESS,EMIS_GUESS,'maxiterations',maxiter)

where maxiter is the maximum number of steps the algorithm executes.

Change the default value of the tolerance with the command:

hmmtrain(seq, TRANS_GUESS, EMIS_GUESS, 'tolerance', tol)

where tol is the desired value of the tolerance. Increasing the value of tol makes the algorithm halt sooner, but the results are less accurate.

Two factors reduce the reliability of the output matrices of hmmtrain:

Estimating Posterior State Probabilities

The posterior state probabilities of an emission sequence seq are the conditional probabilities that the model is in a particular state when it generates a symbol in seq, given that seq is emitted. You compute the posterior state probabilities with hmmdecode:

PSTATES = hmmdecode(seq,TRANS,EMIS)

The output PSTATES is an M-by-L matrix, where M is the number of states and L is the length of seq. PSTATES(i,j) is the conditional probability that the model is in state i when it generates the jth symbol of seq, given that seq is emitted.

hmmdecode begins with the model in state 1 at step 0, prior to the first emission. PSTATES(i,1) is the probability that the model is in state i at the following step 1. To change the initial state, see Changing the Initial State Distribution.

To return the logarithm of the probability of the sequence seq, use the second output argument of hmmdecode:

[PSTATES,logpseq] = hmmdecode(seq,TRANS,EMIS)

The probability of a sequence tends to 0 as the length of the sequence increases, and the probability of a sufficiently long sequence becomes less than the smallest positive number your computer can represent. hmmdecode returns the logarithm of the probability to avoid this problem.

Changing the Initial State Distribution

By default, Statistics and Machine Learning Toolbox hidden Markov model functions begin in state 1. In other words, the distribution of initial states has all of its probability mass concentrated at state 1. To assign a different distribution of probabilities, p = [p₁, p₂, ..., p_M], to the M initial states, do the following:

If the transition and emission matrices are TRANS and EMIS, respectively, you create the augmented matrices with the following commands:

TRANS_HAT = [0 p; zeros(size(TRANS,1),1) TRANS];

EMIS_HAT = [zeros(1,size(EMIS,2)); EMIS];