Example #1
0
def train_hmm_and_keep_track_of_log_likelihood(hmm, obs, n_iter=1, **kwargs):
    hmm.fit(obs, n_iter=1, **kwargs)
    loglikelihoods = []
    for n in xrange(n_iter):
        hmm.fit(obs, n_iter=1, init_params='', **kwargs)
        loglikelihoods.append(sum(hmm.score(x) for x in obs))
    return loglikelihoods
Example #2
0
def train_hmm_and_keep_track_of_log_likelihood(hmm, obs, n_iter=1, **kwargs):
    hmm.fit(obs, n_iter=1, **kwargs)
    loglikelihoods = []
    for n in xrange(n_iter):
        hmm.fit(obs, n_iter=1, init_params='', **kwargs)
        loglikelihoods.append(sum(hmm.score(x) for x in obs))
    return loglikelihoods
Example #3
0
def test_1():
    # creates a 4-state HMM on the ALA2 data. Nothing fancy, just makes
    # sure the code runs without erroring out
    dataset = AlanineDipeptide().get()
    trajectories = dataset.trajectories
    topology = trajectories[0].topology

    indices = topology.select('symbol C or symbol O or symbol N')
    featurizer = SuperposeFeaturizer(indices, trajectories[0][0])

    sequences = featurizer.transform(trajectories)
    hmm = GaussianHMM(n_states=4, n_init=3)
    hmm.fit(sequences)

    assert len(hmm.timescales_ == 3)
    assert np.any(hmm.timescales_ > 50)