Python GaussianHMM.transmat_方法代码示例

# 需要导入模块: from hmmlearn.hmm import GaussianHMM [as 别名]
# 或者: from hmmlearn.hmm.GaussianHMM import transmat_ [as 别名]
def main(args):
    x, X = loadDiffRows(args.diffFile)
    model = GaussianHMM(n_components=3,
                        covariance_type="diag",
                        n_iter=100000000000)
    model.transmat_ = numpy.array([[0.5, 0.5, 0.0],
                                   [0.0, 0.5, 0.5],
                                   [0.0, 0.0, 1.0]])
    model.fit(X)
    print(model.transmat_)
    model.transmat_[0][2] = 0.
    model.transmat_[1][0] = 0.
    model.transmat_[2][0] = 0.
    model.transmat_[2][1] = 0.
    
    exp = args.outFile.split('/')[-1].split('_')[0]
    with open(args.outFile, 'w') as fout:
        print('exp\tbin\treads\tstate', file=fout)
        for seq in X:
            hiddenStates = model.predict(seq)
            for idx,v in enumerate(zip(x,hiddenStates)):
                r,h = v
                print(exp + '\t' + str(idx) + '\t'
                      + str(r) + '\t' + str(h),
                      file=fout)

# 需要导入模块: from hmmlearn.hmm import GaussianHMM [as 别名]
# 或者: from hmmlearn.hmm.GaussianHMM import transmat_ [as 别名]
def calculate_hmm_g(training_set, test_set, taxonomy, cursor, connection, settings):
    da_id_taxonomy = find_da_id(taxonomy, cursor)
    states, start_probability, transition_probability = start_transition_probability_extraction(training_set, taxonomy)
    n_states = len(states)

    feature_list = extract_features_training_set_gaus(training_set, taxonomy, settings)
    n_features = len(feature_list[states[0]][0])
    mean = calculate_means(states, feature_list, n_features)
    covariance = calculate_covariance(states, feature_list, n_features)
    # covariance = diag_cov(states, feature_list, n_features, mean)

    model = GaussianHMM(n_components=n_states, covariance_type='full')
    model.startprob_ = start_probability
    model.transmat_ = transition_probability
    model.means_ = mean
    model.covars_ = covariance

    test_seq, con_pathes = extract_features_test_set_gaus(test_set, taxonomy, settings)
    da_predictions(test_seq, model, con_pathes, states, da_id_taxonomy, taxonomy, cursor, connection)

# 需要导入模块: from hmmlearn.hmm import GaussianHMM [as 别名]
# 或者: from hmmlearn.hmm.GaussianHMM import transmat_ [as 别名]
from hmmlearn.hmm import GaussianHMM
import matplotlib.pyplot as plt
import numpy as np

# Here n_components correspond to number of states in the hidden
# variables.
model_gaussian = GaussianHMM(n_components=3, covariance_type='full')

# Transition probability as specified above
transition_matrix = np.array([[0.2, 0.6, 0.2],
                              [0.4, 0.3, 0.3],
                              [0.05, 0.05, 0.9]])

# Setting the transition probability
model_gaussian.transmat_ = transition_matrix

# Initial state probability
initial_state_prob = np.array([0.1, 0.4, 0.5])

# Setting initial state probability
model_gaussian.startprob_ = initial_state_prob

# As we want to have a 2-D gaussian distribution the mean has to
# be in the shape of (n_components, 2)
mean = np.array([[0.0, 0.0],
                 [0.0, 10.0],
                 [10.0, 0.0]])

# Setting the mean
model_gaussian.means_ = mean

# 需要导入模块: from hmmlearn.hmm import GaussianHMM [as 别名]
# 或者: from hmmlearn.hmm.GaussianHMM import transmat_ [as 别名]

#.........这里部分代码省略.........
    else: # Argument was not passed

        for group in group_list:

            group.flag_multiple_hmms = False
            if(group.dnase_only):
                if(bias_correction): group.hmm = hmm_data.get_default_hmm_dnase_bc()
                else: group.hmm = hmm_data.get_default_hmm_dnase()
            elif(group.histone_only):
                group.hmm = hmm_data.get_default_hmm_histone()
            else: 
                if(bias_correction): group.hmm = hmm_data.get_default_hmm_dnase_histone_bc()
                else: group.hmm = hmm_data.get_default_hmm_dnase_histone()

    # Creating scikit HMM list
    for group in group_list:

        if(group.flag_multiple_hmms):

            hmm_list = []
            for hmm_file_name in group.hmm:

                try:
                    hmm_scaffold = HMM()
                    hmm_scaffold.load_hmm(hmm_file_name)
                    if(int(hmm_ver.split(".")[0]) <= 0 and int(hmm_ver.split(".")[1]) <= 1):
                        scikit_hmm = GaussianHMM(n_components=hmm_scaffold.states, covariance_type="full", 
                                                 transmat=array(hmm_scaffold.A), startprob=array(hmm_scaffold.pi))
                        scikit_hmm.means_ = array(hmm_scaffold.means)
                        scikit_hmm.covars_ = array(hmm_scaffold.covs)
                    else:
                        scikit_hmm = GaussianHMM(n_components=hmm_scaffold.states, covariance_type="full")
                        scikit_hmm.startprob_ = array(hmm_scaffold.pi)
                        scikit_hmm.transmat_ = array(hmm_scaffold.A)
                        scikit_hmm.means_ = array(hmm_scaffold.means)
                        scikit_hmm.covars_ = array(hmm_scaffold.covs)

                except Exception: error_handler.throw_error("FP_HMM_FILES")
                hmm_list.append(scikit_hmm)

            group.hmm = hmm_list

        else:

            scikit_hmm = None
            try:
                hmm_scaffold = HMM()
                hmm_scaffold.load_hmm(group.hmm)
                if(int(hmm_ver.split(".")[0]) <= 0 and int(hmm_ver.split(".")[1]) <= 1):
                    scikit_hmm = GaussianHMM(n_components=hmm_scaffold.states, covariance_type="full", 
                                             transmat=array(hmm_scaffold.A), startprob=array(hmm_scaffold.pi))
                    scikit_hmm.means_ = array(hmm_scaffold.means)
                    scikit_hmm.covars_ = array(hmm_scaffold.covs)
                else:
                    scikit_hmm = GaussianHMM(n_components=hmm_scaffold.states, covariance_type="full")
                    scikit_hmm.startprob_ = array(hmm_scaffold.pi)
                    scikit_hmm.transmat_ = array(hmm_scaffold.A)
                    scikit_hmm.means_ = array(hmm_scaffold.means)
                    scikit_hmm.covars_ = array(hmm_scaffold.covs)


            except Exception: error_handler.throw_error("FP_HMM_FILES")
            group.hmm = scikit_hmm

    ###################################################################################################
    # Main Pipeline

# 需要导入模块: from hmmlearn.hmm import GaussianHMM [as 别名]
# 或者: from hmmlearn.hmm.GaussianHMM import transmat_ [as 别名]
        try:
            obs = numpy.array(analysis)
            obs = obs.T
            obs = obs[1:]
            obs = obs.T
            obs = scale(obs)

            model = GaussianHMM(algorithm='viterbi', covariance_type='diag', covars_prior=0.01,
                  covars_weight=1, init_params='mc', means_prior=0, means_weight=0,
                  min_covar=0.001, n_components=3, n_iter=1000, params='mc',
                  random_state=None, startprob_prior=1.0, tol=0.01, transmat_prior=1.0,
                  verbose=False)

            model.startprob_ = numpy.array([1., 0, 0])
            model.startprob_prior = model.startprob_
            model.transmat_ = numpy.array([[0.9, 0.1, 0], [0, 0.9, 0.1], [0, 0, 1]])
            model.transmat_prior = model.transmat_

            model.fit(obs)

            pi = model.startprob_
            A = model.transmat_
            w = numpy.ones((n, m), dtype=numpy.double)
            hmm_means = numpy.ones((n, m, d), dtype=numpy.double)
            hmm_means[0][0] = model.means_[0]
            hmm_means[1][0] = model.means_[1]
            hmm_means[2][0] = model.means_[2]
            hmm_covars = numpy.array([[ numpy.matrix(numpy.eye(d,d)) for j in xrange(m)] for i in xrange(n)])
            hmm_covars[0][0] = model.covars_[0]
            hmm_covars[1][0] = model.covars_[1]
            hmm_covars[2][0] = model.covars_[2]