def predict(self, X):
'''
Input
@ X: dimension x sample x length #samples x known steps
Output
@ observation distribution: mu, var #samples x 1 [list]
'''
# sample x some length
X_test = util.convert_sequence(X, emission=False)
mu_l = []
cov_l = []
for i in xrange(len(X_test)):
# Past profile
final_ts_obj = ghmm.EmissionSequence(self.F, X_test[i].tolist())
try:
# alpha: X_test length y #latent States at the moment t when state i is ended
# test_profile_length x number_of_hidden_state
(alpha, scale) = self.ml.forward(final_ts_obj)
alpha = np.array(alpha)
scale = np.array(scale)
except:
print "No alpha is available !!"
sys.exit()
## continue
f = lambda x: round(x, 12)
for j in range(len(alpha)):
alpha[j] = map(f, alpha[j])
alpha[-1] = map(f, alpha[-1])
n = len(X_test[i])
t_mu = np.zeros(self.nEmissionDim)
t_cov = np.zeros(self.nEmissionDim * self.nEmissionDim)
t_sum = 0.0
for j in xrange(self.nState): # N+1
total = np.sum(
self.A[:, j] *
alpha[n / self.nEmissionDim - 1, :]) #* scaling_factor
[mu, cov] = self.B[j]
t_mu += np.array(mu) * total
t_cov += np.array(cov) * (total**2)
t_sum += total
mu_l.append(t_mu.tolist())
cov_l.append(t_cov.tolist())
return mu_l, cov_l
def loglikelihoods(self, X, bPosterior=False, bIdx=False, startIdx=1):
'''
@ X: dimension x sample x length
@ bIdx: enable to return indices
return: the likelihoods over time (in single data)
'''
# sample x some length
X_test = util.convert_sequence(X, emission=False)
return self.loglikelihoods_from_seqs(X_test,
bPosterior=bPosterior,
bIdx=bIdx,
startIdx=startIdx)
def computeLikelihood(idx, A, B, pi, F, X, nEmissionDim, nState, startIdx=1, \
bPosterior=False, converted_X=False, cov_type='full'):
'''
This function will be deprecated. Please, use computeLikelihoods.
'''
if nEmissionDim >= 2:
ml = ghmm.HMMFromMatrices(F, ghmm.MultivariateGaussianDistribution(F),
A, B, pi)
if cov_type == 'diag' or cov_type.find('diag') >= 0:
ml.setDiagonalCovariance(1)
else:
ml = ghmm.HMMFromMatrices(F, ghmm.GaussianDistribution(F), A, B, pi)
if converted_X is False:
X_test = util.convert_sequence(X, emission=False)
X_test = np.squeeze(X_test)
X_test = X_test.tolist()
else:
X_test = X
l_idx = []
l_likelihood = []
l_posterior = []
for i in xrange(startIdx, len(X_test) / nEmissionDim):
final_ts_obj = ghmm.EmissionSequence(F, X_test[:i * nEmissionDim])
try:
logp = ml.loglikelihood(final_ts_obj)
if bPosterior: post = np.array(ml.posterior(final_ts_obj))
except:
print "Unexpected profile!! GHMM cannot handle too low probability. Underflow?"
l_idx.append(i)
l_likelihood.append(-100000000)
if bPosterior:
if len(l_posterior) == 0: l_posterior.append(list(pi))
else: l_posterior.append(l_posterior[-1])
## return False, False # anomaly
continue
l_idx.append(i)
l_likelihood.append(logp)
if bPosterior: l_posterior.append(post[i - 1])
if bPosterior:
return idx, l_idx, l_likelihood, l_posterior
else:
return idx, l_idx, l_likelihood
def computeLikelihoods(idx, A, B, pi, F, X, nEmissionDim, nState, startIdx=2, \
bPosterior=False, converted_X=False, cov_type='full'):
'''
Input:
- X: dimension x length
'''
if nEmissionDim >= 2:
ml = ghmm.HMMFromMatrices(F, ghmm.MultivariateGaussianDistribution(F),
A, B, pi)
if cov_type == 'diag': ml.setDiagonalCovariance(1)
else:
ml = ghmm.HMMFromMatrices(F, ghmm.GaussianDistribution(F), A, B, pi)
X_test = util.convert_sequence(X, emission=False)
X_test = np.squeeze(X_test)
l_idx = []
l_likelihood = []
l_posterior = []
for i in xrange(startIdx, len(X[0])):
final_ts_obj = ghmm.EmissionSequence(
F, X_test[:i * nEmissionDim].tolist())
try:
logp = ml.loglikelihood(final_ts_obj)
if bPosterior: post = np.array(ml.posterior(final_ts_obj))
l_likelihood.append(logp)
if bPosterior: l_posterior.append(post[i - 1])
except:
print "Unexpected profile!! GHMM cannot handle too low probability. Underflow?"
## return False, False # anomaly
## continue
# we keep the state as the previous one
l_likelihood.append(-1000000000000)
if bPosterior:
if len(l_posterior) == 0: l_posterior.append(list(pi))
else: l_posterior.append(l_posterior[-1])
l_idx.append(i)
if bPosterior: return idx, l_idx, l_likelihood, l_posterior
else: return idx, l_idx, l_likelihood
def loglikelihood(self, X, bPosterior=False):
'''
shape?
return: the likelihood of a sequence
'''
X_test = util.convert_sequence(X, emission=False)
X_test = np.squeeze(X_test)
final_ts_obj = ghmm.EmissionSequence(self.F, X_test.tolist())
try:
logp = self.ml.loglikelihood(final_ts_obj)
if bPosterior: post = np.array(self.ml.posterior(final_ts_obj))
except:
print 'Likelihood error!!!!'
if bPosterior: return None, None
return None
if bPosterior: return logp, post
return logp
def partial_fit(self, xData, learningRate=0.2, nrSteps=1, max_iter=100):
''' Online update of HMM using online Baum-Welch algorithm
'''
X = [np.array(data) for data in xData]
nData = len(X[0])
# print 'Creating Training Data'
X_train = util.convert_sequence(X) # Training input
X_train = X_train.tolist()
if self.verbose:
print 'Run Baum Welch method with (samples, length)', np.shape(
X_train)
if learningRate < 1e-5: learningRate = 1e-5
final_seq = ghmm.SequenceSet(self.F, X_train)
for i in xrange(max_iter):
ret = self.ml.baumWelch(final_seq,
nrSteps=nrSteps,
learningRate=learningRate)
if np.isnan(ret):
print 'Baum Welch return:', ret
return 'Failure'
if i > 0:
if abs(last_ret - ret) < 1.0:
print "Partial fitting is converged to ", ret, " from ", last_ret
break
last_ret = ret
print 'Baum Welch return:', ret / float(nData)
[self.A, self.B, self.pi] = self.ml.asMatrices()
self.A = np.array(self.A)
self.B = np.array(self.B)
return ret
def getLoglikelihoods(self, xData, posterior=False, startIdx=1, n_jobs=-1):
'''
shape?
'''
warnings.simplefilter("always", DeprecationWarning)
X = [np.array(data) for data in xData]
X_test = util.convert_sequence(X) # Training input
X_test = X_test.tolist()
n, _ = np.shape(X[0])
# Estimate loglikelihoods and corresponding posteriors
r = Parallel(n_jobs=n_jobs)(delayed(computeLikelihood)(i, self.A, self.B, self.pi, self.F, X_test[i], \
self.nEmissionDim, self.nState,\
startIdx=startIdx,\
bPosterior=posterior, converted_X=True)
for i in xrange(n))
if posterior:
_, ll_idx, ll_logp, ll_post = zip(*r)
return ll_idx, ll_logp, ll_post
else:
_, ll_idx, ll_logp = zip(*r)
return ll_idx, ll_logp
cov[:, i, j] *= cov_mult[nEmissionDim*i + j]
# Emission probability matrix
B = [0] * nState
for i in range(nState):
B[i] = [[mu[i] for mu in mus]]
B[i].append(cov[i].flatten())
# pi - initial probabilities per state
pi = [0.0] * nState
pi[0] = 1.0
ml = ghmm.HMMFromMatrices(F, ghmm.MultivariateGaussianDistribution(F), A, B, pi)
print 'Creating Training Data'
X_train = util.convert_sequence(X) # Training input
X_train = X_train.tolist()
print "training data size: ", np.shape(X_train)
## ml.cmodel.getState(0).setOutProb(1, 0, 0.8)
## print ml.cmodel.getState(0).getOutProb(1)
## print ml.cmodel.getState(0).getOutNum(1)
if cov_type=='diag': ml.setDiagonalCovariance(0)
final_seq = ghmm.SequenceSet(F, X_train)
print 'Run Baum Welch method with (samples, length)', np.shape(X_train)
ret = ml.baumWelch(final_seq, 10000, fixedTrans=1)
######################### Test ###########################################
[A_new, B_new, pi_new] = ml.asMatrices()
def fit(self, xData, A=None, B=None, pi=None, cov_mult=None,
ml_pkl=None, use_pkl=False, cov_type='full', fixed_trans=0,\
shuffle=False):
'''
Input :
- xData: dimension x sample x length
Issues:
- If NaN is returned, the reason can be one of followings,
-- lower cov
-- small range of xData (you have to scale it up.)
'''
# Daehyung: What is the shape and type of input data?
if shuffle:
X = xData
X = np.swapaxes(X, 0, 1)
id_list = range(len(X))
random.shuffle(id_list)
X = np.array(X)[id_list]
X = np.swapaxes(X, 0, 1)
else:
X = [np.array(data) for data in xData]
nData = len(xData[0])
param_dict = {}
# Load pre-trained HMM without training
if use_pkl and ml_pkl is not None and os.path.isfile(ml_pkl):
if self.verbose: print "Load HMM parameters without train the hmm"
param_dict = ut.load_pickle(ml_pkl)
self.A = param_dict['A']
self.B = param_dict['B']
self.pi = param_dict['pi']
if self.nEmissionDim == 1:
self.ml = ghmm.HMMFromMatrices(self.F, ghmm.GaussianDistribution(self.F), \
self.A, self.B, self.pi)
else:
self.ml = ghmm.HMMFromMatrices(self.F, ghmm.MultivariateGaussianDistribution(self.F), \
self.A, self.B, self.pi)
out_a_num = param_dict.get('out_a_num', None)
vec_num = param_dict.get('vec_num', None)
mat_num = param_dict.get('mat_num', None)
u_denom = param_dict.get('u_denom', None)
if out_a_num is not None:
self.ml.setBaumWelchParams(out_a_num, vec_num, mat_num,
u_denom)
return True
else:
if ml_pkl is None:
ml_pkl = os.path.join(os.path.dirname(__file__),
'ml_temp_n.pkl')
if cov_mult is None:
cov_mult = [1.0] * (self.nEmissionDim**2)
if A is None:
if self.verbose: print "Generating a new A matrix"
# Transition probability matrix (Initial transition probability, TODO?)
A = util.init_trans_mat(self.nState).tolist()
if B is None:
if self.verbose: print "Generating a new B matrix"
# We should think about multivariate Gaussian pdf.
mus, cov = util.vectors_to_mean_cov(X,
self.nState,
self.nEmissionDim,
cov_type=cov_type)
## print np.shape(mus), np.shape(cov)
# cov: state x dim x dim
for i in xrange(self.nEmissionDim):
for j in xrange(self.nEmissionDim):
cov[:, i, j] *= cov_mult[self.nEmissionDim * i + j]
if self.verbose:
for i, mu in enumerate(mus):
print 'mu%i' % i, mu
## print 'cov', cov
# Emission probability matrix
B = [0] * self.nState
for i in range(self.nState):
if self.nEmissionDim > 1:
B[i] = [[mu[i] for mu in mus]]
B[i].append(cov[i].flatten().tolist())
else:
B[i] = [np.squeeze(mus[0][i]), float(cov[i])]
if pi is None:
# pi - initial probabilities per state
## pi = [1.0/float(self.nState)] * self.nState
pi = [0.0] * self.nState
pi[0] = 1.0
# print 'Generating HMM'
# HMM model object
if self.nEmissionDim == 1:
self.ml = ghmm.HMMFromMatrices(self.F, ghmm.GaussianDistribution(self.F), \
A, B, pi)
else:
self.ml = ghmm.HMMFromMatrices(self.F, ghmm.MultivariateGaussianDistribution(self.F), \
A, B, pi)
if cov_type == 'diag': self.ml.setDiagonalCovariance(1)
# print 'Creating Training Data'
X_train = util.convert_sequence(X) # Training input
X_train = X_train.tolist()
if self.verbose: print "training data size: ", np.shape(X_train)
if self.verbose:
print 'Run Baum Welch method with (samples, length)', np.shape(
X_train)
final_seq = ghmm.SequenceSet(self.F, X_train)
## ret = self.ml.baumWelch(final_seq, loglikelihoodCutoff=2.0)
ret = self.ml.baumWelch(final_seq,
10000) #, fixedTrans=fixed_trans)
if np.isnan(ret):
print 'Baum Welch return:', ret
return 'Failure'
print 'Baum Welch return:', ret / float(nData)
[self.A, self.B, self.pi] = self.ml.asMatrices()
self.A = np.array(self.A)
self.B = np.array(self.B)
param_dict['A'] = self.A
param_dict['B'] = self.B
param_dict['pi'] = self.pi
try:
[out_a_num, vec_num, mat_num,
u_denom] = self.ml.getBaumWelchParams()
param_dict['out_a_num'] = out_a_num
param_dict['vec_num'] = vec_num
param_dict['mat_num'] = mat_num
param_dict['u_denom'] = u_denom
except:
print "Install new ghmm!!"
if ml_pkl is not None: ut.save_pickle(param_dict, ml_pkl)
return ret / float(nData)
