def detect_events_hmm(mahal_timeseries, c_timeseries, global_pace_timeseries, threshold_quant=.95):
#Sort the keys of the timeseries chronologically
sorted_dates = sorted(mahal_timeseries)
(expected_pace_timeseries, sd_pace_timeseries) = getExpectedPace(global_pace_timeseries)
#Generate the list of values of R(t)
mahal_list = [mahal_timeseries[d] for d in sorted_dates]
c_list = [c_timeseries[d] for d in sorted_dates]
global_pace_list = [global_pace_timeseries[d] for d in sorted_dates]
expected_pace_list = [expected_pace_timeseries[d] for d in sorted_dates]
#Use the quantile to determine the threshold
sorted_mahal = sorted(mahal_list)
threshold = getQuantile(sorted_mahal, threshold_quant)
# The symbols array contains "1" if there is an outlier, "0" if there is not
symbols = []
for i in range(len(mahal_list)):
if(mahal_list[i] > threshold or c_list[i]==1):
symbols.append(1)
else:
symbols.append(0)
# Set up the hidden markov model. We are modeling the non-event states as "0"
# and event states as "1"
# Transition matrix with heavy weight on the diagonals ensures that the model
# is likely to stick in the same state rather than rapidly switching. In other
# words, the predictions will be relatively "smooth"
trans_matrix = array([[.999, .001],
[.001,.999]])
# Emission matrix - state 0 is likely to emit symbol 0, and vice versa
# In other words, events are likely to be outliers
emission_matrix = array([[.95, .05],
[.4, .6]])
# Actually set up the hmm
model = MultinomialHMM(n_components=2, transmat=trans_matrix)
model.emissionprob_ = emission_matrix
# Make the predictions
lnl, predictions = model.decode(symbols)
events = get_all_events(predictions, sorted_dates, mahal_list, global_pace_list,
expected_pace_list)
# Sort events by duration, starting with the long events
events.sort(key = lambda x: x[2], reverse=True)
return events, predictions
def run_hmm_model(input_df, n_unique, A_df, Eta, n_iter = 10000,
tol=1e-2, verbose = False, params = 'e', init_params = ''):
'''
Runs the hmm model and returns the predicted results, score and model
input_df : The dataframe of keypresses
n_unique : number of unqique chars
A_df : Dataframe of trasnmission matrix
Eta : Emissions matrix
n_iter : Max number of iterations for hmm
tol : The value to stop the hmm model if score does not improve by more than this
verbose : Whether or not to print out
params : Parameters to tune
init_params : Paramters to initialize
'''
# Propotion of characters starting words in english
char_counts = get_char_counts()
# Construct model
hmm = MultinomialHMM(n_components=n_unique, startprob_prior=np.append(0, char_counts.values),
transmat_prior=A_df.values, algorithm='viterbi',
random_state=None, n_iter=n_iter, tol=tol,
verbose=verbose, params=params, init_params=init_params)
# Set values
hmm.emissionprob_ = Eta
hmm.transmat_ = A_df.values
hmm.startprob_ = np.append(0, char_counts.values)
# Feed in the clusters as the expected output
model_input = input_df['cluster'].values
# Reshape
if len(model_input.shape) == 1:
model_input = model_input.reshape((len(model_input), 1))
# Fit the model
hmm = hmm.fit(model_input)
# Score model
score, results = hmm.decode(model_input)
return score, results, hmm
def detect_events_hmm(mahal_timeseries, c_timeseries, global_pace_timeseries,
threshold_quant=.95, trans_matrix = DEFAULT_TRANS_MATRIX,
emission_matrix=DEFAULT_EMISSION_MATRIX, initial_state=None):
#Sort the keys of the timeseries chronologically
sorted_dates = sorted(mahal_timeseries)
(expected_pace_timeseries, sd_pace_timeseries) = getExpectedPace(global_pace_timeseries)
#Generate the list of values of R(t)
mahal_list = [mahal_timeseries[d] for d in sorted_dates]
c_list = [c_timeseries[d] for d in sorted_dates]
global_pace_list = [global_pace_timeseries[d] for d in sorted_dates]
expected_pace_list = [expected_pace_timeseries[d] for d in sorted_dates]
#Use the quantile to determine the threshold
sorted_mahal = sorted(mahal_list)
threshold = getQuantile(sorted_mahal, threshold_quant)
# The symbols array contains "1" if there is an outlier, "0" if there is not
symbols = []
for i in range(len(mahal_list)):
if(mahal_list[i] > threshold or c_list[i]==1):
symbols.append(1)
else:
symbols.append(0)
# Actually set up the hmm
model = MultinomialHMM(n_components=2, transmat=trans_matrix, startprob=initial_state)
model.emissionprob_ = emission_matrix
# Make the predictions
lnl, predictions = model.decode(symbols)
events = get_all_events(predictions, sorted_dates, mahal_list, global_pace_list,
expected_pace_list)
# Sort events by duration, starting with the long events
events.sort(key = lambda x: x[2], reverse=True)
return events, predictions
def detect_events_hmm(mahal_timeseries,
c_timeseries,
global_pace_timeseries,
threshold_quant=.95,
trans_matrix=DEFAULT_TRANS_MATRIX,
emission_matrix=DEFAULT_EMISSION_MATRIX,
initial_state=None):
#Sort the keys of the timeseries chronologically
sorted_dates = sorted(mahal_timeseries)
(expected_pace_timeseries,
sd_pace_timeseries) = getExpectedPace(global_pace_timeseries)
#Generate the list of values of R(t)
mahal_list = [mahal_timeseries[d] for d in sorted_dates]
c_list = [c_timeseries[d] for d in sorted_dates]
global_pace_list = [global_pace_timeseries[d] for d in sorted_dates]
expected_pace_list = [expected_pace_timeseries[d] for d in sorted_dates]
#Use the quantile to determine the threshold
sorted_mahal = sorted(mahal_list)
threshold = getQuantile(sorted_mahal, threshold_quant)
# The symbols array contains "1" if there is an outlier, "0" if there is not
symbols = []
for i in range(len(mahal_list)):
if (mahal_list[i] > threshold or c_list[i] == 1):
symbols.append(1)
else:
symbols.append(0)
# Actually set up the hmm
model = MultinomialHMM(n_components=2,
transmat=trans_matrix,
startprob=initial_state)
model.emissionprob_ = emission_matrix
# Make the predictions
lnl, predictions = model.decode(symbols)
events = get_all_events(predictions, sorted_dates, mahal_list,
global_pace_list, expected_pace_list)
# Sort events by duration, starting with the long events
events.sort(key=lambda x: x[2], reverse=True)
return events, predictions
def test_DiscreteHMM_decode(cases: str) -> None:
np.random.seed(12346)
cases = int(cases)
i = 1
N_decimal = 4
while i < cases:
tol=1e-3
n_samples = np.random.randint(10, 50)
hidden_states = np.random.randint(3, 6)
# symbols is the number of unqiue observation types.
symbols = np.random.randint(4, 9)
X = []
lengths = []
for _ in range(n_samples):
# the actual length is seq_length + 1
seq_length = symbols
this_x = np.random.choice(range(symbols), size=seq_length, replace=False)
X.append(this_x)
lengths.append(seq_length)
max_iter = 100
hmm_gold = MultinomialHMM(n_components=hidden_states, n_iter=100, tol=tol)
X_gold = np.concatenate(X).reshape((-1,1))
hmm_gold.fit(X_gold, lengths)
gold_A = hmm_gold.transmat_
gold_B = hmm_gold.emissionprob_
gold_pi = hmm_gold.startprob_
gold_logprob, gold_state_sequence = hmm_gold.decode(X_gold, lengths)
hmm_mine = DiscreteHMM(hidden_states=hidden_states,
symbols=symbols,
A=gold_A,
B=gold_B,
pi=gold_pi)
mine_logprob_list = []
mine_state_sequence = []
for this_x in X:
this_mine_logprob, this_mine_state_sequence = hmm_mine.decode(this_x)
mine_logprob_list.append(this_mine_logprob)
mine_state_sequence.append(this_mine_state_sequence)
mine_state_sequence = np.concatenate(mine_state_sequence)
mine_logprob = sum(mine_logprob_list)
assert_almost_equal(mine_logprob, gold_logprob, decimal=N_decimal)
assert_almost_equal(mine_state_sequence, gold_state_sequence, decimal=N_decimal)
i+=1
print('Successfully testing the function of computing decodes in discrete HMM!')
emission_probability[1][2] += 1
if train_data['return'][i] < 0.0 and analysis_data['v'][i] == 3:
emission_probability[1][3] += 1
emission_probability[0] /= sum(1 for e in train_data['return'] if e >= 0.0)
emission_probability[1] /= sum(1 for e in train_data['return'] if e < 0.0)
#print(emission_probability)
hmm = MultinomialHMM(n_components=n_states)
hmm.startprob = start_probability
hmm.transmat = transition_probability
hmm.emissionprob = emission_probability
bob_says = np.array([[0, 2, 1, 1, 2, 0]]).T
hmm = hmm.fit(bob_says)
logprob, alice_hears = hmm.decode(bob_says, algorithm="viterbi")
print("Bob says:", ", ".join(map(lambda x: observations[x], bob_says)))
print("Alice hears:", ", ".join(map(lambda x: states[x], alice_hears)))
'''
law_data['hmm_states'] = hmm.predict(rets)
panel = Figure_Util.Figure()
panel.draw(law_data, title='close', subplots=['hmm_states'], figsize=(20, 10))
'''
db.disconnect()
for sent in test_sents:
inp = []
for i in range(len(sent)):
word = sent[i][0]
try:
k = list(emission_dict.keys()).index(word)
except:
nexcept += 1
k = emission_matrix.shape[0] - 1
inp.append(k)
inp = np.atleast_2d(inp).T
if (len(inp) != 1):
logprob, out_ = model.decode(inp, algorithm='viterbi')
out_ = list(map(lambda x: states[x], out_))
else:
#print(sent[0][-1])
out_ = []
out_.append('O')
for i in range(len(sent)):
word = sent[i][0]
gold = sent[i][-1]
pred = out_[i]
out.write("{}\t{}\t{}\n".format(word, gold, pred))
#j+=1
out.write("\n")
print(nexcept)
model.startprob_ = np.array([1, 0, 0])
model.endprob_ = np.array([0, 0, 0.1])
model.transmat_ = np.array([[0.9, 0.1, 0], [0, 0, 1], [0, 0, 1]])
model.emissionprob_ = np.array([[0.25, 0.25, 0.25, 0.25], [0.05, 0, 0.95, 0],
[0.4, 0.1, 0.1, 0.4]])
# In[121]:
#"CTTCATGTGAAAGCAGACGTAAGTCA" A = 0 , C = 1 , G = 2 , T = 3
sequence = [
1, 3, 3, 1, 0, 3, 2, 3, 2, 0, 0, 0, 2, 1, 0, 2, 0, 1, 2, 3, 0, 0, 2, 3, 1,
0
]
logprob, seq = model.decode(np.array([sequence]).transpose())
print(logprob)
print(seq)
# E = 0 , 5 = 1 , I = 2
print("following sequence correspond to :")
print("EEEEEEEEEEEEEEEEEE5IIIIIII")
# ## Question 1.2 : HMM
# #### based on the following paper :
# https://editorialexpress.com/cgi-bin/conference/download.cgi?db_name=SILC2016&paper_id=38
# In[90]:
# Calculating Mean Absolute Percentage Error of predictions
def calc_mape(predicted_data, true_data):
hits = 0
for seq in validating_sequences:
seq_list = []
for inst in seq:
prob_list = []
len_list = []
pred_list = []
if len(seq_list) > 1:
for i in range(8):
seq_list.append(i)
a = np.array(seq_list).reshape(-1,1)
len_list = []
len_list.append(len(seq_list))
b = np.array(len_list)
prob = model.decode(a , lengths = b)
prob_list.append(prob[0])
seq_list.pop()
max_value = max(prob_list)
pred_value = prob_list.index(max_value)
if pred_value == inst[0]:
hits+=1
count+=1
seq_list.append(inst[0])
else:
seq_list.append(inst[0])
len_list.append(len(seq_list))
print(count)
negative_score = []
negative = []
for i in range(data.shape[0]):
if data['vdjdb.score'].iloc[i] == 0:
negative.append(data['cdr3.alpha'].iloc[i])
for i in range(len(negative)):
test = string2matrix_plain(negative[i]).astype(np.int)
score = model.score(test)
negative_score.append(score)
negative_score = np.array(negative_score)
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.boxplot([train_score, test_score, negative_score],
positions=[1, 2, 3],
labels=['training', 'testing_pos', 'testing_neg'])
x_train = np.random.normal(1, 0.02, size=len(train_score))
ax.plot(x_train, train_score, 'r.', alpha=0.2)
x_test = np.random.normal(2, 0.02, size=len(test_score))
ax.plot(x_test, test_score, 'b.', alpha=0.2)
x_negative = np.random.normal(3, 0.02, size=len(negative_score))
ax.plot(x_negative, negative_score, 'k.', alpha=0.2)
ax.set_title('Observation score from HMM -- "GILGFVFTL"--TCRA')
import scipy.stats as sc
sc.ttest_ind(test_score, negative_score)
model.predict(test1)
model.predict_proba(test1)
model.decode(test1)
d = _data_on_mouse(data, idx, smoothing_time_radius,
smoothing_amplitude_radius, smoothing_tolerance,
sampling_interval, bins)
discrete_obs.append(d[0])
delta_hws.append(d[1])
delta_fas.append(d[2])
X = np.array(discrete_obs)
model = MultinomialHMM(n_components = n_components)
predictions = []
for i in range(7):
held_out_X = np.vstack((X[:i], X[i+1:]))
model.fit(held_out_X)
predictions.append(model.decode(X[i].reshape(X[i].shape[0], 1)))
f, axarr = plt.subplots(7, 1)
yranges = np.arange(n_components+1, dtype=float)/n_components
colors = plt.cm.rainbow(np.linspace(0, 1, n_components))
for i in range(7):
states, indices = _axvspan_maker(predictions[i][1])
for s, idxs in zip(states, indices):
axarr[i].axvspan(idxs[0], idxs[1], ymin=yranges[s], ymax=yranges[s+1], color=colors[s])
plt.show()
# healthy_model = MultinomialHMM(n_components = n_components)
# healthy_model.fit(dos)
# hs_preds = healthy_model.predict(dos.reshape(len(dos), 1))
for idx in mice:
d = _data_on_mouse(data, idx, smoothing_time_radius,
smoothing_amplitude_radius, smoothing_tolerance,
sampling_interval, bins)
discrete_obs.append(d[0])
delta_hws.append(d[1])
delta_fas.append(d[2])
X = np.array(discrete_obs)
model = MultinomialHMM(n_components=n_components)
predictions = []
for i in range(7):
held_out_X = np.vstack((X[:i], X[i + 1:]))
model.fit(held_out_X)
predictions.append(model.decode(X[i].reshape(X[i].shape[0], 1)))
f, axarr = plt.subplots(7, 1)
yranges = np.arange(n_components + 1, dtype=float) / n_components
colors = plt.cm.rainbow(np.linspace(0, 1, n_components))
for i in range(7):
states, indices = _axvspan_maker(predictions[i][1])
for s, idxs in zip(states, indices):
axarr[i].axvspan(idxs[0],
idxs[1],
ymin=yranges[s],
ymax=yranges[s + 1],
color=colors[s])
plt.show()
# healthy_model = MultinomialHMM(n_components = n_components)
class HMM:
def __init__(self):
pass
def train(self, obs_seq_list: list, state_seq_list: list, obs_set: list,
state_set: list, file):
"""
:param obs_seq_list: observation sequence list [[o1, o2, o3], [o1, o2, o3]...]
:param state_seq_list: state sequence list [[s1, s2, s3], [s1, s2, s3]...]
:param obs_set: all possible observation state
:param state_set: all possible state
"""
self.obs_seq_list = obs_seq_list
self.state_seq_list = state_seq_list
self.obs_set = obs_set
self.state_set = state_set
self.counter = Counter(''.join(state_seq_list))
self.hmm = MultinomialHMM(n_components=len(self.state_set))
self.startprob, self.transmat, self.emissionprob = \
self._init_state(), self._trans_state(), self._emit_state()
self.hmm.startprob_ = self.startprob
self.hmm.transmat_ = self.transmat
self.hmm.emissionprob_ = self.emissionprob
if file is not None:
with open(file, 'wb') as f:
pickle.dump(self, f)
@staticmethod
def load_model(file: str = None):
with open(file, 'rb') as f:
return pickle.load(f)
def predict(self, obs):
obs_seq = np.array([self.preprocess(o) for o in obs])
_, b = self.hmm.decode(obs_seq, algorithm='viterbi')
states = [self.state_set[x] for x in b]
return states
"""Methods calculate startprob, transmat and emissionprob"""
def _init_state(self):
"""calculate init state"""
first_states = [s[0] for s in self.state_seq_list]
cnt = Counter(first_states)
seq_amount = len(first_states)
# init_state = {k: log((v+1)/words_count) for k, v in init_counts.items()}
# plus one smooth
init_state = [(cnt[s] + 1) / seq_amount for s in self.state_set]
return np.array(init_state)
def _trans_state(self):
"""calculate trans state"""
end_state_cnt = {state: 0 for state in self.state_set}
# trans_cnt[start_state][end_state]
trans_cnt = {state: dict(end_state_cnt) for state in self.state_set}
for line in self.state_seq_list:
for w1, w2 in zip(line, line[1:]):
trans_cnt[w1][w2] += 1.0
# trans_state = {k: {kk: log((vv+1)/counter[k]) for kk, vv in v.items()} for k, v in trans_counts.items()}
trans_matrix = [[
(trans_cnt[start_s][end_s] + 1) / self.counter[start_s]
for end_s in self.state_set
] for start_s in self.state_set]
return np.array(trans_matrix)
def _emit_state(self):
"""calculate emit state"""
obs_dict = {word: 0.0 for word in self.obs_set}
emit_cnt = {state: dict(obs_dict) for state in self.state_set}
for state_seq, obs_seq in zip(self.state_seq_list, self.obs_seq_list):
for state, obs in zip(state_seq, obs_seq):
emit_cnt[state][obs] += 1
# emit_state = {k: {kk: log((vv+1)/counter[k]) for kk, vv in v.items()} for k, v in emit_counts.items()}
emit_matrix = [[(emit_cnt[s][o] + 1) / self.counter[s]
for o in self.obs_set] for s in self.state_set]
return np.array(emit_matrix)
def preprocess(self, seq: list):
"""handle new observation"""
return [
self.obs_set.index(obs)
if obs in self.obs_set else len(self.obs_set) - 1 for obs in seq
]