def forward(A, B_initial, PI, O):
row = A.shape[0]
col = len(O)
Alpha = np.zeros((row, col)) # Build Alpha
B = getB(B_initial, O)
# Initialize Alpha 1
Alpha[:, 0] = B[:, 0] + PI[:, 0]
# print Alpha[:,0]
for t in range(1, len(O)):
for n in range(row):
loopc = 0
for i, j in zip(Alpha[:, t - 1], A[:, n]):
if loopc == 0:
roni = i + j
loopc += 1
else:
roni = log_sum(roni, i + j)
Alpha[n, t] = roni + B[n, t]
# Logsum the last column:
count = 0
for i in Alpha[:, -1]:
if count == 0:
sumup = i
count += 1
else:
sumup = log_sum(sumup, i)
return sumup
def backward(self):
for line in open(self.dev):
line = line.strip("\n")
line = line.split(" ")
matrix = [[0.0 for _ in xrange(len(line))]
for _ in xrange(self.nState)]
for i in xrange(len(line) - 2, -2, -1):
word = line[i + 1]
for state1 in xrange(self.nState):
p = (matrix[0][i + 1] + log(self.trans_matrix[state1][0]) +
log(self.emit_matrix[0][word]))
for state2 in xrange(1, self.nState):
p = log_sum(
p, matrix[state2][i + 1] +
log(self.trans_matrix[state1][state2]) +
log(self.emit_matrix[state2][word]))
matrix[state1][i] = p
p = log(self.prior_matrix[0]) + log(
self.emit_matrix[0][line[0]]) + matrix[0][0]
for i in xrange(1, self.nState):
p = (log_sum(
p,
log(self.prior_matrix[i]) +
log(self.emit_matrix[i][line[0]]) + matrix[i][0]))
print p
def forward(self):
for line in self.dev_file:
curr_observable_sequence = line.strip().split()
T = len(curr_observable_sequence)
alpha_log = []
init_alpha_log = {}
for i in self.states:
init_alpha_log[i] = ln(self.pie[i]) + ln(self.b[i][curr_observable_sequence[0]])
alpha_log.append(init_alpha_log)
counter = 1
for curr_observable in curr_observable_sequence[1:]:
temp_alpha_log = {}
for i in self.states:
hold = alpha_log[counter-1][self.states[0]] + ln(self.a[self.states[0]][i])
for j in self.states[1:]:
hold = log_sum(hold,(alpha_log[counter-1][j] + ln(self.a[j][i])))
temp_alpha_log[i] = ln(self.b[i][curr_observable])+hold
alpha_log.append(temp_alpha_log)
counter += 1
hold = alpha_log[T-1][self.states[0]]
for k in self.states[1:]:
hold = log_sum(hold,alpha_log[T-1][k])
print(hold)
def backward(self):
for line in self.dev_file:
curr_observable_sequence = line.strip().split()
T = len(curr_observable_sequence)
beta_log = [0] * T
init_beta_log = {}
for i in self.states:
init_beta_log[i] = 0
beta_log[T - 1] = init_beta_log
for t in range(T - 2, -1, -1):
temp_beta_log = {}
for i in self.states:
hold = beta_log[t + 1][self.states[0]] + ln(
self.a[i][self.states[0]]) + ln(self.b[self.states[0]][
curr_observable_sequence[t + 1]])
for j in self.states[1:]:
hold = log_sum(
hold, beta_log[t + 1][j] + ln(self.a[i][j]) +
ln(self.b[j][curr_observable_sequence[t + 1]]))
temp_beta_log[i] = hold
beta_log[t] = temp_beta_log
hold = ln(self.pie[self.states[0]]) + ln(self.b[self.states[0]][
curr_observable_sequence[0]]) + beta_log[0][self.states[0]]
for i in self.states[1:]:
hold = log_sum(
hold,
ln(self.pie[i]) +
ln(self.b[i][curr_observable_sequence[0]]) +
beta_log[0][i])
print(hold)
def forward():
emit = emitMatrix()
trans = transMatrix()
prior = priorMatrix()
for line in devfile:
line = line.split(" ")
o = line[0]
probMatrix = np.log(prior) + np.log(np.array(emit[o]).reshape(8, 1))
# loop throgh words in line
#print probMatrix
#sys.exit(0)
for z in range(1, len(line)):
o = line[z]
emitprob = np.array(emit[o]).reshape(8, 1)
# loop through each t+1 state
m = []
for j in range(0, 8):
temp = np.log(trans[:, j].reshape(8, 1)) + (probMatrix)
sum = temp[0]
# sum up probs
for k in range(1, 8):
sum = log_sum(sum, temp[k])
prob = np.log(emitprob[j]) + sum
m.append(prob[0])
probMatrix = np.array(m).reshape(8, 1)
#print probMatrix
#sys.exit(0)
total = probMatrix[0]
for h in range(1, 8):
total = log_sum(total, probMatrix[h])
print total[0]
def train(initDict,transDict,emitDict,sentence): sentence=sentence.split() currentDict=dict() for key in initDict: currentDict[key]=initDict[key]+emitDict[key][sentence[0]] #Done step1, initializing for word in sentence[1:]: for i in currentDict: alphaCurrent=emitDict[i][word] prevSum=0 for j in currentDict: alphaPrev=initDict[j] transProb=transDict[j][i] if prevSum==0: prevSum=alphaPrev+transProb else: prevSum=logsum.log_sum(prevSum,alphaPrev+transProb) currentDict[i]=prevSum+alphaCurrent initDict=copy.deepcopy(currentDict) totalP=0 for i in currentDict: if totalP==0: totalP=currentDict[i] else: totalP=logsum.log_sum(totalP,currentDict[i]) print totalP
def backward(sentence_l, prior_l, trans_ll, emit_ld):
for sentence in sentence_l:
beta_t = [0] * 8
sentence.reverse()
#print alpha_a
for index, word in enumerate(sentence):
if index != (len(sentence) - 1):
temp = [0] * 8
for i in range(0, 8):
sum_beta_a_b = -1e100
for j in range(0, 8):
beta_a = beta_t[j] + math.log(trans_ll[i][j])
beta_a_b = beta_a + math.log(emit_ld[j][word])
sum_beta_a_b = log_sum(sum_beta_a_b, beta_a_b)
temp[i] = sum_beta_a_b
beta_t[:] = temp[:]
sum_beta = -1e100
for i in range(0, 8):
beta = math.log(prior_l[i]) + math.log(
emit_ld[i][word]) + beta_t[i]
sum_beta = log_sum(sum_beta, beta)
print sum_beta
def forward(sentence_l, prior_l, trans_ll, emit_ld):
for sentence in sentence_l:
alpha_t = []
#print alpha_a
for index, word in enumerate(sentence):
##calculate alpha1
if index == 0:
for i in range(0, 8):
alpha_t.append(
math.log(prior_l[i]) + math.log(emit_ld[i][word]))
#calculate rest of the sentence
else:
temp = [0] * 8
for i in range(0, 8):
sum_alpha_a = -1e100
for j in range(0, 8):
alpha_a = alpha_t[j] + math.log(trans_ll[j][i])
sum_alpha_a = log_sum(sum_alpha_a, alpha_a)
temp[i] = math.log(emit_ld[i][word]) + sum_alpha_a
alpha_t[:] = temp[:]
sum_alpha = -1e100
for i in range(0, 8):
sum_alpha = log_sum(sum_alpha, alpha_t[i])
print sum_alpha
def backward(A, B_initial, PI, O):
row = A.shape[0]
col = len(O)
Beta = np.zeros((row, col)) # Build Beta
B = getB(B_initial, O)
# Initialize Beta 1
Beta[:, (col - 1)] = 0
for t in reversed(range(0, len(O) - 1)):
for n in range(row):
loopc = 0
for i, j, k in zip(Beta[:, (t + 1)], A[n, :], B[:, (t + 1)]):
if loopc == 0:
roni = i + j + k
loopc += 1
else:
roni = log_sum(roni, i + j + k)
Beta[n, t] = roni
# Logsum the first column:
count = 0
for i, j, k in zip(Beta[:, 0], B[:, 0], PI[:, 0]):
if count == 0:
sumup = i + j + k
count += 1
else:
sumup = log_sum(sumup, i + j + k)
print sumup
def main(argv):
devlines = readfiles(argv[1])
translines = readfiles(argv[2])
emitlines = readfiles(argv[3])
priorlines = readfiles(argv[4])
aij = {}
for line in translines:
words = line.strip().split()
probs = {}
for wd in words[1:]:
prob = wd.split(':')
probs[prob[0]] = math.log(float(prob[1]))
aij[words[0]] = probs
bjk = {}
for line in emitlines:
words = line.strip().split()
probs = {}
for wd in words[1:]:
prob = wd.split(':')
probs[prob[0]] = math.log(float(prob[1]))
bjk[words[0]] = probs
pi = {}
for line in priorlines:
words = line.strip().split()
pi[words[0]] = math.log(float(words[1]))
states = bjk.keys()
for line in devlines:
alpha = []
content = line.strip().split()
alphanext = {}
for st in states:
alphanext[st] = pi[st] + bjk[st][content[0]]
alpha.append(alphanext)
index = 0
for word in content[1:]:
index += 1
alphanew = {}
for st in states:
alphanew[st] = 0.0
for oldst in states:
if alphanew[st] == 0.0:
alphanew[st] = alpha[-1][oldst] + aij[oldst][st]
else:
alphanew[st] = log_sum(alphanew[st], alpha[-1][oldst] + aij[oldst][st])
alphanew[st] += bjk[st][content[index]]
alpha.append(alphanew)
result = 0.0
for st in states:
if result == 0.0:
result = alpha[-1][st]
else:
result = log_sum(result, alpha[-1][st])
print result
def backward(sentence="", trans=None, emits=None, prior=None, labels=[]):
os = sentence.split(" ")
matrix = createMatrix(emits, prior, labels, os)
for i in xrange(0, len(labels)):
if(matrix[i][0] == -1):
matrix[i][0] = backward_recursive(os, i, 0, trans, emits, prior, labels, matrix)
# if matrix[i][0] == -1:
# tmp = math.log(prior[labels[i]])
# tmp += math.log(emits[labels[i]][os[0]])
# for j in xrange(0, len(labels)):
# if matrix[j][1] == -1:
# matrix[i][1] = backward_recursive(os, i, 1, trans, emits, prior, labels, matrix)
# tmp += matrix[i][1]
# matrix[i][0] = tmp
result = matrix[0][0]
result += math.log(prior[labels[0]])
result += math.log(emits[labels[0]][os[0]])
for z in xrange(1, len(labels)):
tmp = matrix[z][0]
tmp += math.log(prior[labels[z]])
tmp += math.log(emits[labels[z]][os[0]])
result = log_sum(result, tmp)
result += -1.0
sys.stdout.write(str(result) + "\n")
def calculate_P(self, dev):
T = len(dev)
alpha_T = dev[T - 1]
sum = 0.0
for i in range(len(alpha_T)):
if i == 0:
sum = alpha_T[0]
else:
sum = log_sum(sum, alpha_T[i])
return sum
def _forwardAlg(d):
l = len(hmmPrior)
alpha = [[0] * (len(d)) for _ in range(l)]
#print alpha
for i in range(l):
alpha[i][0] = hmmPrior[i] + hmmEmit[i][d[0]]
for t in range(1, len(d)):
for i in range(l):
#print t, i, d[t], hmmEmit[i][d[t]], alpha[t][i]
alpha[i][t] = hmmEmit[i][d[t]]
x = alpha[0][t - 1] + hmmTrain[0][i]
for j in range(1, l):
x = log_sum(x, alpha[j][t - 1] + hmmTrain[j][i])
alpha[i][t] += x
#print alpha
x = alpha[0][-1]
for i in range(1, l):
x = log_sum(x, alpha[i][-1])
print x
def _backwardAlg(d):
l = len(hmmPrior)
beta = [[0] * (len(d)) for _ in range(l)]
#print alpha
#for i in range(l):
# beta[i][-1] = 1
for t in range(len(d) - 2, -1, -1):
for i in range(l):
#print t, i, d[t], hmmEmit[i][d[t]], alpha[t][i]
x = beta[0][t + 1] + hmmTrain[i][0] + hmmEmit[0][d[t + 1]]
for j in range(1, l):
x = log_sum(
x, beta[j][t + 1] + hmmTrain[i][j] + hmmEmit[j][d[t + 1]])
beta[i][t] = x
#print alpha
x = beta[0][0] + hmmPrior[0] + hmmEmit[0][d[0]]
for i in range(1, l):
x = log_sum(x, beta[i][0] + hmmPrior[i] + hmmEmit[i][d[0]])
print x
def forward(dev_file, trans_file, emit_file, prior_file):
dev = read_dev(dev_file)
trans = read_trans(trans_file)
emit = read_emit(emit_file)
prior = read_prior(prior_file)
result = []
for sentence in range(len(dev)):
alpha_t = {
k1: log(v1) + log(emit[k1][dev[sentence][0]])
for k1, v1 in prior.items()
}
alpha_tp1 = {}
for word in range(1, len(dev[sentence])):
for k in emit.keys():
alpha_tp1[k] = log(emit[k][dev[sentence][word]]) + reduce(
lambda x, y: log_sum(x, y),
[tv + log(trans[tk][k]) for tk, tv in alpha_t.items()])
alpha_t = dict(alpha_tp1)
result.append(reduce(lambda x, y: log_sum(x, y), alpha_t.values()))
print '\n'.join([str(x) for x in result])
def forward(sentence="", trans=None, emits=None, prior=None, labels=[]):
os = sentence.split(" ");
matrix = createMatrix(emits, prior, labels, os)
t = len(os)
for i in xrange(0, len(prior)):
if matrix[i][t-1] == -1:
matrix[i][t-1] = forward_recursive(os, i, t-1, trans, emits, prior, labels, matrix)
tmp = matrix[0][t-1]
for i in xrange(1, len(prior)):
tmp = log_sum(tmp, matrix[i][t-1])
sys.stdout.write(str(tmp) + "\n")
def calculate_P(self, dev, o1):
beta1 = dev[len(dev) - 1]
p = 0.0
for i in range(self.hmm.N):
pii = log(self.hmm.pi[i])
bi = log(self.hmm.b[o1][i])
beta1_i = beta1[i]
sum = pii + bi + beta1_i
if i == 0:
p = sum
else:
p = log_sum(p, sum)
return p
def backward(dev_file, trans_file, emit_file, prior_file):
dev = read_dev(dev_file)
trans = read_trans(trans_file)
emit = read_emit(emit_file)
prior = read_prior(prior_file)
result = []
for sentence in range(len(dev)):
beta_tp1 = {kT: 0 for kT in prior.keys()}
beta_t = {}
for word in range(len(dev[sentence]) - 1, 0, -1):
for k in emit.keys():
beta_t[k] = reduce(lambda x, y: log_sum(x, y), [
v_tp1 + log(trans[k][k_tp1]) +
log(emit[k_tp1][dev[sentence][word]])
for k_tp1, v_tp1 in beta_tp1.items()
])
beta_tp1 = dict(beta_t)
result.append(
reduce(lambda x, y: log_sum(x, y), [
log(v1) + log(emit[k1][dev[sentence][0]]) + beta_tp1[k1]
for k1, v1 in prior.items()
]))
print '\n'.join([str(x) for x in result])
def forward(self):
for line in open(self.dev):
line = line.strip("\n")
line = line.split(" ")
matrix = [[0.0 for _ in xrange(len(line))]
for _ in xrange(self.nState)]
for i in xrange(self.nState):
matrix[i][0] = (log(self.prior_matrix[i]) +
log(self.emit_matrix[i][line[0]]))
for i in xrange(1, len(line)):
for state1 in xrange(self.nState):
p = matrix[0][i - 1] + log(self.trans_matrix[0][state1])
for state2 in xrange(1, self.nState):
trans = self.trans_matrix[state2][state1]
prev = matrix[state2][i - 1]
p = log_sum(prev + log(trans), p)
prob_o = self.emit_matrix[state1][line[i]]
p = p + log(prob_o)
matrix[state1][i] = p
p = matrix[0][-1]
for i in xrange(1, self.nState):
p = log_sum(p, matrix[i][-1])
print p
def forward_recursive(os, i, j, trans={}, emits={}, prior={}, labels=[], matrix=None):
if matrix[i][j] == -1:
if j == 0:
matrix[i][j] = math.log(prior[labels[i]]) + math.log(emits[labels[i]][os[j]])
else:
tmp = math.log(emits[labels[i]][os[j]])
tmp2 = 0
if matrix[0][j-1] != -1:
tmp2 = matrix[0][j-1]
else:
tmp2 = forward_recursive(os, 0, j-1, trans, emits, prior, labels, matrix)
tmp2 += math.log(trans[labels[0]][labels[i]])
for t in xrange(1, len(prior)):
if matrix[t][j-1] != -1:
tmp2 = log_sum(tmp2, matrix[t][j-1] + math.log(trans[labels[t]][labels[i]]))
else:
matrix[t][j-1] = forward_recursive(os, t, j-1, trans, emits, prior, labels, matrix)
tmp2 = log_sum(tmp2, matrix[t][j-1] + math.log(trans[labels[t]][labels[i]]))
tmp += tmp2
matrix[i][j] = tmp
return matrix[i][j]
def calculate_beta(self, dev, o_tp1, t, T):
beta_t = list()
for i in range(self.hmm.N):
beta_ti = 0.0
for j in range(self.hmm.N):
beta_tp1_j = dev[T - (t + 1)][j]
a_ij = log(self.hmm.a[i][j])
b_j = log(self.hmm.b[o_tp1][j])
sum = beta_tp1_j + a_ij + b_j
if j == 0:
beta_ti = sum
else:
beta_ti = log_sum(beta_ti, sum)
beta_t.append(beta_ti)
dev.append(beta_t)
def calculate_alpha(self, o_tp1, tp1, dev):
alpha_tp1 = list()
for i in range(self.hmm.N):
bi = log(self.hmm.b[o_tp1][i])
logsum = 0.0
for j in range(self.hmm.N):
a_tj = dev[tp1 - 2][j]
a_ji = log(self.hmm.a[j][i])
sum = a_tj + a_ji
if j == 0:
logsum = sum
else:
logsum = log_sum(logsum, sum)
alpha_tp1_i = bi + logsum
alpha_tp1.append(alpha_tp1_i)
dev.append(alpha_tp1)
def backward_recursive(os, i, j, trans={}, emits={}, prior={}, labels=[], matrix=None):
tmp = 0
if matrix[0][j+1] == -1:
matrix[0][j+1] = backward_recursive(os, 0, j+1, trans, emits, prior, labels, matrix)
tmp = matrix[0][j+1]
tmp += math.log(emits[labels[0]][os[j+1]])
tmp += math.log(trans[labels[i]][labels[0]])
for z in xrange(1, len(labels)):
if matrix[z][j+1] == -1:
matrix[z][j+1] = backward_recursive(os, z, j+1, trans, emits, prior, labels, matrix)
tmp2 = matrix[z][j+1]
tmp2 += math.log(emits[labels[z]][os[j+1]])
tmp2 += math.log(trans[labels[i]][labels[z]])
tmp = log_sum(tmp, tmp2)
matrix[i][j] = tmp
return matrix[i][j]
def forward_each(sentence, states, words, prior_vec, trans_mat, emit_mat):
o1 = sentence[0]
afa = []
for i in range(len(states)):
index = find_b(o1, words)
ini = math.log(prior_vec[i]) + math.log(emit_mat[i, index])
afa.append(ini)
for t in range(0, len(sentence) - 1):
temp_afa = afa[:]
for i in range(len(states)):
b_j = find_b(sentence[t + 1], words)
temp_list = []
for j in range(len(afa)):
temp_list.append(temp_afa[j] + math.log(trans_mat[j, i]))
afa[i] = log_sum_all(temp_list) + math.log(emit_mat[i, b_j])
temp = afa[0]
final_p = afa[:]
for i in range(1, len(afa)):
temp = log_sum(temp, final_p[i])
print temp
line = reversed(line)
for word in line:
# setting value for other columns over the other states
for state in states:
for previous_state in states:
if states.index(previous_state) == 0:
second_column_dict[state] = first_column_dict[
previous_state] + trans[state][previous_state] + emits[
previous_state][word]
else:
second_column_dict[state] = log_sum(
(first_column_dict[previous_state] +
trans[state][previous_state] +
emits[previous_state][word]),
second_column_dict[state])
first_column_dict = second_column_dict
second_column_dict = {}
first_column = True
for state in states:
if states.index(state) == 0:
output = first_column_dict[state] + priors[state] + emits[state][
first_word]
else:
output = log_sum(
first_column_dict[state] + priors[state] +
emits[state][first_word], output)
for word in line:
# checking if first column and forming first column
if first_column:
for state in states:
first_column_dict[state] = priors[state] + emits[state][word]
first_column = False
# forming other columns over the other states
else:
for state in states: # applying recursive formula
for previous_state in states:
if states.index(previous_state) == 0:
second_column_dict[state] = first_column_dict[previous_state] + trans[previous_state][state]
else:
second_column_dict[state] = log_sum(first_column_dict[previous_state]+ trans[previous_state][state], second_column_dict[state])
# adding the emission probability of a word given a state
second_column_dict[state] += emits[state][word]
first_column_dict = second_column_dict
second_column_dict = {}
first_column = True
for state in states:
if states.index(state) == 0:
output = first_column_dict[state]
else:
output = log_sum(first_column_dict[state], output)
print output
def log_sum_all(n_list):
temp = n_list[0]
for i in range(1, len(n_list)):
temp = log_sum(temp, n_list[i])
return temp