def build_critic(self):
critic_embedding = embed_seq(input_seq=self.input_,
from_=self.dimension,
to_=self.input_embed,
is_training=self.is_training,
BN=True,
initializer=self.initializer)
critic_encoding = encode_seq(input_seq=critic_embedding,
input_dim=self.input_embed,
num_stacks=self.num_stacks,
num_heads=self.num_heads,
num_neurons=self.num_neurons,
is_training=self.is_training)
frame = full_glimpse(
ref=critic_encoding,
from_=self.input_embed,
to_=self.num_units,
initializer=tf.contrib.layers.xavier_initializer(
)) # Glimpse on critic_encoding [Batch_size, input_embed]
with tf.variable_scope("ffn"): # 2 dense layers for predictions
h0 = tf.layers.dense(frame,
self.num_neurons_critic,
activation=tf.nn.relu,
kernel_initializer=self.initializer)
w1 = tf.get_variable("w1", [self.num_neurons_critic, 1],
initializer=self.initializer)
b1 = tf.Variable(self.init_B, name="b1")
self.predictions = tf.squeeze(tf.matmul(h0, w1) + b1)
tf.summary.scalar('predictions_mean',
tf.reduce_mean(self.predictions))
def load_data(parent_id, go_id):
data1 = list()
data2 = list()
labels = list()
positive1 = list()
negative1 = list()
positive2 = list()
negative2 = list()
with open(DATA_ROOT + parent_id + '/' + go_id + '.txt') as f:
for line in f:
line = line.strip().split(' ')
label = int(line[0])
seq = line[2][:MAXLEN]
sq1 = encode_seq_one_hot(seq, maxlen=MAXLEN)
sq2 = encode_seq(OGAK980101, seq, maxlen=MAXLEN)
sq3 = encode_seq(MEHP950102, seq, maxlen=MAXLEN)
sq4 = encode_seq(CROG050101, seq, maxlen=MAXLEN)
sq5 = encode_seq(TOBD000101, seq, maxlen=MAXLEN)
sq6 = encode_seq(ALTS910101, seq, maxlen=MAXLEN)
if label == 1:
positive1.append([sq1])
positive2.append(sq1)
else:
negative1.append([sq1])
negative2.append(sq1)
shuffle(negative1, negative2, seed=0)
n = min(len(positive1), len(negative1))
data1 = negative1[:n] + positive1[:n]
data2 = negative2[:n] + positive2[:n]
labels = [0.0] * n + [1.0] * n
# Previous was 30
shuffle(data1, data2, labels, seed=0)
data = (
numpy.array(data1, dtype='float32'),
numpy.array(data2, dtype='float32'))
return (numpy.array(labels), data)
def load_data(parent_id, go_id):
data1 = list()
data2 = list()
labels = list()
positive1 = list()
negative1 = list()
positive2 = list()
negative2 = list()
with open(DATA_ROOT + parent_id + '/' + go_id + '.txt') as f:
for line in f:
line = line.strip().split(' ')
label = int(line[0])
seq = line[2][:MAXLEN]
sq1 = encode_seq_one_hot(seq, maxlen=MAXLEN)
sq2 = encode_seq(OGAK980101, seq, maxlen=MAXLEN)
sq3 = encode_seq(MEHP950102, seq, maxlen=MAXLEN)
sq4 = encode_seq(CROG050101, seq, maxlen=MAXLEN)
sq5 = encode_seq(TOBD000101, seq, maxlen=MAXLEN)
sq6 = encode_seq(ALTS910101, seq, maxlen=MAXLEN)
if label == 1:
positive1.append([sq1])
positive2.append(sq1)
else:
negative1.append([sq1])
negative2.append(sq1)
shuffle(negative1, negative2, seed=0)
n = min(len(positive1), len(negative1))
data1 = negative1[:n] + positive1[:n]
data2 = negative2[:n] + positive2[:n]
labels = [0.0] * n + [1.0] * n
# Previous was 30
shuffle(data1, data2, labels, seed=0)
data = (numpy.array(data1,
dtype='float32'), numpy.array(data2, dtype='float32'))
return (numpy.array(labels), data)
def encode(self):
encoded_output, encoded_state = utils.encode_seq(
input_seq=self.q1,
seq_len=self.len1,
word_embeddings=self.word_embeddings,
num_neurons=self.num_neurons) # [batch_size, 2*num_neurons]
with tf.variable_scope(
"variational_inference"): # Variational inference
mean = utils.linear(encoded_state, self.hidden_size,
scope='mean') # [batch_size, n_hidden]
logsigm = utils.linear(encoded_state,
self.hidden_size,
scope='logsigm') # [batch_size, n_hidden]
self.mean, self.logsigm = mean, logsigm
# Gaussian Multivariate kld(z,N(0,1)) = -0.5 * [ sum_d(logsigma) + d - sum_d(sigma) - mu_T*mu]
klds = -0.5 * (tf.reduce_sum(logsigm, 1) +
tf.cast(tf.shape(mean)[1], tf.float32) -
tf.reduce_sum(tf.exp(logsigm), 1) -
tf.reduce_sum(tf.square(mean), 1)
) # KLD(q(z|x), N(0,1)) tensor [batch_size]
utils.variable_summaries(
'klds', klds) # posterior distribution close to prior N(0,1)
self.kld = tf.reduce_mean(klds, 0) # mean over batches: scalar
h_ = tf.get_variable("GO", [1, self.hidden_size],
initializer=self.initializer)
h_ = tf.tile(h_, [self.batch_size, 1
]) # trainable tensor: decoder init_state[1]
eps = tf.random_normal((self.batch_size, self.hidden_size), 0, 1)
self.doc_vec = tf.multiply(
tf.exp(logsigm), eps
) + mean # sample from latent intent space: decoder init_state[0]
self.doc_vec = self.doc_vec, h_ # tuple state Z, h
def encode_decode(self):
actor_embedding = embed_seq(input_seq=self.input_,
from_=self.dimension,
to_=self.input_embed,
is_training=self.is_training,
BN=True,
initializer=self.initializer)
actor_encoding = encode_seq(input_seq=actor_embedding,
input_dim=self.input_embed,
num_stacks=self.num_stacks,
num_heads=self.num_heads,
num_neurons=self.num_neurons,
is_training=self.is_training)
if self.is_training == False:
actor_encoding = tf.tile(actor_encoding, [self.batch_size, 1, 1])
idx_list, log_probs, entropies = [], [], [
] # tours index, log_probs, entropies
mask = tf.zeros((self.batch_size, self.max_length)) # mask for actions
n_hidden = actor_encoding.get_shape().as_list()[2] # input_embed
W_ref = tf.get_variable("W_ref", [1, n_hidden, self.num_units],
initializer=self.initializer)
W_q = tf.get_variable("W_q", [self.query_dim, self.num_units],
initializer=self.initializer)
v = tf.get_variable("v", [self.num_units],
initializer=self.initializer)
encoded_ref = tf.nn.conv1d(
actor_encoding, W_ref, 1, "VALID"
) # actor_encoding is the ref for actions [Batch size, seq_length, n_hidden]
query1 = tf.zeros((self.batch_size, n_hidden)) # initial state
query2 = tf.zeros((self.batch_size, n_hidden)) # previous state
query3 = tf.zeros(
(self.batch_size, n_hidden)) # previous previous state
W_1 = tf.get_variable(
"W_1", [n_hidden, self.query_dim],
initializer=self.initializer) # update trajectory (state)
W_2 = tf.get_variable("W_2", [n_hidden, self.query_dim],
initializer=self.initializer)
W_3 = tf.get_variable("W_3", [n_hidden, self.query_dim],
initializer=self.initializer)
for step in range(self.max_length): # sample from POINTER
query = tf.nn.relu(
tf.matmul(query1, W_1) + tf.matmul(query2, W_2) +
tf.matmul(query3, W_3))
logits = pointer(encoded_ref=encoded_ref,
query=query,
mask=mask,
W_ref=W_ref,
W_q=W_q,
v=v,
C=config.C,
temperature=config.temperature)
prob = distr.Categorical(logits) # logits = masked_scores
idx = prob.sample()
idx_list.append(idx) # tour index
log_probs.append(prob.log_prob(idx)) # log prob
entropies.append(prob.entropy()) # entropies
mask = mask + tf.one_hot(idx, self.max_length) # mask
idx_ = tf.stack([tf.range(self.batch_size, dtype=tf.int32), idx],
1) # idx with batch
query3 = query2
query2 = query1
query1 = tf.gather_nd(actor_encoding,
idx_) # update trajectory (state)
idx_list.append(idx_list[0]) # return to start
self.tour = tf.stack(idx_list, axis=1) # permutations
self.log_prob = tf.add_n(
log_probs) # corresponding log-probability for backprop
self.entropies = tf.add_n(entropies)
tf.summary.scalar('log_prob_mean', tf.reduce_mean(self.log_prob))
tf.summary.scalar('entropies_mean', tf.reduce_mean(self.entropies))