def make_model(self):
input = Input(shape=(self.maxlen, self.num_chars))
# "Encode" the input sequence using an RNN, producing an output of HIDDEN_SIZE
# note: in a situation where your input sequences have a variable length,
# use input_shape=(None, nb_feature).
x = recurrent.LSTM(self.hidden_size)(input)
# For the decoder's input, we repeat the encoded input for each time step
x = RepeatVector(self.max_digits + 1)(x)
# The decoder RNN could be multiple layers stacked or a single layer
x = recurrent.LSTM(self.hidden_size, return_sequences=True)(x)
# For each of step of the output sequence, decide which character should be chosen
x = TimeDistributed(Dense(self.num_chars, activation='softmax'))(x)
def full_number_accuracy(y_true, y_pred):
y_true_argmax = K.argmax(y_true)
y_pred_argmax = K.argmax(y_pred)
tfd = K.equal(y_true_argmax, y_pred_argmax)
tfn = K.all(tfd, axis=1)
tfc = K.cast(tfn, dtype='float32')
tfm = K.mean(tfc)
return tfm
self.model = Model(inputs=input, outputs=x)
self.model.compile(loss='categorical_crossentropy',
optimizer=Adam(lr=self.optimizer_lr,
clipnorm=self.clipnorm),
metrics=['accuracy', full_number_accuracy])
def get_model(word_index):
nb_words = min(MAX_NB_WORDS, len(word_index))
if os.path.exists(embedding_matrix_path):
embedding_matrix = np.load(embedding_matrix_path)["arr_0"]
else:
embedding_matrix = get_embedding_matrix(word_index)
# embedding_matrix,nb_words=get_embedding_matrix(word_index)
nb_words = min(MAX_NB_WORDS, len(word_index))
input1 = Input(shape=(MAX_SEQUENCE_LENGTH, ), dtype='int32')
embedding_layer = Embedding(nb_words,
EMBEDDING_DIM,
input_length=MAX_SEQUENCE_LENGTH,
weights=[embedding_matrix],
trainable=True)
x = embedding_layer(input1)
x = Dropout(rate_drop_dense)(x)
x = recurrent.LSTM(lstm_output_size)(x)
x = RepeatVector(MAX_SEQUENCE_LENGTH)(x)
x = recurrent.LSTM(lstm_output_size)(x)
x = Dropout(rate_drop_dense)(x)
out = Dense(6, activation='sigmoid')(x)
model = Model(inputs=input1, outputs=out)
model.compile(loss='binary_crossentropy',
optimizer='rmsprop',
metrics=['mse'])
model.summary()
return model
def generate_model(output_len, chars=None):
"""Generate the model"""
print('Build model...')
chars = chars or CHARS
model = Sequential()
# "Encode" the input sequence using an RNN, producing an output of hidden_size
# note: in a situation where your input sequences have a variable length,
# use input_shape=(None, nb_feature).
for layer_number in range(CONFIG.input_layers):
model.add(recurrent.LSTM(CONFIG.hidden_size, input_shape=(None, len(chars)), kernel_initializer=CONFIG.initialization,
return_sequences=layer_number + 1 < CONFIG.input_layers))
model.add(Dropout(CONFIG.amount_of_dropout))
# For the decoder's input, we repeat the encoded input for each time step
model.add(RepeatVector(output_len))
# The decoder RNN could be multiple layers stacked or a single layer
for _ in range(CONFIG.output_layers):
model.add(recurrent.LSTM(CONFIG.hidden_size, return_sequences=True, kernel_initializer=CONFIG.initialization))
model.add(Dropout(CONFIG.amount_of_dropout))
# For each of step of the output sequence, decide which character should be chosen
model.add(TimeDistributed(Dense(len(chars), kernel_initializer=CONFIG.initialization)))
model.add(Activation('softmax'))
model.compile(loss='categorical_crossentropy', optimizer='adam', metrics=['accuracy'])
return model
def get_rnn_model():
model = Sequential()
model.add(embed_1)
model.add(conv_1)
model.add(conv_2)
model.add(pool_1)
# model.add(conv_3)
# model.add(conv_4)
# model.add(pool_2)
# model.add(conv_5)
model.add(Attention(recurrent.LSTM(256,input_dim=EMBEDDING_DIM,consume_less='mem',return_sequences=True)))
model.add(Attention(recurrent.LSTM(128,input_dim=EMBEDDING_DIM,consume_less='mem',return_sequences=True)))
model.add(Attention(recurrent.LSTM(64,input_dim=EMBEDDING_DIM,consume_less='mem',return_sequences=False)))
# model.add(bi_lstm_1)
# model.add(bi_lstm_2)
# model.add(bi_lstm_3)
model.add(Dense(256))
model.add(drop_1)
model.add(dense_2)
model.compile(loss='mean_squared_error', optimizer="Adam")
return model
def generate_model(output_len, chars=None):
"""Generate the model"""
print('Build model...')
chars = chars or CHARS
model = Sequential()
# "Encode" the input sequence using an RNN, producing an output of HIDDEN_SIZE
# note: in a situation where your input sequences have a variable length,
# use input_shape=(None, nb_feature).
for layer_number in range(INPUT_LAYERS):
model.add(
recurrent.LSTM(HIDDEN_SIZE,
input_shape=(None, len(chars)),
init=INITIALIZATION,
return_sequences=layer_number + 1 < INPUT_LAYERS))
model.add(Dropout(AMOUNT_OF_DROPOUT))
# For the decoder's input, we repeat the encoded input for each time step
model.add(RepeatVector(output_len))
# The decoder RNN could be multiple layers stacked or a single layer
for _ in range(OUTPUT_LAYERS):
model.add(
recurrent.LSTM(HIDDEN_SIZE,
return_sequences=True,
init=INITIALIZATION))
model.add(Dropout(AMOUNT_OF_DROPOUT))
# For each of step of the output sequence, decide which character should be chosen
model.add(TimeDistributed(Dense(len(chars), init=INITIALIZATION)))
model.add(Activation('softmax'))
model.compile(loss='categorical_crossentropy',
optimizer='adam',
metrics=['accuracy'])
return model
def create_model(computed_params, model_params):
max_inputseq_len = computed_params['max_inputseq_len']
max_outputseq_len = computed_params['max_outputseq_len']
nb_labels = computed_params['nb_labels']
word_dims = computed_params['word_dims']
if model_params['arch'] == 'crf':
max_len = max(max_inputseq_len, max_outputseq_len) + 2
input1 = Input(shape=(max_len, word_dims,), dtype='float32', name='input1')
input2 = Input(shape=(max_len, word_dims,), dtype='float32', name='input2')
else:
input1 = Input(shape=(max_inputseq_len, word_dims,), dtype='float32', name='input1')
input2 = Input(shape=(max_inputseq_len, word_dims,), dtype='float32', name='input2')
optimizer = model_params['optimizer']
arch = model_params['arch']
if arch == 'bilstm':
net1 = Bidirectional(recurrent.LSTM(units=model_params['rnn_size'],
dropout=model_params['dropout_rate'],
return_sequences=False))(input1)
net2 = Bidirectional(recurrent.LSTM(units=model_params['rnn_size'],
dropout=model_params['dropout_rate'],
return_sequences=False))(input2)
net = concatenate([net1, net2])
elif arch in ('crf', 'rnn_seq'):
net1 = Bidirectional(recurrent.LSTM(units=model_params['rnn_size'],
dropout=model_params['dropout_rate'],
return_sequences=False))(input1)
net2 = Bidirectional(recurrent.LSTM(units=model_params['rnn_size'],
dropout=model_params['dropout_rate'],
return_sequences=False))(input2)
net = concatenate([net1, net2])
else:
raise NotImplementedError()
if model_params['dense1'] > 0:
net = Dense(units=model_params['dense1'], activation='sigmoid')(net)
if arch == 'crf':
net = RepeatVector(max_len)(net)
net = recurrent.LSTM(model_params['rnn_size'], return_sequences=True)(net)
net = CRF(units=computed_params['nb_terms'], sparse_target=False)(net)
model = Model(inputs=[input1, input2], outputs=net)
model.compile(loss=crf_loss, optimizer=optimizer, metrics=[crf_viterbi_accuracy])
elif arch == 'bilstm':
net = Dense(units=nb_labels, activation='softmax')(net)
model = Model(inputs=[input1, input2], outputs=net)
model.compile(loss='categorical_crossentropy', optimizer=optimizer, metrics=['accuracy'])
return model
def _create_model(self, units, lr, hypothesis_max_length,
sentence_max_length, embeddings, seed):
hyp_inpt = Input([hypothesis_max_length],
name="hypothesis_input",
dtype="int32")
hyp_emb = Dropout(0.5, seed=seed)(Embedding(embeddings.shape[0],
embeddings.shape[1],
weights=[embeddings],
mask_zero=True,
name="hyp_emb")(hyp_inpt))
hyp_bilstm = Bidirectional(
recurrent.LSTM(units[0], return_sequences=False,
name="hyp_lstm"))(hyp_emb)
content_inpt = Input([sentence_max_length],
name="evidence_input",
dtype="int32")
content_emb = Dropout(0.5, seed=seed)(Embedding(
embeddings.shape[0],
embeddings.shape[1],
weights=[embeddings],
mask_zero=True,
name="content_emb")(content_inpt))
evidence_bilstm = Bidirectional(
recurrent.LSTM(units[0],
return_sequences=False,
name="evidence_lstm"))(content_emb)
hidden = Dropout(0.5, seed=seed)(
Concatenate()([hyp_bilstm, evidence_bilstm]))
if len(units) > 1: # add dense layer if required
hidden = Dropout(0.5,
seed=seed)(Dense(units=units[1],
activation="relu",
name="hidden_dense")(hidden))
classifier = Dense(units=2, activation="softmax", name="dense")(hidden)
model = Model(inputs=[hyp_inpt, content_inpt], outputs=classifier)
optimizer = Adam(lr=lr)
model.compile(loss='binary_crossentropy',
optimizer=optimizer,
metrics=['accuracy'])
print(model.summary())
return model
def create_model(params, computed_params):
input = Input(shape=(
computed_params['max_text_len'],
computed_params['nb_features'],
),
dtype='float32',
name='input')
if params['optimizer'] == 'ftml':
opt = keras_contrib.optimizers.FTML()
else:
opt = params['optimizer']
if params['net_arch'] == 'crf':
net = input
for _ in range(params['nb_rnn']):
net = Bidirectional(
recurrent.LSTM(units=params['rnn_units1'],
dropout=params['dropout_rate'],
return_sequences=True))(net)
net = CRF(units=computed_params['nb_labels'], sparse_target=False)(net)
model = Model(inputs=[input], outputs=net)
model.compile(loss=crf_loss,
optimizer=opt,
metrics=[crf_viterbi_accuracy])
model.summary()
elif params['net_arch'] == 'lstm':
net = Bidirectional(
recurrent.LSTM(units=params['rnn_units1'],
dropout=params['dropout_rate'],
return_sequences=False))(input)
for _ in range(params['nb_dense1']):
net = Dense(units=params['rnn_units1'],
activation=params['activation1'])(net)
decoder = RepeatVector(computed_params['max_text_len'])(net)
decoder = recurrent.LSTM(params['rnn_units2'],
return_sequences=True)(decoder)
decoder = TimeDistributed(Dense(units=computed_params['nb_labels'],
activation='softmax'),
name='output')(decoder)
model = Model(inputs=[input], outputs=decoder)
model.compile(loss='categorical_crossentropy', optimizer=opt)
model.summary()
return model
def model(x_train, y_train, x_test, y_test):
"""
Model providing function:
Create Keras model with double curly brackets dropped-in as needed.
Return value has to be a valid python dictionary with two customary keys:
- loss: Specify a numeric evaluation metric to be minimized
- status: Just use STATUS_OK and see hyperopt documentation if not feasible
The last one is optional, though recommended, namely:
- model: specify the model just created so that we can later use it again.
"""
CONFIG = Configuration()
chars = read_top_chars()
model = Sequential()
# "Encode" the input sequence using an RNN, producing an output of hidden_size
# note: in a situation where your input sequences have a variable length,
# use input_shape=(None, nb_feature).
for layer_number in range(CONFIG.input_layers):
model.add(recurrent.LSTM(CONFIG.hidden_size, input_shape=(None, len(chars)), kernel_initializer=CONFIG.initialization,
return_sequences=layer_number + 1 < CONFIG.input_layers))
model.add(Dropout(CONFIG.amount_of_dropout))
# For the decoder's input, we repeat the encoded input for each time step
model.add(RepeatVector(CONFIG.max_input_len))
# The decoder RNN could be multiple layers stacked or a single layer
for _ in range(CONFIG.output_layers):
model.add(recurrent.LSTM(CONFIG.hidden_size, return_sequences=True, kernel_initializer=CONFIG.initialization))
model.add(Dropout(CONFIG.amount_of_dropout))
# For each of step of the output sequence, decide which character should be chosen
model.add(TimeDistributed(Dense(len(chars), kernel_initializer=CONFIG.initialization)))
model.add(Activation('softmax'))
model.compile(loss=CONFIG.loss, optimizer={{choice(['rmsprop', 'adam', 'sgd'])}}, metrics=['accuracy'])
model.fit(x_train, y_train,
batch_size={{choice([100, 200, 300, 400])}},
epochs={{choice([100, 200, 250, 300])}},
verbose=2,
validation_data=(x_test, y_test))
score, acc = model.evaluate(x_test, y_test, verbose=0)
print('Test accuracy:', acc)
print('Random Predictions:')
ctable = CharacterTable(read_top_chars())
print_random_predictions(model, ctable, x_test, y_test)
return {'loss': -acc, 'status': STATUS_OK, 'model': model}
def test_explicit_device_with_go_backward_and_mask(self):
batch_size = 8
timestep = 7
masksteps = 5
units = 4
inputs = np.random.randn(batch_size, timestep,
units).astype(np.float32)
mask = np.ones((batch_size, timestep)).astype(np.bool)
mask[:, masksteps:] = 0
# Test for V1 behavior.
lstm_v1 = rnn_v1.LSTM(units, return_sequences=True, go_backwards=True)
with testing_utils.device(should_use_gpu=True):
outputs_masked_v1 = lstm_v1(inputs, mask=tf.constant(mask))
outputs_trimmed_v1 = lstm_v1(inputs[:, :masksteps])
self.assertAllClose(outputs_masked_v1[:, -masksteps:],
outputs_trimmed_v1)
# Test for V2 behavior.
lstm = rnn.LSTM(units, return_sequences=True, go_backwards=True)
with testing_utils.device(should_use_gpu=True):
outputs_masked = lstm(inputs, mask=tf.constant(mask))
outputs_trimmed = lstm(inputs[:, :masksteps])
self.assertAllClose(outputs_masked[:, -masksteps:], outputs_trimmed)
def _create_model(self, units, max_length):
model = Sequential()
model.add(
Embedding(self.embeddings.shape[0],
self.embeddings.shape[1],
weights=[self.embeddings],
input_length=max_length,
mask_zero=True,
name="emb"))
model.add(Dropout(0.5, name="dropoutemb"))
for i, unit in enumerate(units):
model.add(
recurrent.LSTM(unit,
return_sequences=False,
name="lstm" + str(i)))
# model.add(recurrent.LSTM(5, return_sequences=False, name="lstm", activation="relu"))
model.add(Dropout(0.5, name="dropout" + str(i)))
model.add(Dense(units=2, activation="softmax", name="dense"))
optimizer = Adam(lr=0.01)
model.compile(loss='sparse_categorical_crossentropy',
optimizer=optimizer,
metrics=['accuracy'])
print(model.summary())
return model
def test_explicit_device_with_go_backward_and_mask(self):
if tf.test.is_built_with_rocm():
self.skipTest('Skipping the test as ROCm MIOpen does not '
'support padded input yet.')
batch_size = 8
timestep = 7
masksteps = 5
units = 4
inputs = np.random.randn(batch_size, timestep, units).astype(np.float32)
mask = np.ones((batch_size, timestep)).astype(np.bool)
mask[:, masksteps:] = 0
# Test for V1 behavior.
lstm_v1 = rnn_v1.LSTM(units, return_sequences=True, go_backwards=True)
with testing_utils.device(should_use_gpu=True):
outputs_masked_v1 = lstm_v1(inputs, mask=tf.constant(mask))
outputs_trimmed_v1 = lstm_v1(inputs[:, :masksteps])
self.assertAllClose(outputs_masked_v1[:, -masksteps:], outputs_trimmed_v1)
# Test for V2 behavior.
lstm = rnn.LSTM(units, return_sequences=True, go_backwards=True)
with testing_utils.device(should_use_gpu=True):
outputs_masked = lstm(inputs, mask=tf.constant(mask))
outputs_trimmed = lstm(inputs[:, :masksteps])
self.assertAllClose(outputs_masked[:, -masksteps:], outputs_trimmed)
def create_model(embeddings, units, max_length, seed):
tf.set_random_seed(seed)
session_conf = tf.ConfigProto(intra_op_parallelism_threads=1,
inter_op_parallelism_threads=1)
sess = tf.Session(graph=tf.get_default_graph(), config=session_conf)
K.set_session(sess)
model = Sequential()
emb = Embedding(embeddings.shape[0],
embeddings.shape[1],
weights=[embeddings],
input_length=max_length,
mask_zero=True,
name="foo")
model.add(emb)
model.add(Dropout(0.5, name="dropoutemb"))
for i, unit in enumerate(units):
model.add(
Bidirectional(
recurrent.LSTM(unit,
return_sequences=False,
name="lstm" + str(i))))
# model.add(recurrent.LSTM(5, return_sequences=False, name="lstm", activation="relu"))
model.add(Dropout(0.5, name="dropout" + str(i)))
model.add(Dense(units=2, activation="softmax", name="dense"))
optimizer = Adam(lr=0.01)
model.compile(loss='binary_crossentropy',
optimizer=optimizer,
metrics=['accuracy'])
print(model.summary())
return model
def rnn_att_model(embed,
MAX_LEN,
SENT_HIDDEN_SIZE,
ACTIVATION,
DP,
L2,
LABEL_NUM,
OPTIMIZER,
MLP_LAYER,
LAYERS,
RNN_Cell='LSTM'):
print('Build model...')
RNN = recurrent.LSTM
if RNN_Cell == 'BiLSTM':
RNN = lambda *args, **kwargs: Bidirectional(
recurrent.LSTM(*args, **kwargs))
elif RNN_Cell == 'GRU':
RNN = recurrent.GRU
elif RNN_Cell == 'BiGRU':
RNN = lambda *args, **kwargs: Bidirectional(
recurrent.GRU(*args, **kwargs))
rnn_kwargs = dict(units=SENT_HIDDEN_SIZE, dropout=DP, recurrent_dropout=DP)
translate = TimeDistributed(Dense(SENT_HIDDEN_SIZE, activation=ACTIVATION))
premise = Input(shape=(MAX_LEN, ), dtype='int32')
prem = embed(premise)
# prem = translate(prem)
if LAYERS > 1:
for l in range(LAYERS - 1):
rnn = RNN(return_sequences=True, **rnn_kwargs)
prem = BatchNormalization()(rnn(prem))
rnn = RNN(return_sequences=True, **rnn_kwargs)
prem = rnn(prem)
prem = Attention(MAX_LEN)(prem)
joint = Dropout(DP)(prem)
for i in range(MLP_LAYER):
joint = Dense(2 * SENT_HIDDEN_SIZE,
activation=ACTIVATION,
kernel_regularizer=l2(L2) if L2 else None)(joint)
joint = Dropout(DP)(joint)
# joint = BatchNormalization()(joint)
pred = Dense(LABEL_NUM, activation='softmax')(joint)
model = Model(inputs=premise, outputs=pred)
model.compile(optimizer=OPTIMIZER,
loss='categorical_crossentropy',
metrics=['accuracy'])
model.summary()
return model
def make_model(len_feature):
##########################Parameters for the model and dataset
#TRAINING_SIZE = len(inputs)
# Try replacing JZS1 with LSTM, GRU, or SimpleRNN
HIDDEN_SIZE = node0
RNN = recurrent.LSTM(HIDDEN_SIZE,
input_shape=(None, len(chars)),
return_sequences=False,
kernel_regularizer=l2(l2_c),
bias_regularizer=l2(l2_c),
recurrent_dropout=drop_out_c,
dropout=drop_out_c,
kernel_constraint=maxnorm(constrain_max))
#len0_hla = 34
#ratio_t = 1
###class number = binder or non-binder (1 = binder, 0 = non-binder)
#classes = [0,1]
##########################start a model##########################
##########fixed part
model_fixed = Sequential()
model_fixed.add(
Dense(help_nn,
input_dim=len_feature,
activation=act_fun,
kernel_regularizer=l2(l2_c),
bias_regularizer=l2(l2_c)))
model_fixed.add(Dropout(drop_out_c))
##########recurrent part
model_r = Sequential()
if mask0:
model_r.add(
Masking(mask_value=0., input_shape=(MAXLEN, len(dict_aa['A']))))
model_r.add(RNN)
####merge
merged = Merge([model_fixed, model_r], mode='concat')
###final
final_model = Sequential()
final_model.add(merged)
#, kernel_constraint=maxnorm(constrain_max)
for _ in range(0, help_layer0):
final_model.add(
Dense(help_nn,
kernel_regularizer=l2(l2_c),
bias_regularizer=l2(l2_c)))
final_model.add(Activation(act_fun))
final_model.add(Dropout(drop_out_c))
final_model.add(Dense(1))
final_model.compile(loss=loss_function0, optimizer="adam")
model = final_model
json_string = model.to_json()
open(path_save + file_name0 + out_name + '_model.json',
'w').write(json_string)
return model
def test_masking_layer():
''' This test based on a previously failing issue here:
https://github.com/fchollet/keras/issues/1567
'''
inputs = np.random.random((6, 3, 4))
targets = np.abs(np.random.random((6, 3, 5)))
targets /= targets.sum(axis=-1, keepdims=True)
model = Sequential()
model.add(Masking(input_shape=(3, 4)))
model.add(recurrent.LSTM(units=5, return_sequences=True, unroll=False))
model.compile(loss='categorical_crossentropy', optimizer='adam')
model.fit(inputs, targets, epochs=1, batch_size=100, verbose=1)
model = Sequential()
model.add(Masking(input_shape=(3, 4)))
model.add(recurrent.LSTM(units=5, return_sequences=True, unroll=True))
model.compile(loss='categorical_crossentropy', optimizer='adam')
model.fit(inputs, targets, epochs=1, batch_size=100, verbose=1)
def get_model0(embedding_matrix):
input1 = Input(shape=(MAX_SEQUENCE_LENGTH,), dtype='int32')
# x = Dropout(rate_drop_dense)(input1)
embedding_layer = Embedding(MAX_NB_WORDS,
EMBEDDING_DIM,
input_length=MAX_SEQUENCE_LENGTH,
weights=[embedding_matrix],
trainable=True)
x = embedding_layer(input1)
x = Dropout(rate_drop_dense)(x)
x = recurrent.LSTM(lstm_output_size)(x)
x = RepeatVector(MAX_SEQUENCE_LENGTH)(x)
x = recurrent.LSTM(lstm_output_size)(x)
x = Dropout(rate_drop_dense)(x)
out = Dense(6, activation='sigmoid')(x)
model = Model(inputs=input1, outputs=out)
model.compile(loss='binary_crossentropy', optimizer='rmsprop', metrics=['mse'])
# model.summary()
return model
def create_model(units, lr, hypothesis_max_length, sentence_max_length, embeddings, seed):
# set random seed to Keras and TensorFlow
tf.set_random_seed(seed)
# session_conf = tf.ConfigProto(intra_op_parallelism_threads=1, inter_op_parallelism_threads=1)
# sess = tf.Session(graph=tf.get_default_graph(), config=session_conf)
# K.set_session(sess)
hyp_inpt = Input([hypothesis_max_length], name="hypothesis_input", dtype="int32")
hyp_emb = Dropout(0.5, seed=seed)(Embedding(embeddings.shape[0],
embeddings.shape[1],
weights=[embeddings],
mask_zero=True,
name="hyp_emb")(hyp_inpt))
hyp_bilstm = Bidirectional(recurrent.LSTM(units[0], return_sequences=False, name="hyp_lstm" ))(hyp_emb)
content_inpt = Input([sentence_max_length], name="evidence_input", dtype="int32")
content_emb = Dropout(0.5, seed=seed)(Embedding(embeddings.shape[0],
embeddings.shape[1],
weights=[embeddings],
mask_zero=True,
name="content_emb")(content_inpt))
evidence_bilstm = Bidirectional(recurrent.LSTM(units[0], return_sequences=False, name="evidence_lstm"))(content_emb)
hidden = Dropout(0.5, seed=seed)(Concatenate()([hyp_bilstm, evidence_bilstm]))
if len(units) > 1: # add dense layer if required
hidden = Dropout(0.5, seed=seed)(Dense(units=units[1], activation="relu", name="hidden_dense")(hidden))
classifier = Dense(units=2, activation="softmax", name="dense")(hidden)
model = Model(inputs=[hyp_inpt, content_inpt], outputs=classifier)
optimizer = Adam(lr=lr)
model.compile(loss='binary_crossentropy', optimizer=optimizer, metrics=['accuracy'])
print(model.summary())
return model
def get_model(self, max_size=EMBEDDING_SIZE):
# Defining model
print('Define model')
q1 = Input(shape=(MAX_LEN,), dtype='int32')
q2 = Input(shape=(MAX_LEN,), dtype='int32')
if max_size < EMBEDDING_SIZE:
print('Reduce EMBEDDING_SIZE to %d due to pretrained embedding' % max_size)
if max_size < SENT_HIDDEN_SIZE:
print('Reduce SENT_HIDDEN_SIZE to %d due to pretrained embedding' % max_size)
if self.word_embedding_matrix is None:
embed = Embedding(self.VOCAB_SIZE + 1, min(max_size, EMBEDDING_SIZE),
input_length=MAX_LEN, trainable=TRAIN_EMBED)
else:
embed = Embedding(self.VOCAB_SIZE + 1, min(max_size, EMBEDDING_SIZE), weights=[self.word_embedding_matrix],
input_length=MAX_LEN, trainable=TRAIN_EMBED)
embed_q1 = embed(q1)
embed_q2 = embed(q2)
translate = TimeDistributed(Dense(min(max_size, SENT_HIDDEN_SIZE), activation=ACTIVATION))
sent_q1 = translate(embed_q1)
sent_q2 = translate(embed_q2)
if self.sen_type == 'lstm':
sent_embed = Bidirectional(recurrent.LSTM(units=min(max_size, SENT_HIDDEN_SIZE),
recurrent_dropout=DROPOUT_RATE, dropout=DROPOUT_RATE,
return_sequences=False))
else:
sent_embed = Lambda(lambda x: keras.backend.sum(x, axis=1), output_shape=(min(max_size, SENT_HIDDEN_SIZE),))
sent_q1 = BatchNormalization()(sent_embed(sent_q1))
sent_q2 = BatchNormalization()(sent_embed(sent_q2))
joint = concatenate([sent_q1, sent_q2])
joint = Dropout(DROPOUT_RATE)(joint)
for i in range(3):
joint = Dense(2 * SENT_HIDDEN_SIZE, activation=ACTIVATION, kernel_regularizer=l2(L2) if L2 else None)(joint)
joint = Dropout(DROPOUT_RATE)(joint)
joint = BatchNormalization()(joint)
pred = Dense(1, activation='sigmoid')(joint)
model = Model(inputs=[q1, q2], outputs=pred)
if self.model_type == 'compare':
model.compile(optimizer=OPTIMIZER, loss='binary_crossentropy', metrics=['accuracy'])
else:
model.compile(optimizer=OPTIMIZER, loss='mean_squared_error', metrics=['accuracy'])
return model
def create_seq2seq_model(model_filename, params_filename):
"""Create the model"""
input_token_index,target_token_index,\
input_characters,target_characters,\
max_encoder_seq_length,num_encoder_tokens,\
max_decoder_seq_length,num_decoder_tokens=get_parameters_from_file(params_filename)
initialization = "he_normal"
model = Sequential()
# "Encode" the input sequence using an RNN, producing an output of hidden_size
# note: in a situation where your input sequences have a variable length,
# use input_shape=(None, nb_feature).
model.add(Masking(input_shape=(None, num_encoder_tokens)))
for layer_number in range(LSTM_LAYERS):
model.add(
recurrent.LSTM(latent_dim,
kernel_initializer=initialization,
return_sequences=layer_number + 1 < LSTM_LAYERS))
model.add(Dropout(DROPOUT))
# For the decoder's input, we repeat the encoded input for each time step
model.add(RepeatVector(max_decoder_seq_length))
# The decoder RNN could be multiple layers stacked or a single layer
for _ in range(LSTM_LAYERS):
model.add(
recurrent.LSTM(latent_dim,
return_sequences=True,
kernel_initializer=initialization))
model.add(Dropout(DROPOUT))
# For each of step of the output sequence, decide which character should be chosen
model.add(
TimeDistributed(
Dense(num_decoder_tokens, kernel_initializer=initialization)))
model.add(Activation('softmax'))
model.compile(loss='categorical_crossentropy',
optimizer='adam',
metrics=['accuracy'])
model.save(model_filename)
def test_masking_layer():
''' This test based on a previously failing issue here:
https://github.com/fchollet/keras/issues/1567
'''
model = Sequential()
model.add(Masking(input_shape=(3, 4)))
model.add(recurrent.LSTM(output_dim=5, return_sequences=True))
model.compile(loss='categorical_crossentropy', optimizer='adam')
I = np.random.random((6, 3, 4))
V = np.abs(np.random.random((6, 3, 5)))
V /= V.sum(axis=-1, keepdims=True)
model.fit(I, V, nb_epoch=1, batch_size=100, verbose=1)
def make_model(self, model_type='class2'):
##########################Parameters for the model and dataset
#input layers
seq_input = Input(shape=(self.MAXLEN, len(self.dict_aa['A'])))
fix_input = Input(shape=(self.fix_len, ))
#set RNN layer
if self.mask0:
seq_input0 = Masking(mask_value=0.0)(seq_input)
else:
seq_input0 = seq_input
rnn0 = recurrent.LSTM(
self.node0,
activation=self.act_fun, #recurrent_activation=self.act_fun,
use_bias=True,
kernel_initializer='glorot_uniform',
recurrent_initializer='orthogonal',
bias_initializer='zeros',
unit_forget_bias=True,
kernel_regularizer=None,
recurrent_regularizer=None,
bias_regularizer=None,
activity_regularizer=None,
kernel_constraint=None,
recurrent_constraint=None,
bias_constraint=None,
dropout=self.drop_out_c,
recurrent_dropout=self.drop_r)(seq_input0)
fix0 = Dense(self.fix_node, activation=self.act_fun)(fix_input)
fix0_d = Dropout(self.drop_out_c)(fix0)
merge_layer = concatenate([rnn0, fix0_d])
combine1 = Dense(self.help_nn, activation=self.act_fun)(merge_layer)
combine1_d = Dropout(self.drop_out_c)(combine1)
combine2 = Dense(self.help_nn, activation=self.act_fun)(combine1_d)
combine2_d = Dropout(self.drop_out_c)(combine2)
if model_type == 'regression':
dense0 = Dense(1)(combine2_d)
final_model = Model(inputs=[seq_input, fix_input],
outputs=[dense0])
final_model.compile(loss=self.loss_function0, optimizer='adam')
elif 'class' in model_type:
class_n = int(model_type[-1])
dense0 = Dense(class_n, activation='softmax')(combine2_d)
final_model = Model(inputs=[fix_input, seq_input],
outputs=[dense0])
final_model.compile(loss=self.loss_function0, optimizer="RMSprop")
json_string = final_model.to_json()
open(self.path_save + self.file_name0 + self.out_name + '_model.json',
'w').write(json_string)
return final_model
def test_lstm_v2_feature_parity_with_canonical_lstm(self):
if tf.test.is_built_with_rocm():
self.skipTest('Skipping the test as ROCm MIOpen does not '
'support padded input yet.')
input_shape = 10
rnn_state_size = 8
timestep = 4
batch = 20
(x_train,
y_train), _ = testing_utils.get_test_data(train_samples=batch,
test_samples=0,
input_shape=(timestep,
input_shape),
num_classes=rnn_state_size,
random_seed=87654321)
y_train = np_utils.to_categorical(y_train, rnn_state_size)
# For the last batch item of the test data, we filter out the last
# timestep to simulate the variable length sequence and masking test.
x_train[-2:, -1, :] = 0.0
y_train[-2:] = 0
inputs = keras.layers.Input(shape=[timestep, input_shape],
dtype=tf.float32)
masked_input = keras.layers.Masking()(inputs)
lstm_layer = rnn_v1.LSTM(rnn_state_size,
recurrent_activation='sigmoid')
output = lstm_layer(masked_input)
lstm_model = keras.models.Model(inputs, output)
weights = lstm_model.get_weights()
y_1 = lstm_model.predict(x_train)
lstm_model.compile('rmsprop', 'mse')
lstm_model.fit(x_train, y_train)
y_2 = lstm_model.predict(x_train)
with testing_utils.device(should_use_gpu=True):
cudnn_layer = rnn.LSTM(rnn_state_size)
cudnn_model = keras.models.Model(inputs, cudnn_layer(masked_input))
cudnn_model.set_weights(weights)
y_3 = cudnn_model.predict(x_train)
cudnn_model.compile('rmsprop', 'mse')
cudnn_model.fit(x_train, y_train)
y_4 = cudnn_model.predict(x_train)
self.assertAllClose(y_1, y_3, rtol=1e-5, atol=2e-5)
self.assertAllClose(y_2, y_4, rtol=1e-5, atol=2e-5)
def _time_performance_run_normal_lstm(self, test_config, x_train, y_train):
# Get performance number for standard LSTM on GPU.
input_shape = test_config['input_shape']
rnn_state_size = test_config['rnn_state_size']
timestep = test_config['timestep']
layer = rnn_v1.LSTM(rnn_state_size)
inputs = keras.layers.Input(shape=[timestep, input_shape],
dtype=tf.float32)
outputs = layer(inputs)
model = keras.models.Model(inputs, outputs)
model.compile('sgd', 'mse')
sec_per_epoch = self._measure_performance(test_config, model, x_train,
y_train)
logging.info('Average performance for %s per epoch is: %s',
'Normal LSTM', sec_per_epoch)
return sec_per_epoch
def make_rnn(MAXLEN):
##########################Parameters for the model and dataset
#TRAINING_SIZE = len(inputs)
# Try replacing JZS1 with LSTM, GRU, or SimpleRNN
RNN = recurrent.LSTM(HIDDEN_SIZE, input_shape=(None, len(chars)), return_sequences=False,W_regularizer=l2(l2_c),b_regularizer=l2(l2_c),dropout_W=drop_out_c,dropout_U=drop_out_c)
##########################start a model
model = Sequential()
#masking
if mask0:
model.add(Masking(mask_value=0., input_shape=(MAXLEN, len(dict_aa['A']))))
# "Encode" the input sequence using an RNN, producing an output of HIDDEN_SIZE
#model.add(Masking())
#print(str(LAYERS))
#keras.layers.core.ActivityRegularization(l2=0.0, l2=0.0)
if LAYERS>1:
#print('1')
model.add(RNN(return_sequences=True))
else:
#print('2')
model.add(RNN)
if help_nn >0:
model.add(Dense(help_nn))
model.add(Activation('tanh'))
if LAYERS>2:
for _ in xrange(LAYERS-2):
#print('3')
model.add(RNN(HIDDEN_SIZE, return_sequences=True))
# #model.add(Dropout(0.5))
if LAYERS>1:
#print('4')
model.add(RNN(HIDDEN_SIZE, return_sequences=False))
model.add(Dense(2))
model.add(Activation('softmax'))
model.compile(loss=loss_function0, optimizer='adam')
#save the model
json_string = model.to_json()
open(path_save+file_name0+out_name+'_model.json', 'w+').write(json_string)
return model
def generateModel(X_train, Y_train, X_test, Y_test):
model = Sequential()
model.add(
recurrent.LSTM(32,
input_dim=1,
input_length=99,
activation='sigmoid',
inner_activation='hard_sigmoid'))
model.add(Dropout(0.5))
model.add(Dense(10, activation='softmax'))
# Compile model
model.compile(loss='categorical_crossentropy',
optimizer='adam',
metrics=['accuracy'])
X_train = np.array(X_train).reshape(-1, 99, 1)
X_test = np.array(X_test).reshape(-1, 99, 1)
Y_train = to_categorical(Y_train, 10)
Y_test = to_categorical(Y_test, 10)
# Fit the model
model.fit(X_train, Y_train, nb_epoch=150, batch_size=4)
# model.predict(X_test, batch_size=4, verbose=0)
# model.predict_on_batch(self, x)
model.save('my_model.h5') # creates a HDF5 file 'my_model.h5'
# del model # deletes the existing model
# returns a compiled model
# identical to the previous one
# model = load_model('my_model.h5')
scores = model.evaluate(X_test, Y_test, batch_size=4)
print("%s: %.2f%%" % (model.metrics_names[1], scores[1] * 100))
return model
def __init__(self, load=None):
self.model_path = "../../data/lstm_model.json"
self.params_path = "../../data/lstm_params.h5"
self.vocab, self.max_len = Loader.build_vocab()
print("data loaded!")
print("vocab size: " + str(len(self.vocab)))
print("max sentence length: " + str(self.max_len))
self.w2v = Loader.load_word_vec(self.vocab)
print("word2vec loaded!")
print("num words already in word2vec: " + str(len(self.w2v)))
Loader.add_unknown_words(self.w2v, self.vocab)
self.W, self.word_idx_map = Loader.get_W(self.w2v)
self.c2id, self.id2c = Loader.build_class()
print(self.c2id)
if load:
self.model = Loader.load_model(self.model_path, "lstm",
self.params_path)
return
self.model = Sequential()
self.model.add(
Embedding(len(self.word_idx_map) + 1, 300, weights=[self.W]))
self.model.add(
recurrent.LSTM(output_dim=100,
activation='tanh',
dropout_W=0,
dropout_U=0))
#self.model.add(convolutional.Convolution1D(100, 3, activation='tanh', border_mode='same'))
self.model.add(pooling.GlobalMaxPooling1D())
#self.model.add(Dropout(0.2))
self.model.add(Dense(7))
self.model.add(Activation('softmax'))
print(self.model.summary())
rmsprop = keras.optimizers.rmsprop(lr=0.002)
self.model.compile(loss='categorical_crossentropy',
optimizer=rmsprop,
metrics=["accuracy"])
def build_model(self):
assert self.seq_len > 1
assert len(self.alphabet.alphabet) > 0
bits_per_char = self.alphabet.nb_chars
rnn_size = bits_per_char
model = Sequential()
model.add(
Masking(mask_value=0,
input_shape=(self.seq_len, bits_per_char),
name='input_layer'))
model.add(
recurrent.LSTM(rnn_size,
input_shape=(self.seq_len, bits_per_char),
return_sequences=False))
model.add(Dense(units=rnn_size, activation='sigmoid'))
model.add(
Dense(units=bits_per_char,
activation='softmax',
name='output_layer'))
model.compile(loss='categorical_crossentropy',
optimizer='rmsprop',
metrics=['accuracy'])
return model
def model_init(arguments, prem, hypo, sent1, sent2):
rnn_kwargs = dict(output_dim=300, dropout_W=0.2, dropout_U=0.2)
RNN = lambda *args, **kwargs: Bidirectional(recurrent.LSTM(
*args, **kwargs))
# if RNN and 1 > 1:
# for l in range(1 - 1):
# rnn = RNN(return_sequences=True, **arguments)
# prem = BatchNormalization()(rnn(prem))
# hypo = BatchNormalization()(rnn(hypo))
# rnn = emnd_sum if not RNN else RNN(return_sequences=False, **arguments)
rnn = RNN(return_sequences=False, **rnn_kwargs)
# print("--------------------------------------------------------------------------")
prem = rnn(prem)
# print("--------------------------------------------------------------------------")
prem = BatchNormalization()(prem)
# print("--------------------------------------------------------------------------")
hypo = rnn(hypo)
hypo = BatchNormalization()(hypo)
s1_s2_combined = concatenate([prem, hypo])
s1_s2_combined = Dropout(dropoutt)(s1_s2_combined)
for i in range(3):
s1_s2_combined = Dense(
2 * 300, activation='relu',
W_regularizer=l2(L2) if L2 else None)(s1_s2_combined)
s1_s2_combined = Dropout(dropoutt)(s1_s2_combined)
s1_s2_combined = BatchNormalization()(s1_s2_combined)
pred = Dense(len(B), activation='softmax')(s1_s2_combined)
model = Model(input=[sent1, sent2], output=pred)
model.compile(optimizer=OPTIMIZER,
loss='categorical_crossentropy',
metrics=['accuracy'])
model.summary()
return model
def test_lstm_output_on_multiple_kernel(self):
input_shape = 10
rnn_state_size = 8
timestep = 4
batch = 100
x_train = np.random.random((batch, timestep, input_shape))
inputs = keras.layers.Input(
shape=[timestep, input_shape], dtype=tf.float32)
with testing_utils.device(should_use_gpu=False):
layer = rnn.LSTM(rnn_state_size)
output = layer(inputs)
cpu_model = keras.models.Model(inputs, output)
weights = cpu_model.get_weights()
y_1 = cpu_model.predict(x_train)
with testing_utils.device(should_use_gpu=True):
layer = rnn.LSTM(rnn_state_size)
output = layer(inputs)
gpu_model = keras.models.Model(inputs, output)
gpu_model.set_weights(weights)
y_2 = gpu_model.predict(x_train)
# Note that CuDNN uses 'sigmoid' as activation, so the LSTM V2 uses
# 'sigmoid' as default. Construct the canonical LSTM with sigmoid to achieve
# the same output.
with testing_utils.device(should_use_gpu=True):
layer = rnn_v1.LSTM(rnn_state_size, recurrent_activation='sigmoid')
output = layer(inputs)
canonical_model = keras.models.Model(inputs, output)
# Remove the extra cudnn bias since canonical lstm will not use it.
canonical_model.set_weights(weights[:3])
y_3 = canonical_model.predict(x_train)
self.assertAllClose(y_1, y_2)
self.assertAllClose(y_2, y_3)
