def build_model():
model = None
if embedding_layer:
input = Input(shape=(None, ))
else:
input = Input(shape=(None, n_words))
profiles_input = Input(shape=(None, X_aug_train.shape[2]))
# Defining an embedding layer mapping from the words (n_words) to a vector of len 250
if embedding_layer:
x1 = Embedding(input_dim=n_words, output_dim=250,
input_length=None)(input)
else:
x1 = input
x1 = concatenate([x1, profiles_input])
x1 = Dense(1200, activation="relu")(x1)
x1 = Dropout(0.5)(x1)
# Defining a bidirectional GRU using the embedded representation of the inputs
x1 = Bidirectional(CuDNNGRU(units=500, return_sequences=True))(x1)
x1 = Bidirectional(CuDNNGRU(units=100, return_sequences=True))(x1)
if embedding_layer:
x2 = Embedding(input_dim=n_words, output_dim=125,
input_length=None)(input)
else:
x2 = input
x2 = concatenate([x2, profiles_input])
# Defining a bidirectional GRU using the embedded representation of the inputs
x2 = Bidirectional(CuDNNGRU(units=500, return_sequences=True))(x2)
x2 = Bidirectional(CuDNNGRU(units=100, return_sequences=True))(x2)
COMBO_MOVE = concatenate([x1, x2])
w = Dense(500, activation="relu")(COMBO_MOVE) # try 500
w = Dropout(0.4)(w)
w = tcn.TCN(return_sequences=True)(w)
y = TimeDistributed(Dense(n_tags, activation="softmax"))(w)
# Defining the model as a whole and printing the summary
model = Model([input, profiles_input], y)
# model.summary()
# Setting up the model with categorical x-entropy loss and the custom accuracy function as accuracy
adamOptimizer = Adam(lr=0.001,
beta_1=0.8,
beta_2=0.8,
epsilon=None,
decay=0.0001,
amsgrad=False)
model.compile(optimizer=adamOptimizer,
loss=nll1,
metrics=["accuracy", accuracy])
return model
def build_model():
model = None
input = Input(shape=(
MAXLEN_SEQ,
NB_AS,
))
if hmm:
profiles_input = Input(shape=(
MAXLEN_SEQ,
NB_FEATURES,
))
x1 = concatenate([input, profiles_input])
x2 = concatenate([input, profiles_input])
inp = [input, profiles_input]
else:
x1 = input
x2 = input
inp = input
x1 = Dense(1200, activation="relu")(x1)
x1 = Dropout(0.5)(x1)
# x1 = Bidirectional(CuDNNGRU(units=100, return_sequences=True))(x1)
# Defining a bidirectional LSTM using the embedded representation of the inputs
x2 = Bidirectional(CuDNNGRU(units=500, return_sequences=True))(x2)
# x2 = Dropout(0.5)(x2)
x2 = Bidirectional(CuDNNGRU(units=100, return_sequences=True))(x2)
# x2 = Dropout(0.5)(x2)
COMBO_MOVE = concatenate([x1, x2])
w = Dense(500, activation="relu")(COMBO_MOVE) # try 500
w = Dropout(0.4)(w)
w = tcn.TCN(return_sequences=True)(w)
y = TimeDistributed(Dense(NB_CLASSES_Q8, activation="softmax"))(w)
# Defining the model as a whole and printing the summary
model = Model(inp, y)
# model.summary()
# Setting up the model with categorical x-entropy loss and the custom accuracy function as accuracy
adamOptimizer = Adam(lr=0.001,
beta_1=0.8,
beta_2=0.8,
epsilon=None,
decay=0.0001,
amsgrad=False)
model.compile(optimizer=adamOptimizer,
loss="categorical_crossentropy",
metrics=["accuracy", accuracy])
return model
def createTCNModel (self, embedding_matrix=[],useTrainedEmbedding=False) :
print ("Creating Keras model..\n")
i = Input(batch_shape=(None, self.max_sentence_length))
#If using preTrained embeddings like Glove or Word2Vec, use embeddings as weight
#Else learn weights
if useTrainedEmbedding:
e = Embedding(self.vocab_size, self.embeddingDim, weights=[embedding_matrix], \
input_length=self.max_sentence_length, trainable=False)(i)
else :
e = Embedding(self.vocab_size, self.embeddingDim, \
input_length=self.max_sentence_length, trainable=True)(i)
x = tcn.TCN(e, nb_filters=64, nb_stacks= 2, kernel_size=2, \
activation='tanh',dilations=[1,2,4,8,16,32,64], return_sequences=False)
#Add ANN layer with dropout
x = Dense(units=20,activation='relu')(x)
x = Dropout(0.5)(x)
if (self.num_classes > 2 or self.num_classes == 1) :
output_dim = self.num_classes
elif self.num_classes ==2 :
output_dim = self.num_classes - 1
else :
print ("Invalid number of classes = ",self.num_classes)
exit
#Final output layer
#Use softmax for multiclass and sigmoid for binary classification
if (self.num_classes > 2) :
x = Dense(output_dim, activation='softmax')(x)
else :
x = Dense(output_dim, activation='sigmoid')(x)
self.model = Model(inputs=[i], outputs=[x])
# compile the model
self.model.compile(optimizer='adam', loss='binary_crossentropy', metrics=['acc'])
# summarize the model
print(self.model.summary())
def tcnn_model(dataset):
semantic_dropout = 0.1
lstm_in_dropout = 0.1
final_dropout = 0.1
# Sentence Embeddings
vocab_size = len(dataset.word2index)
inputs1 = Input(shape=(4096, ), name='f_input') # means BATCHx4096
fe1 = Dropout(0.25, name='fe1')(inputs1)
fe2 = Dense(BEFORE_CONCAT, name='fe2', activation='relu')(fe1)
# sequence model.
# Note that shape is of the sample (ignoring batch d). (50, 4096) (50, 62) (50, 62, 3626)
inputs2 = Input(shape=(None, ), name='s_input') # TPDP: remove dim here!!!
se1 = Embedding(vocab_size, EMBEDDING_D, mask_zero=False,
name='se1')(inputs2) # why mask_Zero=True
print("false to masking")
# se2 = Dropout(lstm_in_dropout,name='se2')(se1)
# benchmark adapted from Penn treebank k=3. n=4. hidden=600 dropout=0.5
se = tcn.TCN(input_layer=se1,
nb_filters=BEFORE_CONCAT,
kernel_size=3,
nb_stacks=2,
dilations=[1, 2, 4, 8],
dropout_rate=0.2,
return_sequences=True)
# se3 = TimeDistributed(Dense(BEFORE_CONCAT,name='se4'))(se2)
msk1 = keras.layers.Masking(mask_value=0.0)(se1)
msk1 = keras.layers.Lambda(lambda x: x * 0.0)(msk1)
# decoder model
decoder1 = add([fe2, se, msk1], name='concat/add')
decoder2 = TimeDistributed(
Dense(BEFORE_SOFTMAX_D, activation='relu', name='decoder2'))(decoder1)
decoder2 = TimeDistributed(Dropout(final_dropout,
name='final_dropout'))(decoder2)
outputs = TimeDistributed(
Dense(vocab_size, name='outputs',
activation='softmax'))(decoder2) # activation='softmax
# tie it together [image, seq] [wordo
model = Model(inputs=[inputs1, inputs2], outputs=outputs)
model.summary()
return model
def build_model_ho_3(params):
print(params)
input = Input(shape=(
X_train_aug[0].shape[1],
X_train_aug[0].shape[2],
))
profiles_input = Input(shape=(
X_train_aug[1].shape[1],
X_train_aug[1].shape[2],
))
x1 = concatenate([input, profiles_input])
x2 = concatenate([input, profiles_input])
x1 = Dense(params['dense1'], activation="relu")(x1)
x1 = Dropout(params['dropout1'])(x1)
x2 = Bidirectional(CuDNNGRU(units=params['gru1'],
return_sequences=True))(x2)
if params['gru2']:
x2 = Bidirectional(
CuDNNGRU(units=params['gru2']['gru2_units'],
return_sequences=True))(x2)
if params['gru2'] and params['gru2']['gru3']:
x2 = Bidirectional(
CuDNNGRU(units=params['gru2']['gru3']['gru3_units'],
return_sequences=True))(x2)
COMBO_MOVE = concatenate([x1, x2])
w = Dense(params['dense2'], activation="relu")(COMBO_MOVE)
w = Dropout(params['dropout2'])(w)
w = tcn.TCN(return_sequences=True)(w)
y = TimeDistributed(Dense(8, activation="softmax"))(w)
model = Model([input, profiles_input], y)
adamOptimizer = Adam(lr=params['lr'],
beta_1=0.8,
beta_2=0.8,
epsilon=None,
decay=params['decay'],
amsgrad=False)
model.compile(optimizer=adamOptimizer,
loss="categorical_crossentropy",
metrics=["accuracy", accuracy, matthews_correlation])
earlyStopping = EarlyStopping(monitor='val_accuracy',
patience=3,
verbose=1,
mode='max')
checkpointer = ModelCheckpoint(filepath=load_file,
monitor='val_accuracy',
verbose=1,
save_best_only=True,
mode='max')
model.fit(X_train_aug,
y_train,
validation_data=(X_val_aug, y_val),
epochs=20,
batch_size=params['batch_size'],
callbacks=[checkpointer, earlyStopping],
verbose=1,
shuffle=True)
model.load_weights(load_file)
score = model.evaluate(X_test_aug, y_test)
K.clear_session()
result = {'loss': -score[2], 'status': STATUS_OK}
return result
def build_model(hype_space):
"""Create model according to the hyperparameter space given."""
print("Hyperspace:")
print(hype_space)
#use different inputs according to choice of hyperparameter 'input', 'use profiles'
input_onehot = Input(shape=(None, n_words))
input_seqs = Input(shape=(None, ))
input_elmo = Input(shape=(None, 1024))
input_pssm = Input(shape=(None, 22))
input_hmm = Input(shape=(None, 30))
inp = [input_onehot, input_seqs, input_elmo, input_pssm, input_hmm]
x0 = None
if hype_space['input'] == 'onehot':
x0 = input_onehot
print('Onehot shape:', x0._keras_shape)
if hype_space['input'] == 'seqs':
# have to use embedding
if hype_space['embedding']:
x0 = input_elmo
else:
x0 = Embedding(input_dim=n_words,
output_dim=int(hype_space['dense_output']),
input_length=None)(input_seqs)
print('Seqs shape after embedding:', x0._keras_shape)
if hype_space['input'] == 'both':
# elmo einfügen
if hype_space['embedding']:
x_seq = input_elmo
else:
x_seq = Embedding(input_dim=n_words,
output_dim=int(hype_space['dense_output']),
input_length=None)(input_seqs)
print('Seqs shape after embedding:', x_seq._keras_shape)
print('Onehot shape:', input_onehot._keras_shape)
x0 = concatenate([input_onehot, x_seq])
print('Both concac input shape:', x0._keras_shape)
if hype_space['use_profiles'] is not None:
if hype_space['use_profiles'] == 'pssm':
print('Use pssm profiles.')
x0 = concatenate([x0, input_pssm])
if hype_space['use_profiles'] == 'hmm':
print('Use hmm profiles.')
x0 = concatenate([x0, input_hmm])
if hype_space['use_profiles'] == 'both':
print('Use both profiles.')
x0 = concatenate([x0, input_pssm, input_hmm])
# NN starts here:
if hype_space['tcn_position'] == 'first':
print('TCN first.')
x0 = tcn.TCN(return_sequences=True)(x0)
print('First layer is', hype_space['first_layer']['type'])
x1 = x0
if hype_space['first_layer']['type'] == 'LSTM':
for i in range(hype_space['first_layer']['lstm_nb']):
i = i + 1
print(i)
x1 = Bidirectional(
CuDNNLSTM(units=int(hype_space['first_layer']['lstm_units'] /
i),
return_sequences=True))(x1)
x1 = Dropout(int(hype_space['dropout']))(x1)
x2 = x1
x1 = x0
if hype_space['first_layer']['type'] == 'GRU':
x1 = Bidirectional(
CuDNNGRU(units=int(hype_space['first_layer']['gru1'] * 100),
return_sequences=True))(x1)
if hype_space['first_layer']['gru2']:
x1 = Bidirectional(
CuDNNGRU(units=int(
hype_space['first_layer']['gru2']['gru2_units'] * 100),
return_sequences=True))(x1)
if hype_space['first_layer']['gru2'] and hype_space['first_layer'][
'gru2']['gru3']:
x1 = Bidirectional(
CuDNNGRU(units=int(
hype_space['first_layer']['gru2']['gru3']['gru3_units'] *
100),
return_sequences=True))(x1)
x2 = x1
x1 = x0
COMBO_MOVE = concatenate([x0, x2])
x0 = COMBO_MOVE
if hype_space['second_layer']:
print('Second layer is', hype_space['second_layer']['type'])
x1 = x0
if hype_space['second_layer']['type'] == 'LSTM':
for i in range(hype_space['second_layer']['lstm_nb_2']):
i = i + 1
print(i)
x1 = Bidirectional(
CuDNNLSTM(units=int(
hype_space['second_layer']['lstm_units_2'] / i),
return_sequences=True))(x1)
x1 = Dropout(int(hype_space['dropout']))(x1)
x2 = x1
x1 = x0
if hype_space['second_layer']['type'] == 'GRU':
x1 = Bidirectional(
CuDNNGRU(units=int(hype_space['second_layer']['gru1_2'] * 100),
return_sequences=True))(x1)
if hype_space['second_layer']['gru2_2']:
x1 = Bidirectional(
CuDNNGRU(units=int(
hype_space['second_layer']['gru2_2']['gru2_units_2'] *
100),
return_sequences=True))(x1)
if hype_space['second_layer']['gru2_2'] and hype_space[
'second_layer']['gru2_2']['gru3_2']:
x1 = Bidirectional(
CuDNNGRU(units=int(hype_space['second_layer']['gru2_2']
['gru3_2']['gru3_units_2'] * 100),
return_sequences=True))(x1)
x2 = x1
COMBO_MOVE = concatenate([x0, x2])
'''
current_layer = input
if hype_space['first_conv'] is not None:
k = hype_space['first_conv']
current_layer = keras.layers.convolutional.Conv1D(
filters=16, kernel_size=k, strides=1,
padding='same', activation=hype_space['activation'],
kernel_regularizer=keras.regularizers.l2(
STARTING_L2_REG * hype_space['l2_weight_reg_mult'])
)(current_layer)
# Core loop that stacks multiple conv+pool layers, with maybe some
# residual connections and other fluffs:
n_filters = int(40 * hype_space['conv_hiddn_units_mult'])
for i in range(hype_space['nb_conv_pool_layers']):
print(i)
print(n_filters)
print(current_layer._keras_shape)
current_layer = convolution(current_layer, n_filters, hype_space)
if hype_space['use_BN']:
current_layer = bn(current_layer)
print(current_layer._keras_shape)
n_filters *= 2
# Fully Connected (FC) part:
current_layer = TimeDistributed(Dense(
units=int(1000 * hype_space['fc_units_1_mult']),
activation=hype_space['activation'],
kernel_regularizer=keras.regularizers.l2(
STARTING_L2_REG * hype_space['l2_weight_reg_mult'])
))(current_layer)
print(current_layer._keras_shape)
current_layer = dropout(
current_layer, hype_space, for_convolution_else_fc=False)
if hype_space['one_more_fc'] is not None:
current_layer = TimeDistributed(Dense(
units=int(750 * hype_space['one_more_fc']),
activation=hype_space['activation'],
kernel_regularizer=keras.regularizers.l2(
STARTING_L2_REG * hype_space['l2_weight_reg_mult'])
))(current_layer)
print(current_layer._keras_shape)
current_layer = dropout(
current_layer, hype_space, for_convolution_else_fc=False)
y = TimeDistributed(Dense(
units=NB_CLASSES_Q8,
activation="softmax",
kernel_regularizer=keras.regularizers.l2(
STARTING_L2_REG * hype_space['l2_weight_reg_mult']),
name='y'
))(current_layer)
print(y._keras_shape)
# Finalize model:
inp = [input, profiles_input]
model = Model(inp, y)
model.compile(
optimizer=OPTIMIZER_STR_TO_CLASS[hype_space['optimizer']](
#lr=0.001 * hype_space['lr_rate_mult']
),
loss=LOSS_STR_TO_CLASS[hype_space['loss']],
metrics=[accuracy] #noch andere dazu
)
'''
w = Dense(int(hype_space['dense_output']) * 2,
activation="relu")(COMBO_MOVE) # try 500
w = Dropout(int(hype_space['dropout']))(w)
if hype_space['tcn_position'] == 'last':
print('TCN last.')
w = tcn.TCN(return_sequences=True)(w)
y = TimeDistributed(Dense(n_tags, activation="softmax"))(w)
# Defining the model as a whole and printing the summary
model = Model(inp, y)
# model.summary()
# Setting up the model with categorical x-entropy loss and the custom accuracy function as accuracy
#adamOptimizer = Adam(lr=0.001, beta_1=0.8, beta_2=0.8, epsilon=None, decay=0.0001, amsgrad=False)
model.compile(
optimizer=OPTIMIZER_STR_TO_CLASS[hype_space['optimizer']](
#lr=0.001 * hype_space['lr_rate_mult']
),
loss=LOSS_STR_TO_CLASS[hype_space['loss']],
metrics=[
accuracy,
#weighted_accuracy,
kullback_leibler_divergence
])
return model
