def make_model_bigru(dir_name):
gru_node = lambda x: GRU(64,
kernel_initializer="he_normal",
recurrent_initializer="he_normal",
implementation=2,
bias_initializer="he_normal",
dropout=.2,
recurrent_dropout=.2,
unroll=True,
go_backwards=x)
# MHC BiGRU
mhc_in = Input(shape=(34, 20))
mhc_branch_forw = gru_node(False)(mhc_in)
mhc_branch_forw = BatchNormalization()(mhc_branch_forw)
mhc_branch_forw = PReLU()(mhc_branch_forw)
mhc_branch_back = gru_node(True)(mhc_in)
mhc_branch_back = BatchNormalization()(mhc_branch_back)
mhc_branch_back = PReLU()(mhc_branch_back)
mhc_branch = average([mhc_branch_forw, mhc_branch_back])
# Peptide BiGRU
pep_in = Input(shape=(9, 20))
pep_branch_forw = gru_node(False)(pep_in)
pep_branch_forw = BatchNormalization()(pep_branch_forw)
pep_branch_forw = PReLU()(pep_branch_forw)
pep_branch_back = gru_node(True)(pep_in)
pep_branch_back = BatchNormalization()(pep_branch_back)
pep_branch_back = PReLU()(pep_branch_back)
pep_branch = average([pep_branch_forw, pep_branch_back])
# Merge branches
merged = concatenate([pep_branch, mhc_branch])
merged = Dense(64, kernel_initializer="he_uniform")(merged)
merged = BatchNormalization()(merged)
merged = PReLU()(merged)
merged = Dropout(.3)(merged)
merged = Dense(64, kernel_initializer="he_uniform")(merged)
merged = BatchNormalization()(merged)
merged = PReLU()(merged)
merged = Dropout(.3)(merged)
pred = Dense(1)(merged) #, activation = "sigmoid"
pred = PReLU()(pred)
model = Model([mhc_in, pep_in], pred)
model.compile(loss='kullback_leibler_divergence', optimizer="nadam")
with open(dir_name + "model.json", "w") as outf:
outf.write(model.to_json())
return model
def mean_squared_error(inputs):
if len(inputs) == 2:
[mu1, mu2] = inputs
if isinstance(mu2, list):
return average([mse(mu1, pred) for pred in mu2])
else:
return mse(mu1, mu2)
else:
true = inputs[0]
return average([mse(true, inputs[pred]) for pred in range(1, len(inputs))])
def binary_crossentropy(inputs):
print("Binary cross entropy inputs : ", inputs)
if len(inputs) == 2:
[mu1, mu2] = inputs
if isinstance(mu2, list):
print("**** LOSS AVERAGING BCE ****")
return average([K.binary_crossentropy(mu1, pred) for pred in mu2])
else:
#return -tf.multiply(mu1, tf.log(mu1+10**-7))+10**-10*mu2
return K.binary_crossentropy(mu1, mu2)
else:
true = inputs[0]
return average([K.binary_crossentropy(true, inputs[pred]) for pred in range(1, len(inputs))])
def categorical_crossentropy(inputs):
print("Categorical cross entropy inputs : ", inputs)
if len(inputs) == 2:
[mu1, mu2] = inputs
if isinstance(mu2, list):
return average(
[K.categorical_crossentropy(mu1, pred) for pred in mu2])
else:
return K.categorical_crossentropy(mu1, mu2)
else:
true = inputs[0]
return average([
K.categorical_crossentropy(true, inputs[pred])
for pred in range(1, len(inputs))
])
def get_model(self):
main_input = Input(shape=(
self.input_length,
4,
))
rev_input = kl.Lambda(lambda x: x[:, ::-1, ::-1])(main_input)
s_model = Sequential([
kl.Conv1D(filters=self.filters,
kernel_size=self.kernel_size,
input_shape=(self.input_length, 4),
strides=1),
kl.BatchNormalization(),
kl.core.Activation("relu"),
kl.pooling.MaxPooling1D(pool_size=self.pool_size,
strides=self.strides),
Flatten(),
kl.Dense(units=3),
],
name="shared_layers")
main_output = s_model(main_input)
rev_output = s_model(rev_input)
avg = kl.average([main_output, rev_output])
final_out = kl.core.Activation("sigmoid")(avg)
siamese_model = Model(inputs=main_input, outputs=final_out)
opt = keras.optimizers.Adam(lr=0.001)
siamese_model.compile(optimizer=opt,
loss="binary_crossentropy",
metrics=["accuracy"])
return siamese_model
def binary_crossentropy(inputs):
if len(inputs) == 2:
[mu1, mu2] = inputs
if isinstance(mu2, list):
return average([K.binary_crossentropy(mu1, pred) for pred in mu2])
else:
return K.binary_crossentropy(mu1, mu2)
else:
raise Exception(
"BINARY CROSS ENTROPY HAS MORE THAN 2 ARGUMENTS. ENSURE THIS IS DESIRED"
)
true = inputs[0]
return average([
K.binary_crossentropy(true, inputs[pred])
for pred in range(1, len(inputs))
])
def trainable_net(img_rows, img_cols, color_type, num_classes=None):
small_input = L.Input(shape=(img_rows, img_cols, channel))
small_net = small_model(small_input, num_classes=num_classes)
small_net.load_weights('imagenet_models/multi_cnn_small.h5')
# small_net.layers.pop()
small_net.trainable = True
small_output = small_net.layers[-1].output
medium_input = L.Input(shape=(img_rows * 2, img_cols * 2, channel))
medium_net = medium_model(medium_input, num_classes=num_classes)
medium_net.load_weights('imagenet_models/multi_cnn_medium.h5')
# medium_net.layers.pop()
medium_net.trainable = False
medium_output = medium_net.layers[-1].output
large_input = L.Input(shape=(img_rows * 3, img_cols * 3, channel))
large_net = large_model(large_input, num_classes=num_classes)
large_net.load_weights('imagenet_models/multi_cnn_large.h5')
# large_net.layers.pop()
large_net.trainable = False
large_output = large_net.layers[-1].output
logits = L.average([small_output, medium_output, large_output])
new_model = K.models.Model([small_input, medium_input, large_input],
logits)
sgd = K.optimizers.SGD(lr=0.001, momentum=0.99, decay=1e-4)
new_model.compile(optimizer=sgd,
loss='categorical_crossentropy',
metrics=['acc'])
return new_model
def _getEnsembledModel(ensemble_count, num_features, **kwargs):
kwargs['num_features'] = num_features
if ensemble_count == 1:
return getModel(verbose=True, **kwargs)
model_inputs = [
Input(shape=(None, ), name="input_src"),
Input(shape=(None, ), name="input_mt")
]
if num_features:
model_inputs = [Input(shape=(num_features, ), name="input_features")
] + model_inputs
logger.info("Creating models to ensemble")
verbose = [True] + [False] * (ensemble_count - 1)
models = [
getModel(model_inputs=model_inputs, verbose=v, **kwargs)
for v in verbose
]
output = average([model(model_inputs) for model in models], name='quality')
model = Model(inputs=model_inputs, outputs=output)
_printModelSummary(logger, model, "ensembled_model")
return model
def build(self, input_shape, num_classes):
inp = Input(shape=input_shape)
inp_norm = BatchNormalization()(inp)
outs = [] # the list of ensemble outputs
for i in range(ens_models):
# Conv [32] -> Conv [32] -> Pool (with dropout on the pooling layer)
conv_1 = Convolution2D(conv_depth_1, (kernel_size, kernel_size),
padding='same',
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(l2_lambda))(inp_norm)
conv_1 = BatchNormalization()(conv_1)
conv_2 = Convolution2D(conv_depth_1, (kernel_size, kernel_size),
padding='same',
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(l2_lambda))(conv_1)
conv_2 = BatchNormalization()(conv_2)
pool_1 = MaxPooling2D(pool_size=(pool_size, pool_size))(conv_2)
drop_1 = Dropout(drop_prob_1)(pool_1)
# Conv [64] -> Conv [64] -> Pool (with dropout on the pooling layer)
conv_3 = Convolution2D(conv_depth_2, (kernel_size, kernel_size),
padding='same',
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(l2_lambda))(drop_1)
conv_3 = BatchNormalization()(conv_3)
conv_4 = Convolution2D(conv_depth_2, (kernel_size, kernel_size),
padding='same',
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(l2_lambda))(conv_3)
conv_4 = BatchNormalization()(conv_4)
pool_2 = MaxPooling2D(pool_size=(pool_size, pool_size))(conv_4)
drop_2 = Dropout(drop_prob_1)(pool_2)
# Now flatten to 1D, apply FC -> ReLU (with dropout) -> softmax
flat = Flatten()(drop_2)
hidden = Dense(hidden_size,
activation='relu',
kernel_initializer='he_uniform',
kernel_regularizer=l2(l2_lambda))(flat)
hidden = BatchNormalization()(hidden)
drop_3 = Dropout(drop_prob_2)(hidden)
outs.append(
Dense(num_classes,
kernel_initializer='glorot_uniform',
kernel_regularizer=l2(l2_lambda),
activation='softmax')(drop_3))
out = average(outs)
return Model(inputs=inp, outputs=out)
def ensemble(models, model_inputs):
outputs = [models[0](model_inputs[0]), models[1](model_inputs[1])]
y = layers.average(outputs)
modelEns = Model(model_inputs, y, name='ensemble')
return modelEns
def two_stream(img_input_shape,
coor_input_shape,
num_classes,
l2_regularization=0.001):
regularization = l2(l2_regularization)
img_input = Input(shape=img_input_shape, name='img_input')
coor_input = Input(shape=coor_input_shape, name='coor_input')
img_net = mini_XCEPTION(img_input_shape)
coor_net = coor_covnet(coor_input_shape)
img_stream = img_net(img_input)
coor_stream = coor_net(coor_input)
img_stream = Flatten()(img_stream)
# coor_stream = Flatten()(coor_stream)
img_stream = Dense(14,
activation='relu',
kernel_regularizer=regularization)(img_stream)
coor_stream = Dense(14,
activation='relu',
kernel_regularizer=regularization)(coor_stream)
feature = average([img_stream, coor_stream])
fc_1 = Dense(units=num_classes,
activation='relu',
kernel_regularizer=regularization)(feature)
output = Activation('softmax', name='predictions')(fc_1)
model = Model(inputs=[img_input, coor_input], outputs=output)
return model
def getEnsembledModel(ensemble_count, **kwargs):
if ensemble_count == 1:
return getModel(verbose=True, **kwargs)
src_input = Input(shape=(None, ))
ref_input = Input(shape=(None, ))
model_inputs = [src_input, ref_input]
logger.info("Creating models to ensemble")
verbose = [True] + [False] * (ensemble_count - 1)
models = [
getModel(model_inputs=model_inputs, verbose=v, **kwargs)
for v in verbose
]
output = average([model(model_inputs) for model in models], name='quality')
logger.info("Compiling ensembled model")
model = Model(inputs=model_inputs, outputs=output)
model.compile(optimizer="adadelta",
loss={"quality": "mse"},
metrics={"quality": ["mse", "mae",
getStatefulPearsonr()]})
_printModelSummary(logger, model, "ensembled_model")
return model
def nn_model2(train_x,train_y):
"""建立第二个五层的神经网络"""
inputs=Input(shape=(train_x.shape[1],))
x1 = Dense(500, activation='tanh')(inputs)
x1 = bn_prelu(x1)
x2 = Dense(500, activation='relu')(inputs)
x2 = bn_prelu(x2)
# x=maximum([x1,x2])
# x=multiply([x1,x2])
# x=concatenate([x1,x2],axis=1)
# x=add([x1,x2])
x=average([x1,x2])
x = Dense(50, activation='sigmoid')(x)
x = bn_prelu(x)
# x = Dense(50, activation='relu')(x)
# x = bn_prelu(x)
x = Dense(50, activation='linear')(x)
predictions = Dense(10, activation='softmax')(x)
model = Model(inputs=inputs, outputs=predictions)
model.compile(optimizer=#Adam(lr=0.001, epsilon=1e-09, decay=0.0),
'rmsprop',
#"adam",
loss='categorical_crossentropy',
metrics=['accuracy'])
model.fit(train_x, train_y,epochs=5, batch_size=200, validation_split=0.0)
return model
def SpatialConsensus2(seq_len=3, classes=101, weights='imagenet', dropout=0.5):
mobilenet_no_top = MobileNet(
input_shape=(224,224,3),
pooling='avg',
include_top=False,
weights=weights,
)
# x = Reshape((1,1,1024), name='reshape_1')(mobilenet_no_top.output)
# x = Conv2D(classes, (1, 1),
# padding='same', name='conv_preds')(x)
x = Dropout(dropout, name='dropout')(mobilenet_no_top.output)
# x = Activation('softmax', name='act_softmax')(x)
# x = Reshape((classes,), name='reshape_2')(x)
x = Dense(classes, activation='softmax')(x)
mobilenet = Model(inputs=mobilenet_no_top.input, outputs=x)
# mobilenet.summary()
input_1 = Input((224,224,3))
input_2 = Input((224,224,3))
input_3 = Input((224,224,3))
y_1 = mobilenet(input_1)
y_2 = mobilenet(input_2)
y_3 = mobilenet(input_3)
z = average([y_1, y_2, y_3])
# z = Dropout(dropout, name='dropout')(z)
# z = Activation('softmax')(z)
result_model = Model(inputs=[input_1, input_2, input_3], outputs=z)
return result_model
def get_model(config):
inp = Input(shape=(config.strmaxlen, ), name='input')
emb1 = Embedding(config.max_features, config.embed_size, trainable = True)(inp)
emb1 = SpatialDropout1D(config.prob_dropout)(emb1)
####
l1_G = Bidirectional(CuDNNGRU(config.cell_size_l1, return_sequences=True))(emb1)
l2_LL = Bidirectional(CuDNNLSTM(config.cell_size_l2, return_sequences=True))(l1_G)
l2_LG = Bidirectional(CuDNNGRU(config.cell_size_l2, return_sequences=True))(l1_G)
# avg_pool_L = GlobalAveragePooling1D()(l1_L)
# max_pool_L = GlobalMaxPooling1D()(l1_L)
attention_LL = Attention(config.strmaxlen)(l2_LL)
attention_LG = Attention(config.strmaxlen)(l2_LG)
# avg_pool_LL = GlobalAveragePooling1D()(l2_LL)
# max_pool_LL = GlobalMaxPooling1D()(l2_LL)
# avg_pool_LG = GlobalAveragePooling1D()(l2_LG)
# max_pool_LG = GlobalMaxPooling1D()(l2_LG)
# avg_pool_LLC = GlobalAveragePooling1D()(l3_LLC)
# max_pool_LLC = GlobalMaxPooling1D()(l3_LLC)
# avg_pool_LGC = GlobalAveragePooling1D()(l3_LGC)
# max_pool_LGC = GlobalMaxPooling1D()(l3_LGC)
# conc_LL = concatenate([avg_pool_LL, max_pool_LL])
# conc_LG = concatenate([avg_pool_LG, max_pool_LG])
# conc_GLC = concatenate([avg_pool_G, max_pool_G, avg_pool_GL, max_pool_GL, avg_pool_GLC, max_pool_GLC])
# conc_GGC = concatenate([avg_pool_G, max_pool_G, avg_pool_GG, max_pool_GG, avg_pool_GGC, max_pool_GGC])
out_LL = Dropout(config.prob_dropout)(attention_LL)
out_LL = Dense(1)(out_LL)
out_LG = Dropout(config.prob_dropout)(attention_LG)
out_LG = Dense(1)(out_LG)
####
out_avg = average([out_LL, out_LG])
# # ==================================================================================================
model_avg = Model(inputs=inp, outputs=[out_LL, out_LG, out_avg])
# inp_pre = Input(shape=(config.strmaxlen, ), name='input_pre')
# inp_post = Input(shape=(config.strmaxlen, ), name='input_post')
# model_pre = model_avg(inp_pre)
# model_post = model_avg(inp_post)
# stack_layer = concatenate([model_pre, model_post])
# ens_out = Dense(1, use_bias=False)(stack_layer)
# reg_model = Model(inputs=[inp_pre, inp_post], outputs=ens_out)
model_avg.compile(loss='mean_squared_error', optimizer='adam', loss_weights=[1., 1., 4.] ,metrics=['mean_squared_error', 'accuracy'])
return model_avg
def fconcatenate(path_orig, path_down):
if path_orig._keras_shape == path_down._keras_shape:
path_down_cropped = path_down
else:
crop_x_1 = int(
np.ceil(
(path_down._keras_shape[2] - path_orig._keras_shape[2]) / 2))
crop_x_0 = path_down._keras_shape[2] - path_orig._keras_shape[
2] - crop_x_1
crop_y_1 = int(
np.ceil(
(path_down._keras_shape[3] - path_orig._keras_shape[3]) / 2))
crop_y_0 = path_down._keras_shape[3] - path_orig._keras_shape[
3] - crop_y_1
crop_z_1 = int(
np.ceil(
(path_down._keras_shape[4] - path_orig._keras_shape[4]) / 2))
crop_z_0 = path_down._keras_shape[4] - path_orig._keras_shape[
4] - crop_z_1
path_down_cropped = Cropping3D(cropping=((crop_x_0, crop_x_1),
(crop_y_0, crop_y_1),
(crop_z_0,
crop_z_1)))(path_down)
connected = average([path_orig, path_down_cropped])
return connected
def ensembleModels(ymodel):
model_input = Input(shape=ymodel[0].input_shape[1:])
yModels = [model(model_input) for model in ymodel]
yAvg = layers.average(yModels)
modelEns = Model(inputs=model_input, outputs=yAvg, name='ensemble')
print(modelEns.summary())
modelEns.save(args.model)
def build_super_discriminator(discriminators):
image = Input(shape=(1, 28, 28))
fakes = []
auxes = []
for discriminator in discriminators:
d_fake, d_aux = discriminator(image)
fakes.append(Reshape((-1,))(d_fake))
auxes.append(d_aux)
fake = concatenate(fakes)
# out = []
# for i in range(256):
# out.append(tf.strided_slice(fake,i,2*256+i,256))
# fake = tf.stack(out)
aux = average(auxes)
# def l2norm(a, b):
# return Reshape(())(dot([a - b, a - b], 0))
# diffs = []
# for i in range(len(discriminators)):
# for j in range(i + 1, len(discriminators)):
# diffs.append(l2norm(fakes[i], fakes[j]))
# diff = concatenate(diffs)
return Model(inputs=image, outputs=[fake, aux])
def Conv_filters(x_0):
x_1_1 = Conv2D(filters=16, kernel_size=(3, 4), strides=(2, 2), padding="same", activation="relu")(x_0)
x_1_2 = Conv2D(filters=16, kernel_size=(3, 2), strides=(2, 2), padding="same", activation="relu")(x_0)
x_1 = average([x_1_1, x_1_2])
x_2_1 = Conv2D(filters=16, kernel_size=(3, 4), strides=(2, 2), padding="same", activation="relu")(x_1)
x_2_2 = Conv2D(filters=16, kernel_size=(3, 2), strides=(2, 2), padding="same", activation="relu")(x_1)
x_2 = average([x_2_1, x_2_2])
x_3_1 = Conv2D(filters=16, kernel_size=(3, 4), strides=(2, 2), padding="same", activation="relu")(x_2)
x_3_2 = Conv2D(filters=16, kernel_size=(3, 2), strides=(2, 2), padding="same", activation="relu")(x_2)
x_3 = average([x_3_1, x_3_2])
x_4 = MaxPooling2D(pool_size=(3, 3), padding="same")(x_3)
return x_4
def create_model(self, X, wv_model):
X_preprocessed = super(ModelContainer10,
self).inputs_context_emb_layer_nc(X, wv_model)
X_preprocessed = np.array([
sequence.pad_sequences(subX_prep,
maxlen=maxlen,
padding='post',
truncating='post',
value=-1) for subX_prep in X_preprocessed
])
input = Input(shape=(3, maxlen), dtype='int32')
# Left Context branch
input_L = Lambda(lambda x: x[:, 0], output_shape=(maxlen, ))(input)
embedding_layer_L = wv_model.wv.get_embedding_layer()
mask_L = Masking(mask_value=-1)(input_L)
emb_seq_L = embedding_layer_L(mask_L)
x_L = Conv1D(filters=8, kernel_size=3, activation='relu')(emb_seq_L)
x_L = Dropout(0.4)(x_L)
x_L = GlobalMaxPooling1D()(x_L)
x_L = Dropout(0.2)(x_L)
x_L = Dense(2, activation='sigmoid')(x_L)
# Connective branch
input_NC = Lambda(lambda x: x[:, 1], output_shape=(maxlen, ))(input)
embedding_layer_NC = wv_model.wv.get_embedding_layer()
mask_NC = Masking(mask_value=-1)(input_NC)
emb_seq_NC = embedding_layer_NC(mask_NC)
x_NC = Conv1D(filters=128, kernel_size=4,
activation='relu')(emb_seq_NC)
x_NC = (AveragePooling1D(pool_size=4))(x_NC)
x_NC = (Dropout(0.2))(x_NC)
x_NC = (Conv1D(filters=256, kernel_size=2, activation='relu'))(x_NC)
x_NC = (Dropout(0.5))(x_NC)
x_NC = (Conv1D(filters=32, kernel_size=8, activation='relu'))(x_NC)
x_NC = GlobalMaxPooling1D()(x_NC)
x_NC = Dense(16, activation='tanh')(x_NC)
x_NC = Dropout(0.2)(x_NC)
x_NC = Dense(2, activation='sigmoid')(x_NC)
# Right context branch
input_R = Lambda(lambda x: x[:, 2], output_shape=(maxlen, ))(input)
embedding_layer_R = wv_model.wv.get_embedding_layer()
mask_R = Masking(mask_value=-1)(input_R)
emb_seq_R = embedding_layer_R(mask_R)
x_R = Conv1D(filters=8, kernel_size=3, activation='relu')(emb_seq_R)
x_R = Dropout(0.4)(x_R)
x_R = GlobalMaxPooling1D()(x_R)
x_R = Dropout(0.2)(x_R)
x_R = Dense(2, activation='sigmoid')(x_R)
x = average([x_L, x_R])
x = concatenate([x_NC, x])
preds = (Dense(2, activation='sigmoid'))(x)
model = Model(input, preds, name='Model10_contexts')
return model, X_preprocessed
def ensembleModels(models, model_input): # collect outputs of models in a list yModels=[model(model_input) for model in models] # averaging outputs yAvg=layers.average(yModels) # build model from same input and avg output modelEns = Model(inputs=model_input, outputs=yAvg, name='ensemble') return modelEns
def ensembleModels(models, model_input):
yModels = [model(model_input) for model in models]
yAvg = layers.average(yModels)
modelEns = Model(inputs=model_input, outputs=yAvg, name='ensemble')
# modelEns.compile(optimizer=Adam(lr=1e-4), loss='categorical_crossentropy', metrics=['accuracy'])
print(modelEns.summary())
modelEns.save('mix2_model.h5')
print(type(modelEns))
def ensembleModelsByAverageOutput(self, modelList):
model_input = layers.Input(shape=modelList[0].input_shape[1:]) # c*h*w
yModels = [model(model_input) for model in modelList]
yAvg = layers.average(yModels)
model = models.Model(inputs=model_input, outputs=yAvg, name='ensemble')
return model
def image_entry_model_46(time_steps, data_dim):
inputs = Input(shape=(time_steps, data_dim, 3))
x_0 = inputs
x_1_1 = Conv2D(filters=16, kernel_size=(3, 4), strides=(2, 2), padding="same", activation="relu")(x_0)
x_1_2 = Conv2D(filters=16, kernel_size=(3, 2), strides=(2, 2), padding="same", activation="relu")(x_0)
x_1 = average([x_1_1, x_1_2])
x_2_1 = Conv2D(filters=16, kernel_size=(3, 4), strides=(2, 2), padding="same", activation="relu")(x_1)
x_2_2 = Conv2D(filters=16, kernel_size=(3, 2), strides=(2, 2), padding="same", activation="relu")(x_1)
x_2 = average([x_2_1, x_2_2])
x_3_1 = Conv2D(filters=16, kernel_size=(3, 4), strides=(2, 2), padding="same", activation="relu")(x_2)
x_3_2 = Conv2D(filters=16, kernel_size=(3, 2), strides=(2, 2), padding="same", activation="relu")(x_2)
x_3 = average([x_3_1, x_3_2])
x_4 = MaxPooling2D(pool_size=(3, 3), padding="same")(x_3)
x_4 = Permute((3, 2, 1))(x_4)
x_shape = K.int_shape(x_4)
x_4 = [Lambda(slicer_3D.slice_pieces_3D, output_shape=(x_shape[1],x_shape[2], 1))(x_4) for _ in range(x_shape[3])]
x_4 = [Reshape((1, K.int_shape(Flatten()(each))[1]))(Flatten()(each)) for each in x_4]
x_4 = concatenate(x_4, axis=1)
x_5 = GRU(256, return_sequences=True)(x_4)
x_6 = GRU(128)(x_5)
prediction = Dense(4, activation="softmax")(x_6)
model = Model(inputs=inputs, outputs=prediction)
model.summary()
'''
train = snore_data_extractor(load_folder_path, one_hot=True, data_mode="train", resize=(data_dim, time_steps), timechain=False, duplicate=True)
devel = snore_data_extractor(load_folder_path, one_hot=True, data_mode="devel", resize=(data_dim, time_steps), timechain=False, duplicate=True)
epoch_num = 500
batch_size = 16
regularizer = tf.contrib.layers.l2_regularizer(0.01)
loss = tf.reduce_mean(losses.kullback_leibler_divergence(labels, predicts)) + tf.contrib.layers.apply_regularization(regularizer, weights_list=train_var[:-8])
train_step = tf.train.RMSPropOptimizer(learning_rate=0.001, momentum=0.01).minimize(loss)
'''
return model
def Model_DiscSeg(inputsize=640):
img_input = Input(shape=(inputsize, inputsize, 3))
conv1 = Conv2D(32, (3, 3), activation='relu', padding='same', name='block1_conv1')(img_input)
conv1 = Conv2D(32, (3, 3), activation='relu', padding='same', name='block1_conv2')(conv1)
pool1 = MaxPooling2D(pool_size=(2, 2))(conv1)
conv2 = Conv2D(64, (3, 3), activation='relu', padding='same', name='block2_conv1')(pool1)
conv2 = Conv2D(64, (3, 3), activation='relu', padding='same', name='block2_conv2')(conv2)
pool2 = MaxPooling2D(pool_size=(2, 2))(conv2)
conv3 = Conv2D(128, (3, 3), activation='relu', padding='same', name='block3_conv1')(pool2)
conv3 = Conv2D(128, (3, 3), activation='relu', padding='same', name='block3_conv2')(conv3)
pool3 = MaxPooling2D(pool_size=(2, 2))(conv3)
conv4 = Conv2D(256, (3, 3), activation='relu', padding='same', name='block4_conv1')(pool3)
conv4 = Conv2D(256, (3, 3), activation='relu', padding='same', name='block4_conv2')(conv4)
pool4 = MaxPooling2D(pool_size=(2, 2))(conv4)
conv5 = Conv2D(512, (3, 3), activation='relu', padding='same', name='block5_conv1')(pool4)
conv5 = Conv2D(512, (3, 3), activation='relu', padding='same', name='block5_conv2')(conv5)
up6 = concatenate([Conv2DTranspose(256, (2, 2), strides=(2, 2), padding='same', name='block6_dconv')(conv5), conv4],
axis=3)
conv6 = Conv2D(256, (3, 3), activation='relu', padding='same', name='block6_conv1')(up6)
conv6 = Conv2D(256, (3, 3), activation='relu', padding='same', name='block6_conv2')(conv6)
up7 = concatenate([Conv2DTranspose(128, (2, 2), strides=(2, 2), padding='same', name='block7_dconv')(conv6), conv3],
axis=3)
conv7 = Conv2D(128, (3, 3), activation='relu', padding='same', name='block7_conv1')(up7)
conv7 = Conv2D(128, (3, 3), activation='relu', padding='same', name='block7_conv2')(conv7)
up8 = concatenate([Conv2DTranspose(64, (2, 2), strides=(2, 2), padding='same', name='block8_dconv')(conv7), conv2],
axis=3)
conv8 = Conv2D(64, (3, 3), activation='relu', padding='same', name='block8_conv1')(up8)
conv8 = Conv2D(64, (3, 3), activation='relu', padding='same', name='block8_conv2')(conv8)
up9 = concatenate([Conv2DTranspose(32, (2, 2), strides=(2, 2), padding='same', name='block9_dconv')(conv8), conv1],
axis=3)
conv9 = Conv2D(32, (3, 3), activation='relu', padding='same', name='block9_conv1')(up9)
conv9 = Conv2D(32, (3, 3), activation='relu', padding='same', name='block9_conv2')(conv9)
side6 = UpSampling2D(size=(8, 8))(conv6)
side7 = UpSampling2D(size=(4, 4))(conv7)
side8 = UpSampling2D(size=(2, 2))(conv8)
out6 = Conv2D(1, (1, 1), activation='sigmoid', name='side_6')(side6)
out7 = Conv2D(1, (1, 1), activation='sigmoid', name='side_7')(side7)
out8 = Conv2D(1, (1, 1), activation='sigmoid', name='side_8')(side8)
out9 = Conv2D(1, (1, 1), activation='sigmoid', name='side_9')(conv9)
out10 = average([out6, out7, out8, out9])
# out10 = Conv2D(1, (1, 1), activation='sigmoid', name='side_10')(out10)
model = Model(inputs=[img_input], outputs=[out10])
return model
def __init__(self):
vi = Input(shape=(video_len, video_dim))
qa = Input(shape=(qa_len, ))
subt = Input(shape=(subtitle_len, ))
vp = video_lstm(vi) # the output will be a vector
qa1 = qa_encoder(qa)
qa1 = qa_lstm(qa1)
sub1 = sub_encoder(subt)
sub1 = sub_lstm(sub1)
v0 = p0(pair_average(vp))
u0 = pair_average(sub1)
q0 = pair_average(qa1)
v = v0
u = u0
q = q0
uv = multiply([v, u])
uq = multiply([u, q])
vq = multiply([v, q])
m = average([uv, uq, vq])
for _ in range(K):
v = video_shaper(V_Att([vi, m]))
u = S_Att([sub1, m])
q = Q_Att([qa1, m])
# Multi-modal Fusion
uv = multiply([v, u])
uq = multiply([u, q])
vq = multiply([v, q])
m = add([m, average([uv, uq, vq])])
x = Dense(100, activation='relu')(m)
x = Dense(50, activation='relu')(x)
score = Dense(1)(x)
self.model = Model(inputs=[vi, qa, subt], outputs=score)
print('finished score_model')
def get_model(config):
inp = Input(shape=(config.strmaxlen, ), name='input')
# inp = Input(shape=(config.max_features, ), name='input')
emb = Embedding(config.max_features,
config.max_features,
embeddings_initializer='identity',
trainable=True)(inp)
# emb1 = Embedding(config.max_features, config.embed_size, trainable = True)(inp)
emb1 = SpatialDropout1D(config.prob_dropout)(emb)
####
l1_L = Bidirectional(
CuDNNLSTM(config.cell_size_l1, return_sequences=True))(emb1)
l2_LL = Bidirectional(
CuDNNLSTM(config.cell_size_l2, return_sequences=False))(l1_L)
l2_LG = Bidirectional(
CuDNNGRU(config.cell_size_l2, return_sequences=False))(l1_L)
out_LL = Dropout(config.prob_dropout2)(l2_LL)
out_LG = Dropout(config.prob_dropout2)(l2_LG)
out_LL = Dense(2, activation='softmax')(out_LL)
out_LG = Dense(2, activation='softmax')(out_LG)
####
emb2 = SpatialDropout1D(config.prob_dropout)(emb)
l1_G = Bidirectional(
CuDNNGRU(config.cell_size_l1, return_sequences=True))(emb2)
l2_GL = Bidirectional(
CuDNNLSTM(config.cell_size_l2, return_sequences=False))(l1_G)
l2_GG = Bidirectional(
CuDNNGRU(config.cell_size_l2, return_sequences=False))(l1_G)
out_GL = Dropout(config.prob_dropout2)(l2_GL)
out_GG = Dropout(config.prob_dropout2)(l2_GG)
out_GL = Dense(2, activation='softmax')(out_GL)
out_GG = Dense(2, activation='softmax')(out_GG)
out_avg = average([out_LL, out_LG, out_GL, out_GG])
# # ==================================================================================================
model_avg = Model(inputs=inp,
outputs=[out_LL, out_LG, out_GL, out_GG, out_avg])
model_avg.compile(loss='categorical_crossentropy',
optimizer='adam',
loss_weights=[1., 1., 1., 1., 0.1],
metrics=['accuracy'])
return model_avg
def ensemble_models(input_shape, model_list, rename_model=False):
if rename_model:
for index, model in enumerate(model_list):
model.name = 'ensemble_' + str(index) + '_' + model.name
for layer in model.layers:
layer.name = 'ensemble_' + str(index) + '_' + layer.name
inputs = Input(shape=input_shape)
outputs = average([model(inputs) for model in model_list])
return Model(inputs=inputs, outputs=outputs)
def test_merge_average():
i1 = layers.Input(shape=(4, 5))
i2 = layers.Input(shape=(4, 5))
o = layers.average([i1, i2])
assert o._keras_shape == (None, 4, 5)
model = models.Model([i1, i2], o)
x1 = np.random.random((2, 4, 5))
x2 = np.random.random((2, 4, 5))
out = model.predict([x1, x2])
assert out.shape == (2, 4, 5)
assert_allclose(out, 0.5 * (x1 + x2), atol=1e-4)
def ensemble_models(models, model_input):
# append the output of each model to a list
model_output = [model(model_input) for model in models]
# average the outputs of each model
avg_output = layers.average(model_output)
# build the ensemble model having same input as our models but the average
# of the output of our models as output
ensemble_model = Model(inputs=model_input,
outputs=avg_output,
name='ensemble')
# return the ensembled model
return ensemble_model
def test_merge_average():
i1 = layers.Input(shape=(4, 5))
i2 = layers.Input(shape=(4, 5))
o = layers.average([i1, i2])
assert o._keras_shape == (None, 4, 5)
model = models.Model([i1, i2], o)
x1 = np.random.random((2, 4, 5))
x2 = np.random.random((2, 4, 5))
out = model.predict([x1, x2])
assert out.shape == (2, 4, 5)
assert_allclose(out, 0.5 * (x1 + x2), atol=1e-4)
def eltwise(layer, layer_in, layerId):
out = {}
if (layer['params']['layer_type'] == 'Multiply'):
# This input reverse is to handle visualization
out[layerId] = multiply(layer_in[::-1])
elif (layer['params']['layer_type'] == 'Sum'):
out[layerId] = add(layer_in[::-1])
elif (layer['params']['layer_type'] == 'Average'):
out[layerId] = average(layer_in[::-1])
elif (layer['params']['layer_type'] == 'Dot'):
out[layerId] = dot(layer_in[::-1], -1)
else:
out[layerId] = maximum(layer_in[::-1])
return out