Python keras.layers.merge.concatenate() Examples

def loss_net(x_in, trux_x_in,width, height,style_image_path,content_weight,style_weight):
    # Append the initial input to the FastNet input to the VGG inputs
    x = concatenate([x_in, trux_x_in], axis=0)
    
    # Normalize the inputs via custom VGG Normalization layer
    x = VGGNormalize(name="vgg_normalize")(x)

    vgg = VGG16(include_top=False,input_tensor=x)

    vgg_output_dict = dict([(layer.name, layer.output) for layer in vgg.layers[-18:]])
    vgg_layers = dict([(layer.name, layer) for layer in vgg.layers[-18:]])

    if style_weight > 0:
        add_style_loss(vgg,style_image_path , vgg_layers, vgg_output_dict, width, height,style_weight)   

    if content_weight > 0:
        add_content_loss(vgg_layers,vgg_output_dict,content_weight)

    # Freeze all VGG layers
    for layer in vgg.layers[-19:]:
        layer.trainable = False

    return vgg 

def concat_images_with_tiled_vector(images, vector):
    """Combine a set of images with a vector, tiling the vector at each pixel in the images and concatenating on the channel axis.

    # Params

        images: list of images with the same dimensions
        vector: vector to tile on each image. If you have
            more than one vector, simply concatenate them
            all before calling this function.

    # Returns

    """
    with K.name_scope('concat_images_with_tiled_vector'):
        if not isinstance(images, list):
            images = [images]
        image_shape = K.int_shape(images[0])
        tiled_vector = tile_vector_as_image_channels(vector, image_shape)
        images.append(tiled_vector)
        combined = K.concatenate(images)

        return combined 

def block_inception_a(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 96, 1, 1)

    branch_1 = conv2d_bn(input, 64, 1, 1)
    branch_1 = conv2d_bn(branch_1, 96, 3, 3)

    branch_2 = conv2d_bn(input, 64, 1, 1)
    branch_2 = conv2d_bn(branch_2, 96, 3, 3)
    branch_2 = conv2d_bn(branch_2, 96, 3, 3)

    branch_3 = AveragePooling2D((3,3), strides=(1,1), padding='same')(input)
    branch_3 = conv2d_bn(branch_3, 96, 1, 1)

    x = concatenate([branch_0, branch_1, branch_2, branch_3], axis=channel_axis)
    return x 

def block_reduction_a(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 384, 3, 3, strides=(2,2), padding='valid')

    branch_1 = conv2d_bn(input, 192, 1, 1)
    branch_1 = conv2d_bn(branch_1, 224, 3, 3)
    branch_1 = conv2d_bn(branch_1, 256, 3, 3, strides=(2,2), padding='valid')

    branch_2 = MaxPooling2D((3,3), strides=(2,2), padding='valid')(input)

    x = concatenate([branch_0, branch_1, branch_2], axis=channel_axis)
    return x 

def block_inception_b(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 384, 1, 1)

    branch_1 = conv2d_bn(input, 192, 1, 1)
    branch_1 = conv2d_bn(branch_1, 224, 1, 7)
    branch_1 = conv2d_bn(branch_1, 256, 7, 1)

    branch_2 = conv2d_bn(input, 192, 1, 1)
    branch_2 = conv2d_bn(branch_2, 192, 7, 1)
    branch_2 = conv2d_bn(branch_2, 224, 1, 7)
    branch_2 = conv2d_bn(branch_2, 224, 7, 1)
    branch_2 = conv2d_bn(branch_2, 256, 1, 7)

    branch_3 = AveragePooling2D((3,3), strides=(1,1), padding='same')(input)
    branch_3 = conv2d_bn(branch_3, 128, 1, 1)

    x = concatenate([branch_0, branch_1, branch_2, branch_3], axis=channel_axis)
    return x 

def block_reduction_b(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 192, 1, 1)
    branch_0 = conv2d_bn(branch_0, 192, 3, 3, strides=(2, 2), padding='valid')

    branch_1 = conv2d_bn(input, 256, 1, 1)
    branch_1 = conv2d_bn(branch_1, 256, 1, 7)
    branch_1 = conv2d_bn(branch_1, 320, 7, 1)
    branch_1 = conv2d_bn(branch_1, 320, 3, 3, strides=(2,2), padding='valid')

    branch_2 = MaxPooling2D((3, 3), strides=(2, 2), padding='valid')(input)

    x = concatenate([branch_0, branch_1, branch_2], axis=channel_axis)
    return x 

def forward(self):
        model_input = Input(shape=(self.maxlen,), dtype='int32', name='token')
        x = Token_Embedding(model_input, self.nb_tokens, self.embedding_dim,
                            self.token_embeddings, True, self.maxlen,
                            self.embed_dropout_rate, name='token_embeddings')
        x = Activation('tanh')(x)

        # skip-connection from embedding to output eases gradient-flow and allows access to lower-level features
        # ordering of the way the merge is done is important for consistency with the pretrained model
        lstm_0_output = Bidirectional(
            LSTM(self.rnn_size, return_sequences=True), name="bi_lstm_0")(x)
        lstm_1_output = Bidirectional(
            LSTM(self.rnn_size, return_sequences=True), name="bi_lstm_1")(lstm_0_output)
        x = concatenate([lstm_1_output, lstm_0_output, x], name='concatenate')

        x = self.attention_layer(x)
        if self.return_attention:
            x, weights = x
        outputs = tc_output_logits(x, self.nb_classes, self.final_dropout_rate)
        if self.return_attention:
            outputs.append(weights)
            outputs = concatenate(outputs, axis=-1, name='outputs')

        self.model = Model(inputs=model_input,
                           outputs=outputs, name="Bi_LSTM_Attention") 

def forward(self):
        model_input = Input(shape=(self.maxlen,), dtype='int32', name='token')
        x = Token_Embedding(model_input, self.nb_tokens, self.embedding_dim,
                            self.token_embeddings, False, self.maxlen,
                            self.embed_dropout_rate, name='token_embeddings')
        cnn_combine = []
        for i in range(len(self.conv_kernel_size)):
            cnn = self.cnn_list[i](x)
            pool = self.pool_list[i](cnn)
            cnn_combine.append(pool)
        x = concatenate(cnn_combine, axis=-1)

        x = Flatten()(x)
        x = Dropout(self.final_dropout_rate)(x)
        x = self.fc(x)

        outputs = tc_output_logits(x, self.nb_classes, self.final_dropout_rate)

        self.model = Model(inputs=model_input,
                           outputs=outputs, name="TextCNN") 

def block_reduction_b(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 192, 1, 1)
    branch_0 = conv2d_bn(branch_0, 192, 3, 3, strides=(2, 2), padding='valid')

    branch_1 = conv2d_bn(input, 256, 1, 1)
    branch_1 = conv2d_bn(branch_1, 256, 1, 7)
    branch_1 = conv2d_bn(branch_1, 320, 7, 1)
    branch_1 = conv2d_bn(branch_1, 320, 3, 3, strides=(2,2), padding='valid')

    branch_2 = MaxPooling2D((3, 3), strides=(2, 2), padding='valid')(input)

    x = concatenate([branch_0, branch_1, branch_2], axis=channel_axis)
    return x 

def block_inception_b(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 384, 1, 1)

    branch_1 = conv2d_bn(input, 192, 1, 1)
    branch_1 = conv2d_bn(branch_1, 224, 1, 7)
    branch_1 = conv2d_bn(branch_1, 256, 7, 1)

    branch_2 = conv2d_bn(input, 192, 1, 1)
    branch_2 = conv2d_bn(branch_2, 192, 7, 1)
    branch_2 = conv2d_bn(branch_2, 224, 1, 7)
    branch_2 = conv2d_bn(branch_2, 224, 7, 1)
    branch_2 = conv2d_bn(branch_2, 256, 1, 7)

    branch_3 = AveragePooling2D((3,3), strides=(1,1), padding='same')(input)
    branch_3 = conv2d_bn(branch_3, 128, 1, 1)

    x = concatenate([branch_0, branch_1, branch_2, branch_3], axis=channel_axis)
    return x 

def block_inception_a(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 96, 1, 1)

    branch_1 = conv2d_bn(input, 64, 1, 1)
    branch_1 = conv2d_bn(branch_1, 96, 3, 3)

    branch_2 = conv2d_bn(input, 64, 1, 1)
    branch_2 = conv2d_bn(branch_2, 96, 3, 3)
    branch_2 = conv2d_bn(branch_2, 96, 3, 3)

    branch_3 = AveragePooling2D((3, 3), strides=(1, 1), padding='same')(input)
    branch_3 = conv2d_bn(branch_3, 96, 1, 1)

    x = concatenate([branch_0, branch_1, branch_2, branch_3], axis=channel_axis)
    return x 

def block_inception_b(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 384, 1, 1)

    branch_1 = conv2d_bn(input, 192, 1, 1)
    branch_1 = conv2d_bn(branch_1, 224, 1, 7)
    branch_1 = conv2d_bn(branch_1, 256, 7, 1)

    branch_2 = conv2d_bn(input, 192, 1, 1)
    branch_2 = conv2d_bn(branch_2, 192, 7, 1)
    branch_2 = conv2d_bn(branch_2, 224, 1, 7)
    branch_2 = conv2d_bn(branch_2, 224, 7, 1)
    branch_2 = conv2d_bn(branch_2, 256, 1, 7)

    branch_3 = AveragePooling2D((3, 3), strides=(1, 1), padding='same')(input)
    branch_3 = conv2d_bn(branch_3, 128, 1, 1)

    x = concatenate([branch_0, branch_1, branch_2, branch_3], axis=channel_axis)
    return x 

def yolo_body(inputs, num_anchors, num_classes):
    """Create YOLO_V2 model CNN body in Keras."""
    darknet = Model(inputs, darknet_body()(inputs))
    conv20 = compose(
        DarknetConv2D_BN_Leaky(1024, (3, 3)),
        DarknetConv2D_BN_Leaky(1024, (3, 3)))(darknet.output)

    conv13 = darknet.layers[43].output
    conv21 = DarknetConv2D_BN_Leaky(64, (1, 1))(conv13)
    # TODO: Allow Keras Lambda to use func arguments for output_shape?
    conv21_reshaped = Lambda(
        space_to_depth_x2,
        output_shape=space_to_depth_x2_output_shape,
        name='space_to_depth')(conv21)

    x = concatenate([conv21_reshaped, conv20])
    x = DarknetConv2D_BN_Leaky(1024, (3, 3))(x)
    x = DarknetConv2D(num_anchors * (num_classes + 5), (1, 1))(x)
    return Model(inputs, x) 

def block_reduction_b(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 192, 1, 1)
    branch_0 = conv2d_bn(branch_0, 192, 3, 3, strides=(2, 2), padding='valid')

    branch_1 = conv2d_bn(input, 256, 1, 1)
    branch_1 = conv2d_bn(branch_1, 256, 1, 7)
    branch_1 = conv2d_bn(branch_1, 320, 7, 1)
    branch_1 = conv2d_bn(branch_1, 320, 3, 3, strides=(2, 2), padding='valid')

    branch_2 = MaxPooling2D((3, 3), strides=(2, 2), padding='valid')(input)

    x = concatenate([branch_0, branch_1, branch_2], axis=channel_axis)
    return x 

def block_inception_c(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 256, 1, 1)

    branch_1 = conv2d_bn(input, 384, 1, 1)
    branch_10 = conv2d_bn(branch_1, 256, 1, 3)
    branch_11 = conv2d_bn(branch_1, 256, 3, 1)
    branch_1 = concatenate([branch_10, branch_11], axis=channel_axis)

    branch_2 = conv2d_bn(input, 384, 1, 1)
    branch_2 = conv2d_bn(branch_2, 448, 3, 1)
    branch_2 = conv2d_bn(branch_2, 512, 1, 3)
    branch_20 = conv2d_bn(branch_2, 256, 1, 3)
    branch_21 = conv2d_bn(branch_2, 256, 3, 1)
    branch_2 = concatenate([branch_20, branch_21], axis=channel_axis)

    branch_3 = AveragePooling2D((3, 3), strides=(1, 1), padding='same')(input)
    branch_3 = conv2d_bn(branch_3, 256, 1, 1)

    x = concatenate([branch_0, branch_1, branch_2, branch_3], axis=channel_axis)
    return x 

def block_reduction_a(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 384, 3, 3, strides=(2, 2), padding='valid')

    branch_1 = conv2d_bn(input, 192, 1, 1)
    branch_1 = conv2d_bn(branch_1, 224, 3, 3)
    branch_1 = conv2d_bn(branch_1, 256, 3, 3, strides=(2, 2), padding='valid')

    branch_2 = MaxPooling2D((3, 3), strides=(2, 2), padding='valid')(input)

    x = concatenate([branch_0, branch_1, branch_2], axis=channel_axis)
    return x 

def block_reduction_a(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 384, 3, 3, strides=(2,2), padding='valid')

    branch_1 = conv2d_bn(input, 192, 1, 1)
    branch_1 = conv2d_bn(branch_1, 224, 3, 3)
    branch_1 = conv2d_bn(branch_1, 256, 3, 3, strides=(2,2), padding='valid')

    branch_2 = MaxPooling2D((3,3), strides=(2,2), padding='valid')(input)

    x = concatenate([branch_0, branch_1, branch_2], axis=channel_axis)
    return x 

def block_inception_a(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 96, 1, 1)

    branch_1 = conv2d_bn(input, 64, 1, 1)
    branch_1 = conv2d_bn(branch_1, 96, 3, 3)

    branch_2 = conv2d_bn(input, 64, 1, 1)
    branch_2 = conv2d_bn(branch_2, 96, 3, 3)
    branch_2 = conv2d_bn(branch_2, 96, 3, 3)

    branch_3 = AveragePooling2D((3,3), strides=(1,1), padding='same')(input)
    branch_3 = conv2d_bn(branch_3, 96, 1, 1)

    x = concatenate([branch_0, branch_1, branch_2, branch_3], axis=channel_axis)
    return x 

def interaction(input_1, input_2):
    "Get the interaction then concatenate results"
    mult = Multiply()([input_1, input_2])
    add = Add()([input_1, input_2])
    sub = substract(input_1, input_2)
    #distance = el_distance(input_1, input_2)
    
    out_= Concatenate()([sub, mult, add,])
    return out_ 

def define_model(self, length, vocab_size):

        embedding_size = 100
        cnn_filter_size = 32

        inputs1 = Input(shape=(length,))
        embedding1 = Embedding(vocab_size, embedding_size)(inputs1)
        conv1 = Conv1D(filters=cnn_filter_size, kernel_size=4, activation='relu')(
            embedding1)
        drop1 = Dropout(0.5)(conv1)
        pool1 = MaxPooling1D(pool_size=2)(drop1)
        flat1 = Flatten()(pool1)

        inputs2 = Input(shape=(length,))
        embedding2 = Embedding(vocab_size, embedding_size)(inputs2)
        conv2 = Conv1D(filters=cnn_filter_size, kernel_size=6, activation='relu')(
            embedding2)
        drop2 = Dropout(0.5)(conv2)
        pool2 = MaxPooling1D(pool_size=2)(drop2)
        flat2 = Flatten()(pool2)

        inputs3 = Input(shape=(length,))
        embedding3 = Embedding(vocab_size, embedding_size)(inputs3)
        conv3 = Conv1D(filters=cnn_filter_size, kernel_size=8, activation='relu')(
            embedding3)
        drop3 = Dropout(0.5)(conv3)
        pool3 = MaxPooling1D(pool_size=2)(drop3)
        flat3 = Flatten()(pool3)

        merged = concatenate([flat1, flat2, flat3])
        # interpretation
        dense1 = Dense(10, activation='relu')(merged)

        outputs = Dense(units=len(self.labels), activation='softmax')(dense1)

        model = Model(inputs=[inputs1, inputs2, inputs3], outputs=outputs)
        # compile
        model.compile(loss='categorical_crossentropy', optimizer='adam', metrics=['accuracy'])
        # summarize
        print(model.summary())
        return model 

def _merge_inputs(self, inputs):
        return concatenate(inputs, axis=2) 

def configure(self, observation_space_shape, nb_actions):
        # Next, we build a simple model.
        # actor network
        actor = Sequential()
        actor.add(Flatten(input_shape=(1,) + observation_space_shape))
        actor.add(Dense(16))
        actor.add(Activation('relu'))
        actor.add(Dense(16))
        actor.add(Activation('relu'))
        actor.add(Dense(16))
        actor.add(Activation('relu'))
        actor.add(Dense(nb_actions))
        actor.add(Activation('linear'))
        print(actor.summary())

        # critic network
        action_input = Input(shape=(nb_actions,), name='action_input')
        observation_input = Input(shape=(1,) + observation_space_shape, name='observation_input')
        flattened_observation = Flatten()(observation_input)
        x = concatenate([action_input, flattened_observation])
        x = Dense(32)(x)
        x = Activation('relu')(x)
        x = Dense(32)(x)
        x = Activation('relu')(x)
        x = Dense(32)(x)
        x = Activation('relu')(x)
        x = Dense(1)(x)
        x = Activation('linear')(x)
        critic = Model(input=[action_input, observation_input], output=x)
        print(critic.summary())

        # Finally, we configure and compile our agent. You can use every built-in Keras optimizer and
        # even the metrics!
        memory = SequentialMemory(limit=100000, window_length=1)
        random_process = OrnsteinUhlenbeckProcess(size=nb_actions, theta=.15, mu=0., sigma=.3)
        self.agent = DDPGAgent(nb_actions=nb_actions, actor=actor, critic=critic, critic_action_input=action_input,
                          memory=memory, nb_steps_warmup_critic=100, nb_steps_warmup_actor=100,
                          random_process=random_process, gamma=.99, target_model_update=1e-3)
        self.agent.compile(Adam(lr=.001, clipnorm=1.), metrics=['mae']) 

def _build(self, models, layers=[]):
        for layer in layers:
            layer.name = '%s/%s' % (self.scope, layer.name)

        inputs, outputs = self._get_inputs_outputs(models)
        x = concatenate(outputs)
        for layer in layers:
            x = layer(x)

        model = km.Model(inputs, x, name=self.name)
        return model 

def block_inception_c(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 256, 1, 1)

    branch_1 = conv2d_bn(input, 384, 1, 1)
    branch_10 = conv2d_bn(branch_1, 256, 1, 3)
    branch_11 = conv2d_bn(branch_1, 256, 3, 1)
    branch_1 = concatenate([branch_10, branch_11], axis=channel_axis)


    branch_2 = conv2d_bn(input, 384, 1, 1)
    branch_2 = conv2d_bn(branch_2, 448, 3, 1)
    branch_2 = conv2d_bn(branch_2, 512, 1, 3)
    branch_20 = conv2d_bn(branch_2, 256, 1, 3)
    branch_21 = conv2d_bn(branch_2, 256, 3, 1)
    branch_2 = concatenate([branch_20, branch_21], axis=channel_axis)

    branch_3 = AveragePooling2D((3, 3), strides=(1, 1), padding='same')(input)
    branch_3 = conv2d_bn(branch_3, 256, 1, 1)

    x = concatenate([branch_0, branch_1, branch_2, branch_3], axis=channel_axis)
    return x 

def __dense_block(x, nb_layers, nb_filter, growth_rate, bottleneck=False, dropout_rate=None, weight_decay=1e-4,
                  grow_nb_filters=True, return_concat_list=False):
    ''' Build a dense_block where the output of each conv_block is fed to subsequent ones
    Args:
        x: keras tensor
        nb_layers: the number of layers of conv_block to append to the model.
        nb_filter: number of filters
        growth_rate: growth rate
        bottleneck: bottleneck block
        dropout_rate: dropout rate
        weight_decay: weight decay factor
        grow_nb_filters: flag to decide to allow number of filters to grow
        return_concat_list: return the list of feature maps along with the actual output
    Returns: keras tensor with nb_layers of conv_block appended
    '''
    concat_axis = 1 if K.image_data_format() == 'channels_first' else -1

    x_list = [x]

    for i in range(nb_layers):
        cb = __conv_block(x, growth_rate, bottleneck, dropout_rate, weight_decay)
        x_list.append(cb)

        x = concatenate([x, cb], axis=concat_axis)

        if grow_nb_filters:
            nb_filter += growth_rate

    if return_concat_list:
        return x, nb_filter, x_list
    else:
        return x, nb_filter 

def dense_model(patch_size, num_classes):
    merged_inputs = Input(shape=patch_size + (4,), name='merged_inputs')
    flair = Reshape(patch_size + (1,))(
        Lambda(
            lambda l: l[:, :, :, :, 0],
            output_shape=patch_size + (1,))(merged_inputs),
    )
    t2 = Reshape(patch_size + (1,))(
        Lambda(lambda l: l[:, :, :, :, 1], output_shape=patch_size + (1,))(merged_inputs)
    )
    t1 = Lambda(lambda l: l[:, :, :, :, 2:], output_shape=patch_size + (2,))(merged_inputs)

    flair = dense_net(flair)
    t2 = dense_net(t2)
    t1 = dense_net(t1)

    t2 = concatenate([flair, t2])

    t1 = concatenate([t2, t1])

    tumor = Conv3D(2, kernel_size=1, strides=1, name='tumor')(flair)
    core = Conv3D(3, kernel_size=1, strides=1, name='core')(t2)
    enhancing = Conv3D(num_classes, kernel_size=1, strides=1, name='enhancing')(t1)
    net = Model(inputs=merged_inputs, outputs=[tumor, core, enhancing])

    return net 

def nn_architecture_seg_3d(input_shape, pool_size=(2, 2, 2), n_labels=1, initial_learning_rate=0.00001,
                        depth=3, n_base_filters=16, metrics=dice_coefficient, batch_normalization=True):
    inputs = Input(input_shape)
    current_layer = inputs
    levels = list()

    for layer_depth in range(depth):
        layer1 = create_convolution_block(input_layer=current_layer, n_filters=n_base_filters * (2**layer_depth),
                                          batch_normalization=batch_normalization)
        layer2 = create_convolution_block(input_layer=layer1, n_filters=n_base_filters * (2**layer_depth) * 2,
                                          batch_normalization=batch_normalization)
        if layer_depth < depth - 1:
            current_layer = MaxPooling3D(pool_size=pool_size)(layer2)
            levels.append([layer1, layer2, current_layer])
        else:
            current_layer = layer2
            levels.append([layer1, layer2])

    for layer_depth in range(depth - 2, -1, -1):
        up_convolution = UpSampling3D(size=pool_size)
        concat = concatenate([up_convolution, levels[layer_depth][1]], axis=1)
        current_layer = create_convolution_block(n_filters=levels[layer_depth][1]._keras_shape[1],
                                                 input_layer=concat, batch_normalization=batch_normalization)
        current_layer = create_convolution_block(n_filters=levels[layer_depth][1]._keras_shape[1],
                                                 input_layer=current_layer,
                                                 batch_normalization=batch_normalization)

    final_convolution = Conv3D(n_labels, (1, 1, 1))(current_layer)
    act = Activation('sigmoid')(final_convolution)
    model = Model(inputs=inputs, outputs=act)

    if not isinstance(metrics, list):
        metrics = [metrics]

    model.compile(optimizer=Adam(lr=initial_learning_rate), loss=dice_coefficient_loss, metrics=metrics)
    return model 

def ab_ag_seq_model(max_ag_len, max_cdr_len):
    input_ag = Input(shape=(max_ag_len, NUM_FEATURES))
    ag_seq = Masking()(input_ag)

    enc_ag = Bidirectional(LSTM(128, dropout=0.1, recurrent_dropout=0.1),
                           merge_mode='concat')(ag_seq)

    input_ab = Input(shape=(max_cdr_len, NUM_FEATURES))
    label_mask = Input(shape=(max_cdr_len,))

    seq = Masking()(input_ab)

    loc_fts = MaskedConvolution1D(64, 5, padding='same', activation='elu')(seq)

    glb_fts = Bidirectional(LSTM(256, dropout=0.15, recurrent_dropout=0.2,
                                 return_sequences=True),
                            merge_mode='concat')(loc_fts)

    enc_ag_rep = RepeatVector(max_cdr_len)(enc_ag)
    ab_ag_repr = concatenate([glb_fts, enc_ag_rep])
    ab_ag_repr = MaskingByLambda(mask_by_input(label_mask))(ab_ag_repr)
    ab_ag_repr = Dropout(0.3)(ab_ag_repr)

    aa_probs = TimeDistributed(Dense(1, activation='sigmoid'))(ab_ag_repr)
    model = Model(inputs=[input_ag, input_ab, label_mask], outputs=aa_probs)
    model.compile(loss='binary_crossentropy',
                  optimizer='adam',
                  metrics=['binary_accuracy', false_pos, false_neg],
                  sample_weight_mode="temporal")
    return model 

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
        path_down_cropped = Cropping2D(cropping=((crop_x_0,crop_x_1),(crop_y_0,crop_y_1)))(path_down)
    connected = concatenate([path_orig,path_down_cropped],axis=0)
    return connected 

def block_inception_c(input):
    if K.image_data_format() == 'channels_first':
        channel_axis = 1
    else:
        channel_axis = -1

    branch_0 = conv2d_bn(input, 256, 1, 1)

    branch_1 = conv2d_bn(input, 384, 1, 1)
    branch_10 = conv2d_bn(branch_1, 256, 1, 3)
    branch_11 = conv2d_bn(branch_1, 256, 3, 1)
    branch_1 = concatenate([branch_10, branch_11], axis=channel_axis)


    branch_2 = conv2d_bn(input, 384, 1, 1)
    branch_2 = conv2d_bn(branch_2, 448, 3, 1)
    branch_2 = conv2d_bn(branch_2, 512, 1, 3)
    branch_20 = conv2d_bn(branch_2, 256, 1, 3)
    branch_21 = conv2d_bn(branch_2, 256, 3, 1)
    branch_2 = concatenate([branch_20, branch_21], axis=channel_axis)

    branch_3 = AveragePooling2D((3, 3), strides=(1, 1), padding='same')(input)
    branch_3 = conv2d_bn(branch_3, 256, 1, 1)

    x = concatenate([branch_0, branch_1, branch_2, branch_3], axis=channel_axis)
    return x