def run_dnn(X_train, X_val, y_train, y_val, df_test, n_orgs):
# For use with organization embeddings later:
X_train_array = [X_train['orguuid'], (X_train.drop('orguuid', axis=1))]
X_val_array = [X_val['orguuid'], (X_val.drop('orguuid', axis=1))]
import tensorflow as tf
from tensorflow import keras
# PReLU with constant
from keras.initializers import Constant
# embedding with L2 regularization
from keras.regularizers import l2
# # Gelu
# from keras.utils.generic_utils import get_custom_objects
# def gelu(x):
# return 0.5 * x * (1 + tf.tanh(tf.sqrt(2 / np.pi) * (x + 0.044715 * tf.pow(x, 3))))
# get_custom_objects().update({'gelu': keras.layers.Activation(gelu)})
n_latent_factors_orgs = 30
org_input = keras.layers.Input(shape=[1])
org_embedding = keras.layers.Embedding(
n_orgs + 1,
n_latent_factors_orgs,
embeddings_initializer='he_normal',
embeddings_regularizer=l2(1e-6))(org_input)
org_vec = keras.layers.Flatten()(org_embedding)
org_vec = keras.layers.Dropout(0.2)(org_vec)
other_input = keras.layers.Input(shape=(3, ))
concat = keras.layers.Concatenate()([org_vec, other_input])
dense_1 = keras.layers.Dense(32, name='FullyConnected-1')(concat)
act_1 = keras.layers.PReLU(alpha_initializer=Constant(value=0.25))(dense_1)
dense_2 = keras.layers.Dense(16, name='FullyConnected-2')(act_1)
act_2 = keras.layers.PReLU(alpha_initializer=Constant(value=0.25))(dense_2)
dense_3 = keras.layers.Dense(16, name='FullyConnected-3')(act_2)
act_3 = keras.layers.PReLU(alpha_initializer=Constant(value=0.25))(dense_3)
dense_4 = keras.layers.Dense(16, name='FullyConnected-4')(act_3)
act_4 = keras.layers.PReLU(alpha_initializer=Constant(value=0.25))(dense_4)
output = keras.layers.Dense(1, activation=tf.nn.sigmoid,
name='Output')(act_4)
model = keras.Model([org_input, other_input], output)
model.compile(optimizer='adam',
loss='binary_crossentropy',
metrics=['accuracy'])
history = model.fit(X_train_array,
y_train,
epochs=20,
batch_size=1,
verbose=1,
validation_data=(X_val_array, y_val))
val_loss, val_acc = model.evaluate(X_val_array, y_val)
print('Validation accuracy:', val_acc)
rank_results = test_results(df_test, alg="dnn", model=model)
return rank_results
EPOCHS = 100
modelfile = os.path.basename(__file__).split(".")[0]
loss = "squared_hinge"
optimizer = "nadam"
sequence = Input(shape=(totallen, ))
seqsa = Lambda(lambda x: x[:, 0:5])(sequence)
seqsb = Lambda(lambda x: x[:, 5:])(sequence)
seqsc = Lambda(lambda x: x[:, 5:])(sequence)
network_emb = sparse.load_npz("model/weibo_wembedding.npz").todense()
embedded = Embedding(len(words) + 1,
word_size,
embeddings_initializer=Constant(network_emb),
input_length=seqlen,
mask_zero=False,
trainable=True)(seqsb)
networkcore_emb = sparse.load_npz("model/weibo_coreembedding.npz").todense()
embeddedc = Embedding(len(words) + 1,
actors_size,
embeddings_initializer=Constant(networkcore_emb),
input_length=seqlen,
mask_zero=False,
trainable=True)(seqsc)
#
# concat = concatenate([embedded, embeddedc])
dropout = Dropout(rate=Dropoutrate)(seqsa)
def create_net(self):
e_input = Input(shape=(self.input_shape, self.input_shape, 1))
x = Conv2D(self.filters, (3, 3), padding='same')(e_input)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
shape_before_flatten = K.int_shape(x)[1:]
x = Flatten()(x)
self.encoder_mu = Dense(self.latent_dim)(x)
self.encoder_log_variance = Dense(self.latent_dim)(x)
e_output = Lambda(self.sampling)([self.encoder_mu, self.encoder_log_variance])
# Keep the encoder part
self.e = Model(e_input, e_output)
# And now the decoder part
d_input = Input(shape=[self.latent_dim])
x = Dense(np.prod(shape_before_flatten))(d_input)
x = Reshape(target_shape=shape_before_flatten)(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = UpSampling2D((2, 2))(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = UpSampling2D((2, 2))(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = UpSampling2D((2, 2))(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = UpSampling2D((2, 2))(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = UpSampling2D((2, 2))(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = BatchNormalization()(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = UpSampling2D((2, 2))(x)
d_output = Conv2D(1, (3, 3), activation='sigmoid', padding='same')(x)
self.d = Model(d_input, d_output)
# Finalize the VAE
vae_input = Input(shape=(self.input_shape, self.input_shape, 1))
vae_enc_out = self.e(vae_input)
vae_dec_out = self.d(vae_enc_out)
self.vae = Model(vae_input, vae_dec_out)
return
def build(self, input_shape):
self.temp = self.add_weight(name='temp', shape=[], initializer=Constant(self.start_temp), trainable=False)
self.logits = self.add_weight(name='logits', shape=[self.output_dim, input_shape[1]],
initializer=glorot_normal(), trainable=True)
super(ConcreteSelect, self).build(input_shape)
from keras.models import Sequential
from keras.layers import Dense, Flatten
from keras.callbacks import TensorBoard, EarlyStopping
from keras.optimizers import SGD
from keras.initializers import Constant
import keras.backend as K
import pickle
import time
from copy import deepcopy
from shutil import copy
from random import randint
model = Sequential()
model.add(Flatten(input_shape=(28, 28, 3)))
model.add(Dense(512, kernel_initializer='glorot_normal',
bias_initializer=Constant(0.1), activation='relu'))
model.add(Dense(512, kernel_initializer='glorot_normal',
bias_initializer=Constant(0.1), activation='relu'))
model.add(Dense(512, kernel_initializer='glorot_normal',
bias_initializer=Constant(0.1), activation='relu'))
model.add(Dense(10, kernel_initializer='glorot_normal',
bias_initializer=Constant(0.1), activation='softmax'))
early_stop = EarlyStopping(monitor='loss', min_delta=0.0001, patience=5)
now = str(time.time())
tb_callback = TensorBoard(log_dir='../Tensorboard/mlp3/' + now)
img = tf.placeholder(tf.float32, [28, 28, 3])
norm_image = tf.image.per_image_standardization(img)
opt = SGD(lr=0.01, momentum=0.9)
def build(self, dim_input):
self.bin_map = self.add_weight(name = 'bin_map', shape = [self.dim_output, dim_input[1]], initializer = glorot_normal(), trainable = 1)
self.temp = self.add_weight(name = 'temp', shape = [], initializer = Constant(self.temp_initial), trainable = 0)
super(CoRAESelect, self).build(dim_input)
def build(self, input_shape):
self.p = self.add_weight(shape=(),
name='p',
initializer=Constant(value=self.init_p),
trainable=False)
super(HB, self).build(input_shape)
print('output to file.')
sX = pickle.dumps(X)
fx.write(sX)
sy = pickle.dumps(y)
fy.write(sy)
if MODE==2:
loss = "squared_hinge"
optimizer = "nadam"
metric= "accuracy"
sequence = Input(shape=(maxlen,nFeatures,))
seqsa, seqsb, seqsc, seqsd, seqse = Lambda(lambda x: [x[:,:,0],x[:,:,1],x[:,:,2],x[:,:,3],x[:,:,4]])(sequence)
zhwiki_emb = numpy.load("msr_dic/zhwiki_embedding.npy")
embeddeda = Embedding(len(chars) + 1, word_size,embeddings_initializer=Constant(zhwiki_emb), input_length=maxlen, mask_zero=False)(seqsa)
embeddedb = Embedding(len(chars) + 1, word_size,embeddings_initializer=Constant(zhwiki_emb), input_length=maxlen, mask_zero=False)(seqsb)
embeddedc = Embedding(len(chars) + 1, word_size,embeddings_initializer=Constant(zhwiki_emb), input_length=maxlen, mask_zero=False)(seqsc)
maximuma = Maximum()([embeddeda, embeddedb])
maximumb = Maximum()([embeddedc, embeddedb])
# zhwiki_biemb = numpy.load("model/zhwiki_biembedding.npy")
zhwiki_biemb = sparse.load_npz("model/zhwiki_biembedding.npz").todense()
embeddedd = Embedding(len(bigrams) + 1, word_size, input_length=maxlen,embeddings_initializer=Constant(zhwiki_biemb),
mask_zero=False)(seqsd)
embeddede = Embedding(len(bigrams) + 1, word_size, input_length=maxlen,embeddings_initializer=Constant(zhwiki_biemb),
mask_zero=False)(seqse)
concat = concatenate([embeddeda, maximuma, maximumb, embeddedd, embeddede])
char = TimeDistributed(Flatten())(maxpool_out)
char = Dropout(0.5)(char)
output = concatenate([words, casing,char])
output = Bidirectional(LSTM(200, return_sequences=True, dropout=0.50, recurrent_dropout=0.25))(output)
output = TimeDistributed(Dense(len(label2Idx), activation='softmax'))(output)
model = Model(inputs=[words_input, casing_input,character_input], outputs=[output])
model.compile(loss='sparse_categorical_crossentropy', optimizer='nadam')
model.summary()
'''
sents_input = Input(shape=(5, Maxwordsent), name='sents_input')
#words = TimeDistributed(Embedding(input_dim=wordEmbeddings.shape[0], output_dim=wordEmbeddings.shape[1], weights=[wordEmbeddings], trainable=False))(sents_input)#shape[0]is the vacoabilry size, shape[1] is output size #embedding_1 (Embedding) (None, None, 100) the first None is the batch, the second None is the number of word in a sentence
words = TimeDistributed(
Embedding(input_dim=wordEmbeddings.shape[0],
output_dim=wordEmbeddings.shape[1],
embeddings_initializer=Constant(wordEmbeddings),
trainable=False)
)(
sents_input
) #shape[0]is the vacoabilry size, shape[1] is output size #embedding_1 (Embedding) (None, None, 100) the first None is the batch, the second None is the number of word in a sentence
conv1d_out = TimeDistributed(
Conv1D(kernel_size=3,
filters=Maxwordsent,
padding='same',
activation='tanh',
strides=1)
)(
words
) #(None, None, 52, 30) filters is the kernel number, it decide output how many vecters
maxpool_out = TimeDistributed(MaxPooling1D(Maxwordsent))(
def model_fourth(X,
drop_ra=0.,
l1_reg=0.,
bias=0.1,
g_noise=0.,
nodes=[32, 16, 5, 16, 32]):
#a list of layers, each comprised of a dictionary of layer elements
input_dim = X.shape[1]
layers = []
layers.append({
'layer':
Dense(nodes[0], input_dim=input_dim, kernel_regularizer=l1(0.)),
'advanced_activation':
PReLU(),
'normalisation':
BatchNormalization()
})
layers.append({
'layer':
Dense(nodes[1], bias_initializer=Constant(value=bias)),
'advanced_activation':
PReLU(),
'dropout_rate':
drop_ra,
'normalisation':
BatchNormalization()
})
layers.append({
'layer':
Dense(nodes[2], bias_initializer=Constant(value=bias)),
'advanced_activation':
PReLU()
})
layers.append({
'layer':
Dense(nodes[3], bias_initializer=Constant(value=bias)),
'advanced_activation':
PReLU(),
'dropout_rate':
drop_ra
})
layers.append({
'layer':
Dense(nodes[4], bias_initializer=Constant(value=bias)),
'advanced_activation':
PReLU(),
'dropout_rate':
drop_ra
})
layers.append({
'layer': Dense(input_dim, kernel_regularizer=l1(l1_reg)),
'activation': 'linear'
})
return layers
def model_tenth(X,
drop_ra=0.,
l1_reg=0.,
bias=0.,
g_noise=0.,
ker_init=None,
nodes=[32, 16, 5, 16, 32]):
#a list of layers, each comprised of a dictionary of layer elements
#K.clear_session()
input_dim = X.shape[1]
layers = []
layers.append({
'layer':
Dense(nodes[0],
input_dim=input_dim,
kernel_initializer=ker_init,
bias_initializer=Constant(value=bias)),
'advanced_activation':
PReLU(),
'noise':
GaussianNoise(g_noise)
})
layers.append({
'layer':
Dense(nodes[1],
kernel_initializer=ker_init,
bias_initializer=Constant(value=bias)),
'advanced_activation':
PReLU(),
'noise':
GaussianNoise(g_noise),
'dropout_rate':
drop_ra,
'normalisation':
BatchNormalization()
})
layers.append({'layer': MaxoutDense(nodes[2], init=ker_init)})
layers.append({
'layer':
Dense(nodes[3],
bias_initializer=Constant(value=bias),
kernel_initializer=ker_init),
'advanced_activation':
PReLU(),
'dropout_rate':
drop_ra
})
layers.append({
'layer':
Dense(nodes[4],
bias_initializer=Constant(value=bias),
kernel_initializer=ker_init),
'advanced_activation':
PReLU(),
'dropout_rate':
drop_ra
})
layers.append({
'layer':
Dense(input_dim,
kernel_regularizer=l1(l1_reg),
kernel_initializer=ker_init)
})
return layers
def build_model(embeddings):
# input representation features
words_input = Input(shape=[SEQUENCE_LEN], dtype='int32')
pos1_input = Input(shape=[SEQUENCE_LEN], dtype='int32')
pos2_input = Input(shape=[SEQUENCE_LEN], dtype='int32')
segs_input = Input(shape=[SEQUENCE_LEN, 3], dtype='float32')
# lexical features
e1_input = Input(shape=[ENTITY_LEN], dtype='int32') # L1
e2_input = Input(shape=[ENTITY_LEN], dtype='int32') # L2
e1context_input = Input(shape=[2], dtype='int32') # L3
e2context_input = Input(shape=[2], dtype='int32') # L4
# word embedding
we = embeddings["word_embeddings"]
words_embed = Embedding(we.shape[0], we.shape[1], weights=[we])
words = words_embed(words_input)
e1 = words_embed(e1_input)
e2 = words_embed(e2_input)
e1context = words_embed(e1context_input)
e2context = words_embed(e2context_input)
# lexical feature
e1_flat = Flatten()(e1)
e2_flat = Flatten()(e2)
e1context_flat = Flatten()(e1context)
e2context_flat = Flatten()(e2context)
# position embedding
pe1 = embeddings["position_embeddings_1"]
pos1 = Embedding(pe1.shape[0], pe1.shape[1], weights=[pe1])(pos1_input)
pe2 = embeddings["position_embeddings_2"]
pos2 = Embedding(pe2.shape[0], pe2.shape[1], weights=[pe2])(pos2_input)
# input representation
input_repre = Concatenate()([words, pos1, pos2])
input_repre = Dropout(DROPOUT)(input_repre)
# input attention
e1_repeat = RepeatVector(SEQUENCE_LEN)(e1_flat)
e2_repeat = RepeatVector(SEQUENCE_LEN)(e2_flat)
concat = Concatenate()([words, e1_repeat, e2_repeat])
alpha = Dense(1, activation="softmax")(concat)
alpha = Reshape([SEQUENCE_LEN])(alpha)
alpha = RepeatVector(WORD_REPRE_SIZE)(alpha)
alpha = Permute([2, 1])(alpha)
input_repre = Multiply()([input_repre, alpha])
# word-level convolution
input_conved = Conv1D(filters=NB_FILTERS_WORD,
kernel_size=WINDOW_SIZE_WORD,
padding="same",
activation="relu",
kernel_initializer=TruncatedNormal(stddev=0.1),
bias_initializer=Constant(0.1))(input_repre)
input_pooled = PiecewiseMaxPool()([input_conved, segs_input])
# fully connected
outputs = [input_pooled, e1_flat, e2_flat, e1context_flat, e2context_flat]
output = Concatenate()(outputs)
output = Dropout(DROPOUT)(output)
output = Dense(
units=NB_RELATIONS,
activation="softmax",
kernel_initializer=TruncatedNormal(stddev=0.1),
bias_initializer=Constant(0.1),
kernel_regularizer='l2',
bias_regularizer='l2',
)(output)
model = Model(inputs=[
words_input, pos1_input, pos2_input, e1_input, e2_input,
e1context_input, e2context_input, segs_input
],
outputs=[output])
model.compile(loss="sparse_categorical_crossentropy",
optimizer='sgd',
metrics=['accuracy'])
# model.summary()
return model
from keras.layers import Flatten
from keras.layers import LSTM
from keras.initializers import Constant
from keras.layers.wrappers import Bidirectional
from pickle import dump, load
import json
from keras.preprocessing.sequence import pad_sequences
import numpy as np
from underthesea import word_tokenize
embedding_matrix = load(open(r"app\Controllers\embedding_matrix.pkl", "rb"))
model = Sequential()
model.add(Embedding(4616, 300, embeddings_initializer=Constant(embedding_matrix),
input_length=80))
model.add(Bidirectional(LSTM(64, dropout = 0.2, recurrent_dropout = 0.2)))
model.add(Flatten())
model.add(Dense(5000, activation='relu'))
model.add(Dense(100, activation='relu'))
model.add(Dense(3, activation='softmax'))
model.compile(loss = 'categorical_crossentropy', optimizer='adam', metrics=['accuracy'])
model.load_weights('app\Controllers\model_linhKien.h5')
file = open(r'app\Controllers\list_CORPUS.txt', encoding="utf8")
list_CORPUS = file.read().split('\n')
file.close()
def run_lstm(X_train, X_val, y_train, y_val, df_test, org_features,
proj_features):
import tensorflow as tf
from tensorflow import keras
# PReLU with constant
from keras.initializers import Constant
#Embedding with L2 regularization
from keras.regularizers import l2
# LSTM_a
org_input = keras.layers.Input(shape=(None, len(org_features)))
lstm_org_1 = keras.layers.LSTM(32, name='Left-LSTM')(org_input)
org_vec = keras.layers.Dropout(0.2, name='Left-Dropout')(lstm_org_1)
org_dense_1 = keras.layers.Dense(32, name='Left-FullyConnected-1')(org_vec)
org_act_1 = keras.layers.PReLU(alpha_initializer=Constant(
value=0.25))(org_dense_1)
org_dense_2 = keras.layers.Dense(16,
name='Left-FullyConnected-2')(org_act_1)
org_act_2 = keras.layers.PReLU(alpha_initializer=Constant(
value=0.25))(org_dense_2)
org_fin = keras.layers.Flatten()(org_act_2)
# LSTM_b
proj_input = keras.layers.Input(shape=(None, len(proj_features)))
lstm_proj_1 = keras.layers.Bidirectional(keras.layers.LSTM(
32, name='Right-LSTM'),
merge_mode='sum')(proj_input)
proj_vec = keras.layers.Dropout(0.2, name='Right-Dropout')(lstm_proj_1)
proj_dense_1 = keras.layers.Dense(32,
name='Right-FullyConnected-1')(proj_vec)
proj_act_1 = keras.layers.PReLU(alpha_initializer=Constant(
value=0.25))(proj_dense_1)
proj_dense_2 = keras.layers.Dense(
16, name='Right-FullyConnected-2')(proj_act_1)
proj_act_2 = keras.layers.PReLU(alpha_initializer=Constant(
value=0.25))(proj_dense_2)
proj_fin = keras.layers.Flatten()(proj_act_2)
output = ManDist(name='Combined-Similarity')([org_vec, proj_vec])
model = keras.Model([org_input, proj_input], output)
model.compile(optimizer='adam',
loss='binary_crossentropy',
metrics=['accuracy'])
history = model.fit(X_train,
y_train,
epochs=12,
batch_size=1,
verbose=1,
validation_data=(X_val, y_val))
val_loss, val_acc = model.evaluate(X_val, y_val)
print('Validation accuracy:', val_acc)
rank_results = test_results(df_test,
alg="lstm",
model=model,
org_features=org_features,
proj_features=proj_features)
return rank_results
def build(self, input_shape=None):
self.log_vars = []
for i in range(2):
self.log_vars += [
self.add_weight(name="log_var" + str(i), shape=(1,), initializer=Constant(0.), trainable=False)]
super(MultiLossLayer, self).build(input_shape)
return K.square((K.squeeze(K.batch_dot(y_true, y_pred, axes=1),
axis=-1) / K.sum(y_true, axis=-1)) - K.max(y_true, axis=-1))
# Neural Network Model
if 'model_pong.h5' in os.listdir('.'):
model = load_model('model_pong.h5')
print "\nLoaded model\n"
else:
model = Sequential()
model.add(Conv2D(32, input_shape=(4, 84, 84), kernel_size=8, data_format=\
'channels_first', activation='relu'))
model.add(Conv2D(64, kernel_size=4, activation='relu'))
model.add(Conv2D(64, kernel_size=2, activation='relu'))
model.add(Flatten())
model.add(Dense(128, kernel_initializer=glorot_normal(), bias_initializer=\
Constant(0.1), activation='relu'))
model.add(Dense(6, kernel_initializer=glorot_normal(), bias_initializer=\
Constant(0.001)))
opt = RMSprop()
model.compile(loss='mse', optimizer=opt)
print "\nCreated model\n"
tb_callback = TensorBoard(log_dir='/home/rharish/Programs/Python/RL'\
'/Tensorboard/' + str(time.time()))
pong_experience = deque()
pong_policy_epsilon = 0.6
pong_ep_num = 0
def saver():
#!/usr/bin/env python
from __future__ import print_function
from builtins import input
from keras.models import Sequential
from keras.layers import Dense, Conv2D, MaxPooling2D, Flatten, Dropout
from keras.callbacks import EarlyStopping
from keras.initializers import glorot_normal, Constant
from get_data import get_data
model = Sequential()
model.add(Conv2D(32, 5, strides=5, input_shape=(50, 50, 1),
activation='relu', padding='same',
kernel_initializer=glorot_normal(),
bias_initializer=Constant(0.1)))
model.add(MaxPooling2D((2, 2), padding='same'))
model.add(Dropout(0.25))
model.add(Conv2D(64, 3, strides=3, activation='relu', padding='same',
kernel_initializer=glorot_normal(),
bias_initializer=Constant(0.1)))
model.add(MaxPooling2D((2, 2), padding='same'))
model.add(Dropout(0.25))
model.add(Flatten())
model.add(Dense(100, activation='relu', kernel_initializer=glorot_normal(),
bias_initializer=Constant(0.1)))
model.add(Dropout(0.5))
model.add(Dense(1, activation='sigmoid', kernel_initializer=glorot_normal(),
bias_initializer=Constant(0.1)))
early_stop = EarlyStopping(monitor='loss', min_delta=0.025, patience=5)
model.compile(loss='binary_crossentropy', optimizer='adam',
def build_model_FCN_model_api(batch_size,
optimizer,
patch_size=(128, 128),
base_weight_decay=0.0005,
output_ROI_mask=True):
print('Using build_model_FCN_model_api')
# define the shared model:
net_name = 'Multi-view_FCN'
scale_number = 3
##################### input ###############################################
input_shape0 = (batch_size, patch_size[0], patch_size[1], 1)
input_shape1 = (batch_size, patch_size[0] / 2, patch_size[1] / 2, 1)
input_shape2 = (batch_size, patch_size[0] / 4, patch_size[1] / 4, 1)
input_shape3 = (1, patch_size[0] / 4, patch_size[1] / 4, 1)
input_patches1_s0 = Input(batch_shape=input_shape0, name='patches1_s0')
input_patches1_s1 = Input(batch_shape=input_shape1, name='patches1_s1')
input_patches1_s2 = Input(batch_shape=input_shape2, name='patches1_s2')
input_patches2_s0 = Input(batch_shape=input_shape0, name='patches2_s0')
input_patches2_s1 = Input(batch_shape=input_shape1, name='patches2_s1')
input_patches2_s2 = Input(batch_shape=input_shape2, name='patches2_s2')
input_patches3_s0 = Input(batch_shape=input_shape0, name='patches3_s0')
input_patches3_s1 = Input(batch_shape=input_shape1, name='patches3_s1')
input_patches3_s2 = Input(batch_shape=input_shape2, name='patches3_s2')
input_patches4_s0 = Input(batch_shape=input_shape0, name='patches4_s0')
input_patches4_s1 = Input(batch_shape=input_shape1, name='patches4_s1')
input_patches4_s2 = Input(batch_shape=input_shape2, name='patches4_s2')
input_depth_maps_v1 = Input(batch_shape=input_shape3,
name='depth_ratio_v1')
input_depth_maps_v2 = Input(batch_shape=input_shape3,
name='depth_ratio_v2')
input_depth_maps_v3 = Input(batch_shape=input_shape3,
name='depth_ratio_v3')
input_depth_maps_v4 = Input(batch_shape=input_shape3,
name='depth_ratio_v4')
if output_ROI_mask:
# the output density patch/map is down-sampled by a factor of 4
output_masks = Input(batch_shape=(batch_size, patch_size[0],
patch_size[1], 1),
name='output_masks')
train_flag = False
####################### view 1 #############################################
# image pyramids:
x1_s0_output = feature_extraction_view1(base_weight_decay,
input_patches1_s0, train_flag)
x1_s1_output = feature_extraction_view1(base_weight_decay,
input_patches1_s1, train_flag)
x1_s2_output = feature_extraction_view1(base_weight_decay,
input_patches1_s2, train_flag)
# view 1 decoder
# x1_7 = view1_decoder(base_weight_decay, x1_s0_output)
# conv block 5
x1_5 = Conv2D(data_format='channels_last',
trainable=True,
filters=64,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_5')(x1_s0_output)
x1_5 = Activation('relu', name='conv_block_5_act')(x1_5)
# conv block 6
x1_6 = Conv2D(data_format='channels_last',
trainable=True,
filters=32,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_6')(x1_5)
x1_6 = Activation('relu', name='conv_block_6_act')(x1_6)
# conv block 7
x1_7 = Conv2D(data_format='channels_last',
trainable=True,
filters=1,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_7')(x1_6)
x1_7 = Activation('relu', name='conv_block_7_act')(x1_7)
####################### view 2 #############################################
# image pyramids:
x2_s0_output = feature_extraction_view2(base_weight_decay,
input_patches2_s0, train_flag)
x2_s1_output = feature_extraction_view2(base_weight_decay,
input_patches2_s1, train_flag)
x2_s2_output = feature_extraction_view2(base_weight_decay,
input_patches2_s2, train_flag)
# view 2 decoder
# x2_7 = view2_decoder(base_weight_decay, x2_s0_output)
# dmap
# conv block 5
x2_5 = Conv2D(data_format='channels_last',
trainable=True,
filters=64,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_5_2')(x2_s0_output)
x2_5 = Activation('relu', name='conv_block_5_2_act')(x2_5)
# conv block 6
x2_6 = Conv2D(data_format='channels_last',
trainable=True,
filters=32,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_6_2')(x2_5)
x2_6 = Activation('relu', name='conv_block_6_2_act')(x2_6)
# conv block 7
x2_7 = Conv2D(data_format='channels_last',
trainable=True,
filters=1,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_7_2')(x2_6)
x2_7 = Activation('relu', name='conv_block_7_2_act')(x2_7)
####################### view 3 #############################################
# image pyramids:
x3_s0_output = feature_extraction_view3(base_weight_decay,
input_patches3_s0, train_flag)
x3_s1_output = feature_extraction_view3(base_weight_decay,
input_patches3_s1, train_flag)
x3_s2_output = feature_extraction_view3(base_weight_decay,
input_patches3_s2, train_flag)
# view 3 decoder
# x3_7 = view3_decoder(base_weight_decay, x3_s0_output)
# conv block 5
x3_5 = Conv2D(data_format='channels_last',
trainable=True,
filters=64,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_5_3')(x3_s0_output)
x3_5 = Activation('relu', name='conv_block_5_3_act')(x3_5)
# conv block 6
x3_6 = Conv2D(data_format='channels_last',
trainable=True,
filters=32,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_6_3')(x3_5)
x3_6 = Activation('relu', name='conv_block_6_3_act')(x3_6)
# conv block 7
x3_7 = Conv2D(data_format='channels_last',
trainable=True,
filters=1,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_7_3')(x3_6)
x3_7 = Activation('relu', name='conv_block_7_3_act')(x3_7)
####################### view 4 #############################################
# image pyramids:
x4_s0_output = feature_extraction_view4(base_weight_decay,
input_patches4_s0, train_flag)
x4_s1_output = feature_extraction_view4(base_weight_decay,
input_patches4_s1, train_flag)
x4_s2_output = feature_extraction_view4(base_weight_decay,
input_patches4_s2, train_flag)
# view 4 decoder
# x4_7 = view4_decoder(base_weight_decay, x4_s0_output)
# conv block 5
x4_5 = Conv2D(data_format='channels_last',
trainable=True,
filters=64,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_5_4')(x4_s0_output)
x4_5 = Activation('relu', name='conv_block_5_4_act')(x4_5)
# conv block 6
x4_6 = Conv2D(data_format='channels_last',
trainable=True,
filters=32,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_6_4')(x4_5)
x4_6 = Activation('relu', name='conv_block_6_4_act')(x4_6)
# conv block 7
x4_7 = Conv2D(data_format='channels_last',
trainable=True,
filters=1,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_7_4')(x4_6)
x4_7 = Activation('relu', name='conv_block_7_4_act')(x4_7)
#################################### fusion #############################################
################# get the scale-selection mask #####################
# view depth of image
batch_size = x1_s0_output.shape[0].value
height = x1_s0_output.shape[1].value
width = x1_s0_output.shape[2].value
num_channels = x1_s0_output.shape[3].value
output_shape = [1, height, width, 1]
# view1_depth = feature_scale_fusion_layer_mask(scale_number=scale_number,
# view = 1, output_shape=output_shape)
# view2_depth = feature_scale_fusion_layer_mask(scale_number=scale_number,
# view = 2, output_shape=output_shape)
# view3_depth = feature_scale_fusion_layer_mask(scale_number=scale_number,
# view = 3, output_shape=output_shape)
# view1_scale = scale_selection_mask(base_weight_decay, input_depth_maps_v1)
# view2_scale = scale_selection_mask(base_weight_decay, input_depth_maps_v2)
# view3_scale = scale_selection_mask(base_weight_decay, input_depth_maps_v3)
view1_scale = Conv2D(data_format='channels_last',
trainable=True,
filters=1,
kernel_size=(1, 1),
strides=(1, 1),
kernel_initializer=Constant(value=-1),
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
bias_initializer='ones',
activation=None,
name='scale_fusion1')(input_depth_maps_v1)
view2_scale = Conv2D(data_format='channels_last',
trainable=True,
filters=1,
kernel_size=(1, 1),
strides=(1, 1),
kernel_initializer=Constant(value=-1),
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
bias_initializer='ones',
activation=None,
name='scale_fusion2')(input_depth_maps_v2)
view3_scale = Conv2D(data_format='channels_last',
trainable=True,
filters=1,
kernel_size=(1, 1),
strides=(1, 1),
kernel_initializer=Constant(value=-1),
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
bias_initializer='ones',
activation=None,
name='scale_fusion3')(input_depth_maps_v3)
view4_scale = Conv2D(data_format='channels_last',
trainable=True,
filters=1,
kernel_size=(1, 1),
strides=(1, 1),
kernel_initializer=Constant(value=-1),
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
bias_initializer='ones',
activation=None,
name='scale_fusion4')(input_depth_maps_v4)
view1_scale_mask = feature_scale_fusion_layer_rbm(
scale_number=scale_number)(view1_scale)
view2_scale_mask = feature_scale_fusion_layer_rbm(
scale_number=scale_number)(view2_scale)
view3_scale_mask = feature_scale_fusion_layer_rbm(
scale_number=scale_number)(view3_scale)
view4_scale_mask = feature_scale_fusion_layer_rbm(
scale_number=scale_number)(view4_scale)
#################### fusion with mask ##################
# view 1
## conv
x1_s0_output_fusion = fusion_conv_v1(base_weight_decay, x1_s0_output)
x1_s1_output_fusion = fusion_conv_v1(base_weight_decay, x1_s1_output)
x1_s2_output_fusion = fusion_conv_v1(base_weight_decay, x1_s2_output)
## up sampling
x1_s1_output_fusion = UpSampling_layer(size=[height, width])(
[x1_s1_output_fusion])
x1_s2_output_fusion = UpSampling_layer(size=[height, width])(
[x1_s2_output_fusion])
concatenated_map_v1 = Concatenate(name='cat_map_v1')(
[x1_s0_output_fusion, x1_s1_output_fusion, x1_s2_output_fusion])
fusion_v1 = feature_scale_fusion_layer(scale_number=scale_number)(
[concatenated_map_v1, view1_scale_mask])
## proj
fusion_v1_proj = SpatialTransformer(
1, [int(480 / 4), int(640 / 4)])(fusion_v1)
# view 2
## conv
x2_s0_output_fusion = fusion_conv_v2(base_weight_decay, x2_s0_output)
x2_s1_output_fusion = fusion_conv_v2(base_weight_decay, x2_s1_output)
x2_s2_output_fusion = fusion_conv_v2(base_weight_decay, x2_s2_output)
## up sampling
x2_s1_output_fusion = UpSampling_layer(size=[height, width])(
[x2_s1_output_fusion])
x2_s2_output_fusion = UpSampling_layer(size=[height, width])(
[x2_s2_output_fusion])
concatenated_map_v2 = Concatenate(name='cat_map_v2')(
[x2_s0_output_fusion, x2_s1_output_fusion, x2_s2_output_fusion])
fusion_v2 = feature_scale_fusion_layer(scale_number=scale_number)(
[concatenated_map_v2, view2_scale_mask])
## proj
fusion_v2_proj = SpatialTransformer(
2, [int(480 / 4), int(640 / 4)])(fusion_v2)
# view 3
## conv
x3_s0_output_fusion = fusion_conv_v3(base_weight_decay, x3_s0_output)
x3_s1_output_fusion = fusion_conv_v3(base_weight_decay, x3_s1_output)
x3_s2_output_fusion = fusion_conv_v3(base_weight_decay, x3_s2_output)
## up sampling
x3_s1_output_fusion = UpSampling_layer(size=[height, width])(
[x3_s1_output_fusion])
x3_s2_output_fusion = UpSampling_layer(size=[height, width])(
[x3_s2_output_fusion])
concatenated_map_v3 = Concatenate(name='cat_map_v3')(
[x3_s0_output_fusion, x3_s1_output_fusion, x3_s2_output_fusion])
fusion_v3 = feature_scale_fusion_layer(scale_number=scale_number)(
[concatenated_map_v3, view3_scale_mask])
## proj
fusion_v3_proj = SpatialTransformer(
3, [int(480 / 4), int(640 / 4)])(fusion_v3)
# view 4
## conv
x4_s0_output_fusion = fusion_conv_v4(base_weight_decay, x4_s0_output)
x4_s1_output_fusion = fusion_conv_v4(base_weight_decay, x4_s1_output)
x4_s2_output_fusion = fusion_conv_v4(base_weight_decay, x4_s2_output)
## up sampling
x4_s1_output_fusion = UpSampling_layer(size=[height, width])(
[x4_s1_output_fusion])
x4_s2_output_fusion = UpSampling_layer(size=[height, width])(
[x4_s2_output_fusion])
concatenated_map_v4 = Concatenate(name='cat_map_v4')(
[x4_s0_output_fusion, x4_s1_output_fusion, x4_s2_output_fusion])
fusion_v4 = feature_scale_fusion_layer(scale_number=scale_number)(
[concatenated_map_v4, view4_scale_mask])
## proj
fusion_v4_proj = SpatialTransformer(
4, [int(480 / 4), int(640 / 4)])(fusion_v4)
################# concatenate ################
concatenated_map = Concatenate(name='cat_map_fusion')(
[fusion_v1_proj, fusion_v2_proj, fusion_v3_proj, fusion_v4_proj])
fusion_v123 = Conv2D(data_format='channels_last',
trainable=True,
filters=96,
kernel_size=(1, 1),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='scale_fusion')(concatenated_map)
fusion_v123 = Activation('relu', name='scale_fusion_act')(fusion_v123)
#################### fusion and decode #####################################
# conv block 9
x = Conv2D(data_format='channels_last',
trainable=True,
filters=64,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_fusion1')(fusion_v123)
x = Activation('relu', name='conv_block_fusion1_act')(x)
x = Conv2D(data_format='channels_last',
trainable=True,
filters=32,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_fusion2')(x)
x = Activation('relu', name='conv_block_fusion2_act')(x)
x = Conv2D(data_format='channels_last',
trainable=True,
filters=1,
kernel_size=(5, 5),
strides=(1, 1),
kernel_initializer='he_normal',
padding='same',
kernel_regularizer=l2(base_weight_decay),
use_bias=True,
activation=None,
name='conv_block_fusion3')(x)
x_output = Activation('relu', name='conv_block_fusion3_act')(x)
if output_ROI_mask:
rgr_output = 'den_map_roi'
output = Multiply(name=rgr_output)([x_output, output_masks])
print('Layer name of regression output: {}'.format(rgr_output))
model = Model(inputs=[
input_patches1_s0, input_patches1_s1, input_patches1_s2,
input_patches2_s0, input_patches2_s1, input_patches2_s2,
input_patches3_s0, input_patches3_s1, input_patches3_s2,
input_patches4_s0, input_patches4_s1, input_patches4_s2,
input_depth_maps_v1, input_depth_maps_v2, input_depth_maps_v3,
input_depth_maps_v4, output_masks
],
outputs=[x_output],
name=net_name)
else:
model = Model(
inputs=[
input_patches1_s0,
input_patches1_s1,
input_patches1_s2,
input_patches2_s0,
input_patches2_s1,
input_patches2_s2,
input_patches3_s0,
input_patches3_s1,
input_patches3_s2,
input_patches4_s0,
input_patches4_s1,
input_patches4_s2,
input_depth_maps_v1,
input_depth_maps_v2,
input_depth_maps_v3,
input_depth_maps_v4,
],
outputs=[x_output], #x1_7, x2_7, x3_7, x4_7,
name=net_name + 'overall')
print('Compiling ...')
model.compile(optimizer=optimizer, loss='mse')
return model
str(dropout_reg)
colorprint(Color.BLUE, tmp_str)
#Build the Multi Layer Perceptron model
model = Sequential()
model.add(
Reshape((IMG_SIZE * IMG_SIZE * 3, ),
input_shape=(IMG_SIZE, IMG_SIZE, 3),
name='reshape'))
#model.add(Dense(units=2048, activation='relu',name='second'))
#model.add(Dropout(0.2))
model.add(
Dense(units=DIM_HIDDEN[0],
activation='relu',
kernel_initializer='glorot_normal',
bias_initializer=Constant(value=0.01),
name='first_dense',
kernel_constraint=maxnorm(5),
kernel_regularizer=regularizers.l2(0.01)))
#kernel_constraint=maxnorm(3)))
#kernel_constraint=maxnorm(3)))
#model.add(BatchNormalization())
#kernel_regularizer=regularizers.l2(0.001)))
#kernel_constraint=maxnorm(3)))
# kernel_regularizer=regularizers.l2(0.001)))
model.add(Dropout(drop_prob))
model.add(
Dense(units=DIM_HIDDEN[1],
activation='relu',
kernel_initializer='glorot_normal',
def create_network(self):
# first level convolutional group
conv1a = Conv2D(
64,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
conv1b = Conv2D(
64,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
pool1 = MaxPooling2D(pool_size=(2, 2))
drop1 = Dropout(0.7)
# second level convolutional group
conv2a = Conv2D(
128,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
conv2b = Conv2D(
128,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
pool2 = MaxPooling2D(pool_size=(2, 2))
drop2 = Dropout(0.7)
# third level convolutional group
conv3a = Conv2D(
256,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
conv3b = Conv2D(
256,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
pool3 = MaxPooling2D(pool_size=(2, 2))
drop3 = Dropout(0.7)
# fourth level convolutional group
conv4a = Conv2D(
512,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
conv4b = Conv2D(
512,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
pool4 = MaxPooling2D(pool_size=(2, 2))
drop4 = Dropout(0.7)
# fifth level convolutional group
conv5a = Conv2D(
1024,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
conv5b = Conv2D(
1024,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
# fourth level upsampling
up4 = UpSampling2D(size=(2, 2))
upconv4 = Conv2D(
512,
2,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
# fourth level merge
merge4 = Concatenate(axis=3)
drop42 = Dropout(0.7)
# fourth level second convolutional group
conv42a = Conv2D(
512,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
conv42b = Conv2D(
512,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
# third level upsampling
up3 = UpSampling2D(size=(2, 2))
upconv3 = Conv2D(
256,
2,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
# third level merge
merge3 = Concatenate(axis=3)
drop32 = Dropout(0.7)
# third level second convolutional group
conv32a = Conv2D(
256,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
conv32b = Conv2D(
256,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
# second level upsampling
up2 = UpSampling2D(size=(2, 2))
upconv2 = Conv2D(
128,
2,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
# second level merge
merge2 = Concatenate(axis=3)
drop22 = Dropout(0.7)
# second level second convolutional group
conv22a = Conv2D(
128,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
conv22b = Conv2D(
128,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
# first level upsampling
up1 = UpSampling2D(size=(2, 2))
upconv1 = Conv2D(
64,
2,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
# first level merge
merge1 = Concatenate(axis=3)
drop12 = Dropout(0.7)
# first level second convolutional group
conv12a = Conv2D(
64,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
conv12b = Conv2D(
64,
3,
activation="relu",
padding="same",
kernel_initializer="he_normal",
)
# output layer
convout_mean = Conv2D(
1,
1,
activation=None,
padding="same",
kernel_initializer="he_normal",
)
convout_log_var = Conv2D(
1,
1,
activation=None,
padding="same",
kernel_initializer="he_normal",
bias_initializer=Constant(-3),
)
convout = Concatenate(name="probout")
inputs = Input(self.input_size)
# first level convolutional group
c1 = conv1b(conv1a(inputs))
p1 = drop1(pool1(c1))
# second level convolutional group
c2 = conv2b(conv2a(p1))
p2 = drop2(pool2(c2))
# third level convolutional group
c3 = conv3b(conv3a(p2))
p3 = drop3(pool3(c3))
# fourth level convolutional group
c4 = conv4b(conv4a(p3))
p4 = drop4(pool4(c4))
# fifth level convolutional group
c5 = conv5b(conv5a(p4))
# fourth level upsampling
u4 = upconv4(up4(c5))
m4 = drop42(merge4([c4, u4]))
# fourth level second convolutional group
c42 = conv42b(conv42a(m4))
# third level upsampling
u3 = upconv3(up3(c42))
m3 = drop32(merge3([c3, u3]))
# third level second convolutional group
c32 = conv32b(conv32a(m3))
# second level upsampling
u2 = upconv2(up2(c32))
m2 = drop22(merge2([c2, u2]))
# second level second convolutional group
c22 = conv22b(conv22a(m2))
# first level upsampling
u1 = upconv1(up1(c22))
m1 = drop12(merge1([c1, u1]))
# first level second convolutional group
c12 = conv12b(conv12a(m1))
# output layer
outputs = convout([convout_mean(c12), convout_log_var(c12)])
return Model(inputs, outputs)
def __init__(self):
super().__init__(3, self.lppl, Constant(0.5))
def create_net(self, input_shape):
net_input = Input(shape=input_shape)
x = Conv2D(self.filters, (3, 3), padding='same')(net_input)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = MaxPooling2D((2, 2), padding='same')(x)
x = Conv2D(self.filters, (3, 3), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
self.encoded = MaxPooling2D((2, 2), padding='same')(x)
# Keep the encoder part
self.encoder = Model(net_input, self.encoded)
# And now the decoder part
x = Conv2DTranspose(self.filters, (3,3), strides=(2,2), padding='same')(self.encoded)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = Conv2DTranspose(self.filters, (3,3), strides=(2,2), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = Conv2DTranspose(self.filters, (3,3), strides=(2,2), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = Conv2DTranspose(self.filters, (3,3), strides=(2,2), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = Conv2DTranspose(self.filters, (3,3), strides=(2,2), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = Conv2DTranspose(self.filters, (3,3), strides=(2,2), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = Conv2DTranspose(self.filters, (3,3), strides=(2,2), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
x = Conv2DTranspose(self.filters, (3,3), strides=(2,2), padding='same')(x)
x = PReLU(alpha_initializer=Constant(value=0.25))(x)
self.decoded = Conv2D(1, (3, 3), activation='sigmoid', padding='same')(x)
self.model = Model(net_input, self.decoded)
return
train = y[~y.index.isin(test_index)]
train_index = train.index.values
y_values = y.ix[:, 0].values
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_values[train_index], y_values[test_index]
y_train = np.eye(n_classes)[y_train - 1]
print X_train.shape # (2465, 900)
# input layer
input_signal = Input(shape=(signal_rows, 1))
print K.int_shape(input_signal) # (None, 900, 1)
# define initial parameters
b_init = Constant(value=0.0)
k_init = TruncatedNormal(mean=0.0, stddev=0.01, seed=2018)
# first feature extractor
conv11 = Conv1D(16,
kernel_size=32,
strides=1,
padding='valid',
bias_initializer=b_init,
kernel_initializer=k_init)(input_signal)
bn11 = BatchNormalization()(conv11)
actv11 = Activation('relu')(bn11)
conv12 = Conv1D(32,
kernel_size=32,
strides=1,
padding='valid',
clf = Sequential()
clf.add(InputLayer(input_shape=(1, 28, 28)))
clf.add(BatchNormalization())
clf.add(Conv2D(64, (4, 4), padding='same'))
clf.add(LeakyReLU())
clf.add(MaxPool2D(padding='same'))
clf.add(
Conv2D(
128,
(4, 4),
padding='same',
bias_initializer=Constant(0.01),
kernel_initializer='random_uniform',
))
clf.add(
Conv2D(
64,
(4, 4),
padding='same',
bias_initializer=Constant(0.01),
kernel_initializer='random_uniform',
))
clf.add(LeakyReLU())
clf.add(MaxPool2D(padding='same'))
other_mat_train = np.concatenate((other_mat_train, ncode_mat_train),
axis=1)
other_mat_trn = other_mat_train
other_mat_val = other_mat_tst
y_trn = train_df.readm30.astype(int).values
y_val = y_true
Y_trn = to_categorical(y_trn)
Y_val = to_categorical(y_val)
# model building
if model_name == 'setsum_nn':
input_DX1 = Input(shape=(1, ))
DX1_embed = Embedding(input_dim=n_DX1_cat + len(dx1_ccs_dict) + 1,
output_dim=DX1_dim,
embeddings_initializer=Constant(embeds['DX1_embed']),
name='DX1_embed')(input_DX1)
DX1_embed = Reshape((DX1_dim, ))(DX1_embed)
input_DX = Input(shape=(len(DXs), ))
DX_embed = Embedding(input_dim=n_DX_cat + len(dx_ccs_dict) + 1,
output_dim=DX_dim,
mask_zero=True,
embeddings_initializer=Constant(embeds['DX_embed']),
name='DX_embed')(input_DX)
DX_embed = MaskedDense(DX_dim, activation='relu')(DX_embed)
DX_embed = MaskedSum()(DX_embed)
input_PR = Input(shape=(len(PRs), ))
PR_embed = Embedding(input_dim=n_PR_cat + len(pr_ccs_dict) + 1,
output_dim=PR_dim,
mask_zero=True,
embeddings_initializer=Constant(embeds['PR_embed']),
def FCN_8s_pretrained(classes, in_shape, l2_reg, nopad=False, test=False):
vgg16 = VGG16(include_top=False, weights="imagenet", input_shape=in_shape)
inputs = Input(shape=in_shape)
if nopad:
x = inputs
else:
x = ZeroPadding2D(padding=(100, 100))(inputs)
for layer in vgg16.layers[1:]:
if "conv" in layer.name:
W, b = layer.get_weights()
config = layer.get_config()
config["kernel_regularizer"] = l2(l2_reg)
config["kernel_initializer"] = Constant(W)
config["bias_initializer"] = Constant(b)
conv = Conv2D.from_config(config)
x = conv(x)
elif "pool" in layer.name:
x = MaxPooling2D()(x)
if layer.name == "block3_pool":
feat3 = x
elif layer.name == "block4_pool":
feat4 = x
x = Conv2D(filters=4096,
kernel_size=(7, 7),
padding="valid",
activation="relu",
kernel_regularizer=l2(l2_reg),
name="fc1")(x)
x = Dropout(0.5)(x)
x = Conv2D(filters=4096,
kernel_size=(1, 1),
padding="valid",
activation="relu",
kernel_regularizer=l2(l2_reg),
name="fc2")(x)
x = Dropout(0.5)(x)
score5 = Conv2D(filters=classes,
kernel_size=(1, 1),
kernel_regularizer=l2(l2_reg),
activation="relu")(x)
if nopad:
score5 = Conv2DTranspose(filters=classes,
kernel_size=(14, 14),
strides=(1, 1),
padding="valid",
activation="linear",
kernel_regularizer=l2(l2_reg),
kernel_initializer=Constant(
bilinear_upsample_weights(
"full", classes)
))(score5)
else:
score5 = Conv2DTranspose(filters=classes,
kernel_size=(4, 4),
strides=(2, 2),
padding="same",
activation="linear",
kernel_regularizer=l2(l2_reg),
kernel_initializer=Constant(
bilinear_upsample_weights(2, classes)
))(score5)
# pool3 のfeature mapを次元圧縮
score3 = Conv2D(filters=classes,
kernel_size=(1, 1),
kernel_regularizer=l2(l2_reg),
activation='relu')(feat3)
# pool4のfeature mapを次元圧縮
score4 = Conv2D(filters=classes,
kernel_size=(1, 1),
kernel_regularizer=l2(l2_reg),
activation="relu")(feat4)
# merge p4 and p5
score4 = CroppingLike2D(K.int_shape(score5))(score4)
score45 = Add()([score4, score5])
# p4+p5 を x2 upsampling
if not nopad:
score45 = ZeroPadding2D(padding=(1, 1))(score45)
score45 = Conv2DTranspose(filters=classes,
kernel_size=(4, 4),
strides=(2, 2),
padding="same",
activation="linear",
kernel_regularizer=l2(l2_reg),
kernel_initializer=Constant(
bilinear_upsample_weights(2, classes)
))(score45)
# p3とp45をmerge
score3 = CroppingLike2D(K.int_shape(score45))(score3)
score345 = Add()([score3, score45])
# p3+p4+p5を x8 upsampling
if not nopad:
score345 = ZeroPadding2D(padding=(1, 1))(score345)
x = Conv2DTranspose(filters=classes,
kernel_size=(16, 16),
strides=(8, 8),
padding="same",
activation="linear",
kernel_regularizer=l2(l2_reg),
kernel_initializer=Constant(
bilinear_upsample_weights(8, classes)
))(score345)
x = CroppingLike2D(K.int_shape(inputs))(x)
if test:
x = Activation("softmax")(x)
model = Model(inputs=inputs, outputs=x)
return model
if i > num_words:
continue
embeddings_vector = embeddings_index.get(w)
if embeddings_vector is not None:
embeddings_matrix[i] = embeddings_vector
prob_thresh = (y_train_df.sum() / y_train_df.shape[0]).clip(upper=0.5)
prob_thresh
from keras.initializers import Constant
####################################################################
filter_length = 256
cnn_model = Sequential()
cnn_model.add(
Embedding(vocab_len + 1,
300,
embeddings_initializer=Constant(embeddings_matrix),
input_length=x_train.shape[1]))
cnn_model.add(Dropout(0.2))
cnn_model.add(
Conv1D(filter_length, 5, padding='valid', activation='relu', strides=1))
cnn_model.add(GlobalMaxPool1D())
cnn_model.add(Dense(y_train_df.shape[1]))
cnn_model.add(Activation('sigmoid'))
cnn_model.compile(optimizer='adam',
loss='binary_crossentropy',
metrics=['accuracy'])
cnn_model.summary()
callbacks = [
ReduceLROnPlateau(),
def FCN_8s(classes, in_shape, l2_reg, nopad=False, test=False):
"""
VGG16 based FCN model,
classes: int, number of classes
return: keras Model object
"""
inputs = Input(shape=in_shape)
if nopad:
x = inputs
else:
x = ZeroPadding2D(padding=(100, 100))(inputs)
x = Conv2D(filters=64,
kernel_size=(3, 3),
padding='same',
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Conv2D(filters=64,
kernel_size=(3, 3),
padding='same',
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = MaxPooling2D()(x)
x = Conv2D(filters=128,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Conv2D(filters=128,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = MaxPooling2D()(x)
x = Conv2D(filters=256,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Conv2D(filters=256,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Conv2D(filters=256,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = MaxPooling2D()(x)
# pool3のfeature mapを取得
p3 = x
x = Conv2D(filters=512,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Conv2D(filters=512,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Conv2D(filters=512,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = MaxPooling2D()(x)
# pool4のfeature mapを取得
p4 = x
x = Conv2D(filters=512,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Conv2D(filters=512,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Conv2D(filters=512,
kernel_size=(3, 3),
padding="same",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = MaxPooling2D()(x)
x = Conv2D(filters=4096,
kernel_size=(7, 7),
padding="valid",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Dropout(0.5)(x)
x = Conv2D(filters=4096,
kernel_size=(1, 1),
padding="valid",
kernel_regularizer=l2(l2_reg))(x)
x = Activation("relu")(x)
x = Dropout(0.5)(x)
score_p5 = Conv2D(filters=classes,
kernel_size=(1, 1),
kernel_regularizer=l2(l2_reg),
activation="relu")(x)
if nopad:
score_p5 = Conv2DTranspose(filters=classes,
kernel_size=(14, 14),
strides=(1, 1),
padding="valid",
activation="linear",
kernel_regularizer=l2(l2_reg),
kernel_initializer=Constant(
bilinear_upsample_weights(
"full", classes)
))(score_p5)
else:
score_p5 = Conv2DTranspose(filters=classes,
kernel_size=(4, 4),
strides=(2, 2),
padding="same",
activation="linear",
kernel_regularizer=l2(l2_reg),
kernel_initializer=Constant(
bilinear_upsample_weights(2, classes)
))(score_p5)
# pool3 のfeature mapを次元圧縮
score_p3 = Conv2D(filters=classes,
kernel_size=(1, 1),
kernel_regularizer=l2(l2_reg),
activation='relu')(p3)
# pool4のfeature mapを次元圧縮
score_p4 = Conv2D(filters=classes,
kernel_size=(1, 1),
kernel_regularizer=l2(l2_reg),
activation="relu")(p4)
# merge p4 and p5
score_p4 = CroppingLike2D(K.int_shape(score_p5))(score_p4)
score_p45 = Add()([score_p4, score_p5])
# p4+p5 を x2 upsampling
if not nopad:
score_p45 = ZeroPadding2D(padding=(1, 1))(score_p45)
score_p45 = Conv2DTranspose(filters=classes,
kernel_size=(4, 4),
strides=(2, 2),
padding="same",
activation="linear",
kernel_regularizer=l2(l2_reg),
kernel_initializer=Constant(
bilinear_upsample_weights(2, classes)
))(score_p45)
# p3とp45をmerge
score_p3 = CroppingLike2D(K.int_shape(score_p45))(score_p3)
score_p345 = Add()([score_p3, score_p45])
# p3+p4+p5を x8 upsampling
if not nopad:
score_p345 = ZeroPadding2D(padding=(1, 1))(score_p345)
x = Conv2DTranspose(filters=classes,
kernel_size=(16, 16),
strides=(8, 8),
padding="same",
activation="linear",
kernel_regularizer=l2(l2_reg),
kernel_initializer=Constant(
bilinear_upsample_weights(8, classes)
))(score_p345)
x = CroppingLike2D(K.int_shape(inputs))(x)
if test:
x = Activation("softmax")(x)
model = Model(inputs=inputs, outputs=x)
return model
def make_layers(self):
self.word_embedding_layer = Embedding(
len(self.dataset.word_embedding_matrix),
self.word_embedding_dim,
embeddings_initializer=Constant(
self.dataset.word_embedding_matrix),
trainable=self.trainable_word_emb,
mask_zero=self.flag_embedding_layer_mask_zero,
name='word_emb',
embeddings_regularizer=l2(self.embedding_regularizer_coefficient))
self.word_rnn = self.stack_rnn(self.stack[0])
self.tanh1 = self.make_dense(DIMENSION_ATTENTION, activation='tanh')
self.att1 = AttentionLayer(name='att1')
self.rnn2 = self.stack_rnn(self.stack[1])
self.tanh2 = self.make_dense(DIMENSION_ATTENTION, activation='tanh')
self.att2 = AttentionLayer(name='att2')
self.logit = self.make_dense(self.dataset.n_classes,
activation='softmax',
name='logit')
if self.optimizer_name == 'rmsprop':
self.optimizer = optimizers.RMSprop(lr=self.initial_learning_rate,
**self.optimizer_kwargs)
elif self.optimizer_name == 'sgd':
self.optimizer = optimizers.SGD(lr=self.initial_learning_rate,
momentum=0.9,
**self.optimizer_kwargs)
elif self.optimizer_name == 'adam':
self.optimizer = optimizers.Adam(lr=self.initial_learning_rate,
**self.optimizer_kwargs)
else:
self.log.write('unknown optimizer name')
sys.exit(1)
if self.CHAR:
self.dataset.make_character_embedding_index()
self.character_embedding_layer = Embedding(
len(self.dataset.char_embedding_index),
len(self.dataset.char_embedding_index) - 2,
# weights=[self.dataset.char_embedding_matrix],
embeddings_initializer=Constant(
self.dataset.char_embedding_matrix),
mask_zero=self.char_rnn_flag,
trainable=True,
name='ch_emb',
embeddings_regularizer=l2(
self.embedding_regularizer_coefficient))
if not self.char_rnn_flag: # character cnn
self.conv1 = self.make_conv(self.conv_unit_size, 5)
self.conv2 = self.make_conv(self.conv_unit_size, 2)
else: # character rnn
self.char_rnn = self.make_rnn(self.CHARACTER_RNN_DIMENSION,
False)
# temp
self.word_linear = self.make_dense(self.word_embedding_dim,
activation='linear')
self.char_linear = self.make_dense(self.word_embedding_dim,
activation='linear')
self.max_tanh = self.make_dense(self.word_embedding_dim,
activation='tanh')
# layers for merging words and characters
self.conv_dense = self.make_dense(
self.word_embedding_dim, activation=self.conv_dense_activation)
self.max_relu = self.make_dense(self.word_embedding_dim,
activation='relu')
def fcn_VGG16_8s(INPUT_SIZE,nb_classes): # previous name: fcn8s_take2
""" Returns Keras FCN-8 model definition.
"""
fcn32_flag = False
inputs = Input(shape=(INPUT_SIZE, INPUT_SIZE, 3))
# Start from VGG16 layers
vgg16 = VGG16(weights='imagenet', include_top=False, input_tensor=inputs)
# Skip connections from pool3, 256 channels
vgg16_upto_intermediate_layer_pool3 = Model(inputs=vgg16.input, outputs=vgg16.get_layer('block3_pool').output)
score_pool3 = vgg16_upto_intermediate_layer_pool3.output
# 1x1 conv layer to reduce number of channels to nb_classes:
score_pool3c = Conv2D(filters=nb_classes,kernel_size=(1, 1),name="score_pool3c")(score_pool3)
# Skip connections from pool4, 512 channels
vgg16_upto_intermediate_layer_pool4 = Model(inputs=vgg16.input, outputs=vgg16.get_layer('block4_pool').output)
score_pool4 = vgg16_upto_intermediate_layer_pool4.output
# 1x1 conv layer to reduce number of channels to nb_classes:
score_pool4c = Conv2D(filters=nb_classes, kernel_size=(1, 1))(score_pool4)
# score from the top vgg16 layer:
score_pool5 = vgg16.output
#n = 4096
score6c = Conv2D(filters=4096, kernel_size=(7, 7), padding='same', name="conv6")(score_pool5)
score7c = Conv2D(filters=4096, kernel_size=(1, 1), padding='same', name="conv7")(score6c)
#score7c = Conv2D(filters=nb_classes,kernel_size=(1, 1))(score6c)
score7c_upsample = Conv2DTranspose(filters=nb_classes,
kernel_size=(4, 4),
strides=(2, 2),
padding='same',
activation = None,
kernel_initializer = Constant(bilinear_upsample_weights(2, nb_classes)),
name="score_pool7c_upsample")(score7c)
# Fuse scores
score_7_4 = Add()([score7c_upsample, score_pool4c])
# upsample:
score_7_4_up = Conv2DTranspose(filters=nb_classes,
kernel_size=(4, 4),
strides=(2, 2),
padding='same',
activation= None,
kernel_initializer=Constant(bilinear_upsample_weights(2, nb_classes)),
name="score_7_4_up")(score_7_4)
# Fuse scores
score_7_4_3 = Add()([score_7_4_up, score_pool3c])
# upsample:
score_7_4_3_up = Conv2DTranspose(filters=nb_classes,
kernel_size=(16, 16),
strides=(8, 8),
padding='same',
activation=None,
kernel_initializer=Constant(bilinear_upsample_weights(8, nb_classes)),
name="score_7_4_3_up")(score_7_4_3)
# Batch Normalization: (optional)
#score_7_4_3_up = BatchNormalization()(score_7_4_3_up)
output = (Activation('softmax'))(score_7_4_3_up)
# # -- There's another way to match the tensor sizes from earlier layers, using a Cropping2D layer --
# # e.g., for fcn-16, we can crop layer 'score_pool4c' to get the same size as layer 'score_7c'
# score_pool4c_cropped = Cropping2D((5+3, 5+3))(score_pool4c)
# # fuse layers,
# score_7_4_cropped = Add()([score7c, score_pool4c_cropped])
# # then upsample to input size:
# x = Conv2DTranspose(filters=nb_classes,
# kernel_size=(64, 64),
# strides=(32+2,32+2),
# padding='same',
# activation='sigmoid',
# kernel_initializer=Constant(bilinear_upsample_weights(32, nb_classes)))(score_7_4_cropped)
# Creating the model:
model = Model(inputs=inputs, outputs=output, name='fcn_VGG16_8s')
# Fixing weighs in lower layers
for layer in model.layers[:15]: # sometimes I use it, sometimes not.
layer.trainable = False
return model