def train_repet_network(beat_spectrum_array, sdr_array, n_epochs, take):
"""
:param beat_spectrum_array:
:param sdr_array:
:param n_epochs:
:param take:
:return:
"""
beat_spec_len = 432
with tf.Graph().as_default():
input_layer = input_data(shape=[None, beat_spec_len, 1])
conv1 = conv_1d(input_layer, 32, 4, activation="relu", regularizer="L2")
max_pool1 = max_pool_1d(conv1, 2)
conv2 = conv_1d(max_pool1, 64, 80, activation="relu", regularizer="L2")
max_pool2 = max_pool_1d(conv2, 2)
fully1 = fully_connected(max_pool2, 128, activation="relu")
dropout1 = dropout(fully1, 0.8)
fully2 = fully_connected(dropout1, 256, activation="relu")
dropout2 = dropout(fully2, 0.8)
linear = fully_connected(dropout2, 1, activation="linear")
regress = tflearn.regression(linear, optimizer="rmsprop", loss="mean_square", learning_rate=0.001)
# Training
model = tflearn.DNN(regress) # , session=sess)
model.fit(
beat_spectrum_array,
sdr_array,
n_epoch=n_epochs,
snapshot_step=1000,
show_metric=True,
run_id="repet_choice_{0}_epochs_take_{1}".format(n_epochs, take),
)
return model
def load_audio_convnet(filename):
input_layer = input_data(shape=[None, MAX_CONV, 1])
conv_layer_1 = conv_1d(input_layer, nb_filter=8, filter_size=79, activation='relu', name='conv_layer_1')
pool_layer_1 = max_pool_1d(conv_layer_1, 100, name='pool_layer_1')
conv_layer_2 = conv_1d(pool_layer_1, nb_filter=16, filter_size=11, activation='relu', name='conv_layer_2')
pool_layer_2 = max_pool_1d(conv_layer_2, 5, name='pool_layer_2')
fc_layer_1 = fully_connected(pool_layer_2, 100, activation='tanh', name='fc_layer_1')
fc_layer_2 = fully_connected(fc_layer_1, 3, activation='softmax', name='fc_layer_2')
network = regression(fc_layer_2, optimizer='sgd', loss='categorical_crossentropy', learning_rate=0.1)
model = tflearn.DNN(network)
model.load(filename)
return model
def main():
pickle_folder = '../pickles_rolloff'
pickle_folders_to_load = [f for f in os.listdir(pickle_folder) if os.path.isdir(join(pickle_folder, f))]
pickle_folders_to_load = sorted(pickle_folders_to_load)
# pickle parameters
fg_or_bg = 'background'
sdr_type = 'sdr'
feature = 'beat_spec'
beat_spec_len = 432
# training params
n_classes = 16
training_percent = 0.85
testing_percent = 0.15
validation_percent = 0.00
# set up training, testing, & validation partitions
beat_spec_array, sdr_array = load_beat_spec_and_sdrs(pickle_folders_to_load, pickle_folder,
feature, fg_or_bg, sdr_type)
train, test, validate = split_into_sets(len(pickle_folders_to_load), training_percent,
testing_percent, validation_percent)
trainX = np.expand_dims([beat_spec_array[i] for i in train], -1)
trainY = np.expand_dims([sdr_array[i] for i in train], -1)
testX = np.expand_dims([beat_spec_array[i] for i in test], -1)
testY = np.array([sdr_array[i] for i in test])
# Building convolutional network
network = input_data(shape=[None, beat_spec_len, 1])
network = conv_1d(network, 32, 4, activation='relu', regularizer="L2")
network = max_pool_1d(network, 2)
network = conv_1d(network, 64, 80, activation='relu', regularizer="L2")
network = max_pool_1d(network, 2)
network = fully_connected(network, 128, activation='relu')
network = dropout(network, 0.8)
network = fully_connected(network, 256, activation='relu') # look for non-tanh things???
network = dropout(network, 0.8)
network = fully_connected(network, 1, activation='linear')
regress = tflearn.regression(network, optimizer='sgd', loss='mean_square', learning_rate=0.01)
# Training
model = tflearn.DNN(regress, tensorboard_verbose=1)
model.fit(trainX, trainY, n_epoch=100,
snapshot_step=1000, show_metric=True, run_id='relus_100_3')
predicted = np.array(model.predict(testX))[:,0]
# pprint.pprint()
print("Test MSE: ", np.square(testY - predicted).mean())
plot(testY, predicted)
def main():
pickle_folder = 'pickles_combined'
# pickle parameters
fg_or_bg = 'background'
sdr_type = 'sdr'
feature = 'beat_spec'
# training params
training_percent = 0.85
testing_percent = 0.15
validation_percent = 0.00
beat_spec_max = 355
# set up training, testing, & validation partitions
beat_spec_array, sdr_array = unpickle_beat_spec_and_sdrs(pickle_folder, beat_spec_max)
train, test, validate = split_into_sets(len(beat_spec_array), training_percent,
testing_percent, validation_percent)
trainX = np.expand_dims([beat_spec_array[i] for i in train], -1)
trainY = np.expand_dims([sdr_array[i] for i in train], -1)
testX = np.expand_dims([beat_spec_array[i] for i in test], -1)
testY = np.array([sdr_array[i] for i in test])
# Building convolutional network
network = input_data(shape=[None, beat_spec_max, 1])
network = conv_1d(network, 32, 4, activation='relu', regularizer="L2")
network = max_pool_1d(network, 2)
network = conv_1d(network, 64, 80, activation='relu', regularizer="L2")
network = max_pool_1d(network, 2)
network = fully_connected(network, 128, activation='relu')
network = dropout(network, 0.8)
network = fully_connected(network, 256, activation='relu') # look for non-tanh things???
network = dropout(network, 0.8)
network = fully_connected(network, 1, activation='linear')
regress = tflearn.regression(network, optimizer='sgd', loss='mean_square', learning_rate=0.01)
start = time.time()
# Training
model = tflearn.DNN(regress, tensorboard_verbose=1)
model.fit(trainX, trainY, n_epoch=2000,
snapshot_step=1000, show_metric=True, run_id='mir1k_2000_truncate')
elapsed = (time.time() - start)
predicted = np.array(model.predict(testX))[:,0]
print("Test MSE: ", np.square(testY - predicted).mean())
print(elapsed, "seconds")
plot(testY, predicted)
def build_tflearn_cnn(length):
input_layer = input_data(shape=[None, length, 1])
# Convolution Layer
conv_layer_1 = conv_1d(input_layer,
nb_filter=512,
filter_size=10,
activation='relu',
name='conv_layer_1',
weights_init='xavier',
regularizer="L2")
pool_layer_1 = max_pool_1d(conv_layer_1, 4, name='pool_layer_1')
conv_layer_2 = conv_1d(pool_layer_1,
nb_filter=512,
filter_size=5,
activation='relu',
name='conv_layer_2',
weights_init='xavier',
regularizer="L2")
pool_layer_3 = max_pool_1d(conv_layer_2, 4, name='pool_layer_3')
# flat = flatten(pool_layer_3)
fc_layer_4 = fully_connected(pool_layer_3,
256,
activation='relu',
name='fc_layer_4',
regularizer='L2')
drop_2 = dropout(fc_layer_4, drop_out_prob)
fc_layer_5 = fully_connected(drop_2,
128,
activation='relu',
name='fc_layer_5',
regularizer='L2')
drop_3 = dropout(fc_layer_5, drop_out_prob)
# Output
fc_layer_2 = fully_connected(drop_3,
3,
activation='softmax',
name='output')
network = regression(fc_layer_2,
optimizer='adam',
loss='softmax_categorical_crossentropy',
learning_rate=0.0001,
metric='accuracy')
model = tflearn.DNN(network, tensorboard_verbose=0)
return model
def main():
"""
:return:
"""
pickle_folder = '../Repet/pickles_rolloff'
pickle_folders_to_load = [f for f in os.listdir(pickle_folder) if os.path.isdir(join(pickle_folder, f))]
fg_or_bg = 'background'
sdr_type = 'sdr'
feature = 'beat_spec'
beat_spec_len = 432
n_epochs = 200
take = 1
# set up training, testing, & validation partitions
beat_spec_array, sdr_array = load_beat_spec_and_sdrs(pickle_folders_to_load, pickle_folder,
feature, fg_or_bg, sdr_type)
beat_spec_array = np.expand_dims(beat_spec_array, -1)
sdr_array = np.expand_dims(sdr_array, -1)
# Building convolutional network
network = input_data(shape=[None, beat_spec_len, 1])
network = conv_1d(network, 32, 4, activation='relu', regularizer="L2")
network = max_pool_1d(network, 2)
network = conv_1d(network, 64, 80, activation='relu', regularizer="L2")
network = max_pool_1d(network, 2)
network = fully_connected(network, 128, activation='relu')
network = dropout(network, 0.8)
network = fully_connected(network, 256, activation='relu') # look for non-tanh things???
network = dropout(network, 0.8)
network = fully_connected(network, 1, activation='linear')
regress = tflearn.regression(network, optimizer='rmsprop', loss='mean_square', learning_rate=0.001)
start = time.time()
# Training
model = tflearn.DNN(regress) # , session=sess)
model.fit(beat_spec_array, sdr_array, n_epoch=n_epochs,
snapshot_step=1000, show_metric=True,
run_id='repet_save_{0}_epochs_take_{1}'.format(n_epochs, take))
elapsed = (time.time() - start)
print('Finished training after ' + elapsed + 'seconds. Saving...')
model_output_folder = 'network_outputs/'
model_output_file = join(model_output_folder, 'repet_save_{0}_epochs_take_{1}'.format(n_epochs, take))
model.save(model_output_file)
def transform_embedded_sequences(self, embedded_sequences):
net = conv_1d(embedded_sequences, self.filters, 5, 1, activation='relu', padding="valid")
net = max_pool_1d(net, 5, padding="valid")
if self.dropout_rate > 0:
net = dropout(net, self.dropout_rate)
net = conv_1d(net, self.filters, 5, activation='relu', padding="valid")
net = max_pool_1d(net, 5, padding="valid")
if self.dropout_rate > 0:
net = dropout(net, self.dropout_rate)
net = conv_1d(net, self.filters, 5, activation='relu', padding="valid")
net = max_pool_1d(net, 35)
if self.dropout_rate > 0:
net = dropout(net, self.dropout_rate)
net = fully_connected(net, self.filters, activation='relu')
preds = fully_connected(net, self.class_count, activation='softmax')
return preds
def residual_block_1D(incoming,out_channels,downsample=False, first=False, filt_len=16, dropout_prob=0.85, downsampleSecond=True): resnet = incoming in_channels = incoming.shape[-1].value strides = (2 if downsample else 1) dsLayer = (1 if downsampleSecond else 0) identity = resnet nConv = 2 if first: resnet = conv_1d(resnet, out_channels, filt_len, strides,weights_init="variance_scaling") nConv = 1 for i in range(nConv): resnet = batch_normalization(resnet) resnet = relu(resnet) resnet = dropout(resnet, dropout_prob) if downsample and i==dsLayer: #1 as in, second layer resnet = conv_1d(resnet,out_channels,filt_len, strides=1, weights_init="variance_scaling") #puts the downsampling on the first conv layer only else: resnet = conv_1d(resnet,out_channels,filt_len, strides, weights_init="variance_scaling") #Beginning of skip connection identity = max_pool_1d(identity,strides, strides) if in_channels != out_channels: ch = (out_channels - in_channels) // 2 identity = tf.pad(identity,[[0,0],[0,0],[ch,ch]]) in_channels = out_channels resnet = resnet + identity return resnet
def model_fn(net, X_len, max_reach, block_size, out_classes, batch_size, dtype,
**kwargs):
"""
Args:
net -> Input tensor shaped (batch_size, max_reach + block_size + max_reach, 3)
Returns:
logits -> Unscaled logits tensor in time_major form, (block_size, batch_size, out_classes)
"""
net = batch_normalization(net, decay=0.99, scope="Initial_bn")
for block in range(1, 3):
with tf.variable_scope("block%d" % block):
for layer in range(kwargs['num_layers']):
with tf.variable_scope("layer%d" % layer):
net = conv_1d(net, 64, 9, scope='conv1d')
net = batch_normalization(net, scope='bn')
net = tf.nn.relu(net)
net = max_pool_1d(net, 2)
net = tf.nn.relu(net)
net = central_cut(net, block_size, 4)
net = tf.transpose(net, [1, 0, 2], name="Shift_to_time_major")
net = conv_1d(net, 9, 1, scope='logits')
return {
'logits': net,
'init_state': tf.constant(0),
'final_state': tf.constant(0),
}
def multi_filter_conv_block(input, n_filters, reuse=False,
dropout_keep_prob=0.5, activation='relu',
padding='same', name='mfcb'):
branch1 = conv_1d(input, n_filters, 1, padding=padding,
activation=activation, reuse=reuse,
scope='{}_conv_branch_1'.format(name))
branch2 = conv_1d(input, n_filters, 3, padding=padding,
activation=activation, reuse=reuse,
scope='{}_conv_branch_2'.format(name))
branch3 = conv_1d(input, n_filters, 5, padding=padding,
activation=activation, reuse=reuse,
scope='{}_conv_branch_3'.format(name))
unstacked_b1 = tf.unstack(branch1, axis=1,
name='{}_unstack_b1'.format(name))
unstacked_b2 = tf.unstack(branch2, axis=1,
name='{}_unstack_b2'.format(name))
unstacked_b3 = tf.unstack(branch3, axis=1,
name='{}_unstack_b3'.format(name))
n_grams = []
for t_b1, t_b2, t_b3 in zip(unstacked_b1, unstacked_b2, unstacked_b3):
n_grams.append(tf.stack([t_b1, t_b2, t_b3], axis=0))
n_grams_merged = tf.concat(n_grams, axis=0)
n_grams_merged = tf.transpose(n_grams_merged, perm=[1, 0, 2])
gram_pooled = max_pool_1d(n_grams_merged, kernel_size=3, strides=3)
cnn_out = dropout(gram_pooled, dropout_keep_prob)
return cnn_out
def model_fn(net, X_len, max_reach, block_size, out_classes, batch_size, dtype,
**kwargs):
"""
Args:
net -> Input tensor shaped (batch_size, max_reach + block_size + max_reach, 3)
Returns:
logits -> Unscaled logits tensor in time_major form, (block_size, batch_size, out_classes)
"""
for block in range(1, 4):
with tf.variable_scope("block%d" % block):
for layer in range(1, 1 + 1):
with tf.variable_scope('layer_%d' % layer):
net = conv_1d(net, 32, 3)
net = max_pool_1d(net, 2)
net = tf.nn.relu(net)
net = central_cut(net, block_size, 8)
net = tf.transpose(net, [1, 0, 2], name="Shift_to_time_major")
net = conv_1d(net, 9, 1, scope='logits')
return {
'logits': net,
'init_state': tf.constant(0),
'final_state': tf.constant(0),
}
def sentiment_analysis(self, sentencedata):
unique_words = self.uniqueword_csvload()
neurons = len(unique_words)
reset_default_graph()
network = input_data(shape=[None, 1, neurons])
network = conv_1d(network, 8, 3, activation='relu')
network = max_pool_1d(network, 3)
network = conv_1d(network, 16, 3, activation='relu')
network = max_pool_1d(network, 3)
network = fully_connected(network, 8, activation='relu')
network = dropout(network, 0.5)
network = fully_connected(network, 2, activation='softmax')
network = regression(network,
optimizer='adam',
learning_rate=0.01,
loss='categorical_crossentropy')
model = tflearn.DNN(network)
model.load(
"./model/thaitext-classifier-combined_inhousedata-UTF8-4-100.tfl")
input_sentencedata = self.preprocess_server_2(sentencedata)[0]
#input_uniquewords = self.get_uniquewords(input_sentencedata)
sentences = []
#f = open(file_path, 'r')
for word in input_sentencedata:
sentences.append(word)
vector_one = []
inner_vector = []
for word in unique_words:
if word in sentences:
vector_one.append(1)
else:
vector_one.append(0)
inner_vector.append(vector_one)
inner_vector = np.array(inner_vector, dtype=np.float32)
print("inner_vector:", inner_vector)
label = model.predict_label([inner_vector])
pred = model.predict([inner_vector])
return pred
def main():
"""
:return:
"""
# pickle parameters
fg_or_bg = 'background'
sdr_type = 'sdr'
feature = 'sim_mat'
beat_spec_len = 432
# set up training, testing, & validation partitions
sim_mat_array, sdr_array = get_generated_data(feature, fg_or_bg, sdr_type)
# training params
n_classes = 10
n_training_steps = 1000
training_step_size = 100
training_percent = 0.85
testing_percent = 0.15
validation_percent = 0.00
sdr_array_1h, hist = sdrs_to_one_hots(sdr_array, n_classes, True)
train, test, validate = split_into_sets(len(sim_mat_array), training_percent,
testing_percent, validation_percent)
# Building convolutional network
network = input_data(shape=[None, beat_spec_len, 1], name='input')
network = conv_1d(network, 32, 3, activation='relu', regularizer="L2")
network = max_pool_1d(network, 2)
# network = local_response_normalization(network)
# network = batch_normalization(network)
# network = conv_1d(network, 64, 3, activation='relu', regularizer="L2")
# network = max_pool_1d(network, 2)
# network = local_response_normalization(network)
# network = batch_normalization(network)
# network = fully_connected(network, 128, activation='tanh')
# network = dropout(network, 0.5)
network = fully_connected(network, 512, activation='tanh')
network = dropout(network, 0.5)
network = fully_connected(network, n_classes, activation='softmax')
# network = fully_connected(network, 1, activation='linear')
network = regression(network, optimizer='adagrad', learning_rate=0.01,
loss='categorical_crossentropy', name='target')
X = np.expand_dims(sim_mat_array, -1)
Y = np.array(sdr_array_1h)
# X = np.expand_dims([beat_spec_array[i] for i in train], -1)
# Y = np.array([sdr_array_1h[i] for i in train])
# testX = np.expand_dims([beat_spec_array[i] for i in test], -1)
# testY = np.array([sdr_array[i] for i in test])
# Training
model = tflearn.DNN(network, tensorboard_verbose=1)
model.fit({'input': X}, {'target': Y}, n_epoch=20,
validation_set=0.1,
snapshot_step=1000, show_metric=True, run_id='{} classes'.format(n_classes - 1))
def model_fn(net,
X_len,
max_reach,
block_size,
out_classes,
batch_size,
reuse=False,
**kwargs):
"""
Args:
net -> Input tensor shaped (batch_size, max_reach + block_size + max_reach, 3)
Returns:
logits -> Unscaled logits tensor in time_major form, (block_size, batch_size, out_classes)
"""
print("model in", net.get_shape())
with tf.name_scope("model"):
for j in range(3):
with tf.variable_scope("block%d" % (j + 1)):
for i, no_channel in zip([1, 4, 16],
np.array([64, 64, 128]) * (2**j)):
with tf.variable_scope("atrous_conv1d_%d" % i):
filter = tf.get_variable("W",
shape=(3, net.get_shape()[-1],
no_channel))
bias = tf.get_variable("b", shape=(no_channel, ))
net = atrous_conv1d(net, filter, i,
padding="SAME") + bias
net = tf.nn.relu(net)
net = max_pool_1d(net, 2)
print("after conv", net.get_shape())
net = tf.transpose(net, [1, 0, 2], name="Shift_to_time_major")
outputs = net
# outputs.get_shape()[-1] # Number of output filters
state_size = 128 * 4
init_state = tf.constant(0.1, dtype=tf.float32)
final_state = tf.constant(0.1, dtype=tf.float32)
print("outputs", outputs.get_shape())
with tf.variable_scope("Output"):
W = tf.get_variable("W", shape=[state_size, out_classes])
b = tf.get_variable("b", shape=[out_classes])
logits = tf.nn.conv1d(outputs,
tf.reshape(W, (1, state_size, out_classes)),
1,
padding='SAME')
logits += b
print("model out", logits.get_shape())
return {
'logits': logits,
'init_state': init_state,
'final_state': final_state,
}
def build_model_specific():
### IS ANY OF THIS NECESSARY FOR LIGHT/DARK? IN GENERAL W/ STAIONARY CAMERA?
img_prep = ImagePreprocessing()
img_prep.add_featurewise_zero_center()
img_prep.add_featurewise_stdnorm()
img_aug = ImageAugmentation()
img_aug.add_random_flip_leftright()
# Specify shape of the data, image prep
network = input_data(shape=[None, 52, 64],
data_preprocessing=img_prep,
data_augmentation=img_aug)
# conv_2d incoming, nb_filter, filter_size
# incoming: Tensor. Incoming 4-D Tensor.
# nb_filter: int. The number of convolutional filters. # WHAT IS THIS?
# filter_size: 'intor list ofints`. Size of filters. # WHAT IS THIS?
network = conv_1d(network, 512, 3, activation='relu')
# (incoming, kernel_size)
# incoming: Tensor. Incoming 4-D Layer.
# kernel_size: 'intor list ofints`. Pooling kernel size.
network = max_pool_1d(network, 2)
network = conv_1d(network, 64, 3, activation='relu')
network = conv_1d(network, 64, 3, activation='relu')
network = max_pool_1d(network, 2)
network = fully_connected(network, 512, activation='relu')
network = dropout(network, 0.5)
network = fully_connected(network, 4, activation='softmax')
network = regression(network, optimizer='adam',
loss='categorical_crossentropy',
learning_rate=0.0003)
model = tflearn.DNN(network, tensorboard_verbose=0)
return model
def make_audio_convnet():
global buzz_train_d_conv
buzz_test_d_conv = buzz_train_d_conv
input_layer = input_data(shape=[None, MAX_CONV, 1])
conv_layer_1 = conv_1d(input_layer,
nb_filter=8,
filter_size=79,
activation='relu',
name='conv_layer_1')
pool_layer_1 = max_pool_1d(conv_layer_1, 100, name='pool_layer_1')
conv_layer_2 = conv_1d(pool_layer_1,
nb_filter=16,
filter_size=11,
activation='relu',
name='conv_layer_2')
pool_layer_2 = max_pool_1d(conv_layer_2, 5, name='pool_layer_2')
fc_layer_1 = fully_connected(pool_layer_2,
100,
activation='tanh',
name='fc_layer_1')
fc_layer_2 = fully_connected(fc_layer_1,
3,
activation='softmax',
name='fc_layer_2')
network = regression(fc_layer_2,
optimizer='sgd',
loss='categorical_crossentropy',
learning_rate=0.1)
model = tflearn.DNN(network)
model.fit(buzz_train_d_conv[0],
buzz_train_d_conv[1],
n_epoch=30,
shuffle=True,
validation_set=(buzz_test_d_conv[0], buzz_test_d_conv[1]),
show_metric=True,
batch_size=100,
run_id='audio_convnet')
model.save('pck_nets/AudioConvNet.tfl')
def model_fn(net, X_len, max_reach, block_size, out_classes, batch_size, dtype,
**kwargs):
"""
Args:
net -> Input tensor shaped (batch_size, max_reach + block_size + max_reach, 3)
Returns:
logits -> Unscaled logits tensor in time_major form, (block_size, batch_size, out_classes)
"""
print("model in", net.get_shape())
for block in range(1, 4):
with tf.variable_scope("block%d" % block):
if block > 1:
net = tf.expand_dims(net, 3)
net = tf.layers.max_pooling2d(net, [1, 2], [1, 2])
net = tf.squeeze(net, axis=3)
for layer in range(kwargs['num_layers']):
with tf.variable_scope('layer_%d' % layer):
res = net
for sublayer in range(kwargs['num_sub_layers']):
res = batch_normalization(res,
scope='bn_%d' % sublayer)
res = tf.nn.relu(res)
res = conv_1d(
res,
32 * 2**(4 - block),
3,
scope="conv_1d_%d" % sublayer,
weights_init=variance_scaling_initializer(
dtype=dtype))
k = tf.get_variable(
"k",
initializer=tf.constant_initializer(1.0),
shape=[])
net = tf.nn.relu(k) * res + net
net = max_pool_1d(net, 2)
net = tf.nn.relu(net)
net = central_cut(net, block_size, 8)
print("after slice", net.get_shape())
net = tf.transpose(net, [1, 0, 2], name="Shift_to_time_major")
print("after transpose", net.get_shape())
net = conv_1d(net, 9, 1, scope='logits')
print("model out", net.get_shape())
return {
'logits': net,
'init_state': tf.constant(0),
'final_state': tf.constant(0),
}
def model_fn(net, X_len, max_reach, block_size, out_classes, batch_size, k, reuse=False, **kwargs):
"""
Args:
net -> Input tensor shaped (batch_size, max_reach + block_size + max_reach, 3)
Returns:
logits -> Unscaled logits tensor in time_major form, (block_size, batch_size, out_classes)
"""
print("model in", net.get_shape())
# net = tf.Print(net, [tf.shape(net), tf.shape(X_len)], message="netty")
for j in range(3):
with tf.variable_scope("block%d" % (j + 1)):
for i, no_channel in zip([1, 2, 4], [16, 16, 16]):
with tf.variable_scope("atrous_conv1d_%d" % i):
filter = tf.get_variable("W", shape=(3, net.get_shape()[-1], no_channel))
bias = tf.get_variable("b", shape=(no_channel,))
net = atrous_conv1d(net, filter, i, padding="VALID") + bias
net = tf.nn.relu(net)
tf.get_default_graph().add_to_collection("activations", net)
net = tf.Print(net, [tf.shape(net)], first_n=10, message="net, pre_pool")
net = max_pool_1d(net, 2)
print("after conv", net.get_shape())
net = tf.transpose(net, [1, 0, 2], name="Shift_to_time_major")
state_size = 32 # outputs.get_shape()[-1] # Number of output filters
with tf.name_scope("RNN"):
cell = tf.nn.rnn_cell.GRUCell(state_size)
init_state = cell.zero_state(batch_size, dtype=tf.float32)
outputs, final_state = tf.nn.dynamic_rnn(cell, net, initial_state=init_state, sequence_length=X_len, time_major=True)
# outputs = net
# init_state = tf.constant(0.1, dtype=tf.float32)
# final_state = tf.constant(0.1, dtype=tf.float32)
outputs = tf.Print(outputs, [tf.shape(outputs)], first_n=1, message="outputs_pre_w")
print("outputs", outputs.get_shape())
with tf.variable_scope("Output"):
outputs = tf.reshape(outputs, [-1, state_size])
W = tf.get_variable("W", shape=[state_size, out_classes])
b = tf.get_variable("b", shape=[out_classes])
outputs = tf.matmul(outputs, W) + b
logits = tf.reshape(outputs, [block_size // 8, batch_size, out_classes])
print("model out", logits.get_shape())
return {
'logits': logits,
'init_state': init_state,
'final_state': final_state,
'reg': k * ops.running_mean(logits, [3, 4, 5, 6], [1, 2, 4, 8], out_classes)
}
def model(lr=LEARNING_RATE):
network = input_data(shape=[None, 600, 4], name='features')
network = conv_1d(network, 300, 19, strides=1, activation='relu')
network = max_pool_1d(network, 3, strides=3)
network = conv_1d(network, 200, 11, strides=1, activation='relu')
network = max_pool_1d(network, 4, strides=4)
network = conv_1d(network, 200, 7, strides=1, activation='relu')
network = max_pool_1d(network, 4, strides=4)
network = fully_connected(network, 1000, activation='relu')
network = fully_connected(network, 1000, activation='relu')
network = fully_connected(network, 164, activation='sigmoid')
network = regression(network,
optimizer='rmsprop',
loss='binary_crossentropy',
learning_rate=lr,
name='labels')
model = tflearn.DNN(network,
checkpoint_path=MODEL_PATH,
tensorboard_dir=TRAIN_PATH,
tensorboard_verbose=3,
max_checkpoints=1)
return model
def main():
pickle_folder = '../pickles_rolloff'
pickle_folders_to_load = [f for f in os.listdir(pickle_folder) if os.path.isdir(join(pickle_folder, f))]
pickle_folders_to_load = sorted(pickle_folders_to_load)
# pickle parameters
fg_or_bg = 'background'
sdr_type = 'sdr'
feature = 'beat_spec'
beat_spec_len = 432
# training params
n_classes = 16
training_percent = 0.85
testing_percent = 0.15
validation_percent = 0.00
# set up training, testing, & validation partitions
beat_spec_array, sdr_array = load_beat_spec_and_sdrs(pickle_folders_to_load, pickle_folder,
feature, fg_or_bg, sdr_type)
train, test, validate = split_into_sets(len(pickle_folders_to_load), training_percent,
testing_percent, validation_percent)
trainX = np.expand_dims([beat_spec_array[i] for i in train], -1)
trainY = np.expand_dims([sdr_array[i] for i in train], -1)
testX = np.expand_dims([beat_spec_array[i] for i in test], -1)
testY = np.array([sdr_array[i] for i in test])
# Building convolutional network
input = input_data(shape=[None, beat_spec_len, 1])
conv1 = conv_1d(input, 32, 10, activation='relu', regularizer="L2")
max_pool1 = max_pool_1d(conv1, 2)
full = fully_connected(max_pool1, 512, activation='tanh')
# single = tflearn.single_unit(full)
single = fully_connected(full, 1, activation='linear')
regress = tflearn.regression(single, optimizer='sgd', loss='mean_square', learning_rate=0.01)
# Training
model = tflearn.DNN(regress, tensorboard_verbose=1)
model.fit(trainX, trainY, n_epoch=500,
snapshot_step=1000, show_metric=True, run_id='{} classes'.format(n_classes - 1))
predicted = np.array(model.predict(testX))[:,0]
plot(testY, predicted)
def model_fn(net,
X_len,
max_reach,
block_size,
out_classes,
batch_size,
reuse=False,
**kwargs):
"""
Args:
net -> Input tensor shaped (batch_size, max_reach + block_size + max_reach, 3)
Returns:
logits -> Unscaled logits tensor in time_major form, (block_size, batch_size, out_classes)
"""
print("model in", net.get_shape())
for j in range(3):
with tf.variable_scope("block%d" % (j + 1)):
for i, no_channel in zip([1, 4, 16],
np.array([64, 64, 128]) * (2**j)):
with tf.variable_scope("atrous_conv1d_%d" % i):
filter = tf.get_variable("W",
shape=(3, net.get_shape()[-1],
no_channel))
net = tf.nn.convolution(net,
filter,
padding="SAME",
dilation_rate=[i])
net = batch_normalization(net, scope='bn')
net = tf.nn.relu(net)
net = max_pool_1d(net, 2)
net = central_cut(net, block_size, 8)
net = tf.transpose(net, [1, 0, 2], name="Shift_to_time_major")
net = conv_1d(net, 9, 1, scope='logits')
print("model out", net.get_shape())
return {
'logits': net,
'init_state': tf.constant(0),
'final_state': tf.constant(0),
}
def create1dConvNetNeuralNetworkModel(input_size, output_size, learningRate):
# Specify the log directory
logdir = 'log/1d/' + datetime.now().strftime('%Y%m%d-%H%M%S')
# Limit gpu memory use
#tflearn.init_graph(num_cores=1, gpu_memory_fraction=0.7)
convnet = input_data(shape=[None, input_size], name='input_currentState')
convnet = tflearn.embedding(convnet, input_dim=input_size, output_dim=2)
convnet = conv_1d(convnet,
nb_filter=16,
filter_size=3,
strides=1,
padding='valid',
activation='relu')
convnet = max_pool_1d(convnet, kernel_size=2, strides=2, padding='valid')
convnet = flatten(convnet)
convnet = fully_connected(convnet,
n_units=128,
weights_init='truncated_normal',
activation='relu')
convnet = dropout(convnet, 0.5)
convnet = fully_connected(convnet,
n_units=output_size,
activation='softmax')
convnet = regression(convnet,
optimizer='adam',
learning_rate=learningRate,
loss='categorical_crossentropy',
name='targets')
model = tflearn.DNN(convnet, tensorboard_dir=logdir)
return model
# Preprocess data lendat=len(data) data = preprocess(data, lendat) lendatVal=len(dataVal) dataVal = preprocess(dataVal, lendatVal) W= tflearn.initializations.xavier(uniform=True, seed=None, dtype=tf.float32) # Building convolutional network network = input_data(shape=[None, 1024], name='input') network = tflearn.embedding(network, input_dim=71, output_dim=256) network = conv_1d(network, 256, 7, padding='valid', scope='conv1', activation='relu') network = max_pool_1d(network, 3, strides=3, name='Maxpool1D_1') network = conv_1d(network, 256, 7, padding='valid', scope='conv2', activation='relu') network = max_pool_1d(network, 3, strides=3, name='Maxpool1D_2') network = conv_1d(network, 256, 3, padding='valid', scope='conv3', activation='relu') network = conv_1d(network, 256, 3, padding='valid', scope='conv4', activation='relu') network = conv_1d(network, 256, 3, padding='valid', scope='conv5', activation='relu') network = conv_1d(network, 256, 3, padding='valid', scope='conv6', activation='relu') network = max_pool_1d(network, 3, strides=3, name='Maxpool1D_Last') network = tflearn.fully_connected(network, 1024, name='Fullyconected_0') network = dropout(network, 0.5) network = tflearn.fully_connected(network, 1024, name='Fullyconected_1') network = dropout(network, 0.5) network = fully_connected(network, 14, activation='softmax', name='FullyConected_Last') network = regression(network, optimizer='adam', loss='categorical_crossentropy', name='target')
if i == 0:
VU = temp
else:
VU = merge([VU, temp], mode='concat', axis=0)
alphas_prot = tf.nn.softmax(tf.reduce_max(VU, axis=2), name='alphas')
Attn_prot = tf.reduce_sum(prot_gru_2 * tf.expand_dims(alphas_prot, -1), 1)
Attn_prot_reshape = tflearn.reshape(Attn_prot, [-1, GRU_size_prot, 1])
conv_1 = conv_1d(Attn_prot_reshape,
64,
8,
4,
activation='leakyrelu',
weights_init="xavier",
regularizer="L2",
name='conv1')
pool_1 = max_pool_1d(conv_1, 4, name='pool1')
prot_reshape_6 = tflearn.reshape(pool_1, [-1, 64 * 16])
prot_embd_W = []
prot_gru_1_gate_matrix = []
prot_gru_1_gate_bias = []
prot_gru_1_candidate_matrix = []
prot_gru_1_candidate_bias = []
prot_gru_2_gate_matrix = []
prot_gru_2_gate_bias = []
prot_gru_2_candidate_matrix = []
prot_gru_2_candidate_bias = []
for v in tf.global_variables():
if "GRU/GRU/GRUCell/Gates/Linear/Matrix" in v.name:
prot_gru_1_gate_matrix.append(v)
elif "GRU/GRU/GRUCell/Candidate/Linear/Matrix" in v.name:
from tflearn.data_utils import to_categorical, image_preloader
import tflearn.datasets.mnist as mnist
import time
start_time = time.time()
# Data loading and preprocessing
X, Y = image_preloader('data.txt',
image_shape=(900, 900),
mode='file',
categorical_labels=True,
normalize=False)
# Building 'AlexNet'
network = input_data(shape=[None, 900, 900])
network = conv_1d(network, 96, 11, strides=4, activation='relu')
network = max_pool_1d(network, 1, strides=2)
#network = local_response_normalization(network)
network = conv_1d(network, 256, 5, activation='relu')
network = max_pool_1d(network, 1, strides=2)
#network = local_response_normalization(network)
network = conv_1d(network, 384, 3, activation='relu')
network = conv_1d(network, 384, 3, activation='relu')
network = conv_1d(network, 256, 3, activation='relu')
network = max_pool_1d(network, 1, strides=2)
#network = local_response_normalization(network)
network = fully_connected(network, 4096, activation='tanh')
network = dropout(network, 0.5)
network = fully_connected(network, 4096, activation='tanh')
network = dropout(network, 0.5)
network = fully_connected(network, 3, activation='softmax')
network = regression(network,
def model_fn(net, X_len, max_reach, block_size, out_classes, batch_size, dtype, **kwargs):
"""
Args:
net -> Input tensor shaped (batch_size, max_reach + block_size + max_reach, 3)
Returns:
logits -> Unscaled logits tensor in time_major form, (block_size, batch_size, out_classes)
"""
for block in range(1, 3):
with tf.variable_scope("block%d" % block):
for layer in range(kwargs['num_layers']):
with tf.variable_scope('layer_%d' % layer):
res = net
for sublayer in range(kwargs['num_sub_layers']):
res = batch_normalization(
res, scope='bn_%d' % sublayer)
res = tf.nn.relu(res)
res = conv_1d(
res,
64,
3,
scope="conv_1d_%d" % sublayer,
weights_init=variance_scaling_initializer(
dtype=dtype)
)
k = tf.get_variable(
"k", initializer=tf.constant_initializer(1.0), shape=[])
net = tf.nn.relu(k) * res + net
net = max_pool_1d(net, 2)
net = tf.nn.relu(net)
net = central_cut(net, block_size, 4)
net = tf.transpose(net, [1, 0, 2], name="Shift_to_time_major")
# with tf.name_scope("RNN"):
# from tensorflow.contrib.cudnn_rnn import CudnnGRU, RNNParamsSaveable
# rnn_layer = CudnnGRU(
# num_layers=1,
# num_units=64,
# input_size=64,
# )
#
# print(rnn_layer.params_size())
# import sys
# sys.exit(0)
# rnn_params = tf.get_variable("rnn_params", shape=[rnn_layer.params_size()], validate_shape=False)
# params_saveable = RNNParamsSaveable(
# rnn_layer.params_to_canonical, rnn_layer.canonical_to_params, [rnn_params])
# tf.add_to_collection(tf.GraphKeys.SAVEABLE_OBJECTS, params_saveable)
#
with tf.name_scope("RNN"):
cell = tf.contrib.rnn.GRUCell(64)
init_state = cell.zero_state(batch_size, dtype=tf.float32)
outputs, final_state = tf.nn.dynamic_rnn(cell, net, initial_state=init_state, sequence_length=tf.div(X_len + 3, 4), time_major=True, parallel_iterations=128)
net = conv_1d(outputs, 9, 1, scope='logits')
return {
'logits': net,
'init_state': init_state,
'final_state': final_state
}
class Thai_sentiment():
file_path = './corpus/Combined_inhousedata_UTF8-1.csv'
file_path3 = './trainingdataset/combined_inhousedata-UTF8-traindataset-1.csv'
data, labels = load_csv(file_path, target_column=0, categorical_labels=True, n_classes=2)
testdata, testlabels = load_csv(file_path3, target_column=0, categorical_labels=True, n_classes=2)
def preprocess_server(data):
rlist = []
preprocessdata = []
for i in range(len(data)):
x = requests.get('http://174.138.26.245:5000/preprocess/'+data[i][0])
resu = x.json()
preprocessdata.append(resu['result'])
for i in range(len(preprocessdata)):
r = requests.get('http://174.138.26.245:5000/tokenize/'+preprocessdata[i])
result = r.json()
rlist.append(result['result'])
return rlist
'''def get_uniquewords(listdata):
f = open('./uniqueword/combined_inhousedata_UTF8-1_uniquewords.csv', 'w')
uniquewords = []
for line in range(len(listdata)):
words = listdata[line]
inner_data = []
for word in words:
if word not in uniquewords:
#w = repr(word.encode('utf-8'))
uniquewords.append(word)
f.write(word+'\n')
f.close()
return uniquewords'''
def preprocess_vector(listdata, uniquewords):
sentences = []
vectors = []
mainvector = []
#f = open(file_path, 'r')
for line in range(len(listdata)):
words = listdata[line]
inner_data = []
for word in words:
inner_data.append(word)
sentences.append(inner_data)
for sentence in sentences:
inner_vector = []
vectors = []
for word in uniquewords:
if word in sentence:
inner_vector.append(1)
else:
inner_vector.append(0)
vectors.append(inner_vector)
mainvector.append(vectors)
return np.array(mainvector, dtype=np.float32)
def uniqueword_csvload():
uniquewords = []
f = open('./uniqueword/combined_inhousedata_UTF8-1_uniquewords.csv', 'r')
for word in f:
uniquewords.append(word.strip())
return uniquewords
pdata = preprocess_server(data)
# unique_words = get_uniquewords(pdata)
unique_words = uniqueword_csvload()
data = preprocess_vector(pdata, unique_words)
resultdata = preprocess_server(testdata)
resultdata = preprocess_vector(resultdata, unique_words)
neurons = len(unique_words)
# shuffle the dataset
data, labels = shuffle(data, labels)
reset_default_graph()
network = input_data(shape=[None, 1, neurons])
network = conv_1d(network, 8, 3, activation='relu')
network = max_pool_1d(network, 3)
network = conv_1d(network, 16, 3, activation='relu')
network = max_pool_1d(network, 3)
network = fully_connected(network, 8, activation='relu')
network = dropout(network, 0.5)
network = fully_connected(network, 2, activation='softmax')
network = regression(network, optimizer='adam', learning_rate=0.01, loss='categorical_crossentropy')
model = tflearn.DNN(network)
model.fit(data, labels, n_epoch=100, shuffle=True, validation_set=(resultdata, testlabels) , show_metric=True, batch_size=None, snapshot_epoch=True, run_id='task-classifier')
model.save("./model/thaitext-classifier-combined_inhousedata-UTF8-1-100.tfl")
print("Network trained and saved as thaitext-classifier-combined_inhousedata-UTF8-1-100.tfl")
result = model.evaluate(resultdata, testlabels)
print("Evaluation result: %s" %result)
tp = 0
fp = 0
tn = 0
fn = 0
predict = model.predict(resultdata)
for i in range(0, len(testlabels)):
pred = predict[i]
label = testlabels[i]
if label[1] == 1: # data is supposed be positive
if pred[1] > 0.5: # data is positive
tp += 1
else: # data is negative
fp += 1
else: # data is supposed to negative
if pred[0] > 0.5:
tn += 1 # data is negative
else:
fn += 1 # data is positive
precision = float(tp / (tp + fp))
recall = float(tp / (tp + fn))
accuracy = float((tp + tn)/(tp + fp + tn + fn))
f1 = float((2*precision*recall)/(precision+recall))
print ("Precision: %s; Recall: %s" %(precision, recall))
print("Acc: %s, F1: %s" %(accuracy, f1))
feature_GPCR_compound = tflearn.data_utils.featurewise_std_normalization(feature_GPCR_compound,std_feature_train_compound) feature_GPCR_protein = tflearn.data_utils.featurewise_std_normalization(feature_GPCR_protein,std_feature_train_protein) feature_kinase_compound = tflearn.data_utils.featurewise_zero_center(feature_kinase_compound,mean_feature_train_compound) feature_kinase_protein = tflearn.data_utils.featurewise_zero_center(feature_kinase_protein,mean_feature_train_protein) feature_kinase_compound = tflearn.data_utils.featurewise_std_normalization(feature_kinase_compound,std_feature_train_compound) feature_kinase_protein = tflearn.data_utils.featurewise_std_normalization(feature_kinase_protein,std_feature_train_protein) # Sep model prot_data = input_data(shape=[None, 512]) prot_reshape = tflearn.reshape(prot_data, [-1, 256,2]) conv_1 = conv_1d(prot_reshape, 64, 4,2, activation='leakyrelu',weights_init="xavier", regularizer="L2",name='conv1') pool_1 = max_pool_1d(conv_1, 4,name='pool1') conv_2 = conv_1d(pool_1, 32, 4,2, activation='leakyrelu', weights_init="xavier",regularizer="L2",name='conv2') pool_2 = max_pool_1d(conv_2, 2,name='pool2') prot_reshape_4 = tflearn.reshape(pool_2, [-1, 32*8]) drug_data = input_data(shape=[None,256]) drug_reshape = tflearn.reshape(drug_data, [-1, 128,2]) conv_3 = conv_1d(drug_reshape, 64, 4,2, activation='leakyrelu', weights_init="xavier",regularizer="L2",name='conv3') pool_3 = max_pool_1d(conv_3, 2,name='pool3') conv_4 = conv_1d(pool_3, 32, 4,2, activation='leakyrelu', weights_init="xavier",regularizer="L2",name='conv4') pool_4 = max_pool_1d(conv_4, 2,name='pool4') drug_reshape_4 = tflearn.reshape(pool_4, [-1, 32*8]) merging = merge([prot_reshape_4,drug_reshape_4],mode='concat',axis=1) fc_2 = fully_connected(merging, 200, activation='leakyrelu',weights_init="xavier",name='fully2')
from tflearn.data_augmentation import ImageAugmentation
import time
import h5py
start_time = time.time()
X, Y = image_preloader('data.txt', image_shape=(900, 900), mode='file', categorical_labels=True, normalize=False)
img_aug = ImageAugmentation()
img_aug.add_random_flip_leftright()
img_aug.add_random_rotation(max_angle=25.)
img_aug.add_random_blur(sigma_max=3.)
conv_input = input_data(shape=[None, 900, 900], name='input', data_augmentation=img_aug)
conv = conv_1d(conv_input, 10, filter_size=100, activation='leaky_relu', strides=1)
conv1 = conv_1d(conv_input, 5, filter_size=50, activation='leaky_relu', strides=1)
conv1 = max_pool_1d(conv1, kernel_size=2, strides=1)
convnet = merge([conv, conv1], mode='concat', axis=2)
convnet = conv_1d(convnet, 10, filter_size=20, activation='leaky_relu')
convnet = max_pool_1d(convnet, kernel_size=2, strides=1)
convnet = dropout(convnet, 0.5)
convnet = fully_connected(convnet, 3, activation='softmax')
convnet = regression(convnet, optimizer='adam', learning_rate=0.0001, loss='categorical_crossentropy')
model = tflearn.DNN(convnet, tensorboard_verbose=3, tensorboard_dir='Tensordboard/')
model.fit(X, Y, n_epoch=5, validation_set=0.2, show_metric=True, batch_size=20, shuffle=True,
snapshot_epoch=True, run_id='Digital Mammography ConCaDNet')
model.save('Model/model.tflearn')
end_time = time.time()
print("Training Time:")
print(end_time - start_time)
[GRU_size_prot], stddev=0.1),
restore=False)
V_prot = tf.tanh(tf.tensordot(prot_gru_2, W_prot, axes=1) + b_prot)
VU_prot = tf.tensordot(V_prot, U_prot, axes=1)
alphas_prot = tf.nn.softmax(VU_prot, name='alphas')
Attn_prot = tf.reduce_sum(prot_gru_2 * tf.expand_dims(alphas_prot, -1), 1)
Attn_prot_reshape = tflearn.reshape(Attn_prot, [-1, GRU_size_prot, 1])
conv_1 = conv_1d(Attn_prot_reshape,
64,
8,
4,
activation='leakyrelu',
weights_init="xavier",
regularizer="L2",
name='conv1')
pool_1 = max_pool_1d(conv_1, 4, name='pool1')
prot_reshape_6 = tflearn.reshape(pool_1, [-1, 64 * 16])
prot_embd_W = []
prot_gru_1_gate_matrix = []
prot_gru_1_gate_bias = []
prot_gru_1_candidate_matrix = []
prot_gru_1_candidate_bias = []
prot_gru_2_gate_matrix = []
prot_gru_2_gate_bias = []
prot_gru_2_candidate_matrix = []
prot_gru_2_candidate_bias = []
for v in tf.global_variables():
if "GRU/GRU/GRUCell/Gates/Linear/Matrix" in v.name:
prot_gru_1_gate_matrix.append(v)
elif "GRU/GRU/GRUCell/Candidate/Linear/Matrix" in v.name:
# y_train = load_array(data/+'train_labels.bc')
# x_val = load_array(data/+'val_data.bc')
# y_val = load_array(data/+'val_labels.bc')
# embedding_matrix = load_array(data/+'embedding_matrix.bc')
# The syntax with tflearn is almost identical to keras. Only differences
# are: there is no need to flatten a tensor before passing it to a
# fully_connected layer, since the fc layer will take care of that
# automatically. Also, the default padding in tflearn is 'same', while in
# keras is 'valid'.
net = input_data(shape=[None,MAX_SEQUENCE_LENGTH], name='input')
net = embedding(net, input_dim=MAX_NB_WORDS, output_dim=EMBEDDING_DIM, trainable=False, name="EmbeddingLayer")
net = conv_1d(net, 128, 5, 1, activation='relu', padding="valid")
# one could add regularization as:
# net = conv_1d(net, 128, 5, 1, activation='relu', regularizer="L2", padding="valid")
net = max_pool_1d(net, 5, padding="valid")
net = batch_normalization(net)
net = conv_1d(net, 128, 5, activation='relu', padding="valid")
net = max_pool_1d(net, 5, padding="valid")
net = batch_normalization(net)
net = conv_1d(net, 128, 5, activation='relu', padding="valid")
net = max_pool_1d(net, 35)
net = batch_normalization(net)
net = fully_connected(net, 128, activation='relu')
net = dropout(net, 0.5)
net = fully_connected(net, y_train.shape[1], activation='softmax')
net = regression(net, optimizer='adam', learning_rate=0.01,
loss='categorical_crossentropy', name='target')
model = tflearn.DNN(net, tensorboard_verbose=0)
embeddingWeights = tflearn.get_layer_variables_by_name('EmbeddingLayer')[0]
model.set_weights(embeddingWeights, embedding_matrix)
def model_fn(net,
X_len,
max_reach,
block_size,
out_classes,
batch_size,
k,
reuse=False):
"""
Args:
net -> Input tensor shaped (batch_size, max_reach + block_size + max_reach, 3)
Returns:
logits -> Unscaled logits tensor in time_major form, (block_size, batch_size, out_classes)
"""
print("model in", net.get_shape())
with tf.name_scope("model"):
for j in range(3):
with tf.variable_scope("block%d" % (j + 1)):
for i, no_channel in zip([1, 4, 16],
np.array([64, 64, 128]) * (2**j)):
with tf.variable_scope("atrous_conv1d_%d" % i):
filter = tf.get_variable("W",
shape=(3, net.get_shape()[-1],
no_channel))
bias = tf.get_variable("b", shape=(no_channel, ))
net = atrous_conv1d(net, filter, i,
padding="VALID") + bias
net = tf.nn.relu(net)
net = tf.Print(net, [tf.shape(net)],
first_n=5,
message="net, pre_pool")
net = max_pool_1d(net, 2)
print("after conv", net.get_shape())
net = tf.transpose(net, [1, 0, 2], name="Shift_to_time_major")
outputs = net
state_size = 128
with tf.name_scope("RNN"):
cell = tf.nn.rnn_cell.GRUCell(state_size)
cell = tf.nn.rnn_cell.MultiRNNCell([cell for _ in range(3)])
init_state = cell.zero_state(batch_size, dtype=tf.float32)
outputs, final_state = tf.nn.dynamic_rnn(cell,
net,
initial_state=init_state,
sequence_length=X_len,
time_major=True,
parallel_iterations=128)
outputs = tf.Print(outputs, [tf.shape(outputs)],
first_n=1,
message="outputs_pre_w")
print("outputs", outputs.get_shape())
with tf.variable_scope("Output"):
outputs = tf.reshape(outputs, [-1, state_size])
W = tf.get_variable("W", shape=[state_size, out_classes])
b = tf.get_variable("b", shape=[out_classes])
outputs = tf.matmul(outputs, W) + b
logits = tf.reshape(outputs,
[block_size // 8, batch_size, out_classes])
print("model out", logits.get_shape())
return {
'logits': logits,
'init_state': init_state,
'final_state': final_state,
'reg': k * ops.running_mean(logits, [5, 6, 7], [4, 8, 16], out_classes)
}
def my_model(img_prep, img_aug):
# dropout_probability = 0.5
dropout_probability = 1.0
initial_learning_rate = 0.0001
learning_decay = 1E-5
initializer = 'uniform_scaling'
# initializer = 'truncated_normal'
activation_function = 'relu'
# activation_function = 'sigmoid'
objective_function = 'categorical_crossentropy'
# objective_function = 'mean_square'
chooseme = R2()
network = input_data(shape=[None, 1024, 1],
data_preprocessing=img_prep,
data_augmentation=img_aug)
# network = conv_2d(network, 32, 3, strides=1, padding='same', activation=activation_function,
# bias=True, bias_init='zeros', weights_init=initializer,
# regularizer='L2')
network = conv_1d(network,
32,
4,
strides=1,
padding='same',
activation=activation_function,
bias=True,
bias_init='zeros',
weights_init=initializer)
# network = max_pool_2d(network, 2, strides=None, padding='same')
# temporarily removing this puppy
network = max_pool_1d(network, 2, strides=None, padding='same')
# network = conv_2d(network, 64, 3, strides=1, padding='same', activation=activation_function,
# bias=True, bias_init='zeros', weights_init=initializer)
network = conv_1d(network,
64,
4,
strides=1,
padding='same',
activation=activation_function,
bias=True,
bias_init='zeros',
weights_init=initializer)
# network = conv_2d(network, 64, 3, strides=1, padding='same', activation=activation_function,
# bias=True, bias_init='zeros', weights_init=initializer)
network = conv_1d(network,
64,
4,
strides=1,
padding='same',
activation=activation_function,
bias=True,
bias_init='zeros',
weights_init=initializer)
# network = max_pool_2d(network, 2, strides=None, padding='same')
network = max_pool_1d(network, 2, strides=None, padding='same')
network = fully_connected(network, 512, activation=activation_function)
network = dropout(network, dropout_probability)
network = fully_connected(network, 7, activation='softmax')
network = regression(network,
optimizer='adam',
loss=objective_function,
learning_rate=initial_learning_rate,
metric=chooseme)
# sgd = SGD(learning_rate=initial_learning_rate, lr_decay=learning_decay, decay_step=90)
# network = regression(network, optimizer=sgd,
# loss='categorical_crossentropy')
return network
def build_tflearn_ann(length):
input_layer = input_data(shape=[None, length, 1])
pool_layer_1 = max_pool_1d(input_layer, 10, name='pool_layer_1')
pool_layer_2 = max_pool_1d(pool_layer_1, 5, name='pool_layer_2')
pool_layer_3 = max_pool_1d(pool_layer_2, 5, name='pool_layer_3')
pool_layer_4 = max_pool_1d(pool_layer_3, 5, name='pool_layer_3')
fully_connect_1 = fully_connected(pool_layer_3,
512,
activation='relu',
name='fully_connect_1',
weights_init='xavier',
regularizer="L2")
fully_connect_2 = fully_connected(pool_layer_2,
512,
activation='relu',
name='fully_connect_2',
weights_init='xavier',
regularizer="L2")
fully_connect_3 = fully_connected(pool_layer_1,
512,
activation='relu',
name='fully_connect_3',
weights_init='xavier',
regularizer="L2")
fully_connect_4 = fully_connected(pool_layer_4,
512,
activation='relu',
name='fully_connect_3',
weights_init='xavier',
regularizer="L2")
# Merge above layers
merge_layer = tflearn.merge_outputs(
[fully_connect_1, fully_connect_2, fully_connect_3, fully_connect_4])
# merge_layer = tflearn.merge_outputs(
# [fully_connect_1, fully_connect_2, fully_connect_3, fully_connect_4, fully_connect_5])
# merge_layer = tflearn.merge_outputs(
# [fully_connect_1, fully_connect_2, fully_connect_3, fully_connect_4, fully_connect_5, fully_connect_6,
# fully_connect_7, fully_connect_8, fully_connect_9, fully_connect_10])
drop_2 = dropout(merge_layer, 0.25)
fc_layer_4 = fully_connected(drop_2,
2048,
activation='relu',
name='fc_layer_4',
regularizer='L2',
weights_init='xavier',
weight_decay=0.001)
drop_2 = dropout(fc_layer_4, drop_out_prob)
fc_layer_5 = fully_connected(drop_2,
1024,
activation='relu',
name='fc_layer_5',
regularizer='L2',
weights_init='xavier',
weight_decay=0.001)
drop_3 = dropout(fc_layer_5, drop_out_prob)
fc_layer_6 = fully_connected(drop_3,
128,
activation='relu',
name='fc_layer_5',
regularizer='L2',
weights_init='xavier',
weight_decay=0.001)
drop_4 = dropout(fc_layer_6, drop_out_prob)
# Output
fc_layer_2 = fully_connected(drop_4,
3,
activation='softmax',
name='output')
network = regression(fc_layer_2,
optimizer='adam',
loss='softmax_categorical_crossentropy',
learning_rate=0.0001,
metric='Accuracy')
model = tflearn.DNN(network)
return model
def main():
pickle_folder = '../pickles_rolloff'
pickle_folders_to_load = [f for f in os.listdir(pickle_folder) if os.path.isdir(join(pickle_folder, f))]
pickle_folders_to_load = sorted(pickle_folders_to_load)
length = len(pickle_folders_to_load)
# pickle parameters
fg_or_bg = 'background'
sdr_type = 'sdr'
feature = 'beat_spec'
beat_spec_len = 432
n_folds = 10
n_epochs = 200
take = 1
output_folder = 'cross_{0}_folds_{1}_epochs_take{2}/'.format(n_folds, n_epochs, take)
if not os.path.exists(output_folder):
os.makedirs(output_folder)
summary_file = output_folder + 'summary_{0}_folds_{1}_epochs.txt'.format(n_folds, n_epochs)
# set up training, testing, & validation partitions
beat_spec_array, sdr_array = load_beat_spec_and_sdrs(pickle_folders_to_load, pickle_folder,
feature, fg_or_bg, sdr_type)
perm = np.random.permutation(len(pickle_folders_to_load)) # random permutation of indices
folds = np.array_split(perm, n_folds) # splits into folds
predicted = []
for fold in range(n_folds):
train_beat_spec = np.expand_dims([beat_spec_array[i] for i in range(length) if i not in folds[fold]], -1)
train_sdr = np.expand_dims([sdr_array[i] for i in range(length) if i not in folds[fold]], -1)
test_beat_spec = np.expand_dims([beat_spec_array[i] for i in folds[fold]], -1)
test_sdr = np.expand_dims([sdr_array[i] for i in folds[fold]], -1)
with tf.Graph().as_default():
# Building convolutional network
network = input_data(shape=[None, beat_spec_len, 1])
network = conv_1d(network, 32, 4, activation='relu', regularizer="L2")
network = max_pool_1d(network, 2)
network = conv_1d(network, 64, 80, activation='relu', regularizer="L2")
network = max_pool_1d(network, 2)
network = fully_connected(network, 128, activation='relu')
network = dropout(network, 0.8)
network = fully_connected(network, 256, activation='relu') # look for non-tanh things???
network = dropout(network, 0.8)
network = fully_connected(network, 1, activation='linear')
regress = tflearn.regression(network, optimizer='rmsprop', loss='mean_square', learning_rate=0.001)
start = time.time()
# Training
model = tflearn.DNN(regress)#, session=sess)
model.fit(train_beat_spec, train_sdr, n_epoch=n_epochs,
snapshot_step=1000, show_metric=True,
run_id='relus_{0}_{1}_of_{2}'.format(n_epochs, fold+1, n_folds))
elapsed = (time.time() - start)
prediction = np.array(model.predict(test_beat_spec))[:, 0]
with open(output_folder + 'predictions_fold{}.txt'.format(fold + 1), 'a') as f:
f.write('Training avg = {} \n \n'.format(np.mean(train_sdr)))
f.write('Actual \t Predicted \n')
for i in range(len(prediction)):
f.write('{0} \t {1} \n'.format(test_sdr[i][0], prediction[i]))
pprint.pprint(prediction)
predicted.append(prediction)
with open(summary_file, 'a') as f:
mse = np.square(test_sdr - prediction).mean()
f.write('Fold {0}\t mse = {1} dB \t time = {2} min \n'.format(fold + 1, mse, elapsed / 60.))
plot(test_sdr, prediction, output_folder + 'scatter_fold{}.png'.format(fold + 1))
tf.reset_default_graph()
predicted = np.array(predicted).flatten()
print("Test MSE: ", np.square(sdr_array - predicted).mean())
plot(sdr_array, predicted, output_folder + 'scatter_all_folds_{}_epochs.png'.format(n_epochs))
def main(argv):
inputfile = ''
outputfile = ''
try:
opts, args = getopt.getopt(argv, "hi:o:", ["ifile=", "ofile="])
except getopt.GetoptError:
print 'python cnn-blpred.py -i <inputfile> -o <outputfile>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'test.py -i <inputfile> -o <outputfile>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
#print 'Input file is "', inputfile
#print 'Output file is "', outputfile
if not os.path.exists('infile'):
os.makedirs('infile')
if not os.path.exists('outfile'):
os.makedirs('outfile')
copyfile(inputfile, 'infile/' + inputfile)
print('Extracting CKSAAP features!')
feps.feps('infile/', 'outfile/')
copyfile('outfile/' + inputfile + '_full_features.csv',
inputfile.split('.')[0] + '.csv')
copyfile('outfile/' + inputfile + '_proteinFeaturesList.txt',
inputfile.split('.')[0] + '.txt')
rmtree('infile/')
rmtree('outfile/')
print('Reading Features!!')
f = open(inputfile.split('.')[0] + '.txt', 'r')
trainPFL = f.read().splitlines()
f.close()
df = pd.read_csv(inputfile.split('.')[0] + '.csv',
index_col=False,
names=trainPFL)
filenames = [
'BL_Level_1', 'BL_Class_A', 'BL_Class_B', 'BL_Class_C', 'BL_Class_D',
'BL_Group_2'
]
for filename in filenames:
print('Predicting ' + filename + '!')
f1 = open('models/feature_selection/' + filename + '_XGB_FS.pkl', 'rb')
xgb = pickle.load(f1)
f1.close()
f1 = open('models/feature_selection/' + filename + '_vocabulary.pkl',
'rb')
vocabulary = pickle.load(f1)
f1.close()
model = SelectFromModel(xgb, prefit=True)
df_new = model.transform(df)
input_layer = tflearn.input_data(shape=[None, df_new.shape[1]],
name='input')
embedding_layer = tflearn.embedding(input_layer,
input_dim=vocabulary,
output_dim=128,
validate_indices=True)
conv_layer = conv_1d(embedding_layer,
256,
4,
padding='same',
activation='tanh',
regularizer='L2')
maxpool_layer = max_pool_1d(conv_layer, 2)
dropout = tflearn.dropout(maxpool_layer, 0.5)
softmax = tflearn.fully_connected(dropout, 2, activation='softmax')
regression = tflearn.regression(softmax,
optimizer='adam',
learning_rate=0.001,
loss='categorical_crossentropy',
name='target')
clf = tflearn.DNN(regression, tensorboard_verbose=3)
clf.load('models/classification/' + filename + '/' + filename +
'_model.tfl')
predicted = clf.predict_label(df_new)[:, 1]
score = clf.predict(df_new)
if not os.path.exists('results'):
os.makedirs('results')
np.savetxt('results/' + outputfile + '_' + filename +
'_predict_label.csv',
predicted,
delimiter=',')
np.savetxt('results/' + outputfile + '_' + filename +
'_predict_score.csv',
score,
delimiter=',')
tf.reset_default_graph()
del vocabulary, df_new, f1, input_layer, embedding_layer, conv_layer, maxpool_layer, dropout, softmax, regression, clf, predicted, score, model, xgb
gc.collect()
os.remove(inputfile.split('.')[0] + '.csv')
os.remove(inputfile.split('.')[0] + '.txt')
# Sequence padding
trainX = pad_sequences(trainX, maxlen=10, value=0.)
testX = pad_sequences(testX, maxlen=10, value=0.)
# # # Converting labels to binary vectors
trainY = to_categorical(trainY, 6)
testY = to_categorical(testY, 6)
network = input_data(shape=[None, 10], name='input')
network = tflearn.embedding(network, input_dim=1000, output_dim=128)
branch1 = conv_1d(network,
128,
3,
padding='valid',
activation='relu',
regularizer="L2")
branch1 = max_pool_1d(branch1, 2)
branch2 = conv_1d(network,
128,
4,
padding='valid',
activation='relu',
regularizer="L2")
branch2 = max_pool_1d(branch2, 2)
branch3 = conv_1d(network,
128,
5,
padding='valid',
activation='relu',
regularizer="L2")
branch3 = max_pool_1d(branch3, 2)
network = merge([branch1, branch2, branch3], mode='concat', axis=1)
matrix_size = opts.matrix_size
X, Y = image_preloader('/scratch/data.txt',
image_shape=(matrix_size, matrix_size, 1),
mode='file',
categorical_labels=True,
normalize=False)
conv_input = input_data(shape=[None, matrix_size, matrix_size], name='input')
conv = conv_1d(conv_input,
100,
filter_size=50,
activation='leaky_relu',
strides=2)
conv1 = conv_1d(conv_input, 50, 1, activation='leaky_relu', strides=1)
conv1 = max_pool_1d(conv1, kernel_size=2, strides=2)
convnet = merge([conv, conv1], mode='concat', axis=2)
convnet = conv_1d(convnet, 30, filter_size=1, activation='relu')
#convnet = dropout(convnet, 0.35) -- Currently disabled (can be included if generalization is necessary)
convnet = fully_connected(convnet, 3, activation='softmax')
convnet = regression(convnet,
optimizer='adam',
learning_rate=opts.lr,
loss='categorical_crossentropy')
model = tflearn.DNN(convnet,
tensorboard_verbose=3,
tensorboard_dir='/modelState/Tensordboard/')
'''model.fit(X, Y, n_epoch=opts.epoch, validation_set=0.2, show_metric=True, batch_size=opts.bs, snapshot_step=100,
snapshot_epoch=False, run_id='Digital Mammography ConCaDNet')'''
model.load('/modelState/model.tflearn')