def soft_train(network, args):
device = torch.device("cuda" if args.gpu_flag is True else "cpu")
optimizer, scheduler = get_optimizer(network, args)
train_data_set = get_data_set(args, train_flag=True)
test_data_set = get_data_set(args, train_flag=False)
train_data_loader = torch.utils.data.DataLoader(train_data_set,
batch_size=args.batch_size,
shuffle=True)
test_data_loader = torch.utils.data.DataLoader(test_data_set,
batch_size=args.batch_size,
shuffle=False)
print("-*-" * 10 + "\n\t\tTrain network\n" + "-*-" * 10)
for epoch in range(0, args.epoch):
network = network.cpu()
if args.network is "vgg":
network = soft_prune_vgg_step(network, args.prune_rate[0])
elif args.network == 'resnet':
network = soft_prune_resnet_step(network, args.prune_rate)
network = network.to(device)
train_step(network, train_data_loader, test_data_loader, optimizer,
device, epoch)
if scheduler is not None:
scheduler.step()
return network
def Cell_Segmentation():
print("Start Cell Segmentation.")
print(datetime.now().strftime("%Y/%m/%d %H:%M:%S"))
args = argument()
if not args.flaginfer:
print("Train and infer.")
try:
start = time.time()
train_step(fname_train=os.path.join("data", args.train),
fname_label=os.path.join("data", args.label),
fname_model=os.path.join("data", args.model),
N_test=args.ntest, N_train=args.ntrain, N_epoch=args.nepoch, batchsize=args.nbatch,
hgh=args.height, wid=args.width,
mode=args.mode)
print("train time", time.time() - start)
except Exception as e:
raise Exception(e, "Got an error in training step.")
try:
start = time.time()
infer_step(fname_infer=os.path.join("data", args.infer),
fname_save=os.path.join("result", args.output),
fname_model=os.path.join("data", args.model),
thre_discard=args.discard, wid_dilate=args.close,
fstats=args.nostats)
print("infer time", time.time() - start)
except Exception as e:
raise Exception(e, "Got an error in inference step.")
print("All done.")
else:
print("Only Infer.")
try:
start = time.time()
infer_step(fname_infer=os.path.join("data", args.infer),
fname_save=os.path.join("result", args.output),
fname_model=os.path.join("data", args.model),
thre_discard=args.discard, wid_dilate=args.close,
fstats=args.nostats)
print("infer time", time.time() - start)
except Exception as e:
raise Exception(e, "Got an error in inference step.")
print("All done.")
def test_train_one_step(self):
batch = train.get_batch(128)
optimizer = create_test_optimizer()
key = random.PRNGKey(0)
_, train_metrics = train.train_step(optimizer, batch, key)
self.assertLessEqual(train_metrics['loss'], 5)
self.assertGreaterEqual(train_metrics['accuracy'], 0)
def test_train_one_step(self):
batch = train.get_batch(128)
rng = random.PRNGKey(0)
model = train.create_model(rng)
optimizer = train.create_optimizer(model, 0.003)
optimizer, train_metrics = train.train_step(optimizer, batch)
self.assertLessEqual(train_metrics['loss'], 5)
self.assertGreaterEqual(train_metrics['accuracy'], 0)
def test_train_one_step(self):
batch = train.get_batch(128)
rng = random.PRNGKey(0)
with nn.stochastic(rng):
model = train.create_model(nn.make_rng())
optimizer = train.create_optimizer(model, 0.003)
optimizer, train_metrics = train.train_step(
optimizer, batch, nn.make_rng())
self.assertLessEqual(train_metrics['loss'], 5)
self.assertGreaterEqual(train_metrics['accuracy'], 0)
def train(self, x_train_unlabeled, x_train_labeled, x_val_unlabeled, lr,
drop, patience, num_epochs):
# create handler for early stopping and learning rate scheduling
self.lh = LearningHandler(lr=lr,
drop=drop,
lr_tensor=self.learning_rate,
patience=patience)
losses = np.empty((num_epochs, ))
val_losses = np.empty((num_epochs, ))
# begin spectralnet training loop
self.lh.on_train_begin()
for i in range(num_epochs):
# train spectralnet
losses[i] = train.train_step(return_var=[self.loss],
updates=self.net.updates +
[self.train_step],
x_unlabeled=x_train_unlabeled,
inputs=self.inputs,
y_true=self.y_true,
batch_sizes=self.batch_sizes,
x_labeled=x_train_labeled,
y_labeled=self.y_train_labeled_onehot,
batches_per_epoch=100)[0]
# get validation loss
val_losses[i] = train.predict_sum(
self.loss,
x_unlabeled=x_val_unlabeled,
inputs=self.inputs,
y_true=self.y_true,
x_labeled=x_train_unlabeled[0:0],
y_labeled=self.y_train_labeled_onehot,
batch_sizes=self.batch_sizes)
# do early stopping if necessary
if self.lh.on_epoch_end(i, val_losses[i]):
print('STOPPING EARLY')
break
# print training status
print("Epoch: {}, loss={:2f}, val_loss={:2f}".format(
i, losses[i], val_losses[i]))
return losses[:i], val_losses[:i]
def test_single_train_step(self):
prng = random.PRNGKey(0)
# 0 (0)
# / \
# (0) 1 - 2 (1)
edge_list = [(0, 0), (1, 2), (2, 0)]
node_labels = [0, 0, 1]
node_feats, node_labels, sources, targets = train.create_graph_data(edge_list=edge_list,
node_labels=node_labels)
_, initial_params = GNN.init(prng, node_x=node_feats, edge_x=None,
sources=sources, targets=targets)
model = nn.Model(GNN, initial_params)
optimizer = optim.Adam(learning_rate=0.01).create(model)
_, loss = train.train_step(optimizer=optimizer, node_feats=node_feats,
sources=sources, targets=targets)
self.assertGreater(loss, 0.0)
def test_single_train_step(self):
train_ds, test_ds = train.get_datasets()
batch_size = 32
model = train.create_model(random.PRNGKey(0))
optimizer = train.create_optimizer(model, 0.1, 0.9)
# test single train step.
optimizer, train_metrics = train.train_step(
optimizer=optimizer,
batch={k: v[:batch_size]
for k, v in train_ds.items()})
self.assertLessEqual(train_metrics['loss'], 2.302)
self.assertGreaterEqual(train_metrics['accuracy'], 0.0625)
# Run eval model.
loss, accuracy = train.eval_model(optimizer.target, test_ds)
self.assertLess(loss, 2.252)
self.assertGreater(accuracy, 0.2597)
def translate(args):
if os.path.exists("checkpoint/encoder.h5") and \
os.path.exists("checkpoint/decoder.h5"):
hidden = [tf.zeros((1, 256))]
# runs forward propagation through the models to build the model
_ = train.train_step(encoder, decoder, tf.ones((1, 2)), tf.ones(
(1, 2)), hidden)
encoder.load_weights("checkpoint/encoder.h5")
decoder.load_weights("checkpoint/decoder.h5")
print("models loaded....")
result = ''
attention_plot = np.zeros((10, 10))
sentence = Utils.normalizeString(args.sentence)
sentence = Utils.sentenceToIndexes(sentence, train.input_lang)
sentence = Utils.keras.preprocessing.sequence.pad_sequences(
[sentence], padding='post', maxlen=args.max_length, truncating='post')
hidden = [tf.zeros((1, 256))]
enc_out, enc_hidden = encoder(sentence, hidden)
dec_hidden = enc_hidden
SOS_tensor = np.array([SOS_token])
dec_input = tf.squeeze(tf.expand_dims([SOS_tensor], 1), -1)
for tx in range(args.max_length):
dec_out, dec_hidden, attn_weights = decoder(dec_input, enc_out,
dec_hidden)
attn_weights = tf.reshape(attn_weights, (-1, ))
attention_plot[tx] = attn_weights.numpy()
pred = tf.argmax(dec_out, axis=1).numpy()
result += train.output_lang.index2word[pred[0]] + " "
if train.output_lang.index2word[pred[0]] == "EOS":
break
dec_input = tf.expand_dims(pred, axis=1)
return result, attention_plot
variables = encoder.trainable_variables + decoder.trainable_variables
gradients = tape.gradient(loss, variables)
optimizer.apply_gradients(zip(gradients, variables))
return batch_loss
# train
EPOCHS = 10
for epoch in range(EPOCHS):
start = time.time()
encoded_hidden = encoder.initialize_hidden_state()
total_loss = 0
for (batch, (input, target)) in enumerate(dataset.take(steps_per_epoch)):
batch_loss = train_step(input, target, encoded_hidden)
total_loss += batch_loss
if batch % 100 == 0:
print('Epoch {} Batch {} Loss {:.4f}'.format(epoch + 1,
batch,
batch_loss.numpy()))
# saving (checkpoint) the model every 2 epochs
if (epoch + 1) % 2 == 0:
checkpoint.save(file_prefix=checkpoint_prefix)
print('Epoch {} Loss {:.4f}'.format(epoch + 1,
total_loss / steps_per_epoch))
print('Time taken for 1 epoch {} sec\n'.format(time.time() - start))
def evaluate(sentence):
def main(argv=sys.argv):
''' NeuroNER main method
Args:
parameters_filepath the path to the parameters file
output_folder the path to the output folder
'''
arguments = parse_arguments(argv[1:])
parameters, conf_parameters = load_parameters(
arguments['parameters_filepath'], arguments=arguments)
dataset_filepaths, dataset_brat_folders = get_valid_dataset_filepaths(
parameters)
check_parameter_compatiblity(parameters, dataset_filepaths)
# Load dataset
dataset = ds.Dataset(verbose=parameters['verbose'],
debug=parameters['debug'])
dataset.load_dataset(dataset_filepaths, parameters)
# Create graph and session
with tf.device('/gpu:0'):
with tf.Graph().as_default():
session_conf = tf.ConfigProto(
intra_op_parallelism_threads=parameters[
'number_of_cpu_threads'],
inter_op_parallelism_threads=parameters[
'number_of_cpu_threads'],
device_count={
'CPU': 1,
'GPU': parameters['number_of_gpus']
},
allow_soft_placement=True,
# automatically choose an existing and supported device to run the operations in case the specified one doesn't exist
log_device_placement=False)
sess = tf.Session(config=session_conf)
with sess.as_default():
start_time = time.time()
experiment_timestamp = utils.get_current_time_in_miliseconds()
results = {}
results['epoch'] = {}
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time
results['execution_details'][
'time_stamp'] = experiment_timestamp
results['execution_details']['early_stop'] = False
results['execution_details']['keyboard_interrupt'] = False
results['execution_details']['num_epochs'] = 0
results['model_options'] = copy.copy(parameters)
dataset_name = utils.get_basename_without_extension(
parameters['dataset_text_folder'])
model_name = dataset_name
utils.create_folder_if_not_exists(parameters['output_folder'])
stats_graph_folder = os.path.join(
parameters['output_folder'],
model_name) # Folder where to save graphs
final_weights_folder = os.path.join(
parameters['output_folder'], 'weights')
utils.create_folder_if_not_exists(stats_graph_folder)
utils.create_folder_if_not_exists(final_weights_folder)
model_folder = os.path.join(stats_graph_folder, 'model')
utils.create_folder_if_not_exists(model_folder)
# saving the parameter setting to the output model dir. For later resuming training
with open(os.path.join(model_folder, 'parameters.ini'),
'w') as parameters_file:
conf_parameters.write(parameters_file)
tensorboard_log_folder = os.path.join(stats_graph_folder,
'tensorboard_logs')
utils.create_folder_if_not_exists(tensorboard_log_folder)
tensorboard_log_folders = {}
for dataset_type in dataset_filepaths.keys():
tensorboard_log_folders[dataset_type] = os.path.join(
stats_graph_folder, 'tensorboard_logs', dataset_type)
utils.create_folder_if_not_exists(
tensorboard_log_folders[dataset_type])
pickle.dump(
dataset,
open(os.path.join(model_folder, 'dataset.pickle'), 'wb'))
# Instantiate the model
# graph initialization should be before FileWriter, otherwise the graph will not appear in TensorBoard
model = EntityLSTM(dataset, parameters)
# Instantiate the writers for TensorBoard
writers = {}
for dataset_type in dataset_filepaths.keys():
writers[dataset_type] = tf.summary.FileWriter(
tensorboard_log_folders[dataset_type],
graph=sess.graph)
# embedding_writer has to write in model_folder, otherwise TensorBoard won't be able to view embeddings
embedding_writer = tf.summary.FileWriter(model_folder)
embeddings_projector_config = projector.ProjectorConfig()
tensorboard_token_embeddings = embeddings_projector_config.embeddings.add(
)
tensorboard_token_embeddings.tensor_name = model.token_embedding_weights.name
token_list_file_path = os.path.join(
model_folder, 'tensorboard_metadata_tokens.tsv')
tensorboard_token_embeddings.metadata_path = os.path.relpath(
token_list_file_path, '..')
tensorboard_character_embeddings = embeddings_projector_config.embeddings.add(
)
tensorboard_character_embeddings.tensor_name = model.character_embedding_weights.name
character_list_file_path = os.path.join(
model_folder, 'tensorboard_metadata_characters.tsv')
tensorboard_character_embeddings.metadata_path = os.path.relpath(
character_list_file_path, '..')
projector.visualize_embeddings(embedding_writer,
embeddings_projector_config)
# Write metadata for TensorBoard embeddings
token_list_file = codecs.open(token_list_file_path, 'w',
'latin-1')
for token_index in range(dataset.vocabulary_size):
token_list_file.write('{0}\n'.format(
dataset.index_to_token[token_index]))
token_list_file.close()
character_list_file = codecs.open(character_list_file_path,
'w', 'latin-1')
for character_index in range(dataset.alphabet_size):
if character_index == dataset.PADDING_CHARACTER_INDEX:
character_list_file.write('PADDING\n')
else:
character_list_file.write('{0}\n'.format(
dataset.index_to_character[character_index]))
character_list_file.close()
# Initialize the model
sess.run(tf.global_variables_initializer())
if not parameters['use_pretrained_model']:
model.load_pretrained_token_embeddings(
sess, dataset, parameters)
# Start training + evaluation loop. Each iteration corresponds to 1 epoch.
patience_counter = 0
f1_score_best = 0
f1_scores = {'train-F1': [], 'valid-F1': [], 'test-F1': []}
f1_scores_conll = {
'train-F1': [],
'valid-F1': [],
'test-F1': []
}
transition_params_trained = np.random.rand(
len(dataset.unique_labels) + 2,
len(dataset.unique_labels) + 2)
model_saver = tf.train.Saver(
max_to_keep=parameters['num_of_model_to_keep'])
epoch_number = -1
try:
while True:
step = 0
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
# use pre-trained model and epoch_number = 0
if parameters[
'use_pretrained_model'] and epoch_number == 0:
if parameters['use_adapter']:
parameters['use_adapter'] = False
transition_params_trained = train.restore_pretrained_model(
parameters, dataset, sess, model,
model_saver)
print(
'Getting the 3-label predictions from the step1 model.'
)
all_pred_labels, y_pred_for_adapter, y_true_for_adapter, \
output_filepaths = train.predict_labels(sess, model,
transition_params_trained,
parameters, dataset,
epoch_number,
stats_graph_folder,
dataset_filepaths,
for_adapter=True)
# use the label2idx mapping (for adapter) in the dataset to transform all_pred_labels
all_pred_indices = {}
for dataset_type in dataset_filepaths.keys():
all_pred_indices[dataset_type] = []
for i in range(
len(all_pred_labels[dataset_type])
):
indices = [
dataset.
label_adapter_to_index[label]
for label in
all_pred_labels[dataset_type][i]
]
all_pred_indices[dataset_type].append(
indices)
# and use binarizer to transform to ndarray
label_binarizer_adapter = sklearn.preprocessing.LabelBinarizer(
)
label_binarizer_adapter.fit(
range(
max(dataset.index_to_label_adapter.
keys()) + 1))
predicted_label_adapter_vector_indices = {}
for dataset_type in dataset_filepaths.keys():
predicted_label_adapter_vector_indices[
dataset_type] = []
for label_indices_sequence in all_pred_indices[
dataset_type]:
predicted_label_adapter_vector_indices[
dataset_type].append(
label_binarizer_adapter.
transform(
label_indices_sequence))
parameters['use_adapter'] = True
if parameters['train_model'] and parameters[
'add_class']:
transition_params_trained, model, glo_step = \
train.restore_model_parameters_from_pretrained_model(parameters, dataset, sess,
model, model_saver)
init_new_vars_op = tf.initialize_variables(
[glo_step])
sess.run(init_new_vars_op)
else:
transition_params_trained = \
train.restore_pretrained_model(parameters, dataset, sess, model, model_saver)
for dataset_type in dataset_filepaths.keys():
writers[dataset_type] = tf.summary.FileWriter(
tensorboard_log_folders[dataset_type],
graph=sess.graph)
# embedding_writer has to write in model_folder, otherwise TensorBoard won't be able to view embeddings
embedding_writer = tf.summary.FileWriter(
model_folder)
# epoch_number != 0, no matter use or not use pre-trained model
elif epoch_number != 0:
# Train model: loop over all sequences of training set with shuffling
sequence_numbers = list(
range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
transition_params_trained, W_before_crf = train.train_step(
sess, dataset, sequence_number, model,
transition_params_trained, parameters)
step += 1
epoch_elapsed_training_time = time.time(
) - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(
epoch_elapsed_training_time),
flush=False)
if parameters[
'use_adapter']: # model evaluation, using adapter
# pass the pred_for_adapter as label_indices vector
original_label_adapter_vector_indices = dataset.label_adapter_vector_indices
dataset.label_adapter_vector_indices = predicted_label_adapter_vector_indices
y_pred, y_true, output_filepaths = train.predict_labels(
sess, model, transition_params_trained,
parameters, dataset, epoch_number,
stats_graph_folder, dataset_filepaths)
evaluate.evaluate_model(results, dataset, y_pred,
y_true, stats_graph_folder,
epoch_number,
epoch_start_time,
output_filepaths,
parameters)
dataset.label_adapter_vector_indices = original_label_adapter_vector_indices
else: # model evaluation, not using adapter
y_pred, y_true, output_filepaths = train.predict_labels(
sess, model, transition_params_trained,
parameters, dataset, epoch_number,
stats_graph_folder, dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred,
y_true, stats_graph_folder,
epoch_number,
epoch_start_time,
output_filepaths,
parameters)
summary = sess.run(model.summary_op, feed_dict=None)
writers['train'].add_summary(summary, epoch_number)
writers['train'].flush()
utils.copytree(writers['train'].get_logdir(),
model_folder)
# Early stopping
train_f1_score = results['epoch'][epoch_number][0][
'train']['f1_score']['weighted']
valid_f1_score = results['epoch'][epoch_number][0][
'valid']['f1_score']['weighted']
test_f1_score = results['epoch'][epoch_number][0][
'test']['f1_score']['weighted']
f1_scores['train-F1'].append(train_f1_score)
f1_scores['valid-F1'].append(valid_f1_score)
f1_scores['test-F1'].append(test_f1_score)
train_f1_score_conll = results['epoch'][epoch_number][
0]['train']['f1_conll']['micro']
valid_f1_score_conll = results['epoch'][epoch_number][
0]['valid']['f1_conll']['micro']
test_f1_score_conll = results['epoch'][epoch_number][
0]['test']['f1_conll']['micro']
f1_scores_conll['train-F1'].append(
train_f1_score_conll)
f1_scores_conll['valid-F1'].append(
valid_f1_score_conll)
f1_scores_conll['test-F1'].append(test_f1_score_conll)
if valid_f1_score > f1_score_best:
patience_counter = 0
f1_score_best = valid_f1_score
# Save the best model
model_saver.save(
sess,
os.path.join(model_folder, 'best_model.ckpt'))
print(
'updated model to current epoch : epoch {:d}'.
format(epoch_number))
print('the model is saved in: {:s}'.format(
model_folder))
else:
patience_counter += 1
print("In epoch {:d}, the valid F1 is : {:f}".format(
epoch_number, valid_f1_score))
print(
"The last {0} epochs have not shown improvements on the validation set."
.format(patience_counter))
if patience_counter >= parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
# save last model
model_saver.save(
sess,
os.path.join(model_folder, 'last_model.ckpt'))
print('the last model is saved in: {:s}'.format(
model_folder))
break
if epoch_number >= parameters[
'maximum_number_of_epochs'] and not parameters[
'refine_with_crf']:
break
if not parameters['use_pretrained_model']:
plot_name = 'F1-summary-step1.svg'
else:
plot_name = 'F1-summary-step2.svg'
print('Sklearn result:')
for k, l in f1_scores.items():
print(k, l)
print('Conll result:')
for k, l in f1_scores_conll.items():
print(k, l)
utils_plots.plot_f1(
f1_scores,
os.path.join(stats_graph_folder, '..', plot_name),
'F1 score summary')
# TODO: in step 1, for task a, add the best deploy data to step 2 train set, and call script
print('(sklearn micro) test F1:')
micro_f1 = ','.join([
str(results['epoch'][ep][0]['test']['f1_score']
['micro']) for ep in range(epoch_number + 1)
])
print(micro_f1)
print('(sklearn macro) test F1:')
macro_f1 = ','.join([
str(results['epoch'][ep][0]['test']['f1_score']
['macro']) for ep in range(epoch_number + 1)
])
print(macro_f1)
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
print('Training interrupted')
print('Finishing the experiment')
end_time = time.time()
results['execution_details'][
'train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
evaluate.save_results(results, stats_graph_folder)
for dataset_type in dataset_filepaths.keys():
writers[dataset_type].close()
sess.close() # release the session's resources
model = MobileNetv2().to(device).float()
optimizer = optim.Adam(model.parameters(), lr=0.001)
scheduler = ReduceLROnPlateau(optimizer,
mode='max',
factor=0.1,
patience=2,
verbose=True)
n_epochs = 50
stats = {'epoch': [], 'train_loss': [], 'val_loss': [], 'acc': []}
val_loss_min = np.Inf
for epoch in range(n_epochs):
batch_train_loss = []
epoch_loss = 0
stats['epoch'].append(epoch)
for images, labels in train_loader:
loss = train_step(images, labels, model, criterion, optimizer)
epoch_loss += loss.item()
batch_train_loss.append(loss.item())
stats['train_loss'].append(batch_train_loss)
print(
f'Epoch {epoch+0:03}: | Train Loss: {epoch_loss/len(train_loader):.5f}'
)
model.eval()
with torch.no_grad():
batch_val_loss = []
batch_acc = []
epoch_val_loss = 0
epoch_acc = 0
for images, labels in val_loader:
images, labels = images.to(device).float(), labels.to(
for epoch in range(args.epochs):
#print(exp_name_)
#print(torch.cuda.get_device_name(torch.cuda.current_device()))
for idx, (batch, label) in enumerate(train_loader, 0):
# print("batch {}".format(batch.size()))
# print("label grad{}".format(label.requires_grad))
# print("batch{}".format(idx))
# new_label = label.clone().detach()
# new_label = new_label.to(device)
# print('label size {}'.format(label.size()))
if args.count_shuffled_unshuffled:
new_label = restore_labels(label)
#new_label, ratio = shuffle_batch_label(label, shuffle_ratio, device)
#new_label = new_label.detach()
loss = train_step(model, batch, new_label,
device, model_optimizer,
loss_func)
#del new_label
else:
loss = train_step(model, batch, label, device,
model_optimizer, loss_func)
#del label
#del batch
#print("ratio: {}".format(ratio))
loss = loss.detach() #important!
total_loss += loss.item()
#del batch
del loss
#del label, new_label
#print(epoch)
def main():
torch.manual_seed(233)
torch.cuda.set_device(0)
args = get_args()
print("generating config")
config = Config(
state_dim=args.hidden,
input_dim=args.input_dim,
hidden=args.hidden,
output_dim=args.num_classes,
epsilon=args.epsilon
)
gamma = args.gamma
reward_amplify = args.reward_amplify
passive_drive = args.passive_drive
memory = models.Memory(args.capacity)
m = args.batch_size
print("initializing networks")
E = models.Shared_Encoder(config)
Q = models.Simple_Q_Net(config) # 2-dim x-or problem
Q_t = models.Simple_Q_Net(config)
Q_t.load_state_dict(Q.state_dict()) # let Q and Q_t be identical initially
C = models.SimpleNNClassifier(config)
episode_length = args.episode_length
episode_number = args.episode_number
print("initializing optimizers")
optimizer_E = torch.optim.Adam(E.parameters(), lr=args.lr, betas=(0., 0.999))
optimizer_C = torch.optim.Adam(C.parameters(), lr=args.lr, betas=(0., 0.999))
optimizer_Q = torch.optim.Adam(Q.parameters(), lr=args.lr, betas=(0., 0.999))
# enable gpu
E.cuda()
C.cuda()
Q.cuda()
Q_t.cuda()
#test_C(C, E)
loss_last = Variable(torch.tensor([0.])).cuda()
X_eval, Y_eval = xor_data_generate(args.eval_set_size)
X_eval = X_eval.cuda()
Y_eval = Y_eval.cuda()
for i in range(episode_number):
#X_eval, Y_eval = xor_data_generate(args.eval_set_size)
#X_eval = X_eval.cuda()
#Y_eval = Y_eval.cuda()
X, Y = xor_data_generate(m)
X = X.cuda()
Y = Y.cuda()
for t in range(episode_length):
try:
X, Y, loss_last, reward = train_step(E=E,
C=C,
Q=Q,
Q_t=Q_t,
X=X,
Y=Y,
eval_X=X_eval,
eval_Y=Y_eval,
gamma=gamma,
loss_last=loss_last,
memory=memory,
optimizer_C=optimizer_C,
optimizer_E=optimizer_E,
optimizer_Q=optimizer_Q,
reward_amplify=reward_amplify,
passive_drive=passive_drive)
print("Episode %i step %i, loss=%f, reward=%f" % (
i, t, loss_last.detach().cpu().numpy(), reward.detach().cpu().numpy()))
except Exception as e:
print("Cannot train the model on this step, error:", e)
Q_t = Q
if i % 20 == 0:
test_C(C, E)
state = {
'E_state_dict': E.state_dict(),
'E_optimizer': optimizer_E.state_dict(),
'C_state_dict': C.state_dict(),
'C_optimizer': optimizer_C.state_dict(),
'Q_state_dict': Q.state_dict(),
'Q_optimizer': optimizer_Q.state_dict(),
}
model_name = "cog396test_main_episode_" + str(i) + ".tr"
torch.save(state, model_name)
for batch in range(args.num_batches):
start = batch * args.batch_size
end = (batch + 1) * args.batch_size
train_data = (advantages, rewards_to_go, values, actions, observations,
policy_probs)
# slice out batches from train_data
batch_data = [x[start:end] for x in train_data]
batch_data = [torch.tensor(x).to(device) for x in batch_data]
# flatten (batch_size,num_steps,...) into ((batch_size*num_steps,...)
batch_data = [x.reshape((-1, ) + x.shape[2:]) for x in batch_data]
# Step batch
for epoch in range(args.ppo_epochs):
train_step(model, optim, batch_data, args, i, tracker)
tracker.log_iteration_time(args.num_workers * args.num_steps, i)
if i % 5 == 0:
tracker.add_histogram("episode/episode_length",
game_player.episode_length, i)
tracker.add_histogram("episode/episode_rewards",
game_player.episode_rewards, i)
if i % 25 == 0:
tracker.add_histogram("training/raw_advantages",
raw_advantages, i)
tracker.add_histogram("training/rewards",
rewards, i)
tracker.add_histogram("training/observations",
observations, i)
tracker.add_histogram("training/reward_std",
import tensorflow as tf
from keras.utils import Progbar
from get_data import *
from train import train_step
import numpy as np
from config import *
epochs = train_config.epochs
for epoch in range(epochs):
tf.print("{}/{} epoch".format(epoch+1, epochs))
pbar = Progbar(target = 60000, unit_name = "WGAN_GP")
prev_dis_loss,prev_gen_loss = 0,0
for x in train_x_batched:
dis_loss, gen_loss = train_step(x,prev_dis_loss,prev_gen_loss)
prev_dis_loss = dis_loss
prev_gen_loss = gen_loss
values=[("Critic Loss", np.round(dis_loss.numpy(),4)), ("Generator Loss", np.round(gen_loss.numpy(),4))]
pbar.add(x.shape[0],values=values)
def main():
file_params = 'parameters_yelp_50k.ini'
if len(sys.argv) > 1 and '.ini' in sys.argv[1]:
file_params = sys.argv[1]
# Load config
parameters, conf_parameters = load_parameters(
parameters_filepath=os.path.join('.', file_params))
dataset_filepaths = get_valid_dataset_filepaths(parameters)
#check_parameter_compatiblity(parameters, dataset_filepaths)
if parameters['seed'] != -1:
random.seed(parameters['seed'])
# Create annotator
annotator = stanford_corenlp_pywrapper.CoreNLP(
configdict={
'annotators': 'tokenize, ssplit',
'ssplit.eolonly': True
},
corenlp_jars=[parameters['stanford_folder'] + '/*'])
# Load dataset
dataset = ds.Dataset(verbose=parameters['verbose'],
debug=parameters['debug'])
dataset.load_dataset(dataset_filepaths, parameters, annotator)
# Adapt train/valid/test to be multiple of batch_size
for size in ['train_size', 'valid_size', 'test_size']:
if parameters[size] % parameters['batch_size'] != 0:
parameters[size] = int(
parameters[size] /
parameters['batch_size']) * parameters['batch_size']
print('Changed {}'.format(size))
# Set GPU device if more GPUs are specified
if parameters['number_of_gpus'] > 1 and parameters['gpu_device'] != -1:
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = parameters['gpu_device']
# GPUs
print(device_lib.list_local_devices())
# Create graph and session
with tf.Graph().as_default():
session_conf = tf.ConfigProto(
intra_op_parallelism_threads=parameters['number_of_cpu_threads'],
inter_op_parallelism_threads=parameters['number_of_cpu_threads'],
device_count={
'CPU': 1,
'GPU': parameters['number_of_gpus']
},
allow_soft_placement=
True, # automatically choose an existing and supported device to run the operations in case the specified one doesn't exist
log_device_placement=False)
sess = tf.Session(config=session_conf)
with sess.as_default():
if parameters['seed'] != -1:
tf.set_random_seed(parameters['seed'])
# Initialize and save execution details
start_time = time.time()
experiment_timestamp = utils.get_current_time_in_miliseconds()
results = {}
results['epoch'] = {}
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time
results['execution_details'][
'time_stamp'] = experiment_timestamp
results['execution_details']['early_stop'] = False
results['execution_details']['keyboard_interrupt'] = False
results['execution_details']['num_epochs'] = 0
results['model_options'] = copy.copy(parameters)
dataset_name = utils.get_basename_without_extension(
parameters['dataset_folder'])
model_name = '{0}_{1}'.format(
dataset_name, results['execution_details']['time_stamp'])
output_folder = os.path.join('..', 'output')
utils.create_folder_if_not_exists(output_folder)
stats_graph_folder = os.path.join(
output_folder, model_name) # Folder where to save graphs
utils.create_folder_if_not_exists(stats_graph_folder)
model_folder = os.path.join(stats_graph_folder, 'model')
utils.create_folder_if_not_exists(model_folder)
with open(os.path.join(model_folder, file_params),
'w') as parameters_file:
conf_parameters.write(parameters_file)
pickle.dump(
dataset,
open(os.path.join(model_folder, 'dataset.pickle'), 'wb'))
# Instantiate the model
# graph initialization should be before FileWriter, otherwise the graph will not appear in TensorBoard
model = SelfSent(dataset, parameters)
# Initialize the model
sess.run(tf.global_variables_initializer())
if not parameters['use_pretrained_model']:
model.load_pretrained_token_embeddings(
sess, dataset, parameters)
# Start training + evaluation loop. Each iteration corresponds to 1 epoch.
bad_counter = 0 # number of epochs with no improvement on the validation test
previous_best_valid_accuracy = 0
previous_best_test_accuracy = 0
model_saver = tf.train.Saver(
max_to_keep=parameters['maximum_number_of_epochs']
) # defaults to saving all variables
epoch_number = -1
try:
while True:
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
if parameters[
'use_pretrained_model'] and epoch_number == 0:
# Restore pretrained model parameters
dataset = train.restore_model_parameters_from_pretrained_model(
parameters, dataset, sess, model_saver)
dataset.load_deploy(
os.path.join(parameters['dataset_folder'],
'{0}.json'.format('deploy')),
parameters, annotator)
y_pred, y_true, output_filepaths, attentions = train.predict_labels(
sess,
model,
parameters,
dataset,
epoch_number,
stats_graph_folder,
dataset_filepaths,
only_deploy=True)
y_pred = y_pred['deploy']
with open(
output_filepaths['deploy']
[:output_filepaths['deploy'].rfind('/') + 1] +
'attention.txt',
'w',
encoding='utf-8') as fp:
# Compute attention
tokens_with_attentions = []
for sample_id in range(len(y_pred)):
attention = attentions[int(
sample_id / parameters['batch_size'])][
sample_id %
parameters['batch_size']]
# Remove padded dimension
attention = attention[:dataset.
token_lengths[
'deploy']
[sample_id]]
# Save current attention
fp.write("{}\t{:05.2f}\t".format(
y_pred[sample_id][0],
y_pred[sample_id][1]))
fp.write(' '.join(dataset.tokens['deploy']
[sample_id]) + '\t')
fp.write(' '.join(
[str(a)
for a in attention.flatten()]) + '\n')
# Sum over columns (we combine all the annotation vectors)
attention = np.sum(attention, axis=1)
# Normalize to sum at 1
attention = attention / np.linalg.norm(
attention)
# Keep only high confidence
if y_pred[sample_id][1] >= parameters[
'attention_visualization_conf']:
tokens_with_attentions.append(
(y_pred[sample_id][0],
y_pred[sample_id][1],
dataset.tokens['deploy']
[sample_id], attention))
# Plot attention
utils_plots.visualize_attention(
tokens_with_attentions, dataset.unique_labels,
output_filepaths['deploy']
[:output_filepaths['deploy'].rfind('/') + 1],
parameters['attention_visualization_conf'])
break
elif epoch_number != 0:
total_loss, total_accuracy = train.train_step(
sess, dataset, model, parameters)
print('Mean loss: {:.2f}\tMean accuracy: {:.2f}'.
format(np.mean(total_loss),
100.0 * np.mean(total_accuracy)),
flush=True)
epoch_elapsed_training_time = time.time(
) - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(
epoch_elapsed_training_time),
flush=True)
y_pred, y_true, output_filepaths, _ = train.predict_labels(
sess, model, parameters, dataset, epoch_number,
stats_graph_folder, dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred,
y_true, stats_graph_folder,
epoch_number, epoch_start_time,
output_filepaths, parameters)
# Save model
model_saver.save(
sess,
os.path.join(
model_folder,
'model_{0:05d}.ckpt'.format(epoch_number)))
# Early stop
valid_accuracy = results['epoch'][epoch_number][0][
'valid']['accuracy_score']
if valid_accuracy > previous_best_valid_accuracy:
bad_counter = 0
previous_best_valid_accuracy = valid_accuracy
previous_best_test_accuracy = results['epoch'][
epoch_number][0]['test']['accuracy_score']
else:
bad_counter += 1
print(
"The last {0} epochs have not shown improvements on the validation set."
.format(bad_counter))
print("Best valid with test performances in epoch " +
str(epoch_number - bad_counter) +
": {:05.2f}%\t{:05.2f}%".format(
previous_best_valid_accuracy,
previous_best_test_accuracy))
if bad_counter >= parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
break
if epoch_number >= parameters[
'maximum_number_of_epochs']:
break
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
print('Training interrupted')
print('Finishing the experiment')
end_time = time.time()
results['execution_details'][
'train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
evaluate.save_results(results, stats_graph_folder)
sess.close() # release the session's resources
betas=(0, 0.9))
optimizer_G_y2x = torch.optim.Adam(G_y2x.parameters(),
lr=0.0001,
betas=(0, 0.9))
optimizer_D_x = torch.optim.Adam(D_x.parameters(),
lr=0.0001,
betas=(0, 0.9))
optimizer_D_y = torch.optim.Adam(D_y.parameters(),
lr=0.0001,
betas=(0, 0.9))
criterion_image = nn.L1Loss()
criterion_type = nn.L1Loss()
criterion_identity = nn.L1Loss()
x_fake_sample = Sample_from_Pool()
y_fake_sample = Sample_from_Pool()
for epoch in range(num_epochs):
train_step(epoch,trainloader, G_x2y, G_y2x,D_x,D_y,\
optimizer_G_x2y,optimizer_G_y2x,optimizer_D_x, optimizer_D_y,\
criterion_image,criterion_type,criterion_identity, batch_size,\
x_fake_sample,y_fake_sample,lambda_identity_loss,\
lambda_idt_x,lambda_idt_y, wgan_lambda, save_dir,save_log_file,fh)
fh.close()
else:
#Potential validation code
pass
def fit(self):
'''
Dùng để train data
'''
parameters = self.parameters
conf_parameters = self.conf_parameters
dataset_filepaths = self.dataset_filepaths
dataset = self.dataset
dataset_brat_folders = self.dataset_brat_folders
sess = self.sess
model = self.model
transition_params_trained = self.transition_params_trained
stats_graph_folder, experiment_timestamp = self._create_stats_graph_folder(parameters)
# Khởi tạo và lưu các thông tin của lần chạy
start_time = time.time()
results = {}
results['epoch'] = {}
'''
An epoch, in Machine Learning, is the entire processing by the learning algorithm of the entire train-set.
Ex:
The MNIST train set is composed by 55000 samples. Once the algorithm processed all those 55000 samples an epoch is passed.
'''
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time # Thời gian bắt đầu chạy
results['execution_details']['time_stamp'] = experiment_timestamp # Nhãn thời gian
results['execution_details']['early_stop'] = False # Cho biết có lỗi xảy ra nên bị dừng sớm ko
results['execution_details']['keyboard_interrupt'] = False # Cho biết có bị dừng bởi keyboard
results['execution_details']['num_epochs'] = 0 # Số lượng epoch đã chạy
results['model_options'] = copy.copy(parameters) # Các tham số
model_folder = os.path.join(stats_graph_folder, 'model') # output/en.../model
utils.create_folder_if_not_exists(model_folder)
# Save value cac parameters vao file parameters.ini
with open(os.path.join(model_folder, 'parameters.ini'), 'w') as parameters_file:
conf_parameters.write(parameters_file) # Log các tham số ra file
pickle.dump(dataset, open(os.path.join(model_folder, 'dataset.pickle'), 'wb')) # Dump dataset thành pickle file để lần sau chạy
# Tạo folder tensorboard logs để dùng cho việc vẽ biểu đồ sau này
tensorboard_log_folder = os.path.join(stats_graph_folder, 'tensorboard_logs') # folder lưu file log của tensorboard -> dùng cho việc plot biểu đồ lên
utils.create_folder_if_not_exists(tensorboard_log_folder)
tensorboard_log_folders = {}
for dataset_type in dataset_filepaths.keys():
tensorboard_log_folders[dataset_type] = os.path.join(stats_graph_folder, 'tensorboard_logs', dataset_type)
utils.create_folder_if_not_exists(tensorboard_log_folders[dataset_type])
# Khởi tạo các writers cho tensorboard
writers = {} # Có nhiều nhất 4 writers train, test, valid, deploy
for dataset_type in dataset_filepaths.keys():
writers[dataset_type] = tf.summary.FileWriter(tensorboard_log_folders[dataset_type], graph=sess.graph)
embedding_writer = tf.summary.FileWriter(model_folder) # embedding_writer has to write in model_folder, otherwise TensorBoard won't be able to view embeddings
# Dùng cho việc visualize embedding bằng tensorboard
embeddings_projector_config = projector.ProjectorConfig()
tensorboard_token_embeddings = embeddings_projector_config.embeddings.add()
tensorboard_token_embeddings.tensor_name = model.token_embedding_weights.name
token_list_file_path = os.path.join(model_folder, 'tensorboard_metadata_tokens.tsv')
tensorboard_token_embeddings.metadata_path = 'tensorboard_metadata_tokens.tsv'#os.path.relpath(token_list_file_path, '..')
tensorboard_character_embeddings = embeddings_projector_config.embeddings.add()
tensorboard_character_embeddings.tensor_name = model.character_embedding_weights.name
character_list_file_path = os.path.join(model_folder, 'tensorboard_metadata_characters.tsv')
tensorboard_character_embeddings.metadata_path = 'tensorboard_metadata_characters.tsv'#os.path.relpath(character_list_file_path, '..')
# Saves a configuration file that TensorBoard will read during startup.
projector.visualize_embeddings(embedding_writer, embeddings_projector_config)
# Ghi token vào file tsv dùng làm metadata cho embedding
token_list_file = codecs.open(token_list_file_path,'w', 'UTF-8')
for token_index in range(dataset.vocabulary_size):
token_list_file.write('{0}\n'.format(dataset.index_to_token[token_index]))
token_list_file.close()
# Ghi characters vào file tsv dùng làm metadata cho embedding
character_list_file = codecs.open(character_list_file_path,'w', 'UTF-8')
for character_index in range(dataset.alphabet_size):
if character_index == dataset.PADDING_CHARACTER_INDEX:
character_list_file.write('PADDING\n')
else:
character_list_file.write('{0}\n'.format(dataset.index_to_character[character_index]))
character_list_file.close()
# Start training + evaluation loop. Each iteration corresponds to 1 epoch.
bad_counter = 0 # number of epochs with no improvement on the validation test in terms of F1-score
previous_best_valid_f1_score = 0 # f1-Score tốt nhất ở các lần chạy trước
epoch_number = -1
try:
while True:
step = 0
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
if epoch_number != 0:
# Train model: loop over all sequences of training set with shuffling
sequence_numbers=list(range(len(dataset.token_indices['train'])))
print("----****____")
print(dataset.token_indices['train'][:10])
random.shuffle(sequence_numbers)
# Thuc hien train
for sequence_number in sequence_numbers:
transition_params_trained = train.train_step(sess, dataset, sequence_number, model, parameters)
step += 1
if step % 10 == 0:
print('Training {0:.2f}% done'.format(step/len(sequence_numbers)*100), end='\r', flush=True)
# Tinh thoi gian thuc hien 1 epoch
epoch_elapsed_training_time = time.time() - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(epoch_elapsed_training_time), flush=True)
y_pred, y_true, output_filepaths = train.predict_labels(sess, model, transition_params_trained, parameters, dataset, epoch_number, stats_graph_folder, dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred, y_true, stats_graph_folder, epoch_number, epoch_start_time, output_filepaths, parameters)
if parameters['use_pretrained_model'] and not parameters['train_model']:
conll_to_brat.output_brat(output_filepaths, dataset_brat_folders, stats_graph_folder)
break
# Save model
model.saver.save(sess, os.path.join(model_folder, 'model_{0:05d}.ckpt'.format(epoch_number)))
# Save TensorBoard logs
summary = sess.run(model.summary_op, feed_dict=None)
writers['train'].add_summary(summary, epoch_number)
writers['train'].flush()
utils.copytree(writers['train'].get_logdir(), model_folder)
# Early stop
valid_f1_score = results['epoch'][epoch_number][0]['valid']['f1_score']['micro']
# If do chinh xac cua epoch > do chinh xac cua epoch truoc
if valid_f1_score > previous_best_valid_f1_score:
bad_counter = 0
previous_best_valid_f1_score = valid_f1_score
conll_to_brat.output_brat(output_filepaths, dataset_brat_folders, stats_graph_folder, overwrite=True)
self.transition_params_trained = transition_params_trained
else:
bad_counter += 1
print("The last {0} epochs have not shown improvements on the validation set.".format(bad_counter))
# If bad_counter den mot muc gioi han parameters['patience'] = 10 (gia tri khoi tao) finish train
if bad_counter >= parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
break
# Neu so epoch >= so luong epoch toi da quy dinh --> ket thuc train
if epoch_number >= parameters['maximum_number_of_epochs']: break
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
print('Training interrupted')
# Ket thuc train luu cac tham so time, ket qua
print('Finishing the experiment')
end_time = time.time()
results['execution_details']['train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
evaluate.save_results(results, stats_graph_folder)
for dataset_type in dataset_filepaths.keys():
writers[dataset_type].close()
def main(languages):
#embeddings_type = ['polyglot', 'fasttext']
#embeddings_type = ['fasttext', 'fasttext_noOOV']
embeddings_type = ['fasttext_noOOV']
character_lstm = [True]
embedding_language = ['target', 'source']
combination = product(languages, embeddings_type, embedding_language, character_lstm)
create_folder_if_not_exists(os.path.join("..", "log"))
experiment_timestamp = utils.get_current_time_in_miliseconds()
log_file = os.path.join("..", "log", "experiment-{}.log".format(experiment_timestamp))
for language, emb_type, emb_language, char_lstm in combination:
conf_parameters = load_parameters()
conf_parameters = set_datasets(conf_parameters, language)
conf_parameters.set('ann','use_character_lstm', str(char_lstm))
conf_parameters.set('ann','embedding_type', emb_type)
conf_parameters.set('ann','embedding_language', emb_language)
if emb_type == 'polyglot':
conf_parameters.set('ann', 'embedding_dimension', str(64))
elif 'fasttext' in emb_type:
conf_parameters.set('ann', 'embedding_dimension', str(300))
else:
raise("Uknown embedding type")
if emb_language == 'source':
conf_parameters.set('dataset', 'language', constants.MAPPING_LANGUAGE[language])
else:
conf_parameters.set('dataset', 'language', language)
parameters, conf_parameters = parse_parameters(conf_parameters)
start_time = time.time()
experiment_timestamp = utils.get_current_time_in_miliseconds()
results = {}
results['epoch'] = {}
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time
results['execution_details']['time_stamp'] = experiment_timestamp
results['execution_details']['early_stop'] = False
results['execution_details']['keyboard_interrupt'] = False
results['execution_details']['num_epochs'] = 0
results['model_options'] = copy.copy(parameters)
dataset_name = utils.get_basename_without_extension(parameters['dataset_train'])
model_name = '{0}_{1}_{2}_{3}_{4}'.format(language, emb_type, char_lstm, emb_language,
results['execution_details']['time_stamp'])
sys.stdout = open(os.path.join("..", "log", model_name), "w")
print(language, emb_type, char_lstm, emb_language)
with open(log_file, "a") as file:
file.write("Experiment: {}\n".format(model_name))
file.write("Start time:{}\n".format(experiment_timestamp))
file.write("-------------------------------------\n\n")
pprint(parameters)
dataset_filepaths = get_valid_dataset_filepaths(parameters)
check_parameter_compatiblity(parameters, dataset_filepaths)
previous_best_valid_epoch = -1
# Load dataset
dataset = ds.Dataset(verbose=parameters['verbose'], debug=parameters['debug'])
dataset.load_vocab_word_embeddings(parameters)
dataset.load_dataset(dataset_filepaths, parameters)
# Create graph and session
with tf.Graph().as_default():
session_conf = tf.ConfigProto(
intra_op_parallelism_threads=parameters['number_of_cpu_threads'],
inter_op_parallelism_threads=parameters['number_of_cpu_threads'],
device_count={'CPU': 1, 'GPU': parameters['number_of_gpus']},
allow_soft_placement=True,
# automatically choose an existing and supported device to run the operations in case the specified one doesn't exist
log_device_placement=False
)
session_conf.gpu_options.allow_growth = True
sess = tf.Session(config=session_conf)
with sess.as_default():
# Initialize and save execution details
print(model_name)
output_folder = os.path.join('..', 'output')
utils.create_folder_if_not_exists(output_folder)
stats_graph_folder = os.path.join(output_folder, model_name) # Folder where to save graphs
utils.create_folder_if_not_exists(stats_graph_folder)
model_folder = os.path.join(stats_graph_folder, 'model')
utils.create_folder_if_not_exists(model_folder)
with open(os.path.join(model_folder, 'parameters.ini'), 'w') as parameters_file:
conf_parameters.write(parameters_file)
tensorboard_log_folder = os.path.join(stats_graph_folder, 'tensorboard_logs')
utils.create_folder_if_not_exists(tensorboard_log_folder)
tensorboard_log_folders = {}
for dataset_type in dataset_filepaths.keys():
tensorboard_log_folders[dataset_type] = os.path.join(stats_graph_folder, 'tensorboard_logs',
dataset_type)
utils.create_folder_if_not_exists(tensorboard_log_folders[dataset_type])
# del dataset.embeddings_matrix
if not parameters['use_pretrained_model']:
pickle.dump(dataset, open(os.path.join(model_folder, 'dataset.pickle'), 'wb'))
# dataset.load_pretrained_word_embeddings(parameters)
# Instantiate the model
# graph initialization should be before FileWriter, otherwise the graph will not appear in TensorBoard
model = EntityLSTM(dataset, parameters)
# Instantiate the writers for TensorBoard
writers = {}
for dataset_type in dataset_filepaths.keys():
writers[dataset_type] = tf.summary.FileWriter(tensorboard_log_folders[dataset_type],
graph=sess.graph)
embedding_writer = tf.summary.FileWriter(
model_folder) # embedding_writer has to write in model_folder, otherwise TensorBoard won't be able to view embeddings
embeddings_projector_config = projector.ProjectorConfig()
tensorboard_token_embeddings = embeddings_projector_config.embeddings.add()
tensorboard_token_embeddings.tensor_name = model.token_embedding_weights.name
token_list_file_path = os.path.join(model_folder, 'tensorboard_metadata_tokens.tsv')
tensorboard_token_embeddings.metadata_path = os.path.relpath(token_list_file_path, '..')
if parameters['use_character_lstm']:
tensorboard_character_embeddings = embeddings_projector_config.embeddings.add()
tensorboard_character_embeddings.tensor_name = model.character_embedding_weights.name
character_list_file_path = os.path.join(model_folder, 'tensorboard_metadata_characters.tsv')
tensorboard_character_embeddings.metadata_path = os.path.relpath(character_list_file_path, '..')
projector.visualize_embeddings(embedding_writer, embeddings_projector_config)
# Write metadata for TensorBoard embeddings
token_list_file = codecs.open(token_list_file_path, 'w', 'UTF-8')
for token_index in range(len(dataset.index_to_token)):
token_list_file.write('{0}\n'.format(dataset.index_to_token[token_index]))
token_list_file.close()
if parameters['use_character_lstm']:
character_list_file = codecs.open(character_list_file_path, 'w', 'UTF-8')
for character_index in range(dataset.alphabet_size):
if character_index == dataset.PADDING_CHARACTER_INDEX:
character_list_file.write('PADDING\n')
else:
character_list_file.write('{0}\n'.format(dataset.index_to_character[character_index]))
character_list_file.close()
try:
# Initialize the model
sess.run(tf.global_variables_initializer())
if not parameters['use_pretrained_model']:
model.load_pretrained_token_embeddings(sess, dataset, parameters)
# Start training + evaluation loop. Each iteration corresponds to 1 epoch.
bad_counter = 0 # number of epochs with no improvement on the validation test in terms of F1-score
previous_best_valid_f1_score = -1
transition_params_trained = np.random.rand(len(dataset.unique_labels), len(
dataset.unique_labels)) # TODO np.random.rand(len(dataset.unique_labels)+2,len(dataset.unique_labels)+2)
model_saver = tf.train.Saver(
max_to_keep=None) # parameters['maximum_number_of_epochs']) # defaults to saving all variables
epoch_number = 0
while True:
step = 0
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
if parameters['use_pretrained_model'] and epoch_number == 1:
# Restore pretrained model parameters
transition_params_trained = train.restore_model_parameters_from_pretrained_model(parameters,
dataset,
sess,
model,
model_saver)
elif epoch_number != 0:
# Train model: loop over all sequences of training set with shuffling
sequence_numbers = list(range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
data_counter = 0
sub_id = 0
for i in tqdm(range(0, len(sequence_numbers), parameters['batch_size']), "Training epoch {}".format(epoch_number),
mininterval=1):
data_counter += parameters['batch_size']
if data_counter >= 20000:
data_counter = 0
sub_id += 0.001
print("Intermediate evaluation number: ", sub_id)
epoch_elapsed_training_time = time.time() - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(epoch_elapsed_training_time),
flush=True)
y_pred, y_true, output_filepaths = train.predict_labels(sess, model,
transition_params_trained,
parameters, dataset,
epoch_number + sub_id,
stats_graph_folder,
dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred, y_true, stats_graph_folder,
epoch_number, epoch_start_time, output_filepaths,
parameters)
# Save model
model_saver.save(sess, os.path.join(model_folder,
'model_{0:07.3f}.ckpt'.format(
epoch_number + sub_id)))
# Save TensorBoard logs
summary = sess.run(model.summary_op, feed_dict=None)
writers['train'].add_summary(summary, epoch_number)
writers['train'].flush()
utils.copytree(writers['train'].get_logdir(), model_folder)
# Early stop
valid_f1_score = results['epoch'][epoch_number][0]['valid']['f1_score']['micro']
if valid_f1_score > previous_best_valid_f1_score:
bad_counter = 0
previous_best_valid_f1_score = valid_f1_score
else:
bad_counter += 1
sequence_number = sequence_numbers[i: i + parameters['batch_size']]
transition_params_trained, loss = train.train_step(sess, dataset, sequence_number,
model, transition_params_trained,
parameters)
epoch_elapsed_training_time = time.time() - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(epoch_elapsed_training_time), flush=True)
y_pred, y_true, output_filepaths = train.predict_labels(sess, model, transition_params_trained,
parameters, dataset, epoch_number,
stats_graph_folder, dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred, y_true, stats_graph_folder, epoch_number,
epoch_start_time, output_filepaths, parameters)
# Save model
model_saver.save(sess, os.path.join(model_folder, 'model_{0:05d}.ckpt'.format(epoch_number)))
# Save TensorBoard logs
summary = sess.run(model.summary_op, feed_dict=None)
writers['train'].add_summary(summary, epoch_number)
writers['train'].flush()
utils.copytree(writers['train'].get_logdir(), model_folder)
# Early stop
valid_f1_score = results['epoch'][epoch_number][0]['valid']['f1_score']['micro']
if valid_f1_score > previous_best_valid_f1_score:
bad_counter = 0
previous_best_valid_f1_score = valid_f1_score
previous_best_valid_epoch = epoch_number
else:
bad_counter += 1
print("The last {0} epochs have not shown improvements on the validation set.".format(
bad_counter))
if bad_counter >= parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
break
if epoch_number >= parameters['maximum_number_of_epochs']: break
keep_only_best_model(model_folder,previous_best_valid_epoch ,parameters['maximum_number_of_epochs']+1)
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
print('Training interrupted')
# remove the experiment
remove_experiment = input("Do you want to remove the experiment? (yes/y/Yes)")
if remove_experiment in ["Yes", "yes", "y"]:
shutil.rmtree(stats_graph_folder)
print("Folder removed")
else:
print('Finishing the experiment')
end_time = time.time()
results['execution_details']['train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
evaluate.save_results(results, stats_graph_folder)
sys.stdout.close()
except Exception:
logging.exception("")
remove_experiment = input("Do you want to remove the experiment? (yes/y/Yes)")
if remove_experiment in ["Yes", "yes", "y"]:
shutil.rmtree(stats_graph_folder)
print("Folder removed")
sys.stdout.close()
sess.close() # release the session's resources
sys.stdout.close()
def train(self, max_number_of_epoch, model_folder, dropout_rate=0.5):
# stats_graph_folder, experiment_timestamp = utils.create_stats_graph_folder(parameters)
# Initialize and save execution details
start_time = time.time()
utils.create_folder_if_not_exists(model_folder)
pickle.dump(self.dataset,
open(os.path.join(model_folder, 'dataset.pickle'), 'wb'))
pickle.dump(
self.parameters,
open(os.path.join(model_folder, 'parameters.pickle'), 'wb'))
bad_counter = 0 # number of epochs with no improvement on the validation test in terms of F1-score
previous_best_valid_f1_score = -100
epoch_number = -1
while True:
step = 0
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
if epoch_number != 0:
# Train model: loop over all sequences of training set with shuffling
sequence_numbers = list(
range(len(self.dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
self.transition_params_trained = train.train_step(
self.sess, self.dataset, sequence_number, self.model,
dropout_rate)
step += 1
if step % 10 == 0:
print('Training {0:.2f}% done'.format(
step / len(sequence_numbers) * 100),
end='\r',
flush=True)
epoch_elapsed_training_time = time.time() - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(
epoch_elapsed_training_time),
flush=True)
f1_score = {}
for data_type in ['train', 'valid', 'test']:
if data_type not in self.dataset.label_indices.keys():
continue
_, _, f1_score[data_type] = train.evaluate_step(
sess=self.sess,
dataset_type=data_type,
dataset=self.dataset,
model=self.model,
transition_params_trained=self.transition_params_trained,
tagging_format=self.tagging_format)
# if epoch_number % 3 ==0:
self.model.saver.save(self.sess,
os.path.join(model_folder, 'model.ckpt'))
if abs(f1_score['valid'][-2] - previous_best_valid_f1_score) < 0.1:
bad_counter += 1
else:
bad_counter = 0
if bad_counter > 10:
break
previous_best_valid_f1_score = f1_score['valid'][-2]
if epoch_number > max_number_of_epoch:
break
def main(argv=sys.argv):
arguments = parse_arguments(argv[1:])
parameters, conf_parameters = load_parameters(
arguments['parameters_filepath'], arguments=arguments)
dataset_filepaths, dataset_brat_folders = get_valid_dataset_filepaths(
parameters)
check_parameter_compatiblity(parameters, dataset_filepaths)
# Load dataset
dataset = ds.Dataset(verbose=parameters['verbose'],
debug=parameters['debug'])
dataset.load_dataset(dataset_filepaths, parameters)
# Create graph and session
with tf.device('/gpu:0'):
with tf.Graph().as_default():
session_conf = tf.ConfigProto(
intra_op_parallelism_threads=parameters[
'number_of_cpu_threads'],
inter_op_parallelism_threads=parameters[
'number_of_cpu_threads'],
device_count={
'CPU': 1,
'GPU': parameters['number_of_gpus']
},
allow_soft_placement=True,
log_device_placement=False)
sess = tf.Session(config=session_conf)
with sess.as_default():
start_time = time.time()
experiment_timestamp = utils.get_current_time_in_miliseconds()
results = {}
results['epoch'] = {}
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time
results['execution_details'][
'time_stamp'] = experiment_timestamp
results['execution_details']['early_stop'] = False
results['execution_details']['keyboard_interrupt'] = False
results['execution_details']['num_epochs'] = 0
results['model_options'] = copy.copy(parameters)
dataset_name = utils.get_basename_without_extension(
parameters['dataset_text_folder'])
model_name = dataset_name
utils.create_folder_if_not_exists(parameters['output_folder'])
stats_graph_folder = os.path.join(
parameters['output_folder'],
model_name) # Folder where to save graphs
final_weights_folder = os.path.join(
parameters['output_folder'], 'weights')
utils.create_folder_if_not_exists(stats_graph_folder)
utils.create_folder_if_not_exists(final_weights_folder)
model_folder = os.path.join(stats_graph_folder, 'model')
utils.create_folder_if_not_exists(model_folder)
with open(os.path.join(model_folder, 'parameters.ini'),
'w') as parameters_file:
conf_parameters.write(parameters_file)
tensorboard_log_folder = os.path.join(stats_graph_folder,
'tensorboard_logs')
utils.create_folder_if_not_exists(tensorboard_log_folder)
tensorboard_log_folders = {}
for dataset_type in dataset_filepaths.keys():
tensorboard_log_folders[dataset_type] = os.path.join(
stats_graph_folder, 'tensorboard_logs', dataset_type)
utils.create_folder_if_not_exists(
tensorboard_log_folders[dataset_type])
pickle.dump(
dataset,
open(os.path.join(model_folder, 'dataset.pickle'), 'wb'))
model = EntityLSTM(dataset, parameters)
writers = {}
for dataset_type in dataset_filepaths.keys():
writers[dataset_type] = tf.summary.FileWriter(
tensorboard_log_folders[dataset_type],
graph=sess.graph)
embedding_writer = tf.summary.FileWriter(model_folder)
embeddings_projector_config = projector.ProjectorConfig()
tensorboard_token_embeddings = embeddings_projector_config.embeddings.add(
)
tensorboard_token_embeddings.tensor_name = model.token_embedding_weights.name
token_list_file_path = os.path.join(
model_folder, 'tensorboard_metadata_tokens.tsv')
tensorboard_token_embeddings.metadata_path = os.path.relpath(
token_list_file_path, '..')
tensorboard_character_embeddings = embeddings_projector_config.embeddings.add(
)
tensorboard_character_embeddings.tensor_name = model.character_embedding_weights.name
character_list_file_path = os.path.join(
model_folder, 'tensorboard_metadata_characters.tsv')
tensorboard_character_embeddings.metadata_path = os.path.relpath(
character_list_file_path, '..')
projector.visualize_embeddings(embedding_writer,
embeddings_projector_config)
token_list_file = codecs.open(token_list_file_path, 'w',
'latin-1')
for token_index in range(dataset.vocabulary_size):
token_list_file.write('{0}\n'.format(
dataset.index_to_token[token_index]))
token_list_file.close()
character_list_file = codecs.open(character_list_file_path,
'w', 'latin-1')
for character_index in range(dataset.alphabet_size):
if character_index == dataset.PADDING_CHARACTER_INDEX:
character_list_file.write('PADDING\n')
else:
character_list_file.write('{0}\n'.format(
dataset.index_to_character[character_index]))
character_list_file.close()
# Initialize the model
sess.run(tf.global_variables_initializer())
if not parameters['use_pretrained_model']:
model.load_pretrained_token_embeddings(
sess, dataset, parameters)
patience_counter = 0 # number of epochs with no improvement on the validation test in terms of F1-score
f1_score_best = 0
f1_scores = {'train-F1': [], 'valid-F1': [], 'test-F1': []}
transition_params_trained = np.random.rand(
len(dataset.unique_labels) + 2,
len(dataset.unique_labels) + 2)
model_saver = tf.train.Saver(
max_to_keep=parameters['num_of_model_to_keep']
) #, reshape= True) # defaults to saving all variables
epoch_number = -1
try:
while True:
step = 0
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
if parameters[
'use_pretrained_model'] and epoch_number == 0:
if parameters['use_corrector']:
parameters['use_corrector'] = False
transition_params_trained = train.restore_pretrained_model(
parameters, dataset, sess, model,
model_saver)
print(
'Getting the 3-label predictions from the step1 model.'
)
all_pred_labels, y_pred_for_corrector, y_true_for_corrector, \
output_filepaths = train.predict_labels(sess, model,
transition_params_trained,
parameters, dataset,
epoch_number,
stats_graph_folder,
dataset_filepaths,
for_corrector = True)
all_pred_indices = {} #defaultdict(list)
for dataset_type in dataset_filepaths.keys():
all_pred_indices[dataset_type] = []
for i in range(
len(all_pred_labels[dataset_type])
):
indices = [
dataset.
label_corrector_to_index[label]
for label in
all_pred_labels[dataset_type][i]
]
all_pred_indices[dataset_type].append(
indices)
label_binarizer_corrector = sklearn.preprocessing.LabelBinarizer(
)
label_binarizer_corrector.fit(
range(
max(dataset.index_to_label_corrector.
keys()) + 1))
predicted_label_corrector_vector_indices = {}
for dataset_type in dataset_filepaths.keys():
predicted_label_corrector_vector_indices[
dataset_type] = []
for label_indices_sequence in all_pred_indices[
dataset_type]:
predicted_label_corrector_vector_indices[
dataset_type].append(
label_binarizer_corrector.
transform(
label_indices_sequence))
parameters['use_corrector'] = True
transition_params_trained, model, glo_step = \
train.restore_model_parameters_from_pretrained_model(parameters, dataset, sess, model, model_saver)
for dataset_type in dataset_filepaths.keys():
writers[dataset_type] = tf.summary.FileWriter(
tensorboard_log_folders[dataset_type],
graph=sess.graph)
embedding_writer = tf.summary.FileWriter(
model_folder)
init_new_vars_op = tf.initialize_variables(
[glo_step])
sess.run(init_new_vars_op)
elif epoch_number != 0:
sequence_numbers = list(
range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
transition_params_trained, W_before_crf = train.train_step(
sess, dataset, sequence_number, model,
transition_params_trained, parameters)
step += 1
epoch_elapsed_training_time = time.time(
) - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(
epoch_elapsed_training_time),
flush=False)
if parameters['use_corrector']:
original_label_corrector_vector_indices = dataset.label_corrector_vector_indices
dataset.label_corrector_vector_indices = predicted_label_corrector_vector_indices
y_pred, y_true, output_filepaths = train.predict_labels(
sess, model, transition_params_trained,
parameters, dataset, epoch_number,
stats_graph_folder, dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred,
y_true, stats_graph_folder,
epoch_number,
epoch_start_time,
output_filepaths,
parameters)
dataset.label_corrector_vector_indices = original_label_corrector_vector_indices
else:
y_pred, y_true, output_filepaths = train.predict_labels(
sess, model, transition_params_trained,
parameters, dataset, epoch_number,
stats_graph_folder, dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred,
y_true, stats_graph_folder,
epoch_number,
epoch_start_time,
output_filepaths,
parameters)
summary = sess.run(model.summary_op, feed_dict=None)
writers['train'].add_summary(summary, epoch_number)
writers['train'].flush()
utils.copytree(writers['train'].get_logdir(),
model_folder)
# Early stopping
train_f1_score = results['epoch'][epoch_number][0][
'train']['f1_score']['micro']
valid_f1_score = results['epoch'][epoch_number][0][
'valid']['f1_score']['micro']
test_f1_score = results['epoch'][epoch_number][0][
'test']['f1_score']['micro']
f1_scores['train-F1'].append(train_f1_score)
f1_scores['valid-F1'].append(valid_f1_score)
f1_scores['test-F1'].append(test_f1_score)
if valid_f1_score > f1_score_best:
patience_counter = 0
f1_score_best = valid_f1_score
# Save the best model
model_saver.save(
sess,
os.path.join(model_folder, 'best_model.ckpt'))
print(
'updated model to current epoch : epoch {:d}'.
format(epoch_number))
print('the model is saved in: {:s}'.format(
model_folder))
### newly deleted
else:
patience_counter += 1
print("In epoch {:d}, the valid F1 is : {:f}".format(
epoch_number, valid_f1_score))
print(
"The last {0} epochs have not shown improvements on the validation set."
.format(patience_counter))
if patience_counter >= parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
if epoch_number >= parameters[
'maximum_number_of_epochs'] and parameters[
'refine_with_crf']:
model = train.refine_with_crf(
parameters, sess, model, model_saver)
print('refine model with CRF ...')
for additional_epoch in range(
parameters['additional_epochs_with_crf']):
print('Additional {:d}th epoch'.format(
additional_epoch))
sequence_numbers = list(
range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
transition_params_trained, W_before_crf = train.train_step(
sess, dataset, sequence_number, model,
transition_params_trained, parameters)
step += 1
epoch_elapsed_training_time = time.time(
) - epoch_start_time
print(
'Additional training completed in {0:.2f} seconds'
.format(epoch_elapsed_training_time),
flush=False)
y_pred, y_true, output_filepaths = train.predict_labels(
sess, model, transition_params_trained,
parameters, dataset, epoch_number,
stats_graph_folder, dataset_filepaths)
evaluate.evaluate_model(
results, dataset, y_pred, y_true,
stats_graph_folder, epoch_number,
epoch_start_time, output_filepaths,
parameters)
summary = sess.run(model.summary_op,
feed_dict=None)
writers['train'].add_summary(
summary, epoch_number)
writers['train'].flush()
utils.copytree(writers['train'].get_logdir(),
model_folder)
if epoch_number >= parameters[
'maximum_number_of_epochs'] and not parameters[
'refine_with_crf']:
break
if not parameters['use_pretrained_model']:
plot_name = 'F1-summary-step1.svg'
else:
plot_name = 'F1-summary-step2.svg'
for k, l in f1_scores.items():
print(k, l)
utils_plots.plot_f1(
f1_scores,
os.path.join(stats_graph_folder, '..', plot_name),
'F1 score summary')
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
print('Training interrupted')
print('Finishing the experiment')
end_time = time.time()
results['execution_details'][
'train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
evaluate.save_results(results, stats_graph_folder)
for dataset_type in dataset_filepaths.keys():
writers[dataset_type].close()
sess.close()
def main():
parameters, conf_parameters = load_parameters()
dataset_filepaths, dataset_brat_folders = get_valid_dataset_filepaths(parameters)
check_parameter_compatiblity(parameters, dataset_filepaths)
# Load dataset
dataset = ds.Dataset(verbose=parameters['verbose'], debug=parameters['debug'])
dataset.load_dataset(dataset_filepaths, parameters)
# Create graph and session
with tf.Graph().as_default():
session_conf = tf.ConfigProto(
intra_op_parallelism_threads=parameters['number_of_cpu_threads'],
inter_op_parallelism_threads=parameters['number_of_cpu_threads'],
device_count={'CPU': 1, 'GPU': parameters['number_of_gpus']},
allow_soft_placement=True, # automatically choose an existing and supported device to run the operations in case the specified one doesn't exist
log_device_placement=False
)
sess = tf.Session(config=session_conf)
with sess.as_default():
# Initialize and save execution details
start_time = time.time()
experiment_timestamp = utils.get_current_time_in_miliseconds()
results = {}
results['epoch'] = {}
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time
results['execution_details']['time_stamp'] = experiment_timestamp
results['execution_details']['early_stop'] = False
results['execution_details']['keyboard_interrupt'] = False
results['execution_details']['num_epochs'] = 0
results['model_options'] = copy.copy(parameters)
dataset_name = utils.get_basename_without_extension(parameters['dataset_text_folder'])
model_name = '{0}_{1}'.format(dataset_name, results['execution_details']['time_stamp'])
output_folder=os.path.join('..', 'output')
utils.create_folder_if_not_exists(output_folder)
stats_graph_folder=os.path.join(output_folder, model_name) # Folder where to save graphs
utils.create_folder_if_not_exists(stats_graph_folder)
model_folder = os.path.join(stats_graph_folder, 'model')
utils.create_folder_if_not_exists(model_folder)
with open(os.path.join(model_folder, 'parameters.ini'), 'w') as parameters_file:
conf_parameters.write(parameters_file)
tensorboard_log_folder = os.path.join(stats_graph_folder, 'tensorboard_logs')
utils.create_folder_if_not_exists(tensorboard_log_folder)
tensorboard_log_folders = {}
for dataset_type in dataset_filepaths.keys():
tensorboard_log_folders[dataset_type] = os.path.join(stats_graph_folder, 'tensorboard_logs', dataset_type)
utils.create_folder_if_not_exists(tensorboard_log_folders[dataset_type])
pickle.dump(dataset, open(os.path.join(model_folder, 'dataset.pickle'), 'wb'))
# Instantiate the model
# graph initialization should be before FileWriter, otherwise the graph will not appear in TensorBoard
model = EntityLSTM(dataset, parameters)
# Instantiate the writers for TensorBoard
writers = {}
for dataset_type in dataset_filepaths.keys():
writers[dataset_type] = tf.summary.FileWriter(tensorboard_log_folders[dataset_type], graph=sess.graph)
embedding_writer = tf.summary.FileWriter(model_folder) # embedding_writer has to write in model_folder, otherwise TensorBoard won't be able to view embeddings
embeddings_projector_config = projector.ProjectorConfig()
tensorboard_token_embeddings = embeddings_projector_config.embeddings.add()
tensorboard_token_embeddings.tensor_name = model.token_embedding_weights.name
token_list_file_path = os.path.join(model_folder, 'tensorboard_metadata_tokens.tsv')
tensorboard_token_embeddings.metadata_path = os.path.relpath(token_list_file_path, '..')
tensorboard_character_embeddings = embeddings_projector_config.embeddings.add()
tensorboard_character_embeddings.tensor_name = model.character_embedding_weights.name
character_list_file_path = os.path.join(model_folder, 'tensorboard_metadata_characters.tsv')
tensorboard_character_embeddings.metadata_path = os.path.relpath(character_list_file_path, '..')
projector.visualize_embeddings(embedding_writer, embeddings_projector_config)
# Write metadata for TensorBoard embeddings
token_list_file = codecs.open(token_list_file_path,'w', 'UTF-8')
for token_index in range(dataset.vocabulary_size):
token_list_file.write('{0}\n'.format(dataset.index_to_token[token_index]))
token_list_file.close()
character_list_file = codecs.open(character_list_file_path,'w', 'UTF-8')
for character_index in range(dataset.alphabet_size):
if character_index == dataset.PADDING_CHARACTER_INDEX:
character_list_file.write('PADDING\n')
else:
character_list_file.write('{0}\n'.format(dataset.index_to_character[character_index]))
character_list_file.close()
# Initialize the model
sess.run(tf.global_variables_initializer())
if not parameters['use_pretrained_model']:
model.load_pretrained_token_embeddings(sess, dataset, parameters)
# Start training + evaluation loop. Each iteration corresponds to 1 epoch.
bad_counter = 0 # number of epochs with no improvement on the validation test in terms of F1-score
previous_best_valid_f1_score = 0
transition_params_trained = np.random.rand(len(dataset.unique_labels)+2,len(dataset.unique_labels)+2)
model_saver = tf.train.Saver(max_to_keep=parameters['maximum_number_of_epochs']) # defaults to saving all variables
epoch_number = -1
try:
while True:
step = 0
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
if parameters['use_pretrained_model'] and epoch_number == 0:
# Restore pretrained model parameters
transition_params_trained = train.restore_model_parameters_from_pretrained_model(parameters, dataset, sess, model, model_saver)
elif epoch_number != 0:
# Train model: loop over all sequences of training set with shuffling
sequence_numbers=list(range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
transition_params_trained = train.train_step(sess, dataset, sequence_number, model, transition_params_trained, parameters)
step += 1
if step % 10 == 0:
print('Training {0:.2f}% done'.format(step/len(sequence_numbers)*100), end='\r', flush=True)
epoch_elapsed_training_time = time.time() - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(epoch_elapsed_training_time), flush=True)
y_pred, y_true, output_filepaths = train.predict_labels(sess, model, transition_params_trained, parameters, dataset, epoch_number, stats_graph_folder, dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred, y_true, stats_graph_folder, epoch_number, epoch_start_time, output_filepaths, parameters)
if parameters['use_pretrained_model'] and not parameters['train_model']:
conll_to_brat.output_brat(output_filepaths, dataset_brat_folders, stats_graph_folder)
break
# Save model
model_saver.save(sess, os.path.join(model_folder, 'model_{0:05d}.ckpt'.format(epoch_number)))
# Save TensorBoard logs
summary = sess.run(model.summary_op, feed_dict=None)
writers['train'].add_summary(summary, epoch_number)
writers['train'].flush()
utils.copytree(writers['train'].get_logdir(), model_folder)
# Early stop
valid_f1_score = results['epoch'][epoch_number][0]['valid']['f1_score']['micro']
if valid_f1_score > previous_best_valid_f1_score:
bad_counter = 0
previous_best_valid_f1_score = valid_f1_score
conll_to_brat.output_brat(output_filepaths, dataset_brat_folders, stats_graph_folder, overwrite=True)
else:
bad_counter += 1
print("The last {0} epochs have not shown improvements on the validation set.".format(bad_counter))
if bad_counter >= parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
break
if epoch_number >= parameters['maximum_number_of_epochs']: break
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
print('Training interrupted')
print('Finishing the experiment')
end_time = time.time()
results['execution_details']['train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
print('ok1')
evaluate.save_results(results, stats_graph_folder)
print('ok2')
print('ok3')
#sess.close() # release the session's resources
print('ok4')
def main():
#### Parameters - start
conf_parameters = configparser.ConfigParser()
conf_parameters.read(os.path.join('.', 'parameters.ini'))
nested_parameters = utils.convert_configparser_to_dictionary(
conf_parameters)
parameters = {}
for k, v in nested_parameters.items():
parameters.update(v)
for k, v in parameters.items():
if k in [
'remove_unknown_tokens', 'character_embedding_dimension',
'character_lstm_hidden_state_dimension',
'token_embedding_dimension',
'token_lstm_hidden_state_dimension', 'patience',
'maximum_number_of_epochs', 'maximum_training_time',
'number_of_cpu_threads', 'number_of_gpus'
]:
parameters[k] = int(v)
if k in ['dropout_rate']:
parameters[k] = float(v)
if k in [
'use_character_lstm', 'is_character_lstm_bidirect',
'is_token_lstm_bidirect', 'use_crf'
]:
parameters[k] = distutils.util.strtobool(v)
pprint(parameters)
# Load dataset
dataset_filepaths = {}
dataset_filepaths['train'] = os.path.join(
parameters['dataset_text_folder'], 'train.txt')
dataset_filepaths['valid'] = os.path.join(
parameters['dataset_text_folder'], 'valid.txt')
dataset_filepaths['test'] = os.path.join(parameters['dataset_text_folder'],
'test.txt')
dataset = ds.Dataset()
dataset.load_dataset(dataset_filepaths, parameters)
with tf.Graph().as_default():
session_conf = tf.ConfigProto(
device_count={
'CPU': 1,
'GPU': 1
},
allow_soft_placement=
True, # automatically choose an existing and supported device to run the operations in case the specified one doesn't exist
log_device_placement=False)
sess = tf.Session(config=session_conf)
with sess.as_default():
# Instantiate model
model = EntityLSTM(dataset, parameters)
sess.run(tf.global_variables_initializer())
model.load_pretrained_token_embeddings(sess, dataset, parameters)
# Initialize and save execution details
start_time = time.time()
experiment_timestamp = utils.get_current_time_in_miliseconds()
results = {}
#results['model_options'] = copy.copy(model_options)
#results['model_options'].pop('optimizer', None)
results['epoch'] = {}
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time
results['execution_details']['time_stamp'] = experiment_timestamp
results['execution_details']['early_stop'] = False
results['execution_details']['keyboard_interrupt'] = False
results['execution_details']['num_epochs'] = 0
results['model_options'] = copy.copy(parameters)
dataset_name = utils.get_basename_without_extension(
parameters['dataset_text_folder']
) #opts.train.replace('/', '_').split('.')[0] # 'conll2003en'
model_name = '{0}_{1}'.format(
dataset_name, results['execution_details']['time_stamp'])
output_folder = os.path.join('..', 'output')
utils.create_folder_if_not_exists(output_folder)
stats_graph_folder = os.path.join(
output_folder, model_name) # Folder where to save graphs
#print('stats_graph_folder: {0}'.format(stats_graph_folder))
utils.create_folder_if_not_exists(stats_graph_folder)
# model_folder = os.path.join(stats_graph_folder, 'model')
# utils.create_folder_if_not_exists(model_folder)
step = 0
bad_counter = 0
previous_best_valid_f1_score = 0
transition_params_trained = np.random.rand(
len(dataset.unique_labels), len(dataset.unique_labels))
try:
while True:
epoch_number = math.floor(
step / len(dataset.token_indices['train']))
print('\nStarting epoch {0}'.format(epoch_number), end='')
epoch_start_time = time.time()
#print('step: {0}'.format(step))
# Train model: loop over all sequences of training set with shuffling
sequence_numbers = list(
range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
transition_params_trained = train.train_step(
sess, dataset, sequence_number, model,
transition_params_trained, parameters)
step += 1
if step % 100 == 0:
print('.', end='', flush=True)
#break
print('.', flush=True)
#print('step: {0}'.format(step))
# Predict labels using trained model
all_predictions = {}
all_y_true = {}
output_filepaths = {}
for dataset_type in ['train', 'valid', 'test']:
#print('dataset_type: {0}'.format(dataset_type))
prediction_output = train.prediction_step(
sess, dataset, dataset_type, model,
transition_params_trained, step,
stats_graph_folder, epoch_number, parameters)
all_predictions[dataset_type], all_y_true[
dataset_type], output_filepaths[
dataset_type] = prediction_output
# model_options = None
epoch_elapsed_training_time = time.time(
) - epoch_start_time
print(
'epoch_elapsed_training_time: {0:.2f} seconds'.format(
epoch_elapsed_training_time))
results['execution_details']['num_epochs'] = epoch_number
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, all_predictions,
all_y_true, stats_graph_folder,
epoch_number, epoch_start_time,
output_filepaths)
# Early stop
valid_f1_score = results['epoch'][epoch_number][0][
'valid']['f1_score']['micro']
if valid_f1_score > previous_best_valid_f1_score:
bad_counter = 0
previous_best_valid_f1_score = valid_f1_score
else:
bad_counter += 1
if bad_counter > parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
break
if epoch_number > parameters['maximum_number_of_epochs']:
break
# break # debugging
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
# assess_model.save_results(results, stats_graph_folder)
print('Training interrupted')
print('Finishing the experiment')
end_time = time.time()
results['execution_details'][
'train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
evaluate.save_results(results, stats_graph_folder)
sess.close() # release the session's resources
loss_metric.reset_states()
# Iterate over the batches of the dataset.
for step, x_batch_train in enumerate(train_dataset):
Rinnumpy = x_batch_train[0].numpy()
Idx = comput_inter_list_2d(Rinnumpy, L, radious, max_num_neighs)
neigh_list = tf.Variable(Idx)
# print(neigh_list.shape)
# print(x_batch_train[0].shape)
# print(x_batch_train[1].shape)
loss = train_step(model, optimizer, loss_cross,
x_batch_train[0], neigh_list,
x_batch_train[1])
loss_metric(loss)
if step % 100 == 0:
print('step %s: mean loss = %s' % (step, str(loss_metric.result().numpy())))
# mean loss saved in the metric
meanLossStr = str(loss_metric.result().numpy())
# learning rate using the decay
lrStr = str(optimizer._decayed_lr('float32').numpy())
print('epoch %s: mean loss = %s learning rate = %s'%(epoch,
meanLossStr,
lrStr))
print("saving the weights")
try:
while True:
step = 0
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
if epoch_number != 0:
# Train model: loop over all sequences of training set with shuffling
sequence_numbers = list(range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
transition_params_trained = train.train_step(
sess, dataset, sequence_number, model,
parameters['dropout_rate'])
step += 1
if step % 10 == 0:
print('Training {0:.2f}% done'.format(
step / len(sequence_numbers) * 100),
end='\r',
flush=True)
epoch_elapsed_training_time = time.time() - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(
epoch_elapsed_training_time),
flush=True)
y_pred, y_true, output_filepaths = train.predict_labels_lite(
sess=sess,
def fit(self):
parameters = self.parameters
conf_parameters = self.conf_parameters
dataset_filepaths = self.dataset_filepaths
dataset = self.dataset
dataset_brat_folders = self.dataset_brat_folders
sess = self.sess
model = self.model
transition_params_trained = self.transition_params_trained
stats_graph_folder, experiment_timestamp = self._create_stats_graph_folder(parameters)
# Initialize and save execution details
start_time = time.time()
results = {}
results['epoch'] = {}
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time
results['execution_details']['time_stamp'] = experiment_timestamp
results['execution_details']['early_stop'] = False
results['execution_details']['keyboard_interrupt'] = False
results['execution_details']['num_epochs'] = 0
results['model_options'] = copy.copy(parameters)
model_folder = os.path.join(stats_graph_folder, 'model')
utils.create_folder_if_not_exists(model_folder)
with open(os.path.join(model_folder, 'parameters.ini'), 'w') as parameters_file:
conf_parameters.write(parameters_file)
pickle.dump(dataset, open(os.path.join(model_folder, 'dataset.pickle'), 'wb'))
tensorboard_log_folder = os.path.join(stats_graph_folder, 'tensorboard_logs')
utils.create_folder_if_not_exists(tensorboard_log_folder)
tensorboard_log_folders = {}
for dataset_type in dataset_filepaths.keys():
tensorboard_log_folders[dataset_type] = os.path.join(stats_graph_folder, 'tensorboard_logs', dataset_type)
utils.create_folder_if_not_exists(tensorboard_log_folders[dataset_type])
# Instantiate the writers for TensorBoard
writers = {}
for dataset_type in dataset_filepaths.keys():
writers[dataset_type] = tf.summary.FileWriter(tensorboard_log_folders[dataset_type], graph=sess.graph)
embedding_writer = tf.summary.FileWriter(model_folder) # embedding_writer has to write in model_folder, otherwise TensorBoard won't be able to view embeddings
embeddings_projector_config = projector.ProjectorConfig()
tensorboard_token_embeddings = embeddings_projector_config.embeddings.add()
tensorboard_token_embeddings.tensor_name = model.token_embedding_weights.name
token_list_file_path = os.path.join(model_folder, 'tensorboard_metadata_tokens.tsv')
tensorboard_token_embeddings.metadata_path = os.path.relpath(token_list_file_path, '..')
tensorboard_character_embeddings = embeddings_projector_config.embeddings.add()
tensorboard_character_embeddings.tensor_name = model.character_embedding_weights.name
character_list_file_path = os.path.join(model_folder, 'tensorboard_metadata_characters.tsv')
tensorboard_character_embeddings.metadata_path = os.path.relpath(character_list_file_path, '..')
projector.visualize_embeddings(embedding_writer, embeddings_projector_config)
# Write metadata for TensorBoard embeddings
token_list_file = codecs.open(token_list_file_path,'w', 'UTF-8')
for token_index in range(dataset.vocabulary_size):
token_list_file.write('{0}\n'.format(dataset.index_to_token[token_index]))
token_list_file.close()
character_list_file = codecs.open(character_list_file_path,'w', 'UTF-8')
for character_index in range(dataset.alphabet_size):
if character_index == dataset.PADDING_CHARACTER_INDEX:
character_list_file.write('PADDING\n')
else:
character_list_file.write('{0}\n'.format(dataset.index_to_character[character_index]))
character_list_file.close()
# Start training + evaluation loop. Each iteration corresponds to 1 epoch.
bad_counter = 0 # number of epochs with no improvement on the validation test in terms of F1-score
previous_best_valid_f1_score = 0
epoch_number = -1
try:
while True:
step = 0
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
if epoch_number != 0:
# Train model: loop over all sequences of training set with shuffling
sequence_numbers=list(range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
transition_params_trained = train.train_step(sess, dataset, sequence_number, model, parameters)
step += 1
if step % 10 == 0:
print('Training {0:.2f}% done'.format(step/len(sequence_numbers)*100), end='\r', flush=True)
epoch_elapsed_training_time = time.time() - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(epoch_elapsed_training_time), flush=True)
y_pred, y_true, output_filepaths = train.predict_labels(sess, model, transition_params_trained, parameters, dataset, epoch_number, stats_graph_folder, dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred, y_true, stats_graph_folder, epoch_number, epoch_start_time, output_filepaths, parameters)
if parameters['use_pretrained_model'] and not parameters['train_model']:
conll_to_brat.output_brat(output_filepaths, dataset_brat_folders, stats_graph_folder)
break
# Save model
model.saver.save(sess, os.path.join(model_folder, 'model_{0:05d}.ckpt'.format(epoch_number)))
# Save TensorBoard logs
summary = sess.run(model.summary_op, feed_dict=None)
writers['train'].add_summary(summary, epoch_number)
writers['train'].flush()
utils.copytree(writers['train'].get_logdir(), model_folder)
# Early stop
valid_f1_score = results['epoch'][epoch_number][0]['valid']['f1_score']['micro']
if valid_f1_score > previous_best_valid_f1_score:
bad_counter = 0
previous_best_valid_f1_score = valid_f1_score
conll_to_brat.output_brat(output_filepaths, dataset_brat_folders, stats_graph_folder, overwrite=True)
self.transition_params_trained = transition_params_trained
else:
bad_counter += 1
print("The last {0} epochs have not shown improvements on the validation set.".format(bad_counter))
if bad_counter >= parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
break
if epoch_number >= parameters['maximum_number_of_epochs']: break
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
print('Training interrupted')
print('Finishing the experiment')
end_time = time.time()
results['execution_details']['train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
evaluate.save_results(results, stats_graph_folder)
for dataset_type in dataset_filepaths.keys():
writers[dataset_type].close()
def main():
parameters, conf_parameters = load_parameters()
pprint(parameters)
dataset_filepaths = get_valid_dataset_filepaths(parameters)
check_parameter_compatiblity(parameters, dataset_filepaths)
cross_validation = parameters[
'cross_validation'] if 'cross_validation' in parameters else 1
valid_fscores = []
valid_precisions = []
valid_recalls = []
for cv in range(0, cross_validation):
if "als" in dataset_filepaths['train'] and cross_validation > 1:
train_files = list(range(0, cv)) + list(
range(cv + 1, cross_validation))
test_file = cv
file_train = "tmp_combined.train"
file_valid = "tmp_combined.test"
output = []
for i in train_files:
with open(dataset_filepaths['train'] + "_" + str(i),
"r",
encoding="utf-8") as file:
output.append(file.read())
with open(file_train, "w", encoding="utf-8") as file:
file.write("\n\n".join(output))
output = []
with open(dataset_filepaths['train'] + "_" + str(test_file),
"r",
encoding="utf-8") as file:
output.append(file.read())
with open(file_valid, "w", encoding="utf-8") as file:
file.write("\n\n".join(output))
dataset_filepaths['train'] = file_train
dataset_filepaths['valid'] = file_valid
# Load dataset
dataset = ds.Dataset(verbose=parameters['verbose'],
debug=parameters['debug'])
dataset.load_vocab_word_embeddings(parameters)
dataset.load_dataset(dataset_filepaths, parameters)
# Create graph and session
with tf.Graph().as_default():
session_conf = tf.ConfigProto(
intra_op_parallelism_threads=parameters[
'number_of_cpu_threads'],
inter_op_parallelism_threads=parameters[
'number_of_cpu_threads'],
device_count={
'CPU': 1,
'GPU': parameters['number_of_gpus']
},
allow_soft_placement=
True, # automatically choose an existing and supported device to run the operations in case the specified one doesn't exist
log_device_placement=False)
session_conf.gpu_options.allow_growth = True
sess = tf.Session(config=session_conf)
with sess.as_default():
# Initialize and save execution details
start_time = time.time()
experiment_timestamp = utils.get_current_time_in_miliseconds()
results = {}
results['epoch'] = {}
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time
results['execution_details'][
'time_stamp'] = experiment_timestamp
results['execution_details']['early_stop'] = False
results['execution_details']['keyboard_interrupt'] = False
results['execution_details']['num_epochs'] = 0
results['model_options'] = copy.copy(parameters)
dataset_name = utils.get_basename_without_extension(
parameters['dataset_train'])
if 'data_to_use' in parameters:
model_name = '{0}_{1}'.format(
parameters['language'] + "_" + dataset_name + "_small",
results['execution_details']['time_stamp'])
else:
model_name = '{0}_{1}'.format(
parameters['language'] + "_" + dataset_name,
results['execution_details']['time_stamp'])
output_folder = os.path.join('..', 'output')
utils.create_folder_if_not_exists(output_folder)
stats_graph_folder = os.path.join(
output_folder, model_name) # Folder where to save graphs
utils.create_folder_if_not_exists(stats_graph_folder)
model_folder = os.path.join(stats_graph_folder, 'model')
utils.create_folder_if_not_exists(model_folder)
with open(os.path.join(model_folder, 'parameters.ini'),
'w') as parameters_file:
conf_parameters.write(parameters_file)
tensorboard_log_folder = os.path.join(stats_graph_folder,
'tensorboard_logs')
utils.create_folder_if_not_exists(tensorboard_log_folder)
tensorboard_log_folders = {}
for dataset_type in dataset_filepaths.keys():
tensorboard_log_folders[dataset_type] = os.path.join(
stats_graph_folder, 'tensorboard_logs', dataset_type)
utils.create_folder_if_not_exists(
tensorboard_log_folders[dataset_type])
#del dataset.embeddings_matrix
if not parameters['use_pretrained_model']:
pickle.dump(
dataset,
open(os.path.join(model_folder, 'dataset.pickle'),
'wb'))
#dataset.load_pretrained_word_embeddings(parameters)
# Instantiate the model
# graph initialization should be before FileWriter, otherwise the graph will not appear in TensorBoard
model = EntityLSTM(dataset, parameters)
# Instantiate the writers for TensorBoard
writers = {}
for dataset_type in dataset_filepaths.keys():
writers[dataset_type] = tf.summary.FileWriter(
tensorboard_log_folders[dataset_type],
graph=sess.graph)
embedding_writer = tf.summary.FileWriter(
model_folder
) # embedding_writer has to write in model_folder, otherwise TensorBoard won't be able to view embeddings
embeddings_projector_config = projector.ProjectorConfig()
tensorboard_token_embeddings = embeddings_projector_config.embeddings.add(
)
tensorboard_token_embeddings.tensor_name = model.token_embedding_weights.name
token_list_file_path = os.path.join(
model_folder, 'tensorboard_metadata_tokens.tsv')
tensorboard_token_embeddings.metadata_path = os.path.relpath(
token_list_file_path, '..')
if parameters['use_character_lstm']:
tensorboard_character_embeddings = embeddings_projector_config.embeddings.add(
)
tensorboard_character_embeddings.tensor_name = model.character_embedding_weights.name
character_list_file_path = os.path.join(
model_folder, 'tensorboard_metadata_characters.tsv')
tensorboard_character_embeddings.metadata_path = os.path.relpath(
character_list_file_path, '..')
projector.visualize_embeddings(embedding_writer,
embeddings_projector_config)
# Write metadata for TensorBoard embeddings
token_list_file = codecs.open(token_list_file_path, 'w',
'UTF-8')
for token_index in range(len(dataset.index_to_token)):
token_list_file.write('{0}\n'.format(
dataset.index_to_token[token_index]))
token_list_file.close()
if parameters['use_character_lstm']:
character_list_file = codecs.open(character_list_file_path,
'w', 'UTF-8')
for character_index in range(dataset.alphabet_size):
if character_index == dataset.PADDING_CHARACTER_INDEX:
character_list_file.write('PADDING\n')
else:
character_list_file.write('{0}\n'.format(
dataset.index_to_character[character_index]))
character_list_file.close()
try:
# Initialize the model
sess.run(tf.global_variables_initializer())
if not parameters['use_pretrained_model']:
model.load_pretrained_token_embeddings(
sess, dataset, parameters)
# Start training + evaluation loop. Each iteration corresponds to 1 epoch.
bad_counter = 0 # number of epochs with no improvement on the validation test in terms of F1-score
previous_best_valid_f1_score = 0
transition_params_trained = np.random.rand(
len(dataset.unique_labels), len(dataset.unique_labels)
) #TODO np.random.rand(len(dataset.unique_labels)+2,len(dataset.unique_labels)+2)
model_saver = tf.train.Saver(
max_to_keep=None
) #parameters['maximum_number_of_epochs']) # defaults to saving all variables
epoch_number = 0
while True:
epoch_number += 1
print('\nStarting epoch {0}'.format(epoch_number))
epoch_start_time = time.time()
if parameters[
'use_pretrained_model'] and epoch_number == 1:
# Restore pretrained model parameters
transition_params_trained = train.restore_model_parameters_from_pretrained_model(
parameters, dataset, sess, model, model_saver)
elif epoch_number != 0:
# Train model: loop over all sequences of training set with shuffling
sequence_numbers = list(
range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
data_counter = 0
sub_id = 0
for i in tqdm(range(0, len(sequence_numbers),
parameters['batch_size']),
"Training",
mininterval=1):
data_counter += parameters['batch_size']
if data_counter >= 20000:
data_counter = 0
sub_id += 0.001
print("Intermediate evaluation number: ",
sub_id)
#model_saver.save(sess,
# os.path.join(model_folder, 'model_{0:05d}_{1}.ckpt'.format(epoch_number, len(sequence_numbers)/4/len(sequence_numbers))))
epoch_elapsed_training_time = time.time(
) - epoch_start_time
print(
'Training completed in {0:.2f} seconds'
.format(epoch_elapsed_training_time),
flush=True)
y_pred, y_true, output_filepaths = train.predict_labels(
sess, model, transition_params_trained,
parameters, dataset,
epoch_number + sub_id,
stats_graph_folder, dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(
results, dataset, y_pred, y_true,
stats_graph_folder, epoch_number,
epoch_start_time, output_filepaths,
parameters)
# Save model
model_saver.save(
sess,
os.path.join(
model_folder,
'model_{0:07.3f}.ckpt'.format(
epoch_number + sub_id)))
# Save TensorBoard logs
summary = sess.run(model.summary_op,
feed_dict=None)
writers['train'].add_summary(
summary, epoch_number)
writers['train'].flush()
utils.copytree(
writers['train'].get_logdir(),
model_folder)
# Early stop
valid_f1_score = results['epoch'][
epoch_number][0]['valid']['f1_score'][
'micro']
# valid_precision = results['epoch'][epoch_number][0]['valid']['precision']['micro']
# valid_recall = results['epoch'][epoch_number][0]['valid']['recall']['micro']
# valid_fscores.append(valid_f1_score)
if valid_f1_score > previous_best_valid_f1_score:
bad_counter = 0
previous_best_valid_f1_score = valid_f1_score
# previous_best_valid_precision = valid_precision
# previous_best_valid_recall = valid_recall
else:
bad_counter += 1
sequence_number = sequence_numbers[
i:i + parameters['batch_size']]
transition_params_trained, loss = train.train_step(
sess, dataset, sequence_number, model,
transition_params_trained, parameters)
epoch_elapsed_training_time = time.time(
) - epoch_start_time
print('Training completed in {0:.2f} seconds'.format(
epoch_elapsed_training_time),
flush=True)
y_pred, y_true, output_filepaths = train.predict_labels(
sess, model, transition_params_trained, parameters,
dataset, epoch_number, stats_graph_folder,
dataset_filepaths)
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred,
y_true, stats_graph_folder,
epoch_number, epoch_start_time,
output_filepaths, parameters)
# Save model
model_saver.save(
sess,
os.path.join(
model_folder,
'model_{0:05d}.ckpt'.format(epoch_number)))
# Save TensorBoard logs
summary = sess.run(model.summary_op, feed_dict=None)
writers['train'].add_summary(summary, epoch_number)
writers['train'].flush()
utils.copytree(writers['train'].get_logdir(),
model_folder)
# Early stop
valid_f1_score = results['epoch'][epoch_number][0][
'valid']['f1_score']['micro']
#valid_precision = results['epoch'][epoch_number][0]['valid']['precision']['micro']
#valid_recall = results['epoch'][epoch_number][0]['valid']['recall']['micro']
#valid_fscores.append(valid_f1_score)
if valid_f1_score > previous_best_valid_f1_score:
bad_counter = 0
previous_best_valid_f1_score = valid_f1_score
#previous_best_valid_precision = valid_precision
#previous_best_valid_recall = valid_recall
else:
bad_counter += 1
print(
"The last {0} epochs have not shown improvements on the validation set."
.format(bad_counter))
if bad_counter >= parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
break
if epoch_number >= parameters[
'maximum_number_of_epochs']:
break
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
print('Training interrupted')
# remove the experiment
remove_experiment = input(
"Do you want to remove the experiment? (yes/y/Yes)")
if remove_experiment in ["Yes", "yes", "y"]:
shutil.rmtree(stats_graph_folder)
print("Folder removed")
else:
print('Finishing the experiment')
end_time = time.time()
results['execution_details'][
'train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
evaluate.save_results(results, stats_graph_folder)
except Exception:
logging.exception("")
remove_experiment = input(
"Do you want to remove the experiment? (yes/y/Yes)")
if remove_experiment in ["Yes", "yes", "y"]:
shutil.rmtree(stats_graph_folder)
print("Folder removed")
sess.close() # release the session's resources
if 'cross_validation' in parameters and parameters[
'cross_validation'] > 1:
valid_fscores.append(previous_best_valid_f1_score)
#valid_precisions.append(previous_best_valid_precision)
#valid_recalls.append(previous_best_valid_recall)
if 'cross_validation' in parameters and parameters['cross_validation'] > 1:
print("mean f1score:", np.mean(valid_fscores))
#print("mean precision:", np.mean(valid_precisions))
#print("mean recall:", np.mean(valid_recalls))
with codecs.open(os.path.join(stats_graph_folder, "result_cv.txt"),
"w") as file:
file.write("F1score " + ", ".join(map(str, valid_fscores)))
# file.write("Precision " + valid_precisions)
# file.write("Recall " + valid_recalls)
file.write("Mean F1score " + str(np.mean(valid_fscores)))
ckpt.restore(ckpt_manager.latest_checkpoint)
print('Latest checkpoint restored!!')
# Draw a sample
sample_a = next(iter(train_a))
sample_b = next(iter(train_b))
# Train the models
seed = tf.random.normal([1, 256, 256, 3])
for epoch in range(10):
start = time.time()
n = 0
for image_A, image_B in tf.data.Dataset.zip((train_a, train_b)):
print("trainstep")
train_step(image_A, image_B, gen_a, gen_b, disc_a, disc_b,
generator_a_optimizer, generator_b_optimizer,
discriminator_a_optimizer, discriminator_b_optimizer)
if n % 10 == 0:
print(n / 10, end=' ')
n += 1
# Using a consistent image (sample_horse) so that the progress of the model
# is clearly visible.
generate_and_save_images(gen_a, epoch + 1, sample_a, 'A')
generate_and_save_images(gen_b, epoch + 1, sample_b, 'B')
if (epoch + 1) % 5 == 0:
ckpt_save_path = ckpt_manager.save()
print('Saving checkpoint for epoch {} at {}'.format(
epoch + 1, ckpt_save_path))
def main():
parameters, dataset_filepaths = load_parameters()
# Load dataset
dataset = ds.Dataset()
dataset.load_dataset(dataset_filepaths, parameters)
# Create graph and session
with tf.Graph().as_default():
session_conf = tf.ConfigProto(
device_count={
'CPU': 1,
'GPU': 1
},
allow_soft_placement=
True, # automatically choose an existing and supported device to run the operations in case the specified one doesn't exist
log_device_placement=False)
sess = tf.Session(config=session_conf)
with sess.as_default():
# Initialize and save execution details
start_time = time.time()
experiment_timestamp = utils.get_current_time_in_miliseconds()
results = {}
results['epoch'] = {}
results['execution_details'] = {}
results['execution_details']['train_start'] = start_time
results['execution_details']['time_stamp'] = experiment_timestamp
results['execution_details']['early_stop'] = False
results['execution_details']['keyboard_interrupt'] = False
results['execution_details']['num_epochs'] = 0
results['model_options'] = copy.copy(parameters)
dataset_name = utils.get_basename_without_extension(
parameters['dataset_text_folder'])
model_name = '{0}_{1}'.format(
dataset_name, results['execution_details']['time_stamp'])
output_folder = os.path.join('..', 'output')
utils.create_folder_if_not_exists(output_folder)
stats_graph_folder = os.path.join(
output_folder, model_name) # Folder where to save graphs
utils.create_folder_if_not_exists(stats_graph_folder)
model_folder = os.path.join(stats_graph_folder, 'model')
utils.create_folder_if_not_exists(model_folder)
tensorboard_log_folder = os.path.join(stats_graph_folder,
'tensorboard_logs')
utils.create_folder_if_not_exists(tensorboard_log_folder)
tensorboard_log_folders = {}
for dataset_type in ['train', 'valid', 'test']:
tensorboard_log_folders[dataset_type] = os.path.join(
stats_graph_folder, 'tensorboard_logs', dataset_type)
utils.create_folder_if_not_exists(
tensorboard_log_folders[dataset_type])
pickle.dump(
dataset,
open(os.path.join(stats_graph_folder, 'dataset.pickle'), 'wb'))
# Instantiate the model
# graph initialization should be before FileWriter, otherwise the graph will not appear in TensorBoard
model = EntityLSTM(dataset, parameters)
# Instantiate the writers for TensorBoard
writers = {}
for dataset_type in ['train', 'valid', 'test']:
writers[dataset_type] = tf.summary.FileWriter(
tensorboard_log_folders[dataset_type], graph=sess.graph)
embedding_writer = tf.summary.FileWriter(
model_folder
) # embedding_writer has to write in model_folder, otherwise TensorBoard won't be able to view embeddings
embeddings_projector_config = projector.ProjectorConfig()
tensorboard_token_embeddings = embeddings_projector_config.embeddings.add(
)
tensorboard_token_embeddings.tensor_name = model.token_embedding_weights.name
token_list_file_path = os.path.join(
model_folder, 'tensorboard_metadata_tokens.tsv')
tensorboard_token_embeddings.metadata_path = os.path.relpath(
token_list_file_path, '..')
tensorboard_character_embeddings = embeddings_projector_config.embeddings.add(
)
tensorboard_character_embeddings.tensor_name = model.character_embedding_weights.name
character_list_file_path = os.path.join(
model_folder,
'tensorboard_metadata_characters.tsv') # 'metadata.tsv'
tensorboard_character_embeddings.metadata_path = os.path.relpath(
character_list_file_path, '..')
projector.visualize_embeddings(embedding_writer,
embeddings_projector_config)
# Write metadata for TensorBoard embeddings
token_list_file = open(token_list_file_path, 'w')
for token_index in range(dataset.vocabulary_size):
token_list_file.write('{0}\n'.format(
dataset.index_to_token[token_index]))
token_list_file.close()
character_list_file = open(character_list_file_path, 'w')
print('len(dataset.character_to_index): {0}'.format(
len(dataset.character_to_index)))
print('len(dataset.index_to_character): {0}'.format(
len(dataset.index_to_character)))
for character_index in range(dataset.alphabet_size):
if character_index == dataset.PADDING_CHARACTER_INDEX:
character_list_file.write('PADDING\n')
else:
character_list_file.write('{0}\n'.format(
dataset.index_to_character[character_index]))
character_list_file.close()
# Initialize the model
sess.run(tf.global_variables_initializer())
model.load_pretrained_token_embeddings(sess, dataset, parameters)
# Start training + evaluation loop. Each iteration corresponds to 1 epoch.
step = 0
bad_counter = 0 # number of epochs with no improvement on the validation test in terms of F1-score
previous_best_valid_f1_score = 0
transition_params_trained = np.random.rand(
len(dataset.unique_labels), len(dataset.unique_labels))
model_saver = tf.train.Saver(
max_to_keep=parameters['maximum_number_of_epochs']
) # defaults to saving all variables
epoch_number = -1
try:
while True:
epoch_number += 1
#epoch_number = math.floor(step / len(dataset.token_indices['train']))
print('\nStarting epoch {0}'.format(epoch_number), end='')
epoch_start_time = time.time()
#print('step: {0}'.format(step))
# Train model: loop over all sequences of training set with shuffling
sequence_numbers = list(
range(len(dataset.token_indices['train'])))
random.shuffle(sequence_numbers)
for sequence_number in sequence_numbers:
transition_params_trained = train.train_step(
sess, dataset, sequence_number, model,
transition_params_trained, parameters)
step += 1
if step % 100 == 0:
print('.', end='', flush=True)
#break
print('.', flush=True)
#print('step: {0}'.format(step))
# Predict labels using trained model
y_pred = {}
y_true = {}
output_filepaths = {}
for dataset_type in ['train', 'valid', 'test']:
#print('dataset_type: {0}'.format(dataset_type))
prediction_output = train.prediction_step(
sess, dataset, dataset_type, model,
transition_params_trained, step,
stats_graph_folder, epoch_number, parameters)
y_pred[dataset_type], y_true[
dataset_type], output_filepaths[
dataset_type] = prediction_output
# model_options = None
epoch_elapsed_training_time = time.time(
) - epoch_start_time
print(
'epoch_elapsed_training_time: {0:.2f} seconds'.format(
epoch_elapsed_training_time))
results['execution_details']['num_epochs'] = epoch_number
# Evaluate model: save and plot results
evaluate.evaluate_model(results, dataset, y_pred, y_true,
stats_graph_folder, epoch_number,
epoch_start_time, output_filepaths,
parameters)
# Save model
model_saver.save(
sess,
os.path.join(model_folder,
'model_{0:05d}.ckpt'.format(epoch_number))
) #, global_step, latest_filename, meta_graph_suffix, write_meta_graph, write_state)
# Save TensorBoard logs
summary = sess.run(model.summary_op, feed_dict=None)
writers['train'].add_summary(summary, epoch_number)
# Early stop
valid_f1_score = results['epoch'][epoch_number][0][
'valid']['f1_score']['micro']
if valid_f1_score > previous_best_valid_f1_score:
bad_counter = 0
previous_best_valid_f1_score = valid_f1_score
else:
bad_counter += 1
if bad_counter > parameters['patience']:
print('Early Stop!')
results['execution_details']['early_stop'] = True
break
if epoch_number > parameters['maximum_number_of_epochs']:
break
# break # debugging
except KeyboardInterrupt:
results['execution_details']['keyboard_interrupt'] = True
# assess_model.save_results(results, stats_graph_folder)
print('Training interrupted')
print('Finishing the experiment')
end_time = time.time()
results['execution_details'][
'train_duration'] = end_time - start_time
results['execution_details']['train_end'] = end_time
evaluate.save_results(results, stats_graph_folder)
sess.close() # release the session's resources
