def training(session,
training_op,
cost,
train_data,
valid_data,
y_upper_bound=None,
seed=0,
n_epochs=10,
batch_size=128):
"""
* train_data
* valid_data
はいずれも、
* key : tensorflowのplaceholder
* val : numpyのarray(全データ)
のディクショナリ形式で与える
"""
np.random.seed(seed)
# バッチ数を計算
n_samples_train = len(list(train_data.values())[0])
n_samples_valid = len(list(valid_data.values())[0])
n_batches_train = n_samples_train // batch_size
n_batches_valid = n_samples_valid // batch_size
mb = master_bar(range(n_epochs))
# 学習曲線描画のための前準備
train_costs_lst = []
valid_costs_lst = []
x_bounds = [0, n_epochs]
y_bounds = None
for epoch in mb:
# Train
train_costs = []
for _ in progress_bar(range(n_batches_train), parent=mb):
batch_idx = np.random.randint(n_samples_train, size=batch_size)
# feedするデータを指定
feed_dict = {}
for k, v in train_data.items():
feed_dict[k] = v[batch_idx]
_, train_cost = session.run([training_op, cost],
feed_dict=feed_dict)
train_costs.append(train_cost)
# Valid
valid_costs = []
for i in range(n_batches_valid):
start = i * batch_size
end = start + batch_size
# feedするデータを指定
feed_dict = {}
for k, v in valid_data.items():
feed_dict[k] = v[start:end]
valid_cost = session.run(cost, feed_dict=feed_dict)
valid_costs.append(valid_cost)
# 損失関数の値の計算
train_costs_mean = np.mean(train_costs)
valid_costs_mean = np.mean(valid_costs)
train_costs_lst.append(train_costs_mean)
valid_costs_lst.append(valid_costs_mean)
# learning curveの図示
if y_bounds is None:
# 1エポック目のみ実行
y_bounds = [
0, train_costs_mean *
1.1 if y_upper_bound is None else y_upper_bound
]
t = np.arange(len(train_costs_lst))
graphs = [[t, train_costs_lst], [t, valid_costs_lst]]
mb.update_graph(graphs, x_bounds, y_bounds)
# 学習過程の出力
mb.write(
'EPOCH: {0:02d}, Training cost: {1:10.5f}, Validation cost: {2:10.5f}'
.format(epoch + 1, train_costs_mean, valid_costs_mean))
def main():
now = datetime.datetime.now()
now_date = '{}-{:0>2d}-{:0>2d}_{:0>2d}-{:0>2d}-{:0>2d}'.format(now.year, now.month, now.day, now.hour, now.minute, now.second)
# set logger
logger = logging.getLogger("Log")
logger.setLevel(logging.DEBUG)
handler_format = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')
# stream_handler = logging.StreamHandler()
# stream_handler.setLevel(logging.DEBUG)
# stream_handler.setFormatter(handler_format)
# logger.addHandler(stream_handler)
print('{}-{}-{} {}:{}:{}'.format(now.year, now.month, now.day, now.hour, now.minute, now.second))
with open('../params/exp{}.yaml'.format(EXP_NO), "r+") as f:
param = yaml.load(f, Loader=yaml.FullLoader)
param['date'] = now_date
# seed set
seed_setting(param['seed'])
if torch.cuda.is_available():
torch.backends.cudnn.benchmark = True
local_cv = dict()
for fold in param['fold']:
# /mnt/hdd1/alcon2019/ + exp0/ + 2019-mm-dd_hh-mm-ss/ + foldN
outdir = os.path.join(param['save path'], EXP_NAME ,now_date, 'fold{}'.format(fold))
if os.path.exists(param['save path']):
os.makedirs(outdir, exist_ok=True)
else:
print("Not find {}".format(param['save path']))
raise FileNotFoundError
file_handler = logging.FileHandler(os.path.join(outdir, 'experiment.log'))
file_handler.setLevel(logging.DEBUG)
file_handler.setFormatter(handler_format)
logger.addHandler(file_handler)
logger.debug('============= FOLD {} ============='.format(fold))
logger.debug('{}-{}-{} {}:{}:{}'.format(now.year, now.month, now.day, now.hour, now.minute, now.second))
# Dataset
param['batch size'] = max(param['batch size'], param['batch size'] * param['GPU'])
if param['debug']:
train_dataset = AlconDataset(df=get_train_df(param['tabledir']).query('valid != @fold').iloc[:param['batch size']],
augmentation=get_train_augmentation(*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'],'train','imgs'), mode='train')
valid_dataset = AlconDataset(df=get_train_df(param['tabledir']).query('valid == @fold').iloc[:param['batch size']],
augmentation=get_test_augmentation(*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'],'train','imgs'), mode='valid')
else:
train_dataset = AlconDataset(df=get_train_df(param['tabledir']).query('valid != @fold'),
augmentation=get_train_augmentation(*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'train', 'imgs'), mode='train',
margin_augmentation=True)
valid_dataset = AlconDataset(df=get_train_df(param['tabledir']).query('valid == @fold'),
augmentation=get_test_augmentation(*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'train', 'imgs'), mode='valid',
margin_augmentation=False)
logger.debug('train dataset size: {}'.format(len(train_dataset)))
logger.debug('valid dataset size: {}'.format(len(valid_dataset)))
# Dataloader
train_dataloader = DataLoader(train_dataset, batch_size=param['batch size'], num_workers=param['thread'],
pin_memory=False, drop_last=False)
valid_dataloader = DataLoader(valid_dataset, batch_size=param['batch size'], num_workers=param['thread'],
pin_memory=False, drop_last=False)
logger.debug('train loader size: {}'.format(len(train_dataloader)))
logger.debug('valid loader size: {}'.format(len(valid_dataloader)))
# model
# model = ResNetGRU(num_classes=48, hidden_size=512, bidirectional=True, load_weight=param['load weight'], dropout=param['dropout'])
# model = OctResNetGRU2(num_classes=48, hidden_size=512, bidirectional=True, load_weight=None, dropout=param['dropout'])
# model = ResNetGRU3(num_classes=48, hidden_size=512, bidirectional=True, load_weight=param['load weight'], dropout=param['dropout'])
# model = ResNetLSTM(num_classes=48, hidden_size=512, bidirectional=True, load_weight=param['load weight'], dropout=param['dropout'])
# model = ResNetResLSTM_MLP(num_classes=48, hidden_size=512, bidirectional=True, load_weight=param['load weight'], dropout=param['dropout'])
model = SEResNeXtGRU2(num_classes=48, hidden_size=512, bidirectional=True, load_weight=None, dropout=param['dropout'])
param['model'] = model.__class__.__name__
# optim
if param['optim'].lower() == 'sgd':
optimizer = torch.optim.SGD(model.parameters(), lr=param['lr'], momentum=0.9,
weight_decay=1e-5, nesterov=False)
elif param['optim'].lower() == 'adam':
optimizer = torch.optim.SGD(model.parameters(), lr=param['lr'])
else:
raise NotImplementedError
# scheduler
scheduler = eval(param['scheduler'])
model = model.to(param['device'])
if param['GPU'] > 0:
model = nn.DataParallel(model)
loss_fn = nn.CrossEntropyLoss().to(param['device'])
eval_fn = accuracy_one_character
max_char_acc = -1.
max_3char_acc = -1.
min_loss = 10**5
writer = tbx.SummaryWriter("../log/exp{}/{}/fold{}".format(EXP_NO, now_date, fold))
for key, val in param.items():
writer.add_text('data/hyperparam/{}'.format(key), str(val), 0)
mb = master_bar(range(param['epoch']))
for epoch in mb:
avg_train_loss, avg_train_accuracy, avg_three_train_acc = train_alcon_rnn(model, optimizer, train_dataloader, param['device'],
loss_fn, eval_fn, epoch, scheduler=None, writer=writer, parent=mb) #ok
avg_valid_loss, avg_valid_accuracy, avg_three_valid_acc = valid_alcon_rnn(model, valid_dataloader, param['device'],
loss_fn, eval_fn)
writer.add_scalars("data/metric/valid", {
'loss': avg_valid_loss,
'accuracy': avg_valid_accuracy,
'3accuracy': avg_three_valid_acc
}, epoch)
logger.debug('======================== epoch {} ========================'.format(epoch+1))
logger.debug('lr : {:.5f}'.format(scheduler.get_lr()[0]))
logger.debug('loss : train={:.5f} , test={:.5f}'.format(avg_train_loss, avg_valid_loss))
logger.debug('acc(per 1 char) : train={:.3%} , test={:.3%}'.format(avg_train_accuracy, avg_valid_accuracy))
logger.debug('acc(per 3 char) : train={:.3%} , test={:.3%}'.format(avg_three_train_acc, avg_three_valid_acc))
if min_loss > avg_valid_loss:
logger.debug('update best loss: {:.5f} ---> {:.5f}'.format(min_loss, avg_valid_loss))
min_loss = avg_valid_loss
torch.save(model.state_dict(), os.path.join(outdir, 'best_loss.pth'))
if max_char_acc < avg_valid_accuracy:
logger.debug('update best acc per 1 char: {:.3%} ---> {:.3%}'.format(max_char_acc, avg_valid_accuracy))
max_char_acc = avg_valid_accuracy
torch.save(model.state_dict(), os.path.join(outdir, 'best_acc.pth'))
if max_3char_acc < avg_three_valid_acc:
logger.debug('update best acc per 3 char: {:.3%} ---> {:.3%}'.format(max_3char_acc , avg_three_valid_acc))
max_3char_acc = avg_three_valid_acc
torch.save(model.state_dict(), os.path.join(outdir, 'best_3acc.pth'))
if 1:
if scheduler is not None:
if writer is not None:
writer.add_scalar("data/learning rate", scheduler.get_lr()[0], epoch)
scheduler.step()
writer.add_scalars("data/metric/valid", {
'best loss': min_loss,
'best accuracy': max_char_acc,
'best 3accuracy': max_3char_acc
})
logger.debug('================ FINISH TRAIN ================')
logger.debug('Result')
logger.debug('Best loss : {}'.format(min_loss))
logger.debug('Best 1 acc : {}'.format(max_char_acc))
logger.debug('Best 3 acc : {}'.format(max_3char_acc))
writer.export_scalars_to_json(os.path.join(outdir, 'history.json'))
writer.close()
local_cv['fold{}'.format(fold)] = {'accuracy' : max_3char_acc, 'valid_size' : len(valid_dataset)}
del train_dataset, valid_dataset
del train_dataloader, valid_dataloader
del scheduler, optimizer
gc.collect()
logger.debug('=========== Prediction phrase ===========')
logger.debug('load weight : {}'.format(os.path.join(outdir, 'best_3acc.pth')))
model.load_state_dict(torch.load(os.path.join(outdir, 'best_3acc.pth')))
if param['debug']:
test_dataset = AlconDataset(df=get_test_df(param['tabledir']).iloc[:param['batch size']],
augmentation=get_test_augmentation(*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'test', 'imgs'), mode='test')
else:
test_dataset = AlconDataset(df=get_test_df(param['tabledir']),
augmentation=get_test_augmentation(*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'test', 'imgs'), mode='test')
test_dataloader = DataLoader(test_dataset, batch_size=param['batch size'], num_workers=param['thread'],
pin_memory=False, drop_last=False)
logger.debug('test dataset size: {}'.format(len(test_dataset)))
logger.debug('test loader size: {}'.format(len(test_dataloader)))
output_list = pred_alcon_rnn(model, test_dataloader, param['device'])
torch.save(output_list, os.path.join(outdir, 'prediction.pth'))
pd.DataFrame(output_list).drop('logit', axis=1).sort_values('ID').set_index('ID').to_csv(os.path.join(outdir, 'test_prediction.csv'))
logger.debug('success!')
logger.removeHandler(file_handler)
del test_dataset, test_dataloader
gc.collect()
# Ensemble
print('======== Ensemble phase =========')
prediction_dict = dict()
mb = master_bar(param['fold'])
print('======== Load Vector =========')
for i, fold in enumerate(mb):
outdir = os.path.join(param['save path'], EXP_NAME, now_date,'fold{}'.format(fold))
prediction = torch.load(os.path.join(outdir, 'prediction.pth'))
# prediction is list
# prediction[0] = {'ID' : 0, 'logit' torch.tensor, ...}
if i == 0:
for preds in progress_bar(prediction, parent=mb):
prediction_dict[preds['ID']] = preds['logit'] / len(param['fold'])
else:
for preds in progress_bar(prediction, parent=mb):
prediction_dict[preds['ID']] += preds['logit'] / len(param['fold'])
outdir = os.path.join(param['save path'], EXP_NAME, now_date)
file_handler = logging.FileHandler(os.path.join(outdir, 'result.log'))
file_handler.setLevel(logging.DEBUG)
file_handler.setFormatter(handler_format)
logger.addHandler(file_handler)
logger.info(' ========== RESULT ========== \n')
cv = 0.0
train_data_size = 0
for fold in param['fold']:
acc = local_cv['fold{}'.format(fold)]['accuracy']
valid_size = local_cv['fold{}'.format(fold)]['valid_size']
train_data_size += valid_size
logger.info(' fold {} : {:.3%} \n'.format(fold, acc))
cv += acc * valid_size
logger.info(' Local CV : {:.3%} \n'.format(cv / train_data_size))
logger.info(' ============================== \n')
logger.removeHandler(file_handler)
torch.save(prediction_dict, os.path.join(outdir, 'prediction.pth'))
print('======== make submittion file =========')
vocab = get_vocab(param['vocabdir'])
submit_list = list()
for ID, logits in progress_bar(prediction_dict.items()):
submit_dict = dict()
submit_dict["ID"] = ID
preds = logits.softmax(dim=1).argmax(dim=1)
submit_dict["Unicode1"] = vocab['index2uni'][preds[0]]
submit_dict["Unicode2"] = vocab['index2uni'][preds[1]]
submit_dict["Unicode3"] = vocab['index2uni'][preds[2]]
submit_list.append(submit_dict)
print()
pd.DataFrame(submit_list).sort_values('ID').set_index('ID').to_csv(os.path.join(outdir, 'test_prediction.csv'))
import zipfile
with zipfile.ZipFile(os.path.join(outdir,'submit_{}_{}.zip'.format(EXP_NAME, now_date)), 'w') as zf:
zf.write(os.path.join(outdir, 'test_prediction.csv'))
print('success!')
def _custom_train(
self,
train_dataset,
tokenizer,
model,
num_train_examples,
train_batch_size,
):
config = self.parent.config._asdict()
config["strategy"] = self.parent.config.strategy
config["n_device"] = self.parent.config.n_device
labels = config["ner_tags"]
if config["max_steps"] > 0:
num_train_steps = (
config["max_steps"] * config["gradient_accumulation_steps"]
)
config["epochs"] = 1
else:
num_train_steps = (
math.ceil(num_train_examples / train_batch_size)
// config["gradient_accumulation_steps"]
* config["epochs"]
)
with config["strategy"].scope():
loss_fct = tf.keras.losses.SparseCategoricalCrossentropy(
reduction=tf.keras.losses.Reduction.NONE
)
optimizer = create_optimizer(
config["learning_rate"],
num_train_steps,
config["warmup_steps"],
)
if config["use_fp16"]:
optimizer = tf.keras.mixed_precision.experimental.LossScaleOptimizer(
optimizer, "dynamic"
)
loss_metric = tf.keras.metrics.Mean(name="loss", dtype=tf.float32)
gradient_accumulator = GradientAccumulator()
self.logger.info("***** Running training *****")
self.logger.info(" Num examples = %d", num_train_examples)
self.logger.info(" Num Epochs = %d", config["epochs"])
self.logger.info(
" Instantaneous batch size per device = %d",
config["per_device_train_batch_size"],
)
self.logger.info(
" Total train batch size (w. parallel, distributed & accumulation) = %d",
train_batch_size * config["gradient_accumulation_steps"],
)
self.logger.info(
" Gradient Accumulation steps = %d",
config["gradient_accumulation_steps"],
)
self.logger.info(" Total training steps = %d", num_train_steps)
self.logger.debug(model.summary())
@tf.function
def apply_gradients():
grads_and_vars = []
for gradient, variable in zip(
gradient_accumulator.gradients, model.trainable_variables
):
if gradient is not None:
scaled_gradient = gradient / (
config["n_device"]
* config["gradient_accumulation_steps"]
)
grads_and_vars.append((scaled_gradient, variable))
else:
grads_and_vars.append((gradient, variable))
optimizer.apply_gradients(grads_and_vars, config["max_grad_norm"])
gradient_accumulator.reset()
@tf.function
def train_step(train_features, train_labels):
def step_fn(train_features, train_labels):
inputs = {
"attention_mask": train_features["input_mask"],
"training": True,
}
if config["model_architecture_type"] != "distilbert":
inputs["token_type_ids"] = (
train_features["segment_ids"]
if config["model_architecture_type"]
in ["bert", "xlnet"]
else None
)
with tf.GradientTape() as tape:
logits = model(train_features["input_ids"], **inputs)[0]
logits = tf.reshape(logits, (-1, len(labels) + 1))
active_loss = tf.reshape(
train_features["input_mask"], (-1,)
)
active_logits = tf.boolean_mask(logits, active_loss)
train_labels = tf.reshape(train_labels, (-1,))
active_labels = tf.boolean_mask(train_labels, active_loss)
cross_entropy = loss_fct(active_labels, active_logits)
loss = tf.reduce_sum(cross_entropy) * (
1.0 / train_batch_size
)
grads = tape.gradient(loss, model.trainable_variables)
gradient_accumulator(grads)
return cross_entropy
per_example_losses = config["strategy"].experimental_run_v2(
step_fn, args=(train_features, train_labels)
)
mean_loss = config["strategy"].reduce(
tf.distribute.ReduceOp.MEAN, per_example_losses, axis=0
)
return mean_loss
current_time = datetime.datetime.now()
train_iterator = master_bar(range(config["epochs"]))
global_step = 0
self.logger_loss = 0.0
for epoch in train_iterator:
epoch_iterator = progress_bar(
train_dataset,
total=num_train_steps,
parent=train_iterator,
display=config["n_device"] > 1,
)
step = 1
with config["strategy"].scope():
for train_features, train_labels in epoch_iterator:
loss = train_step(train_features, train_labels)
if step % config["gradient_accumulation_steps"] == 0:
config["strategy"].experimental_run_v2(apply_gradients)
loss_metric(loss)
global_step += 1
if (
config["save_steps"] > 0
and global_step % config["save_steps"] == 0
):
# Save model checkpoint
output_dir = os.path.join(
config["output_dir"],
"checkpoint-{}".format(global_step),
)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
model.save_pretrained(output_dir)
self.logger.info(
"Saving model checkpoint to %s", output_dir
)
train_iterator.child.comment = (
f"loss : {loss_metric.result()}"
)
step += 1
train_iterator.write(
f"loss epoch {epoch + 1}: {loss_metric.result()}"
)
loss_metric.reset_states()
self.logger.debug(
" Training took time = {}".format(
datetime.datetime.now() - current_time
)
)
def begin_fit(self):
self.mbar = master_bar(range(self.epochs))
self.mbar.on_iter_begin()
self.run.logger = partial(self.mbar.write, table=True)
def train(model,
epochs,
learning_rates,
optimizer,
criterion,
dataset,
batch_size=512,
num_workers=0,
drop_last=False,
timer=None):
t = timer or Timer()
train_batches = get_dataloader["train"]
if balance:
train_batches = torch.utils.data.DataLoader(
dataset["train"],
batch_size,
shuffle=False,
pin_memory=True,
num_workers=num_workers,
drop_last=drop_last,
sampler=dataset["train"].get_balanced_sampler())
else:
train_batches = torch.utils.data.DataLoader(dataset["train"],
batch_size,
shuffle=True,
pin_memory=True,
num_workers=num_workers,
drop_last=drop_last)
test_batches = torch.utils.data.DataLoader(dataset["val"],
batch_size,
shuffle=False,
pin_memory=True,
num_workers=num_workers)
train_size, val_size = len(dataset["train"]), len(dataset["val"])
if drop_last: train_size -= (train_size % batch_size)
num_epochs = epochs[-1]
lr_schedule = LinearInterpolation(epochs, learning_rates)
#mo_schedule = LinearInterpolation(epochs, momentum)
mb = master_bar(range(num_epochs))
mb.write("Epoch\tTime\tLearRate\tT_loss\tT_accu\t\tV_loss\tV_accu")
mb.write("-" * 70)
for epoch in mb:
#train_batches.dataset.set_random_choices()
lrs = (lr_schedule(x) / batch_size
for x in np.arange(epoch, epoch + 1, 1 / len(train_batches)))
train_stats, train_time = train_epoch(mb, model, train_batches,
optimizer, criterion, lrs, {
'loss': [],
'correct': []
}), t()
test_stats, test_time = test_epoch(mb, model, test_batches, criterion,
{
'loss': [],
'correct': []
}), t()
metric["epoch"].append(epoch + 1)
metric["learning rate"].append(lr_schedule(epoch + 1))
metric["total time"].append(t.total_time)
metric["train loss"].append(sum(train_stats['loss']) / train_size)
metric["train acc"].append(sum(train_stats['correct']) / train_size)
metric["val loss"].append(sum(test_stats['loss']) / val_size)
metric["val acc"].append(sum(test_stats['correct']) / val_size)
mb.write(
"{}/{}\t{:.0f}:{:.0f}\t{:.4f}\t\t{:.4f}\t{:.4f}\t\t{:.4f}\t{:.4f}".
format(metric["epoch"][-1], num_epochs,
metric["total time"][-1] // 60,
metric["total time"][-1] % 60, metric["learning rate"][-1],
metric["train loss"][-1], metric["train acc"][-1],
metric["val loss"][-1], metric["val acc"][-1]))
graphs = [[metric["epoch"], metric["train acc"]],
[metric["epoch"], metric["val acc"]]]
mb.update_graph(graphs)
return metric
def fit(self, X, y, epochs=100, validation_data=None, batch_size=32, verbose=True, early_stopping=False, trans=None, validation_trans=None):
dataset = self.dataset(X, y, trans=trans)
dataloader = DataLoader(dataset, shuffle=True, batch_size=batch_size)
self.history = {"loss": []}
for metric in self.metrics:
self.history[f'{metric.name}'] = []
if validation_data:
dataset = self.dataset(validation_data[0], validation_data[1], trans=validation_trans)
dataloader_val = DataLoader(dataset, shuffle=False, batch_size=batch_size)
self.history["val_loss"] = []
for metric in self.metrics:
self.history[f'val_{metric.name}'] = []
if self.scheduler:
self.history["lr"] = []
self.net.to(self.device)
mb = master_bar(range(1, epochs+1))
best_loss, step, best_e = 1e10, 0, 0
for epoch in mb:
# train
self.net.train()
train_loss, train_metrics = [], [[] for m in self.metrics]
for X, y in progress_bar(dataloader, parent=mb):
X, y = X.to(self.device), y.to(self.device)
self.optimizer.zero_grad()
output = self.net(X)
loss = self.loss(output, y)
loss.backward()
self.optimizer.step()
train_loss.append(loss.item())
comment = f'train_loss {np.mean(train_loss):.5f}'
for i, metric in enumerate(self.metrics):
train_metrics[i].append(metric.call(output, y))
comment += f' train_{metric.name} {np.mean(train_metrics[i]):.5f}'
mb.child.comment = comment
self.history["loss"].append(np.mean(train_loss))
for i, metric in enumerate(self.metrics):
self.history[f'{metric.name}'].append(np.mean(train_metrics[i]))
bar_text = f'Epoch {epoch}/{epochs} loss {np.mean(train_loss):.5f}'
for i, metric in enumerate(self.metrics):
bar_text += f' {metric.name} {np.mean(train_metrics[i]):.5f}'
if self.scheduler:
self.history["lr"].append(optimizer.param_groups[0]['lr'])
self.scheduler.step()
# eval
if validation_data:
self.net.eval()
val_loss, val_metrics = [], [[] for m in self.metrics]
with torch.no_grad():
for X, y in progress_bar(dataloader_val, parent=mb):
X, y = X.to(self.device), y.to(self.device)
output = self.net(X)
loss = self.loss(output, y)
val_loss.append(loss.item())
comment = f'val_loss {np.mean(val_loss):.5f}'
for i, metric in enumerate(self.metrics):
val_metrics[i].append(metric.call(output, y))
comment += f' val_{metric.name} {np.mean(val_metrics[i]):.5f}'
mb.child.comment = comment
self.history["val_loss"].append(np.mean(val_loss))
for i, metric in enumerate(self.metrics):
self.history[f'val_{metric.name}'].append(np.mean(val_metrics[i]))
bar_text += f' val_loss {np.mean(val_loss):.5f}'
for i, metric in enumerate(self.metrics):
bar_text += f' val_{metric.name} {np.mean(val_metrics[i]):.5f}'
if early_stopping:
step += 1
if np.mean(val_loss) < best_loss:
best_loss = np.mean(val_loss)
torch.save(self.net.state_dict(),'best_dict.pth')
best_e = epoch
step = 0
if step >= early_stopping:
self.net.load_state_dict(torch.load('best_dict.pth'))
print(f"training stopped at epoch {epoch}")
print(f"best model found at epoch {best_e} with val_loss {best_loss:.5f}")
break
if verbose:
mb.write(bar_text)
return self.history
def main(out: Param("dataset folder", Path, required=True),
info: Param('info file', Path, required=True),
tile: Param('generated tile size', int, nargs='+', required=True),
n_train: Param('number of train tiles', int, required=True),
n_valid: Param('number of validation tiles', int, required=True),
crap_func: Param('crappifier name', str) = 'no_crap',
n_frames: Param('number of frames', int) = 1,
lr_type: Param('training input, (s)ingle, (t) multi or (z) multi',
str) = 's',
scale: Param('amount to scale', int) = 4,
ftypes: Param('ftypes allowed e.g. - czi, tif', str,
nargs='+') = None,
upsample: Param('use upsample', action='store_true') = False,
only: Param('limit to these categories', nargs='+') = None,
skip: Param("categories to skip", str,
nargs='+') = ['random', 'ArgoSIMDL'],
clean: Param("wipe existing data first",
action='store_true') = False):
"generate tiles from source tiffs"
up = 'up' if upsample else ''
if lr_type not in ['s', 't', 'z']:
print('lr_type should be s, t or z')
return 1
if lr_type == 's':
z_frames, t_frames = 1, 1
elif lr_type == 't':
z_frames, t_frames = 1, n_frames
elif lr_type == 'z':
z_frames, t_frames = n_frames, 1
out = ensure_folder(out / f'{lr_type}_{n_frames}_{info.stem}_{crap_func}')
if clean:
shutil.rmtree(out)
crap_func = eval(crap_func)
if not crap_func is None:
if not callable(crap_func):
print('crap_func is not callable')
crap_func = None
else:
crap_func = partial(crap_func, scale=scale, upsample=upsample)
info = pd.read_csv(info)
if ftypes: info = info.loc[info.ftype.isin(ftypes)]
if only: info = info.loc[info.category.isin(only)]
elif skip: info = info.loc[~info.category.isin(skip)]
info = info.loc[info.nz >= z_frames]
info = info.loc[info.nt >= t_frames]
tile_infos = []
for mode, n_samples in [('train', n_train), ('valid', n_valid)]:
mode_info = info.loc[info.dsplit == mode]
categories = list(mode_info.groupby('category'))
files_by_category = {
c: list(info.groupby('fn'))
for c, info in categories
}
for i in range(n_samples):
category, cat_df = random.choice(categories)
fn, item_df = random.choice(files_by_category[category])
legal_choices = [
item_info for ix, item_info in item_df.iterrows()
if check_info(item_info, t_frames, z_frames)
]
assert (legal_choices)
item_info = random.choice(legal_choices)
for tile_sz in tile:
item_d = dict(item_info)
item_d['tile_sz'] = tile_sz
tile_infos.append(item_d)
tile_info_df = pd.DataFrame(tile_infos).reset_index()
print('num tile pulls:', len(tile_infos))
print(tile_info_df.groupby('category').fn.count())
last_stat = None
tile_pull_info = []
tile_puller = None
multi_str = f'_{lr_type}_{n_frames}' if lr_type != 's' else ''
mbar = master_bar(tile_info_df.groupby('fn'))
for fn, tile_stats in mbar:
if Path(
fn
).stem == 'high res microtubules for testing before stitching - great quality':
continue
for i, tile_stat in progress_bar(list(tile_stats.iterrows()),
parent=mbar):
try:
mode = tile_stat['dsplit']
category = tile_stat['category']
tile_sz = tile_stat['tile_sz']
tile_folder = ensure_folder(
out / f'hr_t_{tile_sz}{multi_str}' / mode / category)
if crap_func:
crap_folder = ensure_folder(
out / f'lr{up}_t_{tile_sz}{multi_str}' / mode /
category)
else:
crap_folder = None
if need_cache_flush(tile_stat, last_stat):
if tile_puller:
tile_puller(None, None, None, close_me=True)
last_stat = tile_stat.copy()
tile_sz = tile_stat['tile_sz']
tile_puller = get_tile_puller(tile_stat, crap_func,
t_frames, z_frames)
tile_pull_info.append(
tile_puller(tile_stat, tile_folder, crap_folder))
except MemoryError as error:
# some files are too big to read
fn = Path(tile_stat['fn'])
print(f'too big: {fn.stem}')
pd.DataFrame(tile_pull_info).to_csv(out / f'tiles{multi_str}.csv',
index=False)
def begin_fit(self):
self.master_bar = master_bar(range(self.epochs))
self.master_bar.on_iter_begin()
# Callback class stores the Learner() object under self.run
self.run.logger = partial(self.master_bar.write, table=True)
def train(self, num_epochs, max_lr=0.1):
t = Timer()
valid_loss_min = np.Inf
patience = 10
p = 0 # current number of epochs, where validation loss didn't increase
#train_size, val_size = len(self.train_ds), len(self.valid_ds)
#if drop_last: train_size -= (train_size % self.batch_size)
self.epochs = [0, num_epochs / 4, num_epochs] #[0, 15, 30, 35]
self.learning_rates = [0, max_lr, 0] #[0, 0.1, 0.005, 0]
lr_schedule = LinearInterpolation(self.epochs, self.learning_rates)
#mo_schedule = LinearInterpolation(epochs, momentum)
stats = {
"train_it": [],
'train_loss': [],
'train_metric': [],
"valid_it": [],
'valid_loss': [],
'valid_metric': []
}
mb = master_bar(range(num_epochs))
mb.names = ["train loss", "train acc", "val loss", "val acc"]
mb.write("Epoch\tTime\tLearRate\tT_loss\tT_accu\t\tV_loss\tV_accu")
mb.write("-" * 70)
for epoch in mb:
mb.write("epoch")
#self.train_batches.dataset.set_random_choices()
lrs = (lr_schedule(x) / self.batch_size
for x in np.arange(epoch, epoch + 1, 1 /
len(self.train_batches)))
stats, train_time = self.train_epoch(stats, epoch, mb, lrs), t()
stats, valid_time = self.valid_epoch(
stats,
epoch,
mb,
), t()
self.log["epoch"].append(epoch + 1)
self.log["learning rate"].append(lr_schedule(epoch + 1))
self.log["total time"].append(t.total_time)
self.log["train loss"].append(np.mean(
stats['train_loss'])) # or np.mean
self.log["train acc"].append(np.mean(stats['train_metric']))
self.log["val loss"].append(np.mean(stats['valid_loss']))
self.log["val acc"].append(np.mean(stats['valid_metric']))
if self.log["val loss"][-1] <= valid_loss_min: # Val loss improve
mb.write('Saving model!')
self.save_model()
valid_loss_min = self.log["val loss"][-1]
p = 0
else: # Val loss didn't improve
p += 1
if p > patience:
mb.write('Stopping training')
break
mb.write(
"{}/{}\t{:.0f}:{:.0f}\t{:.4f}\t\t{:.4f}\t{:.4f}\t\t{:.4f}\t{:.4f}"
.format(self.log["epoch"][-1], num_epochs,
self.log["total time"][-1] // 60,
self.log["total time"][-1] % 60,
self.log["learning rate"][-1],
self.log["train loss"][-1], self.log["train acc"][-1],
self.log["val loss"][-1], self.log["val acc"][-1]))
#graphs = [[self.log["epoch"], self.log["train acc"]],
# [self.log["epoch"], self.log["val acc"]]]
#mb.update_graph(graphs)
torch.cuda.empty_cache() # free cache mem after train
def training(self):
condition = self.config["train"]["condition"]
best_score = {"epoch": -1, "train_loss": np.inf, "valid_loss": np.inf, "train_qwk": 0.0, "valid_qwk": 0.0}
non_improvement_round = 0
mb = master_bar(range(condition["epoch"]))
for epoch in mb:
temp_score = {"epoch": epoch, "train_loss": 0.0, "valid_loss": 0.0, "train_qwk": 0.0, "valid_qwk": 0.0}
for phase in ["train", "valid"]:
if phase == "train":
data_loader = self.train_loader
self.scheduler.step()
self.model.train()
elif phase == "valid":
data_loader = self.valid_loader
self.model.eval()
running_loss = 0.0
y_true, y_pred = np.array([]).reshape((0, 1)), np.array([]).reshape((0, 1))
for data in progress_bar(data_loader, parent=mb):
mb.child.comment = ">> {} phase".format(phase)
inputs = data["image"].to(self.device, dtype=torch.float)
labels = data["label"].view(-1, 1).to(self.device, dtype=torch.float)
self.optimizer.zero_grad()
outputs = self.model(inputs)
with torch.set_grad_enabled(phase == "train"):
loss = self.criterion(outputs, labels)
if phase == "train":
loss.backward()
self.optimizer.step()
running_loss += loss.item()
if torch.cuda.is_available():
labels = labels.cpu()
outputs = outputs.cpu()
y_true = np.vstack((y_true, labels.detach().numpy()))
y_pred = np.vstack((y_pred, outputs.detach().numpy()))
temp_score["{}_loss".format(phase)] = running_loss / len(data_loader)
temp_score["{}_qwk".format(phase)] = self.__auc_scoring(y_true, y_pred)
super().update_training_log(temp_score)
if best_score["valid_loss"] > temp_score["valid_loss"]:
best_score = temp_score
super().update_best_model(self.model.state_dict())
non_improvement_round = 0
else:
non_improvement_round += 1
if epoch % 10 == 0:
text = "[epoch {}] best epoch:{} train loss:{} valid loss:{} train auc:{} valid auc:{}".format(
epoch,
best_score["epoch"],
np.round(best_score["train_loss"], 5),
np.round(best_score["valid_loss"], 5),
np.round(best_score["train_qwk"], 5),
np.round(best_score["valid_qwk"], 5)
)
mb.write(text)
super().update_learning_curve()
# Early Stopping
if non_improvement_round >= condition["early_stopping_rounds"]:
print("\t Early stopping: {}[epoch]".format(epoch))
break
super().update_learning_curve()
return best_score
def train(
args, strategy, train_dataset, tokenizer, model, num_train_examples, labels, train_batch_size, pad_token_label_id
):
if args["max_steps"] > 0:
num_train_steps = args["max_steps"] * args["gradient_accumulation_steps"]
args["num_train_epochs"] = 1
else:
num_train_steps = (
math.ceil(num_train_examples / train_batch_size)
// args["gradient_accumulation_steps"]
* args["num_train_epochs"]
)
writer = tf.summary.create_file_writer("/tmp/mylogs")
with strategy.scope():
loss_fct = tf.keras.losses.SparseCategoricalCrossentropy(reduction=tf.keras.losses.Reduction.NONE)
optimizer = create_optimizer(args["learning_rate"], num_train_steps, args["warmup_steps"])
if args["fp16"]:
optimizer = tf.keras.mixed_precision.experimental.LossScaleOptimizer(optimizer, "dynamic")
loss_metric = tf.keras.metrics.Mean(name="loss", dtype=tf.float32)
gradient_accumulator = GradientAccumulator()
logging.info("***** Running training *****")
logging.info(" Num examples = %d", num_train_examples)
logging.info(" Num Epochs = %d", args["num_train_epochs"])
logging.info(" Instantaneous batch size per device = %d", args["per_device_train_batch_size"])
logging.info(
" Total train batch size (w. parallel, distributed & accumulation) = %d",
train_batch_size * args["gradient_accumulation_steps"],
)
logging.info(" Gradient Accumulation steps = %d", args["gradient_accumulation_steps"])
logging.info(" Total training steps = %d", num_train_steps)
model.summary()
@tf.function
def apply_gradients():
grads_and_vars = []
for gradient, variable in zip(gradient_accumulator.gradients, model.trainable_variables):
if gradient is not None:
scaled_gradient = gradient / (args["n_device"] * args["gradient_accumulation_steps"])
grads_and_vars.append((scaled_gradient, variable))
else:
grads_and_vars.append((gradient, variable))
optimizer.apply_gradients(grads_and_vars, args["max_grad_norm"])
gradient_accumulator.reset()
@tf.function
def train_step(train_features, train_labels):
def step_fn(train_features, train_labels):
inputs = {"attention_mask": train_features["input_mask"], "training": True}
if args["model_type"] != "distilbert":
inputs["token_type_ids"] = (
train_features["segment_ids"] if args["model_type"] in ["bert", "xlnet"] else None
)
with tf.GradientTape() as tape:
logits = model(train_features["input_ids"], **inputs)[0]
logits = tf.reshape(logits, (-1, len(labels) + 1))
active_loss = tf.reshape(train_features["input_mask"], (-1,))
active_logits = tf.boolean_mask(logits, active_loss)
train_labels = tf.reshape(train_labels, (-1,))
active_labels = tf.boolean_mask(train_labels, active_loss)
cross_entropy = loss_fct(active_labels, active_logits)
loss = tf.reduce_sum(cross_entropy) * (1.0 / train_batch_size)
grads = tape.gradient(loss, model.trainable_variables)
gradient_accumulator(grads)
return cross_entropy
per_example_losses = strategy.experimental_run_v2(step_fn, args=(train_features, train_labels))
mean_loss = strategy.reduce(tf.distribute.ReduceOp.MEAN, per_example_losses, axis=0)
return mean_loss
current_time = datetime.datetime.now()
train_iterator = master_bar(range(args["num_train_epochs"]))
global_step = 0
logging_loss = 0.0
for epoch in train_iterator:
epoch_iterator = progress_bar(
train_dataset, total=num_train_steps, parent=train_iterator, display=args["n_device"] > 1
)
step = 1
with strategy.scope():
for train_features, train_labels in epoch_iterator:
loss = train_step(train_features, train_labels)
if step % args["gradient_accumulation_steps"] == 0:
strategy.experimental_run_v2(apply_gradients)
loss_metric(loss)
global_step += 1
if args["logging_steps"] > 0 and global_step % args["logging_steps"] == 0:
# Log metrics
if (
args["n_device"] == 1 and args["evaluate_during_training"]
): # Only evaluate when single GPU otherwise metrics may not average well
y_true, y_pred, eval_loss = evaluate(
args, strategy, model, tokenizer, labels, pad_token_label_id, mode="dev"
)
report = metrics.classification_report(y_true, y_pred, digits=4)
logging.info("Eval at step " + str(global_step) + "\n" + report)
logging.info("eval_loss: " + str(eval_loss))
precision = metrics.precision_score(y_true, y_pred)
recall = metrics.recall_score(y_true, y_pred)
f1 = metrics.f1_score(y_true, y_pred)
with writer.as_default():
tf.summary.scalar("eval_loss", eval_loss, global_step)
tf.summary.scalar("precision", precision, global_step)
tf.summary.scalar("recall", recall, global_step)
tf.summary.scalar("f1", f1, global_step)
lr = optimizer.learning_rate
learning_rate = lr(step)
with writer.as_default():
tf.summary.scalar("lr", learning_rate, global_step)
tf.summary.scalar(
"loss", (loss_metric.result() - logging_loss) / args["logging_steps"], global_step
)
logging_loss = loss_metric.result()
with writer.as_default():
tf.summary.scalar("loss", loss_metric.result(), step=step)
if args["save_steps"] > 0 and global_step % args["save_steps"] == 0:
# Save model checkpoint
output_dir = os.path.join(args["output_dir"], "checkpoint-{}".format(global_step))
if not os.path.exists(output_dir):
os.makedirs(output_dir)
model.save_pretrained(output_dir)
logging.info("Saving model checkpoint to %s", output_dir)
train_iterator.child.comment = f"loss : {loss_metric.result()}"
step += 1
train_iterator.write(f"loss epoch {epoch + 1}: {loss_metric.result()}")
loss_metric.reset_states()
logging.info(" Training took time = {}".format(datetime.datetime.now() - current_time))
def main(config,
pretrained=False,
patience=1,
lr_scale=1.,
pretrained_path=None,
var_neighbor=5,
random_neighbor=True,
netname='att-gcn'):
# Instantiate the network
# os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
# os.environ["CUDA_VISIBLE_DEVICES"] = str(config.gpu_id)
net = nn.DataParallel(ResidualGatedGCNModel(config, dtypeFloat, dtypeLong))
if torch.cuda.is_available():
net.cuda()
if pretrained:
if pretrained_path is not None:
log_dir = pretrained_path
if torch.cuda.is_available():
checkpoint = torch.load(log_dir)
net.load_state_dict(checkpoint['model_state_dict'])
else:
log_dir = f"./tsp-models/{config.expt_name}/"
if torch.cuda.is_available():
checkpoint = torch.load(log_dir + "best_val_checkpoint.tar")
net.load_state_dict(checkpoint['model_state_dict'])
print(net)
# Compute number of network parameters
nb_param = 0
for param in net.parameters():
nb_param += np.prod(list(param.data.size()))
print('Number of parameters:', nb_param)
# Create log directory
tmp_time = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
tmp_time = '{}-{}'.format(netname, tmp_time)
log_dir = f"./logs/{config.expt_name}/{tmp_time}/"
os.makedirs(log_dir, exist_ok=True)
json.dump(config, open(f"{log_dir}/config.json", "w"), indent=4)
writer = SummaryWriter(log_dir) # Define Tensorboard writer
# Training parameters
#batch_size = config.batch_size
#batches_per_epoch = config.batches_per_epoch
#accumulation_steps = config.accumulation_steps
#num_nodes = config.num_nodes
#num_neighbors = config.num_neighbors
max_epochs = config.max_epochs
val_every = config.val_every
test_every = config.test_every
learning_rate = config.learning_rate * lr_scale
decay_rate = config.decay_rate
num_patience = 0
val_loss_old = 1e6 # For decaying LR based on validation loss
val_loss_best = 1e6
best_pred_tour_len = 1e6 # For saving checkpoints
# Define optimizer
optimizer = torch.optim.Adam(net.parameters(), lr=learning_rate)
# optimizer = torch.optim.SGD(net.parameters(), lr=learning_rate,
# momentum=0.9, weight_decay=0.0005)
print(optimizer)
epoch_bar = master_bar(range(max_epochs))
for epoch in epoch_bar:
# Log to Tensorboard
if random_neighbor:
if epoch % var_neighbor == 0:
num_neighbors = np.random.choice(config.num_neighbors)
else:
num_neighbors = config.num_neighbors
writer.add_scalar('learning_rate', learning_rate, epoch)
# Train
train_time, train_loss, train_err_edges, train_err_tour, train_err_tsp, train_pred_tour_len, train_gt_tour_len = train_one_epoch(
net, optimizer, config, epoch_bar, num_neighbors)
epoch_bar.write('t: ' + metrics_to_str(
epoch, train_time, learning_rate, train_loss, train_err_edges,
train_err_tour, train_err_tsp, train_pred_tour_len,
train_gt_tour_len, num_neighbors))
writer.add_scalar('loss/train_loss', train_loss, epoch)
writer.add_scalar('pred_tour_len/train_pred_tour_len',
train_pred_tour_len, epoch)
writer.add_scalar('optimality_gap/train_opt_gap',
train_pred_tour_len / train_gt_tour_len - 1, epoch)
if epoch % val_every == 0 or epoch == max_epochs - 1:
# Validate
val_time, val_loss, val_err_edges, val_err_tour, val_err_tsp, val_pred_tour_len, val_gt_tour_len = test(
net,
config,
epoch_bar,
mode='val',
num_neighbors=num_neighbors)
epoch_bar.write('v: ' + metrics_to_str(
epoch, val_time, learning_rate, val_loss, val_err_edges,
val_err_tour, val_err_tsp, val_pred_tour_len, val_gt_tour_len,
num_neighbors))
writer.add_scalar('loss/val_loss', val_loss, epoch)
writer.add_scalar('pred_tour_len/val_pred_tour_len',
val_pred_tour_len, epoch)
writer.add_scalar('optimality_gap/val_opt_gap',
val_pred_tour_len / val_gt_tour_len - 1, epoch)
# Save checkpoint
if val_pred_tour_len < best_pred_tour_len:
best_pred_tour_len = val_pred_tour_len # Update best prediction
torch.save(
{
'epoch': epoch,
'model_state_dict': net.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
'train_loss': train_loss,
'val_loss': val_loss,
}, log_dir + "best_val_checkpoint_{}.tar".format(epoch))
# Update learning rate
if val_loss > 0.99 * val_loss_old:
learning_rate /= decay_rate
optimizer = update_learning_rate(optimizer, learning_rate)
val_loss_old = val_loss # Update old validation loss
# Early Stopping
if val_loss_best > val_loss:
num_patience = 0
val_loss_best = val_loss
else:
num_patience += 1
# if epoch % test_every == 0 or epoch == max_epochs-1:
# # Test
# test_time, test_loss, test_err_edges, test_err_tour, test_err_tsp, test_pred_tour_len, test_gt_tour_len = test(net, config, epoch_bar, mode='test')
# epoch_bar.write('T: ' + metrics_to_str(epoch, test_time, learning_rate, test_loss, test_err_edges, test_err_tour, test_err_tsp, test_pred_tour_len, test_gt_tour_len))
# writer.add_scalar('loss/test_loss', test_loss, epoch)
# writer.add_scalar('pred_tour_len/test_pred_tour_len', test_pred_tour_len, epoch)
# writer.add_scalar('optimality_gap/test_opt_gap', test_pred_tour_len/test_gt_tour_len - 1, epoch)
# Save training checkpoint at the end of epoch
torch.save(
{
'epoch': epoch,
'model_state_dict': net.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
'train_loss': train_loss,
'val_loss': val_loss,
}, log_dir + "last_train_checkpoint.tar")
# Save checkpoint after every 250 epochs
if epoch != 0 and (epoch % 250 == 0 or epoch == max_epochs - 1):
torch.save(
{
'epoch': epoch,
'model_state_dict': net.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
'train_loss': train_loss,
'val_loss': val_loss,
}, log_dir + f"checkpoint_epoch{epoch}.tar")
if num_patience >= patience:
break
return net
def begin_fit(self):
self.mbar = master_bar(range(self.epochs))
self.trainer.logger = partial(self.mbar.write, table=True)
return
def train_vcae(n_epochs,
model,
train_iterator,
val_iterator,
optimizer,
device,
criterion,
save_best=True,
verbose=True,
is_nf=False,
nf=None):
model_name = 'NormalizingFlow' + model.__class__.__name__ if is_nf else model.__class__.__name__
writer, experiment_name, best_model_path = setup_experiment(model_name,
log_dir="./tb")
mb = master_bar(range(n_epochs))
train_losses, val_losses = [], []
best_val_loss = float('+inf')
for epoch in mb:
train_loss = run_epoch(model,
train_iterator,
optimizer,
criterion,
mb,
phase='train',
epoch=epoch,
writer=writer,
is_nf=is_nf,
nf=nf,
device=device)
val_loss = run_epoch(model,
val_iterator,
None,
criterion,
mb,
phase='val',
epoch=epoch,
writer=writer,
is_nf=is_nf,
nf=nf,
device=device)
# save logs
dict_saver = {}
dict_saver.update({'train_loss_mean': train_loss})
dict_saver.update({'test_loss_mean': val_loss})
file_to_save_path = ''.join(
[LOG_PATH, FILE_NAME, experiment_name, FILE_EXCITON])
save_to_file(file_to_save_path, dict_saver)
# save the best model
if save_best and (val_loss < best_val_loss):
best_val_loss = val_loss
save_model(nf if is_nf else model, best_model_path)
if verbose:
# append to a list for real-time plotting
train_losses.append(train_loss)
val_losses.append(val_loss)
# start plotting for notebook
mb.main_bar.comment = f'EPOCHS, best_loss:{best_val_loss}'
mb.child.comment = f"train_loss:{round(train_loss, 3)}, val_loss:{round(val_loss, 3)}"
plot_loss_update(epoch, n_epochs, mb, train_losses, val_losses)
return best_model_path
def train(region):
np.random.seed(0)
torch.manual_seed(0)
input_len = 10
encoder_units = 32
decoder_units = 64
encoder_rnn_layers = 3
encoder_dropout = 0.2
decoder_dropout = 0.2
input_size = 2
output_size = 1
predict_len = 5
batch_size = 16
epochs = 500
force_teacher = 0.8
train_dataset, test_dataset, train_max, train_min = create_dataset(
input_len, predict_len, region)
train_loader = DataLoader(
train_dataset, batch_size=batch_size, shuffle=True, drop_last=True)
test_loader = DataLoader(
test_dataset, batch_size=batch_size, shuffle=False, drop_last=True)
enc = Encoder(input_size, encoder_units, input_len,
encoder_rnn_layers, encoder_dropout)
dec = Decoder(encoder_units*2, decoder_units, input_len,
input_len, decoder_dropout, output_size)
optimizer = AdaBound(list(enc.parameters()) +
list(dec.parameters()), 0.01, final_lr=0.1)
# optimizer = optim.Adam(list(enc.parameters()) + list(dec.parameters()), 0.01)
criterion = nn.MSELoss()
mb = master_bar(range(epochs))
for ep in mb:
train_loss = 0
enc.train()
dec.train()
for encoder_input, decoder_input, target in progress_bar(train_loader, parent=mb):
optimizer.zero_grad()
enc_vec = enc(encoder_input)
h = enc_vec[:, -1, :]
_, c = dec.initHidden(batch_size)
x = decoder_input[:, 0]
pred = []
for pi in range(predict_len):
x, h, c = dec(x, h, c, enc_vec)
rand = np.random.random()
pred += [x]
if rand < force_teacher:
x = decoder_input[:, pi]
pred = torch.cat(pred, dim=1)
# loss = quantile_loss(pred, target)
loss = criterion(pred, target)
loss.backward()
optimizer.step()
train_loss += loss.item()
test_loss = 0
enc.eval()
dec.eval()
for encoder_input, decoder_input, target in progress_bar(test_loader, parent=mb):
with torch.no_grad():
enc_vec = enc(encoder_input)
h = enc_vec[:, -1, :]
_, c = dec.initHidden(batch_size)
x = decoder_input[:, 0]
pred = []
for pi in range(predict_len):
x, h, c = dec(x, h, c, enc_vec)
pred += [x]
pred = torch.cat(pred, dim=1)
# loss = quantile_loss(pred, target)
loss = criterion(pred, target)
test_loss += loss.item()
print(
f"Epoch {ep} Train Loss {train_loss/len(train_loader)} Test Loss {test_loss/len(test_loader)}")
if not os.path.exists("models"):
os.mkdir("models")
torch.save(enc.state_dict(), f"models/{region}_enc.pth")
torch.save(dec.state_dict(), f"models/{region}_dec.pth")
test_loader = DataLoader(test_dataset, batch_size=1,
shuffle=False, drop_last=False)
rmse = 0
p = 0
predicted = []
true_target = []
enc.eval()
dec.eval()
for encoder_input, decoder_input, target in progress_bar(test_loader, parent=mb):
with torch.no_grad():
enc_vec = enc(encoder_input)
x = decoder_input[:, 0]
h, c = dec.initHidden(1)
pred = []
for pi in range(predict_len):
x, h, c = dec(x, h, c, enc_vec)
pred += [x]
pred = torch.cat(pred, dim=1)
predicted += [pred[0, p].item()]
true_target += [target[0, p].item()]
predicted = np.array(predicted).reshape(1, -1)
predicted = predicted * (train_max - train_min) + train_min
true_target = np.array(true_target).reshape(1, -1)
true_target = true_target * (train_max - train_min) + train_min
rmse, peasonr = calc_metric(predicted, true_target)
print(f"{region} RMSE {rmse}")
print(f"{region} r {peasonr[0]}")
return f"{region} RMSE {rmse} r {peasonr[0]}"
def main():
now = datetime.datetime.now()
now_date = '{}-{:0>2d}-{:0>2d}_{:0>2d}-{:0>2d}-{:0>2d}'.format(
now.year, now.month, now.day, now.hour, now.minute, now.second)
# set logger
logger = logging.getLogger("Log")
logger.setLevel(logging.DEBUG)
handler_format = logging.Formatter(
'%(asctime)s - %(levelname)s - %(message)s')
# stream_handler = logging.StreamHandler()
# stream_handler.setLevel(logging.DEBUG)
# stream_handler.setFormatter(handler_format)
# logger.addHandler(stream_handler)
print('{}-{}-{} {}:{}:{}'.format(now.year, now.month, now.day, now.hour,
now.minute, now.second))
with open('../params/exp{}.yaml'.format(EXP_NO), "r+") as f:
param = yaml.load(f, Loader=yaml.FullLoader)
param['date'] = now_date
# seed set
seed_setting(param['seed'])
if torch.cuda.is_available():
torch.backends.cudnn.benchmark = True
local_cv = dict()
for fold in param['fold']:
# /mnt/hdd1/alcon2019/ + exp0/ + 2019-mm-dd_hh-mm-ss/ + foldN
outdir = os.path.join(param['save path'], EXP_NAME, now_date,
'fold{}'.format(fold))
if os.path.exists(param['save path']):
os.makedirs(outdir, exist_ok=True)
else:
print("Not find {}".format(param['save path']))
raise FileNotFoundError
file_handler = logging.FileHandler(
os.path.join(outdir, 'experiment.log'))
file_handler.setLevel(logging.DEBUG)
file_handler.setFormatter(handler_format)
logger.addHandler(file_handler)
logger.debug('============= FOLD {} ============='.format(fold))
logger.debug('{}-{}-{} {}:{}:{}'.format(now.year, now.month, now.day,
now.hour, now.minute,
now.second))
# Dataset
param['batch size'] = max(param['batch size'],
param['batch size'] * param['GPU'])
if param['debug']:
train_dataset = AlconDataset(
df=get_train_df(param['tabledir']).query(
'valid != @fold').iloc[:param['batch size'] * 12],
augmentation=get_train_augmentation(
*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'train', 'imgs'),
mode='train')
valid_dataset = AlconDataset(
df=get_train_df(param['tabledir']).query(
'valid == @fold').iloc[:param['batch size'] * 12],
augmentation=get_test_augmentation(
*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'train', 'imgs'),
mode='valid')
else:
train_dataset = AlconDataset(
df=get_train_df(param['tabledir']).query('valid != @fold'),
augmentation=get_train_augmentation(
*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'train', 'imgs'),
mode='train',
margin_augmentation=True)
valid_dataset = AlconDataset(
df=get_train_df(param['tabledir']).query('valid == @fold'),
augmentation=get_test_augmentation(
*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'train', 'imgs'),
mode='valid',
margin_augmentation=False)
logger.debug('train dataset size: {}'.format(len(train_dataset)))
logger.debug('valid dataset size: {}'.format(len(valid_dataset)))
# Dataloader
train_dataloader = DataLoader(train_dataset,
batch_size=param['batch size'],
num_workers=param['thread'],
pin_memory=False,
drop_last=False,
shuffle=True)
valid_dataloader = DataLoader(valid_dataset,
batch_size=param['batch size'],
num_workers=param['thread'],
pin_memory=False,
drop_last=False,
shuffle=False)
logger.debug('train loader size: {}'.format(len(train_dataloader)))
logger.debug('valid loader size: {}'.format(len(valid_dataloader)))
# model
model = DenseNet201GRU2(num_classes=48,
hidden_size=512,
bidirectional=True,
load_weight=None,
dropout=param['dropout'])
param['model'] = model.__class__.__name__
# optim
optimizer = torch.optim.SGD(model.parameters(),
lr=0.001,
momentum=0.9,
weight_decay=1e-5,
nesterov=False)
# scheduler
model = model.to(param['device'])
model, optimizer = amp.initialize(model, optimizer, opt_level="O1")
if param['GPU'] > 0:
model = nn.DataParallel(model)
loss_fn = nn.CrossEntropyLoss().to(param['device'])
eval_fn = accuracy_one_character
max_char_acc = -1.
max_3char_acc = -1.
min_loss = 10**5
writer = tbx.SummaryWriter("../log/exp{}/{}/fold{}".format(
EXP_NO, now_date, fold))
for key, val in param.items():
writer.add_text('data/hyperparam/{}'.format(key), str(val), 0)
max_char_acc = -1e-5
max_3char_acc = -1e-5
min_loss = 1e+5
snapshot = 0
snapshot_loss_list = list()
snapshot_eval_list = list()
snapshot_eval3_list = list()
snapshot_loss = 1e+5
snapshot_eval = -1e-5
snapshot_eval3 = -1e-5
val_iter = math.ceil(len(train_dataloader) / 3)
print('val_iter: {}'.format(val_iter))
# Hyper params
cycle_iter = 5
snap_start = 2
n_snap = 8
mb = master_bar(range((n_snap + snap_start) * cycle_iter))
scheduler = CosineAnnealingWarmUpRestarts(optimizer,
T_0=len(train_dataloader) *
cycle_iter,
T_mult=1,
T_up=500,
eta_max=0.1)
for epoch in mb:
if epoch % cycle_iter == 0 and epoch >= snap_start * cycle_iter:
if snapshot > 1:
snapshot_loss_list.append(snapshot_loss)
snapshot_eval_list.append(snapshot_eval)
snapshot_eval3_list.append(snapshot_eval3)
snapshot += 1
snapshot_loss = 10**5
snapshot_eval = 0.0
snapshot_eval3 = 0.0
model.train()
avg_train_loss = 10**5
avg_train_accuracy = 0.0
avg_three_train_acc = 0.0
for step, (inputs, targets, indice) in enumerate(
progress_bar(train_dataloader, parent=mb)):
model.train()
inputs = inputs.to(param['device'])
targets = targets.to(param['device'])
optimizer.zero_grad()
logits = model(inputs) # logits.size() = (batch*3, 48)
preds = logits.view(targets.size(0), 3, -1).softmax(dim=2)
loss = loss_fn(logits,
targets.view(-1, targets.size(2)).argmax(dim=1))
with amp.scale_loss(loss, optimizer) as scaled_loss:
scaled_loss.backward()
# loss.backward()
# torch.nn.utils.clip_grad_norm_(model.parameters(), 1.0)
optimizer.step()
avg_train_loss += loss.item()
_avg_accuracy = eval_fn(preds, targets.argmax(dim=2)).item()
avg_train_accuracy += _avg_accuracy
_three_char_accuracy = accuracy_three_character(
preds, targets.argmax(dim=2), mean=True).item()
avg_three_train_acc += _three_char_accuracy
writer.add_scalar("data/learning rate",
scheduler.get_lr()[0],
step + epoch * len(train_dataloader))
scheduler.step()
writer.add_scalars(
"data/metric/train", {
'loss': loss.item(),
'accuracy': _avg_accuracy,
'3accuracy': _three_char_accuracy
}, step + epoch * len(train_dataloader))
if step % val_iter == 0 and step != 0:
avg_valid_loss, avg_valid_accuracy, avg_three_valid_acc = valid_alcon_rnn(
model, valid_dataloader, param['device'], loss_fn,
eval_fn)
writer.add_scalars(
"data/metric/valid", {
'loss': avg_valid_loss,
'accuracy': avg_valid_accuracy,
'3accuracy': avg_three_valid_acc
}, epoch)
logger.debug(
'======================== epoch {} | step {} ========================'
.format(epoch + 1, step + 1))
logger.debug('lr : {:.5f}'.format(
scheduler.get_lr()[0]))
logger.debug(
'loss : test={:.5f}'.format(avg_valid_loss))
logger.debug('acc(per 1 char) : test={:.3%}'.format(
avg_valid_accuracy))
logger.debug('acc(per 3 char) : test={:.3%}'.format(
avg_three_valid_acc))
if min_loss > avg_valid_loss:
logger.debug(
'update best loss: {:.5f} ---> {:.5f}'.format(
min_loss, avg_valid_loss))
min_loss = avg_valid_loss
torch.save(model.state_dict(),
os.path.join(outdir, 'best_loss.pth'))
if max_char_acc < avg_valid_accuracy:
logger.debug(
'update best acc per 1 char: {:.3%} ---> {:.3%}'.
format(max_char_acc, avg_valid_accuracy))
max_char_acc = avg_valid_accuracy
torch.save(model.state_dict(),
os.path.join(outdir, 'best_acc.pth'))
if max_3char_acc < avg_three_valid_acc:
logger.debug(
'update best acc per 3 char: {:.3%} ---> {:.3%}'.
format(max_3char_acc, avg_three_valid_acc))
max_3char_acc = avg_three_valid_acc
torch.save(model.state_dict(),
os.path.join(outdir, 'best_3acc.pth'))
if snapshot > 0:
if snapshot_loss > avg_valid_loss:
logger.debug(
'[snap] update best loss: {:.5f} ---> {:.5f}'.
format(snapshot_loss, avg_valid_loss))
snapshot_loss = avg_valid_loss
torch.save(
model.state_dict(),
os.path.join(outdir,
f'best_loss_{snapshot}.pth'))
if snapshot_eval < avg_valid_accuracy:
logger.debug(
'[snap] update best acc per 1 char: {:.3%} ---> {:.3%}'
.format(snapshot_eval, avg_valid_accuracy))
snapshot_eval = avg_valid_accuracy
torch.save(
model.state_dict(),
os.path.join(outdir,
f'best_acc_{snapshot}.pth'))
if snapshot_eval3 < avg_three_valid_acc:
logger.debug(
'[snap] update best acc per 3 char: {:.3%} ---> {:.3%}'
.format(snapshot_eval3, avg_three_valid_acc))
snapshot_eval3 = avg_three_valid_acc
torch.save(
model.state_dict(),
os.path.join(outdir,
f'best_3acc_{snapshot}.pth'))
avg_train_loss /= len(train_dataloader)
avg_train_accuracy /= len(train_dataloader)
avg_three_train_acc /= len(train_dataloader)
avg_valid_loss, avg_valid_accuracy, avg_three_valid_acc = valid_alcon_rnn(
model, valid_dataloader, param['device'], loss_fn, eval_fn)
writer.add_scalars(
"data/metric/valid", {
'loss': avg_valid_loss,
'accuracy': avg_valid_accuracy,
'3accuracy': avg_three_valid_acc
}, epoch)
logger.debug(
'======================== epoch {} ========================'.
format(epoch + 1))
logger.debug('lr : {:.5f}'.format(
scheduler.get_lr()[0]))
logger.debug(
'loss : train={:.5f} , test={:.5f}'.format(
avg_train_loss, avg_valid_loss))
logger.debug(
'acc(per 1 char) : train={:.3%} , test={:.3%}'.format(
avg_train_accuracy, avg_valid_accuracy))
logger.debug(
'acc(per 3 char) : train={:.3%} , test={:.3%}'.format(
avg_three_train_acc, avg_three_valid_acc))
if epoch == cycle_iter * snap_start:
torch.save(
model.state_dict(),
os.path.join(outdir,
f'model_epoch_{cycle_iter * snap_start}.pth'))
if min_loss > avg_valid_loss:
logger.debug('update best loss: {:.5f} ---> {:.5f}'.format(
min_loss, avg_valid_loss))
min_loss = avg_valid_loss
torch.save(model.state_dict(),
os.path.join(outdir, 'best_loss.pth'))
if max_char_acc < avg_valid_accuracy:
logger.debug(
'update best acc per 1 char: {:.3%} ---> {:.3%}'.format(
max_char_acc, avg_valid_accuracy))
max_char_acc = avg_valid_accuracy
torch.save(model.state_dict(),
os.path.join(outdir, 'best_acc.pth'))
if max_3char_acc < avg_three_valid_acc:
logger.debug(
'update best acc per 3 char: {:.3%} ---> {:.3%}'.format(
max_3char_acc, avg_three_valid_acc))
max_3char_acc = avg_three_valid_acc
torch.save(model.state_dict(),
os.path.join(outdir, 'best_3acc.pth'))
if snapshot > 0:
if snapshot_loss > avg_valid_loss:
logger.debug(
'[snap] update best loss: {:.5f} ---> {:.5f}'.format(
snapshot_loss, avg_valid_loss))
snapshot_loss = avg_valid_loss
torch.save(
model.state_dict(),
os.path.join(outdir, f'best_loss_{snapshot}.pth'))
if snapshot_eval < avg_valid_accuracy:
logger.debug(
'[snap] update best acc per 1 char: {:.3%} ---> {:.3%}'
.format(snapshot_eval, avg_valid_accuracy))
snapshot_eval = avg_valid_accuracy
torch.save(
model.state_dict(),
os.path.join(outdir, f'best_acc_{snapshot}.pth'))
if snapshot_eval3 < avg_three_valid_acc:
logger.debug(
'[snap] update best acc per 3 char: {:.3%} ---> {:.3%}'
.format(snapshot_eval3, avg_three_valid_acc))
snapshot_eval3 = avg_three_valid_acc
torch.save(
model.state_dict(),
os.path.join(outdir, f'best_3acc_{snapshot}.pth'))
snapshot_loss_list.append(snapshot_loss)
snapshot_eval_list.append(snapshot_eval)
snapshot_eval3_list.append(snapshot_eval3)
writer.add_scalars(
"data/metric/valid", {
'best loss': min_loss,
'best accuracy': max_char_acc,
'best 3accuracy': max_3char_acc
})
logger.debug('================ FINISH TRAIN ================')
logger.debug('Result')
logger.debug('Best loss : {}'.format(min_loss))
logger.debug('Best 1 acc : {}'.format(max_char_acc))
logger.debug('Best 3 acc : {}'.format(max_3char_acc))
writer.export_scalars_to_json(os.path.join(outdir, 'history.json'))
writer.close()
# Local cv
target_list = list()
for _, targets, _ in valid_dataloader:
targets = targets.argmax(dim=2)
target_list.append(targets)
target_list = torch.cat(target_list)
mb = master_bar(range(n_snap))
valid_logit_dict = dict()
init = True
for i in mb:
model.load_state_dict(
torch.load(os.path.join(outdir, f'best_loss_{i+1}.pth')))
logit_alcon_rnn(model,
valid_dataloader,
param['device'],
valid_logit_dict,
div=n_snap,
init=init)
init = False
pred_list = torch.stack(list(valid_logit_dict.values()))
pred_list = pred_list.softmax(dim=2)
local_accuracy = accuracy_three_character(pred_list, target_list)
logger.debug('LOCAL CV : {:5%}'.format(local_accuracy))
torch.save(valid_logit_dict,
os.path.join(outdir, f'fold{fold}_valid_logit.pth'))
local_cv['fold{}'.format(fold)] = {
'accuracy': local_accuracy,
'valid_size': len(valid_dataset)
}
del train_dataset, valid_dataset
del train_dataloader, valid_dataloader
del scheduler, optimizer
del valid_logit_dict, target_list
gc.collect()
logger.debug('=========== Prediction phrase ===========')
if param['debug']:
test_dataset = AlconDataset(
df=get_test_df(param['tabledir']).iloc[:param['batch size'] *
12],
augmentation=get_test_augmentation(
*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'test', 'imgs'),
mode='test')
else:
test_dataset = AlconDataset(
df=get_test_df(param['tabledir']),
augmentation=get_test_augmentation(
*get_resolution(param['resolution'])),
datadir=os.path.join(param['dataroot'], 'test', 'imgs'),
mode='test')
test_dataloader = DataLoader(test_dataset,
batch_size=param['batch size'],
num_workers=param['thread'],
pin_memory=False,
drop_last=False,
shuffle=False)
logger.debug('test dataset size: {}'.format(len(test_dataset)))
logger.debug('test loader size: {}'.format(len(test_dataloader)))
test_logit_dict = dict()
init = True
for i in range(n_snap):
logger.debug('load weight : {}'.format(
os.path.join(outdir, f'best_loss_{i+1}.pth')))
model.load_state_dict(
torch.load(os.path.join(outdir, f'best_loss_{i+1}.pth')))
logit_alcon_rnn(model,
test_dataloader,
param['device'],
test_logit_dict,
div=n_snap,
init=init)
init = False
torch.save(test_logit_dict, os.path.join(outdir, 'prediction.pth'))
output_list = make_submission(test_logit_dict)
pd.DataFrame(output_list).sort_values('ID').set_index('ID').to_csv(
os.path.join(outdir, 'test_prediction.csv'))
logger.debug('success!')
logger.removeHandler(file_handler)
del test_dataset, test_dataloader
gc.collect()
# Ensemble
print('======== Ensemble phase =========')
emsemble_prediction = dict()
mb = master_bar(param['fold'])
print('======== Load Vector =========')
for i, fold in enumerate(mb):
outdir = os.path.join(param['save path'], EXP_NAME, now_date,
'fold{}'.format(fold))
prediction = torch.load(os.path.join(outdir, 'prediction.pth'))
# prediction is list
# prediction[0] = {'ID' : 0, 'logit' torch.tensor, ...}
if i == 0:
for ID, logit in progress_bar(prediction.items(), parent=mb):
emsemble_prediction[ID] = logit / len(param['fold'])
else:
for ID, logit in progress_bar(prediction.items(), parent=mb):
emsemble_prediction[ID] += logit / len(param['fold'])
#
outdir = os.path.join(param['save path'], EXP_NAME, now_date)
#
file_handler = logging.FileHandler(os.path.join(outdir, 'result.log'))
file_handler.setLevel(logging.DEBUG)
file_handler.setFormatter(handler_format)
logger.addHandler(file_handler)
logger.info(' ========== RESULT ========== \n')
#
cv = 0.0
train_data_size = 0
for fold in param['fold']:
acc = local_cv['fold{}'.format(fold)]['accuracy']
valid_size = local_cv['fold{}'.format(fold)]['valid_size']
train_data_size += valid_size
logger.info(' fold {} : {:.3%} \n'.format(fold, acc))
cv += acc * valid_size
logger.info(' Local CV : {:.3%} \n'.format(cv / train_data_size))
logger.info(' ============================== \n')
#
logger.removeHandler(file_handler)
#
#
torch.save(emsemble_prediction, os.path.join(outdir, 'prediction.pth'))
#
print('======== make submittion file =========')
submit_list = make_submission(emsemble_prediction)
pd.DataFrame(submit_list).sort_values('ID').set_index('ID').to_csv(
os.path.join(outdir, 'test_prediction.csv'))
print('success!')
def calculate_map(self,
model: nn.Module,
conf_threshold: float = 0.01,
iou_threshold: float = 0.50,
same_threshold: float = 0.45,
max_preds: float = 200,
plot: bool = True,
use_gpu: bool = True) -> float:
"""Compute the mean average precision (mAP) achieved by a model on
this dataset"""
model.eval()
dl = DataLoader(self, batch_size=32, drop_last=False, num_workers=32)
# First, populate a dictionary with class ids as keys, and tuples of
# the form (confidence, is_correct, bbox) for each bounding box
# predicted for that class
predictions = defaultdict(list)
num_targs = defaultdict(
int) # Dict with number of ground truth boxes for each class
mb = master_bar(dl)
for imgs, targs in mb:
if use_gpu: imgs = imgs.cuda()
preds = model(imgs).cpu()
for pred, targ in progress_bar(list(zip(preds, targs)), parent=mb):
# Process Targets
targ_boxes, targ_classes, _ = tensor2boxes(
self.matcher.default_boxes, targ)
targ_boxes, filtered_idxs = filter_overlapping_boxes(
targ_boxes, iou_threshold=0.95)
targ_classes = targ_classes[filtered_idxs]
for targ_class in targ_classes:
num_targs[targ_class.item()] += 1
# Process Predictions
pred_boxes, pred_classes, pred_confs = nms(
pred, self.matcher.default_boxes, conf_threshold,
same_threshold, max_preds)
# Match Prediction to Targets for each Class
matched_targs = set()
for pred_box, pred_class, pred_conf in zip(
pred_boxes, pred_classes, pred_confs):
# Indices of targets in the same class as the current prediction
same_classes = (targ_classes == pred_class).float()
same_class_idxs = set(
same_classes.nonzero().flatten().numpy())
# Indices of targets that overlap sufficiently with the current prediction
overlaps = jaccard_overlap(pred_box, targ_boxes)
above_thresholds = (overlaps > iou_threshold).float()
above_threshold_idxs = set(
above_thresholds.nonzero().flatten().numpy())
# Indices of targets that are both in the same class and overlap sufficiently
# with the current prediction
valid_idxs = same_class_idxs.intersection(
above_threshold_idxs)
# Target indices in order of decreasing overlap with the current prediction
valid_idxs = list(valid_idxs)
valid_idxs.sort(key=lambda idx: overlaps[idx],
reverse=True)
valid_idxs = [
idx for idx in valid_idxs if idx not in matched_targs
]
pred_box_matched = False
if len(valid_idxs):
targ_idx = valid_idxs[0]
matched_targs.add(targ_idx)
pred_box_matched = True
pred_conf = pred_conf.item()
pred_box = pred_box.detach().cpu().numpy().tolist()
predictions[pred_class].append(
(pred_conf, pred_box_matched, pred_box))
# Calculate Average Precision for each Class
all_classes = set(num_targs.keys()).union(predictions.keys())
avg_precisions = []
for class_idx in all_classes:
tps, fps, fns = 0, 0, num_targs[class_idx]
if fns == 0:
avg_precisions.append(1)
continue
precisions, recalls = [], []
# Sort Predictions in order of decreasing confidence
class_preds = predictions[class_idx]
class_preds = [(conf, is_correct)
for conf, is_correct, _ in class_preds]
class_preds.sort(
reverse=True) # Sort in order of decreasing confidence
for _, is_correct in class_preds:
if is_correct:
tps += 1
fns -= 1
else:
fps += 1
precision = tps / (tps + fps) if tps + fps > 0 else 0
recall = tps / (tps + fns) if tps + fns > 0 else 0
if not (recalls and recalls[-1] == recall):
precisions.append(precision)
recalls.append(recall)
precisions_adj = [
max(precisions[idx:]) for idx in range(len(precisions))
]
avg_precision = 0
for idx, precision in enumerate(precisions_adj[:-1]):
increment = recalls[idx + 1] - recalls[idx]
avg_precision += precision * increment
print(
f"\nAP for {self.categories[class_idx].capitalize()}: {round(avg_precision, 4)}"
)
if plot:
plt.plot(recalls, precisions_adj)
plt.title(self.categories[class_idx].capitalize())
plt.xlabel("Recall")
plt.ylim(0, 1)
plt.xlim(0, 1)
plt.ylabel("Precision")
plt.show()
avg_precisions.append(avg_precision)
mean_avg_precision = np.mean(avg_precisions)
return mean_avg_precision
def train(self, train_df, target_df):
oof = np.zeros((len(train_df), self.cfg.model.n_classes))
cv = 0
for fold_, col in enumerate(self.fold_df.columns):
print(
f'\n========================== FOLD {fold_} ... ==========================\n'
)
logging.debug(
f'\n========================== FOLD {fold_} ... ==========================\n'
)
trn_x, val_x = train_df[self.fold_df[col] == 0], train_df[
self.fold_df[col] > 0]
val_y = target_df[self.fold_df[col] > 0].values
train_loader = factory.get_dataloader(trn_x, self.cfg.data.train)
valid_loader = factory.get_dataloader(val_x, self.cfg.data.valid)
model = factory.get_nn_model(self.cfg).to(device)
criterion = factory.get_loss(self.cfg)
optimizer = factory.get_optim(self.cfg, model.parameters())
scheduler = factory.get_scheduler(self.cfg, optimizer)
best_epoch = -1
best_val_score = -np.inf
mb = master_bar(range(self.cfg.model.epochs))
train_loss_list = []
val_loss_list = []
val_score_list = []
for epoch in mb:
start_time = time.time()
model, avg_loss = self._train_epoch(model, train_loader,
criterion, optimizer, mb)
valid_preds, avg_val_loss = self._val_epoch(
model, valid_loader, criterion)
val_score = factory.get_metrics(self.cfg.common.metrics.name)(
val_y, valid_preds)
train_loss_list.append(avg_loss)
val_loss_list.append(avg_val_loss)
val_score_list.append(val_score)
if self.cfg.scheduler.name != 'ReduceLROnPlateau':
scheduler.step()
elif self.cfg.scheduler.name == 'ReduceLROnPlateau':
scheduler.step(avg_val_loss)
elapsed = time.time() - start_time
mb.write(
f'Epoch {epoch+1} - avg_train_loss: {avg_loss:.4f} avg_val_loss: {avg_val_loss:.4f} val_score: {val_score:.4f} time: {elapsed:.0f}s'
)
logging.debug(
f'Epoch {epoch+1} - avg_train_loss: {avg_loss:.4f} avg_val_loss: {avg_val_loss:.4f} val_score: {val_score:.4f} time: {elapsed:.0f}s'
)
if val_score > best_val_score:
best_epoch = epoch + 1
best_val_score = val_score
best_valid_preds = valid_preds
if self.cfg.model.multi_gpu:
best_model = model.module.state_dict()
else:
best_model = model.state_dict()
oof[val_x.index, :] = best_valid_preds
cv += best_val_score * self.fold_df[col].max()
torch.save(best_model,
f'../logs/{self.run_name}/weight_best_{fold_}.pt')
self._save_loss_png(train_loss_list, val_loss_list, val_score_list,
fold_)
print(f'\nEpoch {best_epoch} - val_score: {best_val_score:.4f}')
logging.debug(
f'\nEpoch {best_epoch} - val_score: {best_val_score:.4f}')
print('\n\n===================================\n')
print(f'CV: {cv:.6f}')
logging.debug(f'\n\nCV: {cv:.6f}')
print('\n===================================\n\n')
self.oof = oof.reshape(-1, 5)
return cv
def get_opt_rf_params(x_trn:np.ndarray, y_trn:np.ndarray, x_val:np.ndarray, y_val:np.ndarray, objective:str,
w_trn:Optional[np.ndarray]=None, w_val:Optional[np.ndarray]=None,
params:Optional[OrderedDict]=None, n_estimators:int=40, verbose=True) \
-> Tuple[Dict[str,float],Union[RandomForestRegressor,RandomForestClassifier]]:
r'''
Use an ordered parameter-scan to roughly optimise Random Forest hyper-parameters.
Arguments:
x_trn: training input data
y_trn: training target data
x_val: validation input data
y_val: validation target data
objective: string representation of objective: either 'classification' or 'regression'
w_trn: training weights
w_val: validation weights
params: ordered dictionary mapping parameters to optimise to list of values to cosnider
n_estimators: number of trees to use in each forest
verbose: Print extra information and show a live plot of model performance
Returns:
params: dictionary mapping parameters to their optimised values
rf: best performing Random Forest
'''
if params is None:
params = OrderedDict({
'min_samples_leaf': [1, 3, 5, 10, 25, 50, 100],
'max_features': [0.3, 0.5, 0.7, 0.9]
})
rf = RandomForestClassifier if 'class' in objective.lower(
) else RandomForestRegressor
best_params = {
'n_estimators': n_estimators,
'n_jobs': -1,
'max_features': 'sqrt'
}
best_scores = []
scores = []
mb = master_bar(params)
mb.names = ['Best', 'Scores']
if verbose: mb.update_graph([[[], []], [[], []]])
for param in mb:
pb = progress_bar(params[param], parent=mb)
pb.comment = f'{param} = {params[param][0]}'
for i, value in enumerate(pb):
pb.comment = f'{param} = {params[param][min(i+1, len(params[param])-1)]}'
m = rf(**{**best_params, param: value})
m.fit(X=x_trn, y=y_trn, sample_weight=w_trn)
scores.append(m.score(X=x_val, y=y_val, sample_weight=w_val))
if len(best_scores) == 0 or scores[-1] > best_scores[-1]:
best_scores.append(scores[-1])
best_params[param] = value
if verbose:
print(
f'Better score schieved: {param} @ {value} = {best_scores[-1]:.4f}'
)
best_m = m
else:
best_scores.append(best_scores[-1])
if verbose:
mb.update_graph([[range(len(best_scores)), best_scores],
[range(len(scores)), scores]])
if verbose: delattr(mb, 'fig')
if verbose: plt.clf()
return best_params, best_m
def begin_fit(self, e: Event):
self.mbar = master_bar(range(e.learn.epochs))
self.mbar.on_iter_begin()
e.learn.logger = partial(self.mbar.write, table=True)
def run_training(model, optimizer, loss_function, device, num_epochs,
train_dataloader, val_dataloader, early_stopper=None, verbose=False):
"""Run model training.
Args:
model (nn.Module): Torch model to train
optimizer: Torch optimizer object
loss_fn: Torch loss function for training
device (torch.device): Torch device to use for training
num_epochs (int): Max. number of epochs to train
train_dataloader (DataLoader): Torch DataLoader object to load the
training data
val_dataloader (DataLoader): Torch DataLoader object to load the
validation data
early_stopper (EarlyStopper, optional): If passed, model will be trained
with early stopping. Defaults to None.
verbose (bool, optional): Print information about model training.
Defaults to False.
Returns:
list, list, list, list, torch.Tensor shape (10,10): Return list of train
losses, validation losses, train accuracies, validation accuracies
per epoch and the confusion matrix evaluated in the last epoch.
"""
start_time = time.time()
master_bar = fastprogress.master_bar(range(num_epochs))
train_losses, val_losses, train_accs, val_accs = [],[],[],[]
for epoch in master_bar:
# Train the model
epoch_train_loss, epoch_train_acc = train(train_dataloader, optimizer, model,
loss_function, device, master_bar)
# Validate the model
epoch_val_loss, epoch_val_acc, confusion_matrix = validate(val_dataloader,
model, loss_function,
device, master_bar)
# Save loss and acc for plotting
train_losses.append(epoch_train_loss)
val_losses.append(epoch_val_loss)
train_accs.append(epoch_train_acc)
val_accs.append(epoch_val_acc)
if verbose:
master_bar.write(f'Train loss: {epoch_train_loss:.2f}, val loss: {epoch_val_loss:.2f}, train acc: {epoch_train_acc:.3f}, val acc {epoch_val_acc:.3f}')
if early_stopper:
####################
## YOUR CODE HERE ##
####################
early_stopper.update(epoch_val_acc, model)
if early_stopper.early_stop:
early_stopper.load_checkpoint(model)
print("Early stopping, since the validation accuracy did not increase. Epoch: {}".format(epoch))
break
# END OF YOUR CODE #
time_elapsed = np.round(time.time() - start_time, 0).astype(int)
print(f'Finished training after {time_elapsed} seconds.')
return train_losses, val_losses, train_accs, val_accs, confusion_matrix
mito_train = [fn for fn in hr_mito]
neuron_path = datasources / 'live_neuron_mito_timelapse_for_deep_learning'
two_channel = list(neuron_path.glob('*MTGreen*.czi'))
one_channel = [x for x in neuron_path.glob('*.czi') if x not in two_channel]
airyscan_path = datasources / 'Airyscan_processed_data_from_the_server'
hr_airyscan = list(airyscan_path.glob('*.czi'))
for fn in hr_mito:
if '03-Airyscan' in fn.stem: valid_files.append(fn)
else: train_files.append(fn)
for lst in [hr_airyscan, one_channel, two_channel]:
lst.sort()
random.shuffle(lst)
split_idx = int(valid_pct * len(lst))
print(split_idx)
valid_files += lst[-split_idx:]
train_files += lst[:-split_idx]
for subdir, file_list in [('train', train_files), ('valid', valid_files)]:
print(f'\n\ncopy, crappify and upsample {subdir} files\n\n')
pbar = master_bar(file_list)
for czi_fn in pbar:
czi_to_multiframe(czi_fn,
hr_path / subdir,
lr_path / subdir,
lr_up_path / subdir,
pbar=pbar)
def train_old(model,
optimizer,
criterion,
dataset,
batch_size,
num_epochs,
num_workers=0,
half=True):
dataloader = {
x: torch.utils.data.DataLoader(dataset[x],
batch_size=batch_size,
shuffle=True,
num_workers=num_workers)
for x in ['train', 'val']
}
dataset_sizes = {x: len(dataset[x]) for x in ['train', 'val']}
# Decay LR by a factor of 0.1 every 7 epochs
scheduler = torch.optim.lr_scheduler.StepLR(optimizer,
step_size=7,
gamma=0.1)
since = time.time()
best_acc = 0.0
#best_model_wts = copy.deepcopy(model.state_dict())
mb = master_bar(range(num_epochs))
mb.names = ['train', 'val']
mb.write("Epoch\tTrn_loss\tVal_loss\tTrn_acc\t\tVal_acc")
# Iterate epochs
#for epoch in range(num_epochs):
for epoch in mb:
# Each epoch has a training and validation phase
for phase in ['train', 'val']:
if phase == 'train':
scheduler.step() # Scheduling the learning rate
model.train() # Set model to training mode
else:
model.eval() # Set model to evaluate mode
running_loss = 0.0
running_corrects = 0
# Iterate over data
#for inputs, labels in dataloader[phase]:
for inputs, labels in progress_bar(dataloader[phase], parent=mb):
inputs = inputs.to(device)
labels = labels.to(device)
if half: inputs = inputs.half()
optimizer.zero_grad() # zero the parameter gradients
outputs = model(inputs) # forward
preds = torch.argmax(outputs, dim=1) # prediction
loss = criterion(outputs, labels) # loss
if phase == 'train': loss.backward() # backward
if phase == 'train': optimizer.step() # optimize
# statistics
running_loss += loss.item() * inputs.size(
0
) # multiplicar si nn.CrossEntropyLoss(size_average=True) que es lo default
running_corrects += torch.sum(preds == labels.data)
epoch_loss = running_loss / dataset_sizes[phase]
epoch_acc = running_corrects.double() / dataset_sizes[phase]
metrics[phase]["loss"].append(epoch_loss)
metrics[phase]["acc"].append(epoch_acc)
#draw_plot(metrics)
# deep copy the model
if phase == 'val' and epoch_acc > best_acc:
best_acc = epoch_acc
#best_model_wts = copy.deepcopy(model.state_dict())
x = list(range(len(metrics["train"]["acc"])))
graphs = [[x, metrics["train"]["acc"]], [x, metrics["val"]["acc"]]]
mb.update_graph(graphs)
mb.write("{}/{}\t{:06.6f}\t{:06.6f}\t{:06.6f}\t{:06.6f}".format(
epoch + 1, num_epochs, metrics["train"]["loss"][-1],
metrics["val"]["loss"][-1], metrics["train"]["acc"][-1],
metrics["val"]["acc"][-1]))
time_elapsed = time.time() - since
print('Training complete in {:.0f}m {:.0f}s'.format(
time_elapsed // 60, time_elapsed % 60))
print('Best val Acc: {:4f}'.format(best_acc))
def main(args):
if args.deterministic:
set_seed(42)
# Set device
if args.device is None:
if torch.cuda.is_available():
args.device = 'cuda:0'
else:
args.device = 'cpu'
normalize = transforms.Normalize(mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225])
train_transforms = transforms.Compose([
transforms.RandomResizedCrop((args.resize, args.resize)),
transforms.RandomHorizontalFlip(),
transforms.RandomRotation(10),
transforms.ToTensor(), normalize
])
test_transforms = transforms.Compose([
transforms.Resize((args.resize, args.resize)),
transforms.ToTensor(), normalize
])
# Train & test sets
train_set = OpenFire(root=args.data_path,
train=True,
download=True,
valid_pct=0.2,
transform=train_transforms)
val_set = OpenFire(root=args.data_path,
train=False,
download=True,
valid_pct=0.2,
transform=test_transforms)
num_classes = len(train_set.classes)
# Samplers
train_sampler = torch.utils.data.RandomSampler(train_set)
test_sampler = torch.utils.data.SequentialSampler(val_set)
# Data loader
train_loader = torch.utils.data.DataLoader(train_set,
batch_size=args.batch_size,
sampler=train_sampler,
num_workers=args.workers,
pin_memory=True)
test_loader = torch.utils.data.DataLoader(val_set,
batch_size=args.batch_size,
sampler=test_sampler,
num_workers=args.workers,
pin_memory=True)
# Model definition
model = torchvision.models.__dict__[args.model](pretrained=args.pretrained)
# Change fc
in_features = getattr(model, 'fc').in_features
setattr(model, 'fc', nn.Linear(in_features, num_classes))
model.to(args.device)
# Loss function
criterion = nn.CrossEntropyLoss()
# optimizer
optimizer = optim.Adam(model.parameters(),
betas=(0.9, 0.99),
weight_decay=args.weight_decay)
# Scheduler
lr_scheduler = optim.lr_scheduler.OneCycleLR(
optimizer,
max_lr=args.lr,
epochs=args.epochs,
steps_per_epoch=len(train_loader),
cycle_momentum=(not isinstance(optimizer, optim.Adam)),
div_factor=args.div_factor,
final_div_factor=args.final_div_factor)
best_loss = math.inf
mb = master_bar(range(args.epochs))
for epoch_idx in mb:
# Training
train_loss = train_epoch(model,
train_loader,
optimizer,
criterion,
master_bar=mb,
epoch=epoch_idx,
scheduler=lr_scheduler,
device=args.device)
# Evaluation
val_loss, acc = evaluate(model,
test_loader,
criterion,
device=args.device)
mb.first_bar.comment = f"Epoch {epoch_idx+1}/{args.epochs}"
mb.write(
f'Epoch {epoch_idx+1}/{args.epochs} - Training loss: {train_loss:.4} | Validation loss: {val_loss:.4} | Error rate: {1 - acc:.4}'
)
# State saving
if val_loss < best_loss:
print(
f"Validation loss decreased {best_loss:.4} --> {val_loss:.4}: saving state..."
)
best_loss = val_loss
if args.output_dir:
torch.save(
dict(model=model.state_dict(),
optimizer=optimizer.state_dict(),
lr_scheduler=lr_scheduler.state_dict(),
epoch=epoch_idx,
args=args),
Path(args.output_dir, f"{args.checkpoint}.pth"))
def experiment_blue_print(
output_root_dir=None,
cv_run_num=None,
ds_train_name=None,
ds_test_name=None,
ds_normalization=None,
num_train_samples=None,
num_augmentations=None,
type_augmentation=None,
num_intra_samples=None,
model_name=None,
batch_size=None,
num_epochs=None,
cls_loss_fn=None,
lr_init=None,
w_top_loss=None,
top_scale=None,
weight_decay_cls=None,
weight_decay_feat_ext=None,
normalize_gradient=None,
pers_type=None,
compute_persistence=None,
track_model=None,
tag=''):
args = dict(locals())
print(args)
if not all(((v is not None) for k, v in args.items())):
s = ', '.join((k for k, v in args.items() if v is None))
raise AssertionError("Some kwargs are None: {}!".format(s))
if w_top_loss > 0 and not compute_persistence:
raise AssertionError('w_top_loss > 0 and compute_persistence == False')
exp_id = get_experiment_id(tag)
output_dir = Path(output_root_dir) / exp_id
output_dir.mkdir()
logger = ExperimentLogger(output_dir, args)
track_accuracy = True
"""
Get the splits for the training data.
"""
DS_TRAIN_ORIGINAL_SPLITS = ds_factory_stratified_shuffle_split(
ds_train_name, num_train_samples)
DS_TEST_ORIGINAL = ds_factory(ds_test_name)
assert len(DS_TRAIN_ORIGINAL_SPLITS) >= cv_run_num
DS_TRAIN_ORIGINAL_SPLITS = DS_TRAIN_ORIGINAL_SPLITS[:cv_run_num]
pers_fn = persistence_fn_factory(args['pers_type'])
cls_loss_fn = cls_loss_fn_factory(args['cls_loss_fn'])
"""
Run over the dataset splits; the splits are fixed for each number of
training samples (500,1000,4000, etc.)
"""
for run_i, DS_TRAIN_ORIGINAL in enumerate(DS_TRAIN_ORIGINAL_SPLITS):
assert len(DS_TRAIN_ORIGINAL) == num_train_samples
logger.new_run()
dl_train, DS_TRAIN, DS_TEST, num_classes = setup_data_for_training(
ds_train_original=DS_TRAIN_ORIGINAL,
ds_test_original=DS_TEST_ORIGINAL,
ds_normalization=ds_normalization,
type_augmentation=type_augmentation,
num_augmentations=num_augmentations,
num_intra_samples=num_intra_samples,
batch_size=batch_size
)
model = model_factory(model_name, num_classes)
model = model.to(DEVICE)
print(model)
opt = torch.optim.SGD(
[
{'params': model.feat_ext.parameters(
), 'weight_decay': weight_decay_feat_ext},
{'params': model.cls.parameters(), 'weight_decay': weight_decay_cls}
],
lr=lr_init,
momentum=0.9,
nesterov=True)
scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(
opt,
T_max=num_epochs,
eta_min=0,
last_epoch=-1)
mb = master_bar(range(num_epochs))
mb_comment = ''
for epoch_i in mb:
model.train()
epoch_loss = 0
L = len(dl_train)-1
for b_i, ((batch_x, batch_y), _) in enumerate(zip(dl_train, progress_bar(range(L), parent=mb))):
n = batch_x[0].size(0)
assert n == num_intra_samples*num_augmentations
assert all(((x.size(0) == n) for x in batch_x))
x, y = torch.cat(batch_x, dim=0), torch.cat(batch_y, dim=0)
x, y = x.to(DEVICE), y.to(DEVICE)
y_hat, z = model(x)
l_cls = cls_loss_fn(y_hat, y)
l_top = torch.tensor(0.0).to(DEVICE)
if compute_persistence:
for i in range(batch_size):
z_sample = z[i*n: (i+1)*n, :].contiguous()
lt = pers_fn(z_sample)[0][0][:, 1]
logger.log_value('batch_lt', lt)
l_top = l_top + (lt-top_scale).abs().sum()
l_top = l_top / float(batch_size)
l = l_cls + w_top_loss * l_top
opt.zero_grad()
l.backward()
# gradient norm and normalization aa
grad_vec_abs = torch.cat(
[p.grad.data.view(-1) for p in model.parameters()], dim=0).abs()
grad_norm = grad_vec_abs.pow(2).sum().sqrt().item()
if grad_norm > 0 and normalize_gradient:
for p in model.parameters():
p.grad.data /= grad_norm
opt.step()
epoch_loss += l.item()
logger.log_value('batch_cls_loss', l_cls)
logger.log_value('batch_top_loss', l_top)
logger.log_value('batch_grad_norm', grad_norm)
logger.log_value('batch_grad_abs_max', grad_vec_abs.max())
logger.log_value('batch_grad_abs_min', grad_vec_abs.min())
logger.log_value('batch_grad_abs_mean', grad_vec_abs.mean())
logger.log_value('batch_grad_abs_std', grad_vec_abs.std())
logger.log_value('lr', scheduler.get_last_lr()[0])
logger.log_value(
'cls_norm', model.cls[0].weight.data.view(-1).norm())
scheduler.step()
mb_comment = "Last loss: {:.2f} {:.4f} ".format(
epoch_loss,
w_top_loss)
track_accuracy = True
if track_accuracy:
X, Y = apply_model(model, DS_TRAIN, device=DEVICE)
acc_train = argmax_and_accuracy(X, Y)
logger.log_value('acc_train', acc_train)
mb_comment += " | acc. train {:.2f} ".format(acc_train)
X, Y = apply_model(model, DS_TEST, device=DEVICE)
acc_test = argmax_and_accuracy(X, Y)
logger.log_value('acc_test', acc_test)
mb_comment += " | acc. test {:.2f} ".format(acc_test)
logger.log_value('epoch_i', epoch_i)
mb.main_bar.comment = mb_comment
logger.write_logged_values_to_disk()
if track_model:
logger.write_model_to_disk('model_epoch_{}'.format(epoch_i),
model)
logger.write_model_to_disk('model', model)
3,
skip=0,
is_transform=True,
crop=CROP_SIZE)
train = torch.utils.data.DataLoader(train_folder,
batch_size=BATCH_SIZE,
shuffle=True,
num_workers=12)
valid = torch.utils.data.DataLoader(valid_folder,
batch_size=BATCH_SIZE,
shuffle=True,
num_workers=12)
lr = INIT_LR
#loss = torch.nn.MSELoss(reduction='mean')
loss = torch.nn.MSELoss(reduction='mean')
mb = master_bar(range(EPOCHS))
best_loss = float('inf')
valid_loss = float('inf')
count = 0
sum_loss = 0
model = model.eval()
for X, Y in progress_bar(valid, parent=mb, txt_len=100):
X = X.cuda() #*2/255-1
#E = E.cuda()
Y = Y.cuda() #*2/255-1
with torch.set_grad_enabled(False):
out = model(X, None)
l = loss(out, Y) * X.size()[0]
count += X.size()[0]
sum_loss += l
def train_model(x_trn, x_val, config, num_classes, weights, device):
y_gr_val = x_val['grapheme_root']
y_vo_val = x_val['vowel_diacritic']
y_co_val = x_val['consonant_diacritic']
model_params = config.model_params
train_dataset = BengaliDataset(x_trn,
n_channels=model_params.n_channels,
img_size=config.img_size,
transforms=config.augmentation)
valid_dataset = BengaliDataset(x_val,
n_channels=model_params.n_channels,
img_size=config.img_size,
transforms=None)
train_loader = DataLoader(train_dataset,
batch_size=config.batch_size,
shuffle=True,
num_workers=3)
valid_loader = DataLoader(valid_dataset,
batch_size=config.batch_size,
shuffle=False,
num_workers=3)
del train_dataset, valid_dataset
gc.collect()
if 'se_resnext' in model_params.model_name:
model = SeNet(model_name=model_params.model_name,
n_channels=model_params.n_channels,
n_classes=model_params.n_classes,
pretrained=model_params.pretrained).to(device)
elif 'resnetd' in model_params.model_name:
model = ResNetD(model_name=model_params.model_name,
n_channels=model_params.n_channels,
n_classes=model_params.n_classes).to(device)
elif 'resne' in model_params.model_name:
model = ResNet(model_name=model_params.model_name,
n_channels=model_params.n_channels,
n_classes=model_params.n_classes,
pretrained=model_params.pretrained).to(device)
elif 'densenet' in model_params.model_name:
model = DenseNet(model_name=model_params.model_name,
n_channels=model_params.n_channels,
n_classes=model_params.n_classes,
pretrained=model_params.pretrained).to(device)
elif 'efficient' in model_params.model_name:
model = ENet(model_name=model_params.model_name,
n_channels=model_params.n_channels,
n_classes=model_params.n_classes,
pretrained=model_params.pretrained).to(device)
if config.model_state_fname is not None:
model.load_state_dict(
torch.load(f'../logs/{config.model_state_fname}/weight_best.pt'))
# relu_replace(model)
# bn_replace(model)
weights_gr = torch.from_numpy(weights['grapheme_root']).cuda()
weights_vo = torch.from_numpy(weights['vowel_diacritic']).cuda()
weights_co = torch.from_numpy(weights['consonant_diacritic']).cuda()
if config.loss == 'CrossEntropyLoss':
# criterion_gr = nn.CrossEntropyLoss(weight=weights_gr)
# criterion_vo = nn.CrossEntropyLoss(weight=weights_vo)
# criterion_co = nn.CrossEntropyLoss(weight=weights_co)
criterion_gr = nn.CrossEntropyLoss()
criterion_vo = nn.CrossEntropyLoss()
criterion_co = nn.CrossEntropyLoss()
elif config.loss == 'SmoothCrossEntropyLoss':
criterion_gr = SmoothCrossEntropyLoss()
criterion_vo = SmoothCrossEntropyLoss()
criterion_co = SmoothCrossEntropyLoss()
elif config.loss == 'FocalLoss':
criterion_gr = FocalLoss()
criterion_vo = FocalLoss()
criterion_co = FocalLoss()
elif config.loss == 'ClassBalancedLoss':
criterion_gr = ClassBalancedLoss(samples_per_cls=weights_gr,
no_of_classes=num_classes[0],
loss_type='focal',
beta=0.999,
gamma=2.0)
criterion_vo = ClassBalancedLoss(samples_per_cls=weights_vo,
no_of_classes=num_classes[1],
loss_type='focal',
beta=0.999,
gamma=2.0)
criterion_co = ClassBalancedLoss(samples_per_cls=weights_co,
no_of_classes=num_classes[2],
loss_type='focal',
beta=0.999,
gamma=2.0)
elif config.loss == 'OhemLoss':
criterion_gr = OhemLoss(rate=1.0)
criterion_vo = OhemLoss(rate=1.0)
criterion_co = OhemLoss(rate=1.0)
if config.optimizer.type == 'Adam':
optimizer = Adam(params=model.parameters(),
lr=config.optimizer.lr,
amsgrad=False,
weight_decay=1e-4)
elif config.optimizer.type == 'SGD':
optimizer = SGD(params=model.parameters(),
lr=config.optimizer.lr,
momentum=0.9,
weight_decay=1e-4,
nesterov=True)
scheduler_flg = False
if config.scheduler.type == 'cosine':
scheduler_flg = True
scheduler = CosineAnnealingLR(optimizer,
T_max=config.scheduler.t_max,
eta_min=config.scheduler.eta_min)
elif config.scheduler.type == 'cosine-warmup':
scheduler_flg = True
scheduler = CosineAnnealingWarmUpRestarts(
optimizer,
T_0=config.scheduler.t_0,
T_mult=config.scheduler.t_mult,
eta_max=config.scheduler.eta_max,
T_up=config.scheduler.t_up,
gamma=config.scheduler.gamma)
elif config.scheduler.type == 'step':
scheduler_flg = True
scheduler = StepLR(optimizer,
step_size=config.scheduler.step_size,
gamma=config.scheduler.gamma)
elif config.scheduler.type == 'reduce':
scheduler_flg = True
scheduler = ReduceLROnPlateau(optimizer,
factor=config.scheduler.factor,
patience=config.scheduler.patience,
min_lr=config.scheduler.min_lr)
best_epoch = -1
best_val_score = -np.inf
mb = master_bar(range(config.epochs))
train_loss_list = []
val_loss_list = []
val_score_list = []
counter = 0
for epoch in mb:
start_time = time.time()
model.train()
avg_loss = 0.
for images, labels_gr, labels_vo, labels_co in progress_bar(
train_loader, parent=mb):
images = Variable(images).to(device)
labels_gr = Variable(labels_gr).to(device)
labels_vo = Variable(labels_vo).to(device)
labels_co = Variable(labels_co).to(device)
if config.loss == 'OhemLoss':
if epoch < config.epochs * 0.2:
new_rate = 1.0
elif epoch < config.epochs * 0.4:
new_rate = 0.8
elif epoch < config.epochs * 0.6:
new_rate = 0.75
elif epoch < config.epochs * 0.8:
new_rate = 0.7
else:
new_rate = 0.6
criterion_gr.update_rate(new_rate)
criterion_vo.update_rate(new_rate)
criterion_co.update_rate(new_rate)
r = np.random.rand()
mix_params = config.augmentation.mix_params
if r < mix_params.mixup:
images, targets = mixup(images, labels_gr, labels_vo,
labels_co, 1.0)
preds_gr, preds_vo, preds_co = model(images)
loss = mixup_criterion(preds_gr, preds_vo, preds_co, targets,
criterion_gr, criterion_vo,
criterion_co)
elif r < (mix_params.mixup + mix_params.cutmix):
images, targets = cutmix(images, labels_gr, labels_vo,
labels_co, 1.0)
preds_gr, preds_vo, preds_co = model(images)
loss = cutmix_criterion(preds_gr, preds_vo, preds_co, targets,
criterion_gr, criterion_vo,
criterion_co)
else:
preds_gr, preds_vo, preds_co = model(images.float())
loss = criterion_gr(preds_gr, labels_gr) \
+ criterion_vo(preds_vo, labels_vo) \
+ criterion_co(preds_co, labels_co)
optimizer.zero_grad()
loss.backward()
optimizer.step()
avg_loss += loss.item() / len(train_loader)
train_loss_list.append(avg_loss)
model.eval()
valid_gr_preds = np.zeros((len(valid_loader.dataset), num_classes[0]))
valid_vo_preds = np.zeros((len(valid_loader.dataset), num_classes[1]))
valid_co_preds = np.zeros((len(valid_loader.dataset), num_classes[2]))
avg_val_loss = 0.
for i, (images, labels_gr, labels_vo,
labels_co) in enumerate(valid_loader):
images = Variable(images).to(device)
labels_gr = Variable(labels_gr).to(device)
labels_vo = Variable(labels_vo).to(device)
labels_co = Variable(labels_co).to(device)
preds_gr, preds_vo, preds_co = model(images.float())
loss_gr = criterion_gr(preds_gr, labels_gr)
loss_vo = criterion_vo(preds_vo, labels_vo)
loss_co = criterion_co(preds_co, labels_co)
valid_gr_preds[i * config.batch_size:(
i + 1) * config.batch_size] = preds_gr.cpu().detach().numpy()
valid_vo_preds[i * config.batch_size:(
i + 1) * config.batch_size] = preds_vo.cpu().detach().numpy()
valid_co_preds[i * config.batch_size:(
i + 1) * config.batch_size] = preds_co.cpu().detach().numpy()
avg_val_loss += (loss_gr.item() + loss_vo.item() +
loss_co.item()) / len(valid_loader)
recall_gr = recall_score(y_gr_val,
np.argmax(valid_gr_preds, axis=1),
average='macro')
recall_vo = recall_score(y_vo_val,
np.argmax(valid_vo_preds, axis=1),
average='macro')
recall_co = recall_score(y_co_val,
np.argmax(valid_co_preds, axis=1),
average='macro')
val_score = np.average([recall_gr, recall_vo, recall_co],
weights=[2, 1, 1])
val_loss_list.append(avg_val_loss)
val_score_list.append(val_score)
if scheduler_flg and config.scheduler.type != 'reduce':
scheduler.step()
elif scheduler_flg and config.scheduler.type == 'reduce':
scheduler.step(avg_val_loss)
elapsed = time.time() - start_time
mb.write(
f'Epoch {epoch+1} - avg_train_loss: {avg_loss:.4f} avg_val_loss: {avg_val_loss:.4f} val_score: {val_score:.4f} val_gr_score: {recall_gr:.4f} val_vo_score: {recall_vo:.4f} val_co_score: {recall_co:.4f} time: {elapsed:.0f}s'
)
logging.debug(
f'Epoch {epoch+1} - avg_train_loss: {avg_loss:.4f} avg_val_loss: {avg_val_loss:.4f} val_score: {val_score:.4f} val_gr_score: {recall_gr:.4f} val_vo_score: {recall_vo:.4f} val_co_score: {recall_co:.4f} time: {elapsed:.0f}s'
)
if best_val_score < val_score:
best_epoch = epoch + 1
best_val_score = val_score
best_recall_gr = recall_gr
best_recall_vo = recall_vo
best_recall_co = recall_co
best_valid_gr_preds = valid_gr_preds
best_valid_vo_preds = valid_vo_preds
best_valid_co_preds = valid_co_preds
best_model = model.state_dict()
counter = 0
counter += 1
if counter == config.early_stopping:
break
print('\n\n===================================\n')
print(f'CV: {best_val_score}\n')
print(f'BEST EPOCH: {best_epoch}')
print(f'BEST RECALL GR: {best_recall_gr}')
print(f'BEST RECALL VO: {best_recall_vo}')
print(f'BEST RECALL CO: {best_recall_co}')
logging.debug(f'\n\nCV: {best_val_score}\n')
logging.debug(f'BEST EPOCH: {best_epoch}')
logging.debug(f'BEST RECALL GR: {best_recall_gr}')
logging.debug(f'BEST RECALL VO: {best_recall_vo}')
logging.debug(f'BEST RECALL CO: {best_recall_co}\n\n')
print('\n===================================\n\n')
return best_model, [
best_valid_gr_preds, best_valid_vo_preds, best_valid_co_preds
], best_val_score, train_loss_list, val_loss_list, val_score_list
def train_model(x_train, y_train, train_transforms):
num_epochs = 80
batch_size = 64
test_batch_size = 256
lr = 3e-3
eta_min = 1e-5
t_max = 10
num_classes = y_train.shape[1]
x_trn, x_val, y_trn, y_val = train_test_split(x_train,
y_train,
test_size=0.2,
random_state=SEED)
train_dataset = FATTrainDataset(x_trn, y_trn, train_transforms)
valid_dataset = FATTrainDataset(x_val, y_val, train_transforms)
train_loader = DataLoader(train_dataset,
batch_size=batch_size,
shuffle=True)
valid_loader = DataLoader(valid_dataset,
batch_size=test_batch_size,
shuffle=False)
model = Classifier(num_classes=num_classes).cuda()
criterion = nn.BCEWithLogitsLoss().cuda()
optimizer = Adam(params=model.parameters(), lr=lr, amsgrad=False)
scheduler = CosineAnnealingLR(optimizer, T_max=t_max, eta_min=eta_min)
best_epoch = -1
best_lwlrap = 0.
mb = master_bar(range(num_epochs))
for epoch in mb:
start_time = time.time()
model.train()
avg_loss = 0.
for x_batch, y_batch in progress_bar(train_loader, parent=mb):
preds = model(x_batch.cuda())
loss = criterion(preds, y_batch.cuda())
optimizer.zero_grad()
loss.backward()
optimizer.step()
avg_loss += loss.item() / len(train_loader)
model.eval()
valid_preds = np.zeros((len(x_val), num_classes))
avg_val_loss = 0.
for i, (x_batch, y_batch) in enumerate(valid_loader):
preds = model(x_batch.cuda()).detach()
loss = criterion(preds, y_batch.cuda())
preds = torch.sigmoid(preds)
valid_preds[i * test_batch_size:(i + 1) *
test_batch_size] = preds.cpu().numpy()
avg_val_loss += loss.item() / len(valid_loader)
score, weight = calculate_per_class_lwlrap(y_val, valid_preds)
lwlrap = (score * weight).sum()
scheduler.step()
if (epoch + 1) % 5 == 0:
elapsed = time.time() - start_time
mb.write(
f'Epoch {epoch+1} - avg_train_loss: {avg_loss:.4f} avg_val_loss: {avg_val_loss:.4f} val_lwlrap: {lwlrap:.6f} time: {elapsed:.0f}s'
)
if lwlrap > best_lwlrap:
best_epoch = epoch + 1
best_lwlrap = lwlrap
torch.save(model.state_dict(), 'weight_best.pt')
return {
'best_epoch': best_epoch,
'best_lwlrap': best_lwlrap,
}
args,
abs_,
optimize_both_exp=False,
batchnorm=True,
prior_var=80,
device=device)
model = model.to(device)
model.apply(EXPVAEWAVE.weight_init)
optimizer = optim.Adam(list(model.parameters()) + [model.exps],
lr=args.learning_rate,
weight_decay=0,
betas=(args.beta_one, args.beta_two))
train_losses = []
n_epochs = args.epochs
mb = master_bar(range(20))
y_ax_index = 0
for i in mb:
epoch = i
for j in progress_bar(range(int(n_epochs / 20)), parent=mb):
model = EXPVAEWAVE.train(model, device, args, optimizer, train_loader,
epoch, train_losses)
# x = range(len(train_losses))
# y = train_losses
# graphs = [[x,y]]
# y_bounds = [0,train_losses[0]]
# mb.update_graph(graphs, y_bounds=y_bounds)
mb.write(f'Avg. Training Loss: {train_losses[-1]}.')
# To get the location estimates for each spike in the recording, we run them through the inference network and then average the location estimates belonging to the same event (this is described in the manuscript in the amplitude jitter portion of the paper).
def main():
n_epoch = 10
now = datetime.datetime.now()
now_date = '{}-{:0>2d}-{:0>2d}_{:0>2d}-{:0>2d}-{:0>2d}'.format(
now.year, now.month, now.day, now.hour, now.minute, now.second)
# set logger
logger = logging.getLogger("Log")
logger.setLevel(logging.DEBUG)
handler_format = logging.Formatter(
'%(asctime)s - %(levelname)s - %(message)s')
print('{}-{}-{} {}:{}:{}'.format(now.year, now.month, now.day, now.hour,
now.minute, now.second))
with open('../params/stacking.yaml', "r+") as f:
param = yaml.load(f, Loader=yaml.FullLoader)
seed_setting(param['seed'])
if torch.cuda.is_available():
torch.backends.cudnn.benchmark = True
local_cv = dict()
for fold in range(5):
outdir = os.path.join(param['save path'], EXP_NAME, now_date,
'fold{}'.format(fold))
if os.path.exists(param['save path']):
os.makedirs(outdir, exist_ok=True)
else:
print("Not find {}".format(param['save path']))
raise FileNotFoundError
file_handler = logging.FileHandler(
os.path.join(outdir, 'experiment.log'))
file_handler.setLevel(logging.DEBUG)
file_handler.setFormatter(handler_format)
logger.addHandler(file_handler)
logger.debug('============= FOLD {} ============='.format(fold))
logger.debug('{}-{}-{} {}:{}:{}'.format(now.year, now.month, now.day,
now.hour, now.minute,
now.second))
print(f'fold - {fold}')
print('load data set')
train_dataset = StackingDataset(
df=get_train_df(param['tabledir']).query('valid != @fold'),
logit_path='/mnt/hdd1/alcon2019/logits_for_oof.pth',
mode='train')
valid_dataset = StackingDataset(
df=get_train_df(param['tabledir']).query('valid == @fold'),
logit_path='/mnt/hdd1/alcon2019/logits_for_oof.pth',
mode='valid')
print('load data loader')
train_dataloader = DataLoader(train_dataset,
batch_size=param['batch size'],
num_workers=param['thread'],
pin_memory=False,
drop_last=False,
shuffle=True)
valid_dataloader = DataLoader(valid_dataset,
batch_size=param['batch size'],
num_workers=param['thread'],
pin_memory=False,
drop_last=False,
shuffle=False)
print('model set')
model = MLP()
optimizer = torch.optim.Adam(model.parameters(), lr=1e-4)
model = model.to(param['device'])
loss_fn = nn.CrossEntropyLoss().to(param['device'])
eval_fn = accuracy_one_character
max_char_acc = -1e-5
max_3char_acc = -1e-5
min_loss = 1e+5
mb = master_bar(range(n_epoch))
for epoch in mb:
model.train()
avg_train_loss = 10**5
avg_train_accuracy = 0.0
avg_three_train_acc = 0.0
for step, (inputs, targets, indice) in enumerate(
progress_bar(train_dataloader, parent=mb)):
model.train()
inputs = inputs.to(param['device'])
targets = targets.to(param['device'])
optimizer.zero_grad()
logits = model(inputs) # logits.size() = (batch*3, 48)
preds = logits.view(targets.size(0), 3, -1).softmax(dim=2)
loss = loss_fn(logits,
targets.view(-1, targets.size(2)).argmax(dim=1))
loss.backward()
avg_train_loss += loss.item()
_avg_accuracy = eval_fn(preds, targets.argmax(dim=2)).item()
avg_train_accuracy += _avg_accuracy
_three_char_accuracy = accuracy_three_character(
preds, targets.argmax(dim=2), mean=True).item()
avg_three_train_acc += _three_char_accuracy
avg_train_loss /= len(train_dataloader)
avg_train_accuracy /= len(train_dataloader)
avg_three_train_acc /= len(train_dataloader)
avg_valid_loss, avg_valid_accuracy, avg_three_valid_acc = valid_alcon_rnn(
model, valid_dataloader, param['device'], loss_fn, eval_fn)
if min_loss > avg_valid_loss:
logger.debug('update best loss: {:.5f} ---> {:.5f}'.format(
min_loss, avg_valid_loss))
min_loss = avg_valid_loss
torch.save(model.state_dict(),
os.path.join(outdir, 'best_loss.pth'))
if max_char_acc < avg_valid_accuracy:
logger.debug(
'update best acc per 1 char: {:.3%} ---> {:.3%}'.format(
max_char_acc, avg_valid_accuracy))
max_char_acc = avg_valid_accuracy
torch.save(model.state_dict(),
os.path.join(outdir, 'best_acc.pth'))
if max_3char_acc < avg_three_valid_acc:
logger.debug(
'update best acc per 3 char: {:.3%} ---> {:.3%}'.format(
max_3char_acc, avg_three_valid_acc))
max_3char_acc = avg_three_valid_acc
torch.save(model.state_dict(),
os.path.join(outdir, 'best_3acc.pth'))
logger.debug(
'======================== epoch {} ========================'.
format(epoch + 1))
logger.debug('lr : {:.5f}'.format(
scheduler.get_lr()[0]))
logger.debug(
'loss : train={:.5f} , test={:.5f}'.format(
avg_train_loss, avg_valid_loss))
logger.debug(
'acc(per 1 char) : train={:.3%} , test={:.3%}'.format(
avg_train_accuracy, avg_valid_accuracy))
logger.debug(
'acc(per 3 char) : train={:.3%} , test={:.3%}'.format(
avg_three_train_acc, avg_three_valid_acc))
logger.debug('================ FINISH TRAIN ================')
logger.debug('Result')
logger.debug('Best loss : {}'.format(min_loss))
logger.debug('Best 1 acc : {}'.format(max_char_acc))
logger.debug('Best 3 acc : {}'.format(max_3char_acc))
