def convert_examples_to_features(
examples: List[InputExample],
tokenizer: PreTrainedTokenizer,
slot_label_encoder: LabelEncoder,
intent_label_encoder: LabelEncoder,
max_length: Optional[int] = None
):
if max_length is None:
max_length = tokenizer.max_len
# slot / intent label id generate.
truncation_size = max_length // 2
features = []
for example in examples:
tmp_label_slot_origin = slot_label_encoder.batch_encode(example.label_slot_raw).numpy().tolist()
if example.label_intent_raw:
tmp_label_intent_origin = intent_label_encoder.batch_encode(example.label_intent_raw).numpy().tolist()
else:
tmp_label_intent_origin = []
# 手动对query/context进行截断，截断长度分别为`max_length // 2`
tmp_text_query = example.text_query[:truncation_size] # query向后截断
tmp_label_slot_origin = tmp_label_slot_origin[:truncation_size]
tmp_text_context = example.text_context[-truncation_size:] # context向前截断
# TODO: 可选query/context顺序交换
tokenizer_outputs = tokenizer.encode_plus(list(tmp_text_query), list(tmp_text_context), padding='max_length',
max_length=max_length)
# 处理slot_mask
tmp_slot_mask = np.asarray([0] * max_length)
tmp_slot_mask[1:len(tmp_text_query) + 1] = 1
# tmp_slot_mask[len(tmp_text_context)+2: len(tmp_text_context)+len(tmp_text_query)+2] = 1
tmp_slot_mask = list(tmp_slot_mask)
# 处理tmp_label_slot
tmp_label_slot = [0] * max_length
tmp_label_slot[1:len(tmp_text_query) + 1] = tmp_label_slot_origin
# 处理tmp_label_intent
tmp_label_intent = np.asarray([0] * intent_label_encoder.vocab_size)
tmp_label_intent[tmp_label_intent_origin] = 1
tmp_label_intent = list(tmp_label_intent)
feature = InputFeatures(**tokenizer_outputs, slot_mask=tmp_slot_mask, label_slot=tmp_label_slot,
label_intent=tmp_label_intent)
features.append(feature)
for i, example in enumerate(examples[:5]):
logger.info("*** Example ***")
logger.info("guid: %s" % example.guid)
logger.info("features: %s" % features[i])
return features
def prepare_sample(
sample: dict, text_encoder: WhitespaceEncoder, label_encoder: LabelEncoder,
max_length: int
) -> (torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor):
"""
Function that receives a sample from the Dataset iterator and prepares t
he input to feed the transformer model.
:param sample: dictionary containing the inputs to build the batch
(e.g: [{'source': 'This flight was amazing!', 'target': 'pos'},
{'source': 'I hate Iberia', 'target': 'neg'}])
:param text_encoder: Torch NLP text encoder for tokenization and vectorization.
:param label_encoder: Torch NLP label encoder for vectorization of labels.
:param max_length: Max length of the input sequences.
If a sequence passes that value it is truncated.
"""
sample = collate_tensors(sample)
input_seqs, input_lengths = text_encoder.batch_encode(sample['source'])
target_seqs = label_encoder.batch_encode(sample['target'])
# Truncate Inputs
if input_seqs.size(1) > max_length:
input_seqs = input_seqs[:, :max_length]
input_mask = lengths_to_mask(input_lengths).unsqueeze(1)
return input_seqs, input_mask, target_seqs
class Tagger(CaptionModelBase):
"""
Tagger base class.
:param hparams: HyperOptArgumentParser containing the hyperparameters.
"""
def __init__(
self,
hparams: HyperOptArgumentParser,
) -> None:
super().__init__(hparams)
def _build_model(self):
self.label_encoder = LabelEncoder(self.hparams.tag_set.split(","),
reserved_labels=[])
def _build_loss(self):
""" Initializes the loss function/s. """
weights = (np.array([
float(x) for x in self.hparams.class_weights.split(",")
]) if self.hparams.class_weights != "ignore" else np.array([]))
if self.hparams.loss == "cross_entropy":
self.loss = nn.CrossEntropyLoss(
reduction="sum",
ignore_index=self.label_encoder.vocab_size,
weight=torch.tensor(weights, dtype=torch.float32)
if weights.any() else None,
)
else:
raise Exception(f"{self.hparams.loss} is not a valid loss option.")
def _retrieve_dataset(self, data_hparams, train=True, val=True, test=True):
""" Retrieves task specific dataset """
return sequence_tagging_dataset(data_hparams, train, val, test)
@property
def default_slot_index(self):
""" Index of the default slot to be ignored. (e.g. 'O' in 'B-I-O' tags) """
return 0
def predict(self, sample: dict) -> list:
""" Function that runs a model prediction,
:param sample: a dictionary that must contain the the 'source' sequence.
Return: list with predictions
"""
if self.training:
self.eval()
return_dict = False
if isinstance(sample, dict):
sample = [sample]
return_dict = True
with torch.no_grad():
model_input, _ = self.prepare_sample(sample, prepare_target=False)
model_out = self.forward(**model_input)
tag_logits = model_out["tags"]
_, pred_labels = tag_logits.topk(1, dim=-1)
for i in range(pred_labels.size(0)):
sample_tags = pred_labels[i, :, :].view(-1)
tags = [
self.label_encoder.index_to_token[sample_tags[j]]
for j in range(model_input["word_lengths"][i])
]
sample[i]["predicted_tags"] = " ".join(tags)
sample[i]["tagged_sequence"] = " ".join([
word + "/" + tag
for word, tag in zip(sample[i]["text"].split(), tags)
])
sample[i][
"encoded_ground_truth_tags"] = self.label_encoder.batch_encode(
[tag for tag in sample[i]["tags"].split()])
if self.hparams.ignore_last_tag:
if (sample[i]["encoded_ground_truth_tags"][
model_input["word_lengths"][i] - 1] == 1):
sample[i]["encoded_ground_truth_tags"][
model_input["word_lengths"][i] -
1] = self.label_encoder.vocab_size
if return_dict:
return sample[0]
return sample
def _compute_loss(self, model_out: dict, targets: dict) -> torch.tensor:
"""
Computes Loss value according to a loss function.
:param model_out: model specific output with predicted tag logits
a tensor [batch_size x seq_length x num_tags]
:param targets: Target tags [batch_size x seq_length]
"""
logits = model_out["tags"].view(-1, model_out["tags"].size(-1))
labels = targets["tags"].view(-1)
return self.loss(logits, labels)
def prepare_sample(self,
sample: list,
prepare_target: bool = True) -> (dict, dict):
"""
Function that prepares a sample to input the model.
:param sample: list of dictionaries.
Returns:
- dictionary with the expected model inputs.
- dictionary with the expected target values.
"""
sample = collate_tensors(sample)
inputs = self.encoder.prepare_sample(sample["text"], trackpos=True)
if not prepare_target:
return inputs, {}
tags, _ = stack_and_pad_tensors(
[
self.label_encoder.batch_encode(tags.split())
for tags in sample["tags"]
],
padding_index=self.label_encoder.vocab_size,
)
if self.hparams.ignore_first_title:
first_tokens = tags[:, 0].clone()
tags[:, 0] = first_tokens.masked_fill_(
first_tokens == self._label_encoder.token_to_index["T"],
self.label_encoder.vocab_size,
)
# TODO is this still needed ?
if self.hparams.ignore_last_tag:
lengths = [len(tags.split()) for tags in sample["tags"]]
lengths = np.asarray(lengths)
k = 0
for length in lengths:
if tags[k][length - 1] == 1:
tags[k][length - 1] = self.label_encoder.vocab_size
k += 1
targets = {"tags": tags}
return inputs, targets
def _compute_metrics(self, outputs: list) -> dict:
"""
Private function that computes metrics of interest based on model predictions
and respective targets.
"""
predictions = [
batch_out["val_prediction"]["tags"] for batch_out in outputs
]
targets = [batch_out["val_target"]["tags"] for batch_out in outputs]
predicted_tags, ground_truth = [], []
for i in range(len(predictions)):
# Get logits and reshape predictions
batch_predictions = predictions[i]
logits = batch_predictions.view(-1,
batch_predictions.size(-1)).cpu()
_, pred_labels = logits.topk(1, dim=-1)
# Reshape targets
batch_targets = targets[i].view(-1).cpu()
assert batch_targets.size() == pred_labels.view(-1).size()
ground_truth.append(batch_targets)
predicted_tags.append(pred_labels.view(-1))
return classification_report(
torch.cat(predicted_tags).numpy(),
torch.cat(ground_truth).numpy(),
padding=self.label_encoder.vocab_size,
labels=self.label_encoder.token_to_index,
ignore=self.default_slot_index,
)
@classmethod
def add_model_specific_args(
cls, parser: HyperOptArgumentParser) -> HyperOptArgumentParser:
""" Parser for Estimator specific arguments/hyperparameters.
:param parser: HyperOptArgumentParser obj
Returns:
- updated parser
"""
parser = super(Tagger, Tagger).add_model_specific_args(parser)
parser.add_argument(
"--tag_set",
type=str,
default="L,U,T",
help="Task tags we want to use.\
Note that the 'default' label should appear first",
)
# Loss
parser.add_argument(
"--loss",
default="cross_entropy",
type=str,
help="Loss function to be used.",
choices=["cross_entropy"],
)
parser.add_argument(
"--class_weights",
default="ignore",
type=str,
help=
'Weights for each of the classes we want to tag (e.g: "1.0,7.0,8.0").',
)
## Data args:
parser.add_argument(
"--data_type",
default="csv",
type=str,
help="The type of the file containing the training/dev/test data.",
choices=["csv"],
)
parser.add_argument(
"--train_path",
default="data/dummy_train.csv",
type=str,
help="Path to the file containing the train data.",
)
parser.add_argument(
"--dev_path",
default="data/dummy_test.csv",
type=str,
help="Path to the file containing the dev data.",
)
parser.add_argument(
"--test_path",
default="data/dummy_test.csv",
type=str,
help="Path to the file containing the test data.",
)
parser.add_argument(
"--loader_workers",
default=0,
type=int,
help=("How many subprocesses to use for data loading. 0 means that"
"the data will be loaded in the main process."),
)
# Metric args:
parser.add_argument(
"--ignore_first_title",
default=False,
help="When used, this flag ignores T tags in the first position.",
action="store_true",
)
parser.add_argument(
"--ignore_last_tag",
default=False,
help="When used, this flag ignores S tags in the last position.",
action="store_true",
)
return parser
with open(fn, 'rb') as f:
model, criterion, optimizer = torch.load(f)
from torchnlp import datasets
from torchnlp.encoders import LabelEncoder
from torchnlp.samplers import BPTTBatchSampler
print('Producing dataset...')
train, val, test = getattr(datasets, args.data)(train=True,
dev=True,
test=True)
encoder = LabelEncoder(train + val + test)
train_data = encoder.batch_encode(train)
val_data = encoder.batch_encode(val)
test_data = encoder.batch_encode(test)
eval_batch_size = 10
test_batch_size = 1
train_source_sampler, val_source_sampler, test_source_sampler = tuple([
BPTTBatchSampler(d, args.bptt, args.batch_size, True, 'source')
for d in (train, val, test)
])
train_target_sampler, val_target_sampler, test_target_sampler = tuple([
BPTTBatchSampler(d, args.bptt, args.batch_size, True, 'target')
for d in (train, val, test)
])
class BERTClassifier(pl.LightningModule):
"""
Sample model to show how to use BERT to classify sentences.
:param hparams: ArgumentParser containing the hyperparameters.
"""
def __init__(self, hparams) -> None:
super(BERTClassifier, self).__init__()
self.hparams = hparams
self.batch_size = hparams.batch_size
# build model
self.__build_model()
# Loss criterion initialization.
self.__build_loss()
if hparams.nr_frozen_epochs > 0:
self.freeze_encoder()
else:
self._frozen = False
self.nr_frozen_epochs = hparams.nr_frozen_epochs
def __build_model(self) -> None:
""" Init BERT model + tokenizer + classification head."""
self.bert = AutoModel.from_pretrained(self.hparams.encoder_model,
output_hidden_states=True,
num_labels=11)
# set the number of features our encoder model will return...
if self.hparams.encoder_model == "google/bert_uncased_L-2_H-128_A-2":
self.encoder_features = 128
else:
self.encoder_features = 768
# Tokenizer
self.tokenizer = BERTTextEncoder("bert-base-uncased")
# Label Encoder
self.label_encoder = LabelEncoder(self.hparams.label_set.split(","),
reserved_labels=[])
self.label_encoder.unknown_index = None
# Classification head
self.classification_head = nn.Sequential(
nn.Linear(self.encoder_features, self.encoder_features * 2),
nn.Tanh(),
nn.Linear(self.encoder_features * 2, self.encoder_features),
nn.Tanh(),
nn.Linear(self.encoder_features, self.label_encoder.vocab_size),
)
def __build_loss(self):
""" Initializes the loss function/s. """
self._loss = nn.CrossEntropyLoss()
def unfreeze_encoder(self) -> None:
""" un-freezes the encoder layer. """
if self._frozen:
log.info(f"\n-- Encoder model fine-tuning")
for param in self.bert.parameters():
param.requires_grad = True
self._frozen = False
def freeze_encoder(self) -> None:
""" freezes the encoder layer. """
for param in self.bert.parameters():
param.requires_grad = False
self._frozen = True
def predict(self, sample: dict) -> dict:
""" Predict function.
:param sample: dictionary with the text we want to classify.
Returns:
Dictionary with the input text and the predicted label.
"""
if self.training:
self.eval()
with torch.no_grad():
model_input, _ = self.prepare_sample([sample],
prepare_target=False)
model_out = self.forward(**model_input)
logits = model_out["logits"].numpy()
predicted_labels = [
self.label_encoder.index_to_token[prediction]
for prediction in np.argmax(logits, axis=1)
]
sample["predicted_label"] = predicted_labels[0]
return sample
def forward(self, tokens, lengths):
""" Usual pytorch forward function.
:param tokens: text sequences [batch_size x src_seq_len]
:param lengths: source lengths [batch_size]
Returns:
Dictionary with model outputs (e.g: logits)
"""
tokens = tokens[:, :lengths.max()]
# When using just one GPU this should not change behavior
# but when splitting batches across GPU the tokens have padding
# from the entire original batch
mask = lengths_to_mask(lengths, device=tokens.device)
# Run BERT model.
word_embeddings = self.bert(tokens, mask)[0]
# Average Pooling
word_embeddings = mask_fill(0.0, tokens, word_embeddings,
self.tokenizer.padding_index)
sentemb = torch.sum(word_embeddings, 1)
sum_mask = mask.unsqueeze(-1).expand(
word_embeddings.size()).float().sum(1)
sentemb = sentemb / sum_mask
return {"logits": self.classification_head(sentemb)}
def loss(self, predictions: dict, targets: dict) -> torch.tensor:
"""
Computes Loss value according to a loss function.
:param predictions: model specific output. Must contain a key 'logits' with
a tensor [batch_size x 1] with model predictions
:param labels: Label values [batch_size]
Returns:
torch.tensor with loss value.
"""
return self._loss(predictions["logits"], targets["labels"])
def prepare_sample(self,
sample: list,
prepare_target: bool = True) -> (dict, dict):
"""
Function that prepares a sample to input the model.
:param sample: list of dictionaries.
Returns:
- dictionary with the expected model inputs.
- dictionary with the expected target labels.
"""
sample = collate_tensors(sample)
tokens, lengths = self.tokenizer.batch_encode(sample["text"])
inputs = {"tokens": tokens, "lengths": lengths}
if not prepare_target:
return inputs, {}
# Prepare target:
try:
targets = {
"labels": self.label_encoder.batch_encode(sample["label"])
}
return inputs, targets
except RuntimeError:
raise Exception("Label encoder found an unknown label.")
def training_step(self, batch: tuple, batch_nb: int, *args,
**kwargs) -> dict:
"""
Runs one training step. This usually consists in the forward function followed
by the loss function.
:param batch: The output of your dataloader.
:param batch_nb: Integer displaying which batch this is
Returns:
- dictionary containing the loss and the metrics to be added to the lightning logger.
"""
inputs, targets = batch
model_out = self.forward(**inputs)
loss_val = self.loss(model_out, targets)
# in DP mode (default) make sure if result is scalar, there's another dim in the beginning
if self.trainer.use_dp or self.trainer.use_ddp2:
loss_val = loss_val.unsqueeze(0)
tqdm_dict = {"train_loss": loss_val}
output = OrderedDict({
"loss": loss_val,
"progress_bar": tqdm_dict,
"log": tqdm_dict
})
# can also return just a scalar instead of a dict (return loss_val)
return output
def validation_step(self, batch: tuple, batch_nb: int, *args,
**kwargs) -> dict:
""" Similar to the training step but with the model in eval mode.
Returns:
- dictionary passed to the validation_end function.
"""
inputs, targets = batch
model_out = self.forward(**inputs)
loss_val = self.loss(model_out, targets)
y = targets["labels"]
y_hat = model_out["logits"]
# acc
labels_hat = torch.argmax(y_hat, dim=1)
val_acc = torch.sum(y == labels_hat).item() / (len(y) * 1.0)
val_acc = torch.tensor(val_acc)
if self.on_gpu:
val_acc = val_acc.cuda(loss_val.device.index)
# in DP mode (default) make sure if result is scalar, there's another dim in the beginning
if self.trainer.use_dp or self.trainer.use_ddp2:
loss_val = loss_val.unsqueeze(0)
val_acc = val_acc.unsqueeze(0)
output = OrderedDict({
"val_loss": loss_val,
"val_acc": val_acc,
})
# can also return just a scalar instead of a dict (return loss_val)
return output
def validation_end(self, outputs: list) -> dict:
""" Function that takes as input a list of dictionaries returned by the validation_step
function and measures the model performance accross the entire validation set.
Returns:
- Dictionary with metrics to be added to the lightning logger.
"""
val_loss_mean = 0
val_acc_mean = 0
for output in outputs:
val_loss = output["val_loss"]
# reduce manually when using dp
if self.trainer.use_dp or self.trainer.use_ddp2:
val_loss = torch.mean(val_loss)
val_loss_mean += val_loss
# reduce manually when using dp
val_acc = output["val_acc"]
if self.trainer.use_dp or self.trainer.use_ddp2:
val_acc = torch.mean(val_acc)
val_acc_mean += val_acc
val_loss_mean /= len(outputs)
val_acc_mean /= len(outputs)
tqdm_dict = {"val_loss": val_loss_mean, "val_acc": val_acc_mean}
result = {
"progress_bar": tqdm_dict,
"log": tqdm_dict,
"val_loss": val_loss_mean,
}
return result
def configure_optimizers(self):
""" Sets different Learning rates for different parameter groups. """
parameters = [
{
"params": self.classification_head.parameters()
},
{
"params": self.bert.parameters(),
"lr": self.hparams.encoder_learning_rate,
},
]
optimizer = optim.Adam(parameters, lr=self.hparams.learning_rate)
return [optimizer], []
def on_epoch_end(self):
""" Pytorch lightning hook """
if self.current_epoch + 1 >= self.nr_frozen_epochs:
self.unfreeze_encoder()
def __retrieve_dataset(self, train=True, val=True, test=True):
""" Retrieves task specific dataset """
return sentiment_analysis_dataset(self.hparams, train, val, test)
@pl.data_loader
def train_dataloader(self) -> DataLoader:
""" Function that loads the train set. """
self._train_dataset = self.__retrieve_dataset(val=False, test=False)[0]
return DataLoader(
dataset=self._train_dataset,
sampler=RandomSampler(self._train_dataset),
batch_size=self.hparams.batch_size,
collate_fn=self.prepare_sample,
num_workers=self.hparams.loader_workers,
)
@pl.data_loader
def val_dataloader(self) -> DataLoader:
""" Function that loads the validation set. """
self._dev_dataset = self.__retrieve_dataset(train=False, test=False)[0]
return DataLoader(
dataset=self._dev_dataset,
batch_size=self.hparams.batch_size,
collate_fn=self.prepare_sample,
num_workers=self.hparams.loader_workers,
)
@pl.data_loader
def test_dataloader(self) -> DataLoader:
""" Function that loads the validation set. """
self._test_dataset = self.__retrieve_dataset(train=False, val=False)[0]
return DataLoader(
dataset=self._test_dataset,
batch_size=self.hparams.batch_size,
collate_fn=self.prepare_sample,
num_workers=self.hparams.loader_workers,
)
@classmethod
def add_model_specific_args(
cls, parser: HyperOptArgumentParser) -> HyperOptArgumentParser:
""" Parser for Estimator specific arguments/hyperparameters.
:param parser: HyperOptArgumentParser obj
Returns:
- updated parser
"""
parser.add_argument(
"--encoder_model",
default="bert-base-uncased",
type=str,
help="Encoder model to be used.",
)
parser.add_argument(
"--encoder_learning_rate",
default=1e-05,
type=float,
help="Encoder specific learning rate.",
)
parser.add_argument(
"--learning_rate",
default=3e-05,
type=float,
help="Classification head learning rate.",
)
parser.opt_list(
"--nr_frozen_epochs",
default=1,
type=int,
help="Number of epochs we want to keep the encoder model frozen.",
tunable=True,
options=[0, 1, 2, 3, 4, 5],
)
# Data Args:
parser.add_argument(
"--label_set",
default="pos,neg",
type=str,
help="Classification labels set.",
)
parser.add_argument(
"--train_csv",
default="data/imdb_reviews_train.csv",
type=str,
help="Path to the file containing the train data.",
)
parser.add_argument(
"--dev_csv",
default="data/imdb_reviews_test.csv",
type=str,
help="Path to the file containing the dev data.",
)
parser.add_argument(
"--test_csv",
default="data/imdb_reviews_test.csv",
type=str,
help="Path to the file containing the dev data.",
)
parser.add_argument(
"--loader_workers",
default=8,
type=int,
help="How many subprocesses to use for data loading. 0 means that \
the data will be loaded in the main process.",
)
return parser
class UniProtData():
def __init__(self, tokenizer, sequence_length):
self.tokenizer = tokenizer
self.sequence_length = sequence_length
def from_file(self, fasta_file, reduce_to_binary=False):
sequence_labels, sequence_strs = [], []
cur_seq_label = None
buf = []
def _flush_current_seq(reduce_to_binary):
nonlocal cur_seq_label, buf
if cur_seq_label is None:
return
if reduce_to_binary:
if cur_seq_label == "0":
sequence_labels.append(cur_seq_label)
else:
sequence_labels.append("1")
else:
sequence_labels.append(cur_seq_label)
sequence_strs.append("".join(buf))
cur_seq_label = None
buf = []
with open(fasta_file, "r") as infile:
for line_idx, line in enumerate(infile):
if line.startswith(">"): # label line
_flush_current_seq(reduce_to_binary)
line = line[1:].strip()
if len(line) > 0:
cur_seq_label = line.split("|")[-1]
else:
cur_seq_label = f"seqnum{line_idx:09d}"
else: # sequence line
buf.append(" ".join(line.strip()))
_flush_current_seq(reduce_to_binary)
# More usefull is to check if we have equal number of sequences and labels
assert len(sequence_strs) == len(sequence_labels)
# Create label encoder from unique strings in the label list
self.label_encoder = LabelEncoder(np.unique(sequence_labels),
reserved_labels=[])
self.data = []
for i in range(len(sequence_strs)):
self.data.append({
"seq": str(sequence_strs[i]),
"label": str(sequence_labels[i])
})
return self.data
def prepare_sample(self,
sample: list,
prepare_target: bool = True) -> (dict, dict):
"""
Function that prepares a sample to input the model.
:param sample: list of dictionaries.
Returns:
- dictionary with the expected model inputs.
- dictionary with the expected target labels.
"""
sample = collate_tensors(sample)
# Tokenize the input, return dict with 3 entries:
# input_ids: tokenized matrix
# token_input_id: matrix of 0,1 indicating if the element belongs to seq0 or eq1
# attention_mask: matrix of 0,1 indicating if a token ist masked (0) or not (1)
# Convert to PT tensor
inputs = self.tokenizer.batch_encode_plus(
sample["seq"],
add_special_tokens=True,
padding=True,
truncation=True,
max_length=self.sequence_length,
return_tensors="pt")
if prepare_target is False:
return inputs, {}
# Prepare target:
try:
targets = {
"labels": self.label_encoder.batch_encode(sample["label"])
}
return inputs, targets
except RuntimeError:
print(sample["label"])
raise Exception("Label encoder found an unknown label.")
def get_dataloader(self, file_path, batch_size, num_worker=4):
data = self.from_file(file_path)
data_loader = DataLoader(data,
batch_size=batch_size,
sampler=RandomSampler(data),
collate_fn=self.prepare_sample,
num_workers=num_worker)
return data_loader
