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Add new token classification example (#8340) 

* Add new token classification example

* Remove txt file

* Add test

* With actual testing done

* Less warmup is better

* Update examples/token-classification/run_ner_new.py

Co-authored-by: Thomas Wolf <thomwolf@users.noreply.github.com>

* Address review comments

* Fix test

* Make Lysandre happy

* Last touches and rename

* Rename in tests

* Address review comments

* More run_ner -> run_ner_old

Co-authored-by: Thomas Wolf <thomwolf@users.noreply.github.com>
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Sylvain Gugger 2020-11-09 11:39:55 -05:00 committed by GitHub
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2
examples/README.md
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@ -37,7 +37,7 @@ git checkout tags/v3.4.0
|---|---|:---:|:---:|:---:|:---:|
| [**`language-modeling`**](https://github.com/huggingface/transformers/tree/master/examples/language-modeling) | Raw text | ✅ | - | ✅ | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/blog/blob/master/notebooks/01_how_to_train.ipynb)
| [**`text-classification`**](https://github.com/huggingface/transformers/tree/master/examples/text-classification) | GLUE, XNLI | ✅ | ✅ | ✅ | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://github.com/huggingface/notebooks/blob/master/examples/text_classification.ipynb)
| [**`token-classification`**](https://github.com/huggingface/transformers/tree/master/examples/token-classification) | CoNLL NER | ✅ | ✅ | - | -
| [**`token-classification`**](https://github.com/huggingface/transformers/tree/master/examples/token-classification) | CoNLL NER | ✅ | ✅ | ✅ | -
| [**`multiple-choice`**](https://github.com/huggingface/transformers/tree/master/examples/multiple-choice) | SWAG, RACE, ARC | ✅ | ✅ | - | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ViktorAlm/notebooks/blob/master/MPC_GPU_Demo_for_TF_and_PT.ipynb)
| [**`question-answering`**](https://github.com/huggingface/transformers/tree/master/examples/question-answering) | SQuAD | ✅ | ✅ | - | -
| [**`text-generation`**](https://github.com/huggingface/transformers/tree/master/examples/text-generation) | - | n/a | n/a | - | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/blog/blob/master/notebooks/02_how_to_generate.ipynb)

39
examples/test_examples.py
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@ -28,7 +28,13 @@ from transformers.testing_utils import TestCasePlus, torch_device
SRC_DIRS = [
os.path.join(os.path.dirname(__file__), dirname)
for dirname in ["text-generation", "text-classification", "language-modeling", "question-answering"]
for dirname in [
"text-generation",
"text-classification",
"token-classification",
"language-modeling",
"question-answering",
]
]
sys.path.extend(SRC_DIRS)
@ -38,6 +44,7 @@ if SRC_DIRS is not None:
import run_generation
import run_glue
import run_mlm
import run_ner
import run_pl_glue
import run_squad
@ -185,6 +192,36 @@ class ExamplesTests(TestCasePlus):
result = run_mlm.main()
self.assertLess(result["perplexity"], 42)
def test_run_ner(self):
stream_handler = logging.StreamHandler(sys.stdout)
logger.addHandler(stream_handler)
tmp_dir = self.get_auto_remove_tmp_dir()
testargs = f"""
run_ner.py
--model_name_or_path bert-base-uncased
--train_file tests/fixtures/tests_samples/conll/sample.json
--validation_file tests/fixtures/tests_samples/conll/sample.json
--output_dir {tmp_dir}
--overwrite_output_dir
--do_train
--do_eval
--warmup_steps=2
--learning_rate=2e-4
--per_gpu_train_batch_size=2
--per_gpu_eval_batch_size=2
--num_train_epochs=2
""".split()
if torch_device != "cuda":
testargs.append("--no_cuda")
with patch.object(sys, "argv", testargs):
result = run_ner.main()
self.assertGreaterEqual(result["eval_accuracy_score"], 0.75)
self.assertGreaterEqual(result["eval_precision"], 0.75)
self.assertLess(result["eval_loss"], 0.5)
def test_run_squad(self):
stream_handler = logging.StreamHandler(sys.stdout)
logger.addHandler(stream_handler)

48
examples/token-classification/README.md
View File

@ -1,6 +1,40 @@
## Named Entity Recognition
## Token classification
Based on the scripts [`run_ner.py`](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py) for Pytorch and
Fine-tuning the library models for token classification task such as Named Entity Recognition (NER) or Parts-of-speech
tagging (POS). The main scrip `run_ner.py` leverages the 🤗 Datasets library and the Trainer API. You can easily
customize it to your needs if you need extra processing on your datasets.
It will either run on a datasets hosted on our [hub](https://huggingface.co/datasets) or with your own text files for
training and validation.
The following example fine-tunes BERT on CoNLL-2003:
```bash
python run_ner.py \
--model_name_or_path bert-base-uncased \
--dataset_name conll2003 \
--output_dir /tmp/test-ner \
--do_train \
--do_eval
```
or just can just run the bash script `run.sh`.
To run on your own training and validation files, use the following command:
```bash
python run_ner.py \
--model_name_or_path bert-base-uncased \
--train_file path_to_train_file \
--validation_file path_to_validation_file \
--output_dir /tmp/test-ner \
--do_train \
--do_eval
```
## Old version of the script
Based on the scripts [`run_ner_old.py`](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py) for Pytorch and
[`run_tf_ner.py`](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_tf_ner.py) for Tensorflow 2.
The following examples are covered in this section:
@ -69,7 +103,7 @@ export SEED=1
To start training, just run:
```bash
python3 run_ner.py --data_dir ./ \
python3 run_ner_old.py --data_dir ./ \
--labels ./labels.txt \
--model_name_or_path $BERT_MODEL \
--output_dir $OUTPUT_DIR \
@ -87,7 +121,7 @@ If your GPU supports half-precision training, just add the `--fp16` flag. After
#### JSON-based configuration file
Instead of passing all parameters via commandline arguments, the `run_ner.py` script also supports reading parameters from a json-based configuration file:
Instead of passing all parameters via commandline arguments, the `run_ner_old.py` script also supports reading parameters from a json-based configuration file:
```json
{
@ -106,7 +140,7 @@ Instead of passing all parameters via commandline arguments, the `run_ner.py` sc
}
```
It must be saved with a `.json` extension and can be used by running `python3 run_ner.py config.json`.
It must be saved with a `.json` extension and can be used by running `python3 run_ner_old.py config.json`.
#### Evaluation
@ -250,7 +284,7 @@ cat data_wnut_17/train.txt data_wnut_17/dev.txt data_wnut_17/test.txt | cut -d "
#### Run the Pytorch version
Fine-tuning with the PyTorch version can be started using the `run_ner.py` script. In this example we use a JSON-based configuration file.
Fine-tuning with the PyTorch version can be started using the `run_ner_old.py` script. In this example we use a JSON-based configuration file.
This configuration file looks like:
@ -274,7 +308,7 @@ This configuration file looks like:
If your GPU supports half-precision training, please set `fp16` to `true`.
Save this JSON-based configuration under `wnut_17.json`. The fine-tuning can be started with `python3 run_ner.py wnut_17.json`.
Save this JSON-based configuration under `wnut_17.json`. The fine-tuning can be started with `python3 run_ner_old.py wnut_17.json`.
#### Evaluation

40
examples/token-classification/run.sh
View File

@ -1,36 +1,6 @@
## The relevant files are currently on a shared Google
## drive at https://drive.google.com/drive/folders/1kC0I2UGl2ltrluI9NqDjaQJGw5iliw_J
## Monitor for changes and eventually migrate to nlp dataset
curl -L 'https://drive.google.com/uc?export=download&id=1Jjhbal535VVz2ap4v4r_rN1UEHTdLK5P' \
| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > train.txt.tmp
curl -L 'https://drive.google.com/uc?export=download&id=1ZfRcQThdtAR5PPRjIDtrVP7BtXSCUBbm' \
| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > dev.txt.tmp
curl -L 'https://drive.google.com/uc?export=download&id=1u9mb7kNJHWQCWyweMDRMuTFoOHOfeBTH' \
| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > test.txt.tmp
export MAX_LENGTH=128
export BERT_MODEL=bert-base-multilingual-cased
python3 scripts/preprocess.py train.txt.tmp $BERT_MODEL $MAX_LENGTH > train.txt
python3 scripts/preprocess.py dev.txt.tmp $BERT_MODEL $MAX_LENGTH > dev.txt
python3 scripts/preprocess.py test.txt.tmp $BERT_MODEL $MAX_LENGTH > test.txt
cat train.txt dev.txt test.txt | cut -d " " -f 2 | grep -v "^$"| sort | uniq > labels.txt
export OUTPUT_DIR=germeval-model
export BATCH_SIZE=32
export NUM_EPOCHS=3
export SAVE_STEPS=750
export SEED=1
python3 run_ner.py \
--task_type NER \
--data_dir . \
--labels ./labels.txt \
--model_name_or_path $BERT_MODEL \
--output_dir $OUTPUT_DIR \
--max_seq_length $MAX_LENGTH \
--num_train_epochs $NUM_EPOCHS \
--per_gpu_train_batch_size $BATCH_SIZE \
--save_steps $SAVE_STEPS \
--seed $SEED \
--do_train \
--do_eval \
--do_predict
--model_name_or_path bert-base-uncased \
--dataset_name conll2003 \
--output_dir /tmp/test-ner \
--do_train \
--do_eval

2
examples/token-classification/run_chunk.sh
View File

@ -21,7 +21,7 @@ export NUM_EPOCHS=3
export SAVE_STEPS=750
export SEED=1
python3 run_ner.py \
python3 run_ner_old.py \
--task_type Chunk \
--data_dir . \
--model_name_or_path $BERT_MODEL \

328
examples/token-classification/run_ner.py
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@ -1,6 +1,5 @@
# coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
# Copyright 2020 The HuggingFace Team All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
@ -13,29 +12,33 @@
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
""" Fine-tuning the library models for named entity recognition on CoNLL-2003. """
"""
Fine-tuning the library models for token classification.
"""
# You can also adapt this script on your own token classification task and datasets. Pointers for this are left as comments.
import logging
import os
import sys
from dataclasses import dataclass, field
from importlib import import_module
from typing import Dict, List, Optional, Tuple
from typing import Optional
import numpy as np
from datasets import load_dataset
from seqeval.metrics import accuracy_score, f1_score, precision_score, recall_score
from torch import nn
import transformers
from transformers import (
AutoConfig,
AutoModelForTokenClassification,
AutoTokenizer,
EvalPrediction,
DataCollatorForTokenClassification,
HfArgumentParser,
Trainer,
TrainingArguments,
set_seed,
)
from utils_ner import Split, TokenClassificationDataset, TokenClassificationTask
from transformers.trainer_utils import is_main_process
logger = logging.getLogger(__name__)
@ -53,15 +56,9 @@ class ModelArguments:
config_name: Optional[str] = field(
default=None, metadata={"help": "Pretrained config name or path if not the same as model_name"}
)
task_type: Optional[str] = field(
default="NER", metadata={"help": "Task type to fine tune in training (e.g. NER, POS, etc)"}
)
tokenizer_name: Optional[str] = field(
default=None, metadata={"help": "Pretrained tokenizer name or path if not the same as model_name"}
)
use_fast: bool = field(default=False, metadata={"help": "Set this flag to use fast tokenization."})
# If you want to tweak more attributes on your tokenizer, you should do it in a distinct script,
# or just modify its tokenizer_config.json.
cache_dir: Optional[str] = field(
default=None, metadata={"help": "Where do you want to store the pretrained models downloaded from s3"}
)
@ -73,23 +70,58 @@ class DataTrainingArguments:
Arguments pertaining to what data we are going to input our model for training and eval.
"""
data_dir: str = field(
metadata={"help": "The input data dir. Should contain the .txt files for a CoNLL-2003-formatted task."}
task_name: Optional[str] = field(default="ner", metadata={"help": "The name of the task (ner, pos...)."})
dataset_name: Optional[str] = field(
default=None, metadata={"help": "The name of the dataset to use (via the datasets library)."}
)
labels: Optional[str] = field(
dataset_config_name: Optional[str] = field(
default=None, metadata={"help": "The configuration name of the dataset to use (via the datasets library)."}
)
train_file: Optional[str] = field(
default=None, metadata={"help": "The input training data file (a csv or JSON file)."}
)
validation_file: Optional[str] = field(
default=None,
metadata={"help": "Path to a file containing all labels. If not specified, CoNLL-2003 labels are used."},
metadata={"help": "An optional input evaluation data file to evaluate on (a csv or JSON file)."},
)
max_seq_length: int = field(
default=128,
metadata={
"help": "The maximum total input sequence length after tokenization. Sequences longer "
"than this will be truncated, sequences shorter will be padded."
},
test_file: Optional[str] = field(
default=None,
metadata={"help": "An optional input test data file to predict on (a csv or JSON file)."},
)
overwrite_cache: bool = field(
default=False, metadata={"help": "Overwrite the cached training and evaluation sets"}
)
preprocessing_num_workers: Optional[int] = field(
default=None,
metadata={"help": "The number of processes to use for the preprocessing."},
)
pad_to_max_length: bool = field(
default=False,
metadata={
"help": "Whether to pad all samples to model maximum sentence length. "
"If False, will pad the samples dynamically when batching to the maximum length in the batch. More "
"efficient on GPU but very bad for TPU."
},
)
label_all_tokens: bool = field(
default=False,
metadata={
"help": "Whether to put the label for one word on all tokens of generated by that word or just on the "
"one (in which case the other tokens will have a padding index)."
},
)
def __post_init__(self):
if self.dataset_name is None and self.train_file is None and self.validation_file is None:
raise ValueError("Need either a dataset name or a training/validation file.")
else:
if self.train_file is not None:
extension = self.train_file.split(".")[-1]
assert extension in ["csv", "json"], "`train_file` should be a csv or a json file."
if self.validation_file is not None:
extension = self.validation_file.split(".")[-1]
assert extension in ["csv", "json"], "`validation_file` should be a csv or a json file."
self.task_name = self.task_name.lower()
def main():
@ -112,60 +144,90 @@ def main():
and not training_args.overwrite_output_dir
):
raise ValueError(
f"Output directory ({training_args.output_dir}) already exists and is not empty. Use --overwrite_output_dir to overcome."
)
module = import_module("tasks")
try:
token_classification_task_clazz = getattr(module, model_args.task_type)
token_classification_task: TokenClassificationTask = token_classification_task_clazz()
except AttributeError:
raise ValueError(
f"Task {model_args.task_type} needs to be defined as a TokenClassificationTask subclass in {module}. "
f"Available tasks classes are: {TokenClassificationTask.__subclasses__()}"
f"Output directory ({training_args.output_dir}) already exists and is not empty."
"Use --overwrite_output_dir to overcome."
)
# Setup logging
logging.basicConfig(
format="%(asctime)s - %(levelname)s - %(name)s - %(message)s",
datefmt="%m/%d/%Y %H:%M:%S",
level=logging.INFO if training_args.local_rank in [-1, 0] else logging.WARN,
level=logging.INFO if is_main_process(training_args.local_rank) else logging.WARN,
)
# Log on each process the small summary:
logger.warning(
"Process rank: %s, device: %s, n_gpu: %s, distributed training: %s, 16-bits training: %s",
training_args.local_rank,
training_args.device,
training_args.n_gpu,
bool(training_args.local_rank != -1),
training_args.fp16,
f"Process rank: {training_args.local_rank}, device: {training_args.device}, n_gpu: {training_args.n_gpu}"
+ f"distributed training: {bool(training_args.local_rank != -1)}, 16-bits training: {training_args.fp16}"
)
# Set the verbosity to info of the Transformers logger (on main process only):
if is_main_process(training_args.local_rank):
transformers.utils.logging.set_verbosity_info()
logger.info("Training/evaluation parameters %s", training_args)
# Set seed
# Set seed before initializing model.
set_seed(training_args.seed)
# Prepare CONLL-2003 task
labels = token_classification_task.get_labels(data_args.labels)
label_map: Dict[int, str] = {i: label for i, label in enumerate(labels)}
num_labels = len(labels)
# Get the datasets: you can either provide your own CSV/JSON/TXT training and evaluation files (see below)
# or just provide the name of one of the public datasets available on the hub at https://huggingface.co/datasets/
# (the dataset will be downloaded automatically from the datasets Hub).
#
# For CSV/JSON files, this script will use the column called 'text' or the first column if no column called
# 'text' is found. You can easily tweak this behavior (see below).
#
# In distributed training, the load_dataset function guarantee that only one local process can concurrently
# download the dataset.
if data_args.dataset_name is not None:
# Downloading and loading a dataset from the hub.
datasets = load_dataset(data_args.dataset_name, data_args.dataset_config_name)
else:
data_files = {}
if data_args.train_file is not None:
data_files["train"] = data_args.train_file
if data_args.validation_file is not None:
data_files["validation"] = data_args.validation_file
if data_args.test_file is not None:
data_files["test"] = data_args.test_file
extension = data_args.train_file.split(".")[-1]
datasets = load_dataset(extension, data_files=data_files)
# See more about loading any type of standard or custom dataset (from files, python dict, pandas DataFrame, etc) at
# https://huggingface.co/docs/datasets/loading_datasets.html.
if training_args.do_train:
column_names = datasets["train"].column_names
else:
column_names = datasets["validation"].column_names
text_column_name = "words" if "words" in column_names else column_names[0]
label_column_name = data_args.task_name if data_args.task_name in column_names else column_names[1]
# Labeling (this part will be easier when https://github.com/huggingface/datasets/issues/797 is solved)
def get_label_list(labels):
unique_labels = set()
for label in labels:
unique_labels = unique_labels | set(label)
label_list = list(unique_labels)
label_list.sort()
return label_list
label_list = get_label_list(datasets["train"][label_column_name])
label_to_id = {l: i for i, l in enumerate(label_list)}
num_labels = len(label_list)
# Load pretrained model and tokenizer
#
# Distributed training:
# The .from_pretrained methods guarantee that only one local process can concurrently
# download model & vocab.
config = AutoConfig.from_pretrained(
model_args.config_name if model_args.config_name else model_args.model_name_or_path,
num_labels=num_labels,
id2label=label_map,
label2id={label: i for i, label in enumerate(labels)},
finetuning_task=data_args.task_name,
cache_dir=model_args.cache_dir,
)
tokenizer = AutoTokenizer.from_pretrained(
model_args.tokenizer_name if model_args.tokenizer_name else model_args.model_name_or_path,
cache_dir=model_args.cache_dir,
use_fast=model_args.use_fast,
use_fast=True,
)
model = AutoModelForTokenClassification.from_pretrained(
model_args.model_name_or_path,
@ -174,67 +236,85 @@ def main():
cache_dir=model_args.cache_dir,
)
# Get datasets
train_dataset = (
TokenClassificationDataset(
token_classification_task=token_classification_task,
data_dir=data_args.data_dir,
tokenizer=tokenizer,
labels=labels,
model_type=config.model_type,
max_seq_length=data_args.max_seq_length,
overwrite_cache=data_args.overwrite_cache,
mode=Split.train,
# Preprocessing the dataset
# Padding strategy
padding = "max_length" if data_args.pad_to_max_length else False
# Tokenize all texts and align the labels with them.
def tokenize_and_align_labels(examples):
tokenized_inputs = tokenizer(
examples[text_column_name],
padding=padding,
truncation=True,
# We use this argument because the texts in our dataset are lists of words (with a label for each word).
is_split_into_words=True,
return_offsets_mapping=True,
)
if training_args.do_train
else None
)
eval_dataset = (
TokenClassificationDataset(
token_classification_task=token_classification_task,
data_dir=data_args.data_dir,
tokenizer=tokenizer,
labels=labels,
model_type=config.model_type,
max_seq_length=data_args.max_seq_length,
overwrite_cache=data_args.overwrite_cache,
mode=Split.dev,
)
if training_args.do_eval
else None
offset_mappings = tokenized_inputs.pop("offset_mapping")
labels = []
for label, offset_mapping in zip(examples[label_column_name], offset_mappings):
label_index = 0
current_label = -100
label_ids = []
for offset in offset_mapping:
# We set the label for the first token of each word. Special characters will have an offset of (0, 0)
# so the test ignores them.
if offset[0] == 0 and offset[1] != 0:
current_label = label_to_id[label[label_index]]
label_index += 1
label_ids.append(current_label)
# For special tokens, we set the label to -100 so it's automatically ignored in the loss function.
elif offset[0] == 0 and offset[1] == 0:
label_ids.append(-100)
# For the other tokens in a word, we set the label to either the current label or -100, depending on
# the label_all_tokens flag.
else:
label_ids.append(current_label if data_args.label_all_tokens else -100)
labels.append(label_ids)
tokenized_inputs["labels"] = labels
return tokenized_inputs
tokenized_datasets = datasets.map(
tokenize_and_align_labels,
batched=True,
num_proc=data_args.preprocessing_num_workers,
load_from_cache_file=not data_args.overwrite_cache,
)
def align_predictions(predictions: np.ndarray, label_ids: np.ndarray) -> Tuple[List[int], List[int]]:
preds = np.argmax(predictions, axis=2)
# Data collator
data_collator = DataCollatorForTokenClassification(tokenizer)
batch_size, seq_len = preds.shape
# Metrics
def compute_metrics(p):
predictions, labels = p
predictions = np.argmax(predictions, axis=2)
out_label_list = [[] for _ in range(batch_size)]
preds_list = [[] for _ in range(batch_size)]
# Remove ignored index (special tokens)
true_predictions = [
[label_list[p] for (p, l) in zip(prediction, label) if l != -100]
for prediction, label in zip(predictions, labels)
]
true_labels = [
[label_list[l] for (p, l) in zip(prediction, label) if l != -100]
for prediction, label in zip(predictions, labels)
]
for i in range(batch_size):
for j in range(seq_len):
if label_ids[i, j] != nn.CrossEntropyLoss().ignore_index:
out_label_list[i].append(label_map[label_ids[i][j]])
preds_list[i].append(label_map[preds[i][j]])
return preds_list, out_label_list
def compute_metrics(p: EvalPrediction) -> Dict:
preds_list, out_label_list = align_predictions(p.predictions, p.label_ids)
return {
"accuracy_score": accuracy_score(out_label_list, preds_list),
"precision": precision_score(out_label_list, preds_list),
"recall": recall_score(out_label_list, preds_list),
"f1": f1_score(out_label_list, preds_list),
"accuracy_score": accuracy_score(true_labels, true_predictions),
"precision": precision_score(true_labels, true_predictions),
"recall": recall_score(true_labels, true_predictions),
"f1": f1_score(true_labels, true_predictions),
}
# Initialize our Trainer
trainer = Trainer(
model=model,
args=training_args,
train_dataset=train_dataset,
eval_dataset=eval_dataset,
train_dataset=tokenized_datasets["train"] if training_args.do_train else None,
eval_dataset=tokenized_datasets["validation"] if training_args.do_eval else None,
tokenizer=tokenizer,
data_collator=data_collator,
compute_metrics=compute_metrics,
)
@ -243,58 +323,50 @@ def main():
trainer.train(
model_path=model_args.model_name_or_path if os.path.isdir(model_args.model_name_or_path) else None
)
trainer.save_model()
# For convenience, we also re-save the tokenizer to the same directory,
# so that you can share your model easily on huggingface.co/models =)
if trainer.is_world_master():
tokenizer.save_pretrained(training_args.output_dir)
trainer.save_model() # Saves the tokenizer too for easy upload
# Evaluation
results = {}
if training_args.do_eval:
logger.info("*** Evaluate ***")
result = trainer.evaluate()
results = trainer.evaluate()
output_eval_file = os.path.join(training_args.output_dir, "eval_results.txt")
if trainer.is_world_master():
output_eval_file = os.path.join(training_args.output_dir, "eval_results_ner.txt")
if trainer.is_world_process_zero():
with open(output_eval_file, "w") as writer:
logger.info("***** Eval results *****")
for key, value in result.items():
logger.info(" %s = %s", key, value)
writer.write("%s = %s\n" % (key, value))
results.update(result)
for key, value in results.items():
logger.info(f" {key} = {value}")
writer.write(f"{key} = {value}\n")
# Predict
if training_args.do_predict:
test_dataset = TokenClassificationDataset(
token_classification_task=token_classification_task,
data_dir=data_args.data_dir,
tokenizer=tokenizer,
labels=labels,
model_type=config.model_type,
max_seq_length=data_args.max_seq_length,
overwrite_cache=data_args.overwrite_cache,
mode=Split.test,
)
logger.info("*** Predict ***")
predictions, label_ids, metrics = trainer.predict(test_dataset)
preds_list, _ = align_predictions(predictions, label_ids)
test_dataset = datasets["test"]
predictions, labels, metrics = trainer.predict(test_dataset)
predictions = np.argmax(predictions, axis=2)
# Remove ignored index (special tokens)
true_predictions = [
[label_list[p] for (p, l) in zip(prediction, label) if l != -100]
for prediction, label in zip(predictions, labels)
]
output_test_results_file = os.path.join(training_args.output_dir, "test_results.txt")
if trainer.is_world_master():
with open(output_test_results_file, "w") as writer:
for key, value in metrics.items():
logger.info(" %s = %s", key, value)
writer.write("%s = %s\n" % (key, value))
logger.info(f" {key} = {value}")
writer.write(f"{key} = {value}\n")
# Save predictions
output_test_predictions_file = os.path.join(training_args.output_dir, "test_predictions.txt")
if trainer.is_world_master():
with open(output_test_predictions_file, "w") as writer:
with open(os.path.join(data_args.data_dir, "test.txt"), "r") as f:
token_classification_task.write_predictions_to_file(writer, f, preds_list)
for prediction in true_predictions:
writer.write(" ".join(prediction) + "\n")
return results

308
examples/token-classification/run_ner_old.py Normal file
View File

@ -0,0 +1,308 @@
# coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
""" Fine-tuning the library models for named entity recognition on CoNLL-2003. """
import logging
import os
import sys
from dataclasses import dataclass, field
from importlib import import_module
from typing import Dict, List, Optional, Tuple
import numpy as np
from seqeval.metrics import accuracy_score, f1_score, precision_score, recall_score
from torch import nn
from transformers import (
AutoConfig,
AutoModelForTokenClassification,
AutoTokenizer,
EvalPrediction,
HfArgumentParser,
Trainer,
TrainingArguments,
set_seed,
)
from utils_ner import Split, TokenClassificationDataset, TokenClassificationTask
logger = logging.getLogger(__name__)
@dataclass
class ModelArguments:
"""
Arguments pertaining to which model/config/tokenizer we are going to fine-tune from.
"""
model_name_or_path: str = field(
metadata={"help": "Path to pretrained model or model identifier from huggingface.co/models"}
)
config_name: Optional[str] = field(
default=None, metadata={"help": "Pretrained config name or path if not the same as model_name"}
)
task_type: Optional[str] = field(
default="NER", metadata={"help": "Task type to fine tune in training (e.g. NER, POS, etc)"}
)
tokenizer_name: Optional[str] = field(
default=None, metadata={"help": "Pretrained tokenizer name or path if not the same as model_name"}
)
use_fast: bool = field(default=False, metadata={"help": "Set this flag to use fast tokenization."})
# If you want to tweak more attributes on your tokenizer, you should do it in a distinct script,
# or just modify its tokenizer_config.json.
cache_dir: Optional[str] = field(
default=None, metadata={"help": "Where do you want to store the pretrained models downloaded from s3"}
)
@dataclass
class DataTrainingArguments:
"""
Arguments pertaining to what data we are going to input our model for training and eval.
"""
data_dir: str = field(
metadata={"help": "The input data dir. Should contain the .txt files for a CoNLL-2003-formatted task."}
)
labels: Optional[str] = field(
default=None,
metadata={"help": "Path to a file containing all labels. If not specified, CoNLL-2003 labels are used."},
)
max_seq_length: int = field(
default=128,
metadata={
"help": "The maximum total input sequence length after tokenization. Sequences longer "
"than this will be truncated, sequences shorter will be padded."
},
)
overwrite_cache: bool = field(
default=False, metadata={"help": "Overwrite the cached training and evaluation sets"}
)
def main():
# See all possible arguments in src/transformers/training_args.py
# or by passing the --help flag to this script.
# We now keep distinct sets of args, for a cleaner separation of concerns.
parser = HfArgumentParser((ModelArguments, DataTrainingArguments, TrainingArguments))
if len(sys.argv) == 2 and sys.argv[1].endswith(".json"):
# If we pass only one argument to the script and it's the path to a json file,
# let's parse it to get our arguments.
model_args, data_args, training_args = parser.parse_json_file(json_file=os.path.abspath(sys.argv[1]))
else:
model_args, data_args, training_args = parser.parse_args_into_dataclasses()
if (
os.path.exists(training_args.output_dir)
and os.listdir(training_args.output_dir)
and training_args.do_train
and not training_args.overwrite_output_dir
):
raise ValueError(
f"Output directory ({training_args.output_dir}) already exists and is not empty. Use --overwrite_output_dir to overcome."
)
module = import_module("tasks")
try:
token_classification_task_clazz = getattr(module, model_args.task_type)
token_classification_task: TokenClassificationTask = token_classification_task_clazz()
except AttributeError:
raise ValueError(
f"Task {model_args.task_type} needs to be defined as a TokenClassificationTask subclass in {module}. "
f"Available tasks classes are: {TokenClassificationTask.__subclasses__()}"
)
# Setup logging
logging.basicConfig(
format="%(asctime)s - %(levelname)s - %(name)s - %(message)s",
datefmt="%m/%d/%Y %H:%M:%S",
level=logging.INFO if training_args.local_rank in [-1, 0] else logging.WARN,
)
logger.warning(
"Process rank: %s, device: %s, n_gpu: %s, distributed training: %s, 16-bits training: %s",
training_args.local_rank,
training_args.device,
training_args.n_gpu,
bool(training_args.local_rank != -1),
training_args.fp16,
)
logger.info("Training/evaluation parameters %s", training_args)
# Set seed
set_seed(training_args.seed)
# Prepare CONLL-2003 task
labels = token_classification_task.get_labels(data_args.labels)
label_map: Dict[int, str] = {i: label for i, label in enumerate(labels)}
num_labels = len(labels)
# Load pretrained model and tokenizer
#
# Distributed training:
# The .from_pretrained methods guarantee that only one local process can concurrently
# download model & vocab.
config = AutoConfig.from_pretrained(
model_args.config_name if model_args.config_name else model_args.model_name_or_path,
num_labels=num_labels,
id2label=label_map,
label2id={label: i for i, label in enumerate(labels)},
cache_dir=model_args.cache_dir,
)
tokenizer = AutoTokenizer.from_pretrained(
model_args.tokenizer_name if model_args.tokenizer_name else model_args.model_name_or_path,
cache_dir=model_args.cache_dir,
use_fast=model_args.use_fast,
)
model = AutoModelForTokenClassification.from_pretrained(
model_args.model_name_or_path,
from_tf=bool(".ckpt" in model_args.model_name_or_path),
config=config,
cache_dir=model_args.cache_dir,
)
# Get datasets
train_dataset = (
TokenClassificationDataset(
token_classification_task=token_classification_task,
data_dir=data_args.data_dir,
tokenizer=tokenizer,
labels=labels,
model_type=config.model_type,
max_seq_length=data_args.max_seq_length,
overwrite_cache=data_args.overwrite_cache,
mode=Split.train,
)
if training_args.do_train
else None
)
eval_dataset = (
TokenClassificationDataset(
token_classification_task=token_classification_task,
data_dir=data_args.data_dir,
tokenizer=tokenizer,
labels=labels,
model_type=config.model_type,
max_seq_length=data_args.max_seq_length,
overwrite_cache=data_args.overwrite_cache,
mode=Split.dev,
)
if training_args.do_eval
else None
)
def align_predictions(predictions: np.ndarray, label_ids: np.ndarray) -> Tuple[List[int], List[int]]:
preds = np.argmax(predictions, axis=2)
batch_size, seq_len = preds.shape
out_label_list = [[] for _ in range(batch_size)]
preds_list = [[] for _ in range(batch_size)]
for i in range(batch_size):
for j in range(seq_len):
if label_ids[i, j] != nn.CrossEntropyLoss().ignore_index:
out_label_list[i].append(label_map[label_ids[i][j]])
preds_list[i].append(label_map[preds[i][j]])
return preds_list, out_label_list
def compute_metrics(p: EvalPrediction) -> Dict:
preds_list, out_label_list = align_predictions(p.predictions, p.label_ids)
return {
"accuracy_score": accuracy_score(out_label_list, preds_list),
"precision": precision_score(out_label_list, preds_list),
"recall": recall_score(out_label_list, preds_list),
"f1": f1_score(out_label_list, preds_list),
}
# Initialize our Trainer
trainer = Trainer(
model=model,
args=training_args,
train_dataset=train_dataset,
eval_dataset=eval_dataset,
compute_metrics=compute_metrics,
)
# Training
if training_args.do_train:
trainer.train(
model_path=model_args.model_name_or_path if os.path.isdir(model_args.model_name_or_path) else None
)
trainer.save_model()
# For convenience, we also re-save the tokenizer to the same directory,
# so that you can share your model easily on huggingface.co/models =)
if trainer.is_world_master():
tokenizer.save_pretrained(training_args.output_dir)
# Evaluation
results = {}
if training_args.do_eval:
logger.info("*** Evaluate ***")
result = trainer.evaluate()
output_eval_file = os.path.join(training_args.output_dir, "eval_results.txt")
if trainer.is_world_master():
with open(output_eval_file, "w") as writer:
logger.info("***** Eval results *****")
for key, value in result.items():
logger.info(" %s = %s", key, value)
writer.write("%s = %s\n" % (key, value))
results.update(result)
# Predict
if training_args.do_predict:
test_dataset = TokenClassificationDataset(
token_classification_task=token_classification_task,
data_dir=data_args.data_dir,
tokenizer=tokenizer,
labels=labels,
model_type=config.model_type,
max_seq_length=data_args.max_seq_length,
overwrite_cache=data_args.overwrite_cache,
mode=Split.test,
)
predictions, label_ids, metrics = trainer.predict(test_dataset)
preds_list, _ = align_predictions(predictions, label_ids)
output_test_results_file = os.path.join(training_args.output_dir, "test_results.txt")
if trainer.is_world_master():
with open(output_test_results_file, "w") as writer:
for key, value in metrics.items():
logger.info(" %s = %s", key, value)
writer.write("%s = %s\n" % (key, value))
# Save predictions
output_test_predictions_file = os.path.join(training_args.output_dir, "test_predictions.txt")
if trainer.is_world_master():
with open(output_test_predictions_file, "w") as writer:
with open(os.path.join(data_args.data_dir, "test.txt"), "r") as f:
token_classification_task.write_predictions_to_file(writer, f, preds_list)
return results
def _mp_fn(index):
# For xla_spawn (TPUs)
main()
if __name__ == "__main__":
main()

36
examples/token-classification/run_old.sh Executable file
View File

@ -0,0 +1,36 @@
## The relevant files are currently on a shared Google
## drive at https://drive.google.com/drive/folders/1kC0I2UGl2ltrluI9NqDjaQJGw5iliw_J
## Monitor for changes and eventually migrate to nlp dataset
curl -L 'https://drive.google.com/uc?export=download&id=1Jjhbal535VVz2ap4v4r_rN1UEHTdLK5P' \
| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > train.txt.tmp
curl -L 'https://drive.google.com/uc?export=download&id=1ZfRcQThdtAR5PPRjIDtrVP7BtXSCUBbm' \
| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > dev.txt.tmp
curl -L 'https://drive.google.com/uc?export=download&id=1u9mb7kNJHWQCWyweMDRMuTFoOHOfeBTH' \
| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > test.txt.tmp
export MAX_LENGTH=128
export BERT_MODEL=bert-base-multilingual-cased
python3 scripts/preprocess.py train.txt.tmp $BERT_MODEL $MAX_LENGTH > train.txt
python3 scripts/preprocess.py dev.txt.tmp $BERT_MODEL $MAX_LENGTH > dev.txt
python3 scripts/preprocess.py test.txt.tmp $BERT_MODEL $MAX_LENGTH > test.txt
cat train.txt dev.txt test.txt | cut -d " " -f 2 | grep -v "^$"| sort | uniq > labels.txt
export OUTPUT_DIR=germeval-model
export BATCH_SIZE=32
export NUM_EPOCHS=3
export SAVE_STEPS=750
export SEED=1
python3 run_ner_old.py \
--task_type NER \
--data_dir . \
--labels ./labels.txt \
--model_name_or_path $BERT_MODEL \
--output_dir $OUTPUT_DIR \
--max_seq_length $MAX_LENGTH \
--num_train_epochs $NUM_EPOCHS \
--per_gpu_train_batch_size $BATCH_SIZE \
--save_steps $SAVE_STEPS \
--seed $SEED \
--do_train \
--do_eval \
--do_predict

2
examples/token-classification/run_pos.sh
View File

@ -21,7 +21,7 @@ export NUM_EPOCHS=3
export SAVE_STEPS=750
export SEED=1
python3 run_ner.py \
python3 _old.py \
--task_type POS \
--data_dir . \
--model_name_or_path $BERT_MODEL \

2
examples/token-classification/test_ner_examples.py
View File

@ -3,7 +3,7 @@ import sys
import unittest
from unittest.mock import patch
import run_ner
import run_ner_old as run_ner
from transformers.testing_utils import slow

2
model_cards/mrm8488/RuPERTa-base-finetuned-ner/README.md
View File

@ -17,7 +17,7 @@ This model is a fine-tuned on [NER-C](https://www.kaggle.com/nltkdata/conll-corp
| Dev | 40 K |
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py)
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py)
- Labels covered:

2
model_cards/mrm8488/RuPERTa-base-finetuned-pos/README.md
View File

@ -16,7 +16,7 @@ This model is a fine-tuned on [CONLL CORPORA](https://www.kaggle.com/nltkdata/co
| Train | 445 K |
| Dev | 55 K |
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py)
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py)
- Labels covered:

2
model_cards/mrm8488/TinyBERT-spanish-uncased-finetuned-ner/README.md
View File

@ -19,7 +19,7 @@ I preprocessed the dataset and split it as train / dev (80/20)
| Dev | 2.2 K |
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py)
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py)
- Labels covered:

2
model_cards/mrm8488/bert-base-german-finetuned-ler/README.md
View File

@ -18,7 +18,7 @@ Court decisions from 2017 and 2018 were selected for the dataset, published onli
| Train | 1657048 |
| Eval | 500000 |
- Training script: [Fine-tuning script for NER provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py)
- Training script: [Fine-tuning script for NER provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py)
Colab: [How to fine-tune a model for NER using HF scripts](https://colab.research.google.com/drive/156Qrd7NsUHwA3nmQ6gXdZY0NzOvqk9AT?usp=sharing)
- Labels covered (and its distribution):

2
model_cards/mrm8488/bert-small-finetuned-typo-detection/README.md
View File

@ -11,7 +11,7 @@ thumbnail:
- Dataset: [GitHub Typo Corpus](https://github.com/mhagiwara/github-typo-corpus) 📚
- [Fine-tune script on NER dataset provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py) 🏋️‍♂️
- [Fine-tune script on NER dataset provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py) 🏋️‍♂️
## Metrics on test set 📋

2
model_cards/mrm8488/bert-spanish-cased-finetuned-ner/README.md
View File

@ -19,7 +19,7 @@ I preprocessed the dataset and split it as train / dev (80/20)
| Dev | 2.2 K |
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py)
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py)
- Labels covered:

2
model_cards/mrm8488/bert-spanish-cased-finetuned-pos-syntax/README.md
View File

@ -11,7 +11,7 @@ This model is a fine-tuned version of the Spanish BERT [(BETO)](https://github.c
- [Dataset: CONLL Corpora ES](https://www.kaggle.com/nltkdata/conll-corpora)
#### [Fine-tune script on NER dataset provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py)
#### [Fine-tune script on NER dataset provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py)
#### 21 Syntax annotations (Labels) covered:

2
model_cards/mrm8488/bert-spanish-cased-finetuned-pos/README.md
View File

@ -19,7 +19,7 @@ I preprocessed the dataset and split it as train / dev (80/20)
| Dev | 50 K |
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py)
- [Fine-tune on NER script provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py)
- **60** Labels covered:

2
model_cards/mrm8488/distilbert-base-multi-cased-finetuned-typo-detection/README.md
View File

@ -11,7 +11,7 @@ thumbnail:
- Dataset: [GitHub Typo Corpus](https://github.com/mhagiwara/github-typo-corpus) 📚 for 15 languages
- [Fine-tune script on NER dataset provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.py) 🏋️‍♂️
- [Fine-tune script on NER dataset provided by Huggingface](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner_old.py) 🏋️‍♂️
## Metrics on test set 📋

2
model_cards/savasy/bert-base-turkish-ner-cased/README.md
View File

@ -32,7 +32,7 @@ export SEED=1
```
Then run pre-training:
```
python3 run_ner.py --data_dir ./tr-data3 \
python3 run_ner_old.py --data_dir ./tr-data3 \
--model_type bert \
--labels ./tr-data/labels.txt \
--model_name_or_path $BERT_MODEL \

10
tests/fixtures/tests_samples/conll/sample.json vendored Normal file
View File

@ -0,0 +1,10 @@
{"words": ["He", "was", "the", "27th", "pitcher", "used", "by", "the", "Angels", "this", "season", ",", "tying", "a", "major-league", "record", "."], "ner": ["O", "O", "O", "O", "O", "O", "O", "O", "B-ORG", "O", "O", "O", "O", "O", "O", "O", "O"]}
{"words": ["CHICAGO", "AT", "ATLANTA"], "ner": ["B-ORG", "O", "B-LOC"]}
{"words": ["President", "Bill", "Clinton", "earlier", "this", "month", "invoked", "special", "powers", "to", "appoint", "Fowler", "during", "the", "congressional", "recess", "because", "the", "Senate", "delayed", "confirming", "his", "nomination", "."], "ner": ["O", "B-PER", "I-PER", "O", "O", "O", "O", "O", "O", "O", "O", "B-PER", "O", "O", "O", "O", "O", "O", "B-ORG", "O", "O", "O", "O", "O"]}
{"words": ["goals", "for", ",", "goals", "against", ",", "points", ")", "."], "ner": ["O", "O", "O", "O", "O", "O", "O", "O", "O"]}
{"words": ["\"", "It", "is", "one", "step", "short", "of", "an", "emergency", "situation", ",", "\"", "a", "police", "spokesman", "said", "via", "telephone", "from", "a", "command", "post", "in", "the", "bush", "."], "ner": ["O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O", "O"]}
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