tune_rales_ner.py

"""
Perform evaluation on RaLEs NER tasks

Adapted from:
transformers/examples/pytorch/token-classification/run_ner.py  (358478e)

Changes:
    -modified for command line support
    -adapted for hyperparameter exploration with optuna
    -added support for RaLEs datasets
    -adding specific path for cache
"""

#!/usr/bin/env python
# coding=utf-8
# 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.
# 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.

import logging
import os
import sys
from dataclasses import dataclass, field
from typing import Optional

import datasets
import numpy as np
from datasets import ClassLabel, load_dataset

import evaluate
import transformers
from transformers import (
    AutoConfig,
    AutoModelForTokenClassification,
    AutoTokenizer,
    DataCollatorForTokenClassification,
    HfArgumentParser,
    PretrainedConfig,
    PreTrainedTokenizerFast,
    Trainer,
    TrainingArguments,
    set_seed,
)
from transformers.trainer_utils import get_last_checkpoint
from transformers.utils import check_min_version, send_example_telemetry
from transformers.utils.versions import require_version
from constants import TRANSFORMERS_DOWNLOAD_PATH, RADGRAPH_DIR, STANZA_DIR

logger = logging.getLogger(__name__)

os.environ['TRANSFORMERS_CACHE'] = TRANSFORMERS_DOWNLOAD_PATH
os.environ['TOKENIZERS_PARALLELISM']="true"

@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"}
    )
    tokenizer_name: Optional[str] = field(
        default=None, metadata={"help": "Pretrained tokenizer name or path if not the same as model_name"}
    )
    cache_dir: Optional[str] = field(
        default=None,
        metadata={"help": "Where do you want to store the pretrained models downloaded from huggingface.co"},
    )
    model_revision: str = field(
        default="main",
        metadata={"help": "The specific model version to use (can be a branch name, tag name or commit id)."},
    )
    use_auth_token: bool = field(
        default=False,
        metadata={
            "help": (
                "Will use the token generated when running `huggingface-cli login` (necessary to use this script "
                "with private models)."
            )
        },
    )
    ignore_mismatched_sizes: bool = field(
        default=False,
        metadata={"help": "Will enable to load a pretrained model whose head dimensions are different."},
    )
    linear_probe: bool = field(
        default=False,
        metadata={"help": "If true freezes base model weights and enables linear probe training."}
    )


@dataclass
class DataTrainingArguments:
    """
    Arguments pertaining to what data we are going to input our model for training and eval.
    """

    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)."}
    )
    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": "An optional input evaluation data file to evaluate on (a csv or JSON file)."},
    )
    test_file: Optional[str] = field(
        default=None,
        metadata={"help": "An optional input test data file to predict on (a csv or JSON file)."},
    )
    text_column_name: Optional[str] = field(
        default=None, metadata={"help": "The column name of text to input in the file (a csv or JSON file)."}
    )
    label_column_name: Optional[str] = field(
        default=None, metadata={"help": "The column name of label to input in the file (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."},
    )
    max_seq_length: int = field(
        default=None,
        metadata={
            "help": (
                "The maximum total input sequence length after tokenization. If set, sequences longer "
                "than this will be truncated, sequences shorter will be padded."
            )
        },
    )
    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."
            )
        },
    )
    max_train_samples: Optional[int] = field(
        default=None,
        metadata={
            "help": (
                "For debugging purposes or quicker training, truncate the number of training examples to this "
                "value if set."
            )
        },
    )
    max_eval_samples: Optional[int] = field(
        default=None,
        metadata={
            "help": (
                "For debugging purposes or quicker training, truncate the number of evaluation examples to this "
                "value if set."
            )
        },
    )
    max_predict_samples: Optional[int] = field(
        default=None,
        metadata={
            "help": (
                "For debugging purposes or quicker training, truncate the number of prediction examples to this "
                "value if set."
            )
        },
    )
    do_crossval: str = field(
        default=False,
        metadata={
            "help": "Whether to do crossvalidation with the training dataset, outputting statistics for all folds (relevant for RadSpRl). Seeds will be set arbitrarily."
        },
    )
    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)."
            )
        },
    )
    return_entity_level_metrics: bool = field(
        default=True,
        metadata={"help": "Whether to return all the entity levels during evaluation or just the overall ones."},
    )

    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 run_ner(config_mods=None, eval_name=None, task=None):
    parser = HfArgumentParser((ModelArguments, DataTrainingArguments, TrainingArguments))
    if len(sys.argv) == 2 and sys.argv[1].endswith(".json"):
        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()

    send_example_telemetry("run_ner", model_args, data_args)
    if config_mods is not None:
        model_args = config_mods(model_args)
        data_args = config_mods(data_args)
        training_args = config_mods(training_args)
    # Setup logging
    logging.basicConfig(
        format="%(asctime)s - %(levelname)s - %(name)s - %(message)s",
        datefmt="%m/%d/%Y %H:%M:%S",
        handlers=[logging.StreamHandler(sys.stdout)],
    )

    log_level = training_args.get_process_log_level()
    logger.setLevel(log_level)
    
    transformers.utils.logging.set_verbosity(log_level)
    transformers.utils.logging.enable_default_handler()
    transformers.utils.logging.enable_explicit_format()

    # Log on each process the small summary:
    logger.warning(
        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}"
    )
    logger.info(f"Training/evaluation parameters {training_args}")

    # Detecting last checkpoint.
    last_checkpoint = None
    if os.path.isdir(training_args.output_dir) and training_args.do_train and not training_args.overwrite_output_dir:
        last_checkpoint = get_last_checkpoint(training_args.output_dir)
        if last_checkpoint is None and len(os.listdir(training_args.output_dir)) > 0:
            raise ValueError(
                f"Output directory ({training_args.output_dir}) already exists and is not empty. "
                "Use --overwrite_output_dir to overcome."
            )
        elif last_checkpoint is not None and training_args.resume_from_checkpoint is None:
            logger.info(
                f"Checkpoint detected, resuming training at {last_checkpoint}. To avoid this behavior, change "
                "the `--output_dir` or add `--overwrite_output_dir` to train from scratch."
            )

    # Set seed before initializing model.
    set_seed(training_args.seed)

    if data_args.dataset_name is not None:
        # Downloading and loading a dataset from the hub.
        raw_datasets = load_dataset(
            data_args.dataset_name,
            data_args.dataset_config_name,
            cache_dir=model_args.cache_dir,
            use_auth_token=True if model_args.use_auth_token else None,
        )
    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]

        if bool(data_args.do_crossval): #10-fold CV
            datasets = {}
            datasets['validation'] = load_dataset(extension, data_files=data_files['train'], split=[
                            f'train[{k}%:{k+10}%]' for k in range(0, 100, 10)
                        ])
            datasets['train'] = load_dataset(extension, data_files=data_files['train'], split=[
                            f'train[:{k}%]+train[{k+10}%:]' for k in range(0, 100, 10)
                        ])
        else:
            raw_datasets = load_dataset(extension, data_files=data_files, cache_dir=model_args.cache_dir)

    if training_args.do_train:
        column_names = raw_datasets["train"].column_names
        features = raw_datasets["train"].features
    elif bool(data_args.do_crossval):
        column_names = datasets['train'][0].column_names
        features = datasets['train'][0].features
    else:
        column_names = raw_datasets["validation"].column_names
        features = raw_datasets["validation"].features

    if data_args.text_column_name is not None:
        text_column_name = data_args.text_column_name
    elif "tokens" in column_names:
        text_column_name = "tokens"
    else:
        text_column_name = column_names[0]

    if data_args.label_column_name is not None:
        label_column_name = data_args.label_column_name
    elif f"{data_args.task_name}_tags" in column_names:
        label_column_name = f"{data_args.task_name}_tags"
    elif "tokens" in column_names:
        label_column_name = "tokens"
    else:
        label_column_name = column_names[1]

    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

    labels_are_int = isinstance(features[label_column_name].feature, ClassLabel)
    if labels_are_int:
        label_list = features[label_column_name].feature.names
        label_to_id = {i: i for i in range(len(label_list))}
    else:
        label_list = get_label_list(raw_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
    config = AutoConfig.from_pretrained(
        model_args.config_name if model_args.config_name else model_args.model_name_or_path,
        num_labels=num_labels,
        finetuning_task=data_args.task_name,
        cache_dir=model_args.cache_dir,
        revision=model_args.model_revision,
        use_auth_token=True if model_args.use_auth_token else None,
    )

    tokenizer_name_or_path = model_args.tokenizer_name if model_args.tokenizer_name else model_args.model_name_or_path
    if config.model_type in {"bloom", "gpt2", "roberta"}:
        tokenizer = AutoTokenizer.from_pretrained(
            tokenizer_name_or_path,
            cache_dir=model_args.cache_dir,
            use_fast=True,
            revision=model_args.model_revision,
            use_auth_token=True if model_args.use_auth_token else None,
            add_prefix_space=True,
        )
    else:
        tokenizer = AutoTokenizer.from_pretrained(
            tokenizer_name_or_path,
            cache_dir=model_args.cache_dir,
            use_fast=True,
            revision=model_args.model_revision,
            use_auth_token=True if model_args.use_auth_token else None,
        )

    # Tokenizer check: this script requires a fast tokenizer.
    if not isinstance(tokenizer, PreTrainedTokenizerFast):
        raise ValueError(
            "This example script only works for models that have a fast tokenizer. Checkout the big table of models at"
            " https://huggingface.co/transformers/index.html#supported-frameworks to find the model types that meet"
            " this requirement"
        )

    # Model has labels -> use them.
    if config.label2id != PretrainedConfig(num_labels=num_labels).label2id:
        if list(sorted(config.label2id.keys())) == list(sorted(label_list)):
            # Reorganize `label_list` to match the ordering of the model.
            if labels_are_int:
                label_to_id = {i: int(config.label2id[l]) for i, l in enumerate(label_list)}
                label_list = [config.id2label[i] for i in range(num_labels)]
            else:
                label_list = [config.id2label[i] for i in range(num_labels)]
                label_to_id = {l: i for i, l in enumerate(label_list)}
        else:
            logger.warning(
                "Your model seems to have been trained with labels, but they don't match the dataset: ",
                f"model labels: {list(sorted(config.label2id.keys()))}, dataset labels:"
                f" {list(sorted(label_list))}.\nIgnoring the model labels as a result.",
            )

    # Set the correspondences label/ID inside the model config
    config.label2id = {l: i for i, l in enumerate(label_list)}
    config.id2label = {i: l for i, l in enumerate(label_list)}
    
    def model_init(lp=model_args.linear_probe):
        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,
            revision=model_args.model_revision,
            use_auth_token=True if model_args.use_auth_token else None,
            ignore_mismatched_sizes=model_args.ignore_mismatched_sizes,
        )
        if lp:
            for param in model.base_model.parameters():
                param.requires_grad = False
        return model
    
    # Map that sends B-Xxx label to its I-Xxx counterpart
    b_to_i_label = []
    for idx, label in enumerate(label_list):
        if label.startswith("B-") and label.replace("B-", "I-") in label_list:
            b_to_i_label.append(label_list.index(label.replace("B-", "I-")))
        else:
            b_to_i_label.append(idx)
    
    # 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,
            max_length=data_args.max_seq_length,
            is_split_into_words=True,
        )
        labels = []
        for i, label in enumerate(examples[label_column_name]):
            word_ids = tokenized_inputs.word_ids(batch_index=i)
            previous_word_idx = None
            label_ids = []
            for word_idx in word_ids:
                # Special tokens have a word id that is None. We set the label to -100 so they are automatically
                # ignored in the loss function.
                if word_idx is None:
                    label_ids.append(-100)
                # We set the label for the first token of each word.
                elif word_idx != previous_word_idx:
                    label_ids.append(label_to_id[label[word_idx]])
                else:
                    if data_args.label_all_tokens:
                        label_ids.append(b_to_i_label[label_to_id[label[word_idx]]])
                    else:
                        label_ids.append(-100)
                previous_word_idx = word_idx

            labels.append(label_ids)
        tokenized_inputs["labels"] = labels
        return tokenized_inputs

    if training_args.do_train:
        if "train" not in raw_datasets:
            raise ValueError("--do_train requires a train dataset")
        train_dataset = raw_datasets["train"]
        if data_args.max_train_samples is not None:
            max_train_samples = min(len(train_dataset), data_args.max_train_samples)
            train_dataset = train_dataset.select(range(max_train_samples))
        with training_args.main_process_first(desc="train dataset map pre-processing"):
            train_dataset = train_dataset.map(
                tokenize_and_align_labels,
                batched=True,
                num_proc=data_args.preprocessing_num_workers,
                load_from_cache_file=not data_args.overwrite_cache,
                desc="Running tokenizer on train dataset",
            )

    if training_args.do_eval:
        if "validation" not in raw_datasets:
            raise ValueError("--do_eval requires a validation dataset")
        eval_dataset = raw_datasets["validation"]
        if data_args.max_eval_samples is not None:
            max_eval_samples = min(len(eval_dataset), data_args.max_eval_samples)
            eval_dataset = eval_dataset.select(range(max_eval_samples))
        with training_args.main_process_first(desc="validation dataset map pre-processing"):
            eval_dataset = eval_dataset.map(
                tokenize_and_align_labels,
                batched=True,
                num_proc=data_args.preprocessing_num_workers,
                load_from_cache_file=not data_args.overwrite_cache,
                desc="Running tokenizer on validation dataset",
            )

    if training_args.do_predict:
        if "test" not in raw_datasets:
            raise ValueError("--do_predict requires a test dataset")
        predict_dataset = raw_datasets["test"]
        if data_args.max_predict_samples is not None:
            max_predict_samples = min(len(predict_dataset), data_args.max_predict_samples)
            predict_dataset = predict_dataset.select(range(max_predict_samples))
        with training_args.main_process_first(desc="prediction dataset map pre-processing"):
            predict_dataset = predict_dataset.map(
                tokenize_and_align_labels,
                batched=True,
                num_proc=data_args.preprocessing_num_workers,
                load_from_cache_file=not data_args.overwrite_cache,
                desc="Running tokenizer on prediction dataset",
            )

    # Data collator
    data_collator = DataCollatorForTokenClassification(tokenizer, pad_to_multiple_of=8 if training_args.fp16 else None)

    # Metrics
    metric = evaluate.load("seqeval")

    def compute_metrics(p):
        predictions, labels = p
        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)
        ]
        true_labels = [
            [label_list[l] for (p, l) in zip(prediction, label) if l != -100]
            for prediction, label in zip(predictions, labels)
        ]

        results = metric.compute(predictions=true_predictions, references=true_labels)
        if data_args.return_entity_level_metrics:
            # Unpack nested dictionaries
            final_results = {}
            for key, value in results.items():
                if isinstance(value, dict):
                    for n, v in value.items():
                        final_results[f"{key}_{n}"] = v
                else:
                    final_results[key] = value
            return final_results
        else:
            return {
                "precision": results["overall_precision"],
                "recall": results["overall_recall"],
                "f1": results["overall_f1"],
                "accuracy": results["overall_accuracy"],
            }

    # Initialize our Trainer
    trainer = Trainer(
        model_init=model_init,
        args=training_args,
        train_dataset=train_dataset if training_args.do_train else None,
        eval_dataset=eval_dataset if training_args.do_eval else None,
        tokenizer=tokenizer,
        data_collator=data_collator,
        compute_metrics=compute_metrics,
    )

    def hp_space(trial):
        """
        formatted as optuna objective (see https://optuna.readthedocs.io/en/stable/tutorial/10_key_features/002_configurations.html#sphx-glr-tutorial-10-key-features-002-configurations-py)
        """
        return {
            "learning_rate": trial.suggest_float("learning_rate", 1e-5, 1e-4, log=True),
            "num_train_epochs": trial.suggest_int("num_train_epochs", 3, 5),
            "per_device_train_batch_size": trial.suggest_categorical("per_device_train_batch_size", [16, 32]),
            "weight_decay": trial.suggest_float("weight_decay", 1e-12, 1e-1, log=True)
        }

    

    # Training
    if training_args.do_train:
        checkpoint = None
        if training_args.resume_from_checkpoint is not None:
            checkpoint = training_args.resume_from_checkpoint
        elif last_checkpoint is not None:
            checkpoint = last_checkpoint
        train_result = trainer.hyperparameter_search(
                            direction='maximize',
                            n_trials=10, 
                            hp_space=hp_space,
                            compute_objective= lambda metrics: metrics['eval_overall_f1'],
                            study_name= f'{training_args.output_dir}_{eval_name}_{task}'
                            )
        #model is saved automatically

    # Evaluation
    if training_args.do_eval:
        logger.info("*** Evaluate ***")

        metrics = trainer.evaluate()

        max_eval_samples = data_args.max_eval_samples if data_args.max_eval_samples is not None else len(eval_dataset)
        metrics["eval_samples"] = min(max_eval_samples, len(eval_dataset))

        trainer.log_metrics("eval", metrics)
        trainer.save_metrics("eval", metrics)

    kwargs = {"finetuned_from": model_args.model_name_or_path, "tasks": "token-classification"}
    if data_args.dataset_name is not None:
        kwargs["dataset_tags"] = data_args.dataset_name
        if data_args.dataset_config_name is not None:
            kwargs["dataset_args"] = data_args.dataset_config_name
            kwargs["dataset"] = f"{data_args.dataset_name} {data_args.dataset_config_name}"
        else:
            kwargs["dataset"] = data_args.dataset_name

    
    trainer.create_model_card(**kwargs)

def do_ner_rales(task, config):
    # add the model attributes to arguments for HF argparser compatibility   
    
    sys.argv = ['tune_rales_ner.py'] 
    sys.argv += ['--model_name_or_path', config['model_name_or_path']]
    sys.argv += ['--tokenizer_name', config['tokenizer_path']]
    sys.argv += ['--cache_dir', config['cache_dir']]
    sys.argv += ['--output_dir', os.path.join(config['output_dir'], config['eval_name']+'_'+task)]
    
    sys.argv += ['--evaluation_strategy', 'epoch']
    sys.argv += ['--logging_strategy', 'epoch']
    sys.argv += ['--save_strategy', 'epoch']
    sys.argv += ['--load_best_model_at_end', 'True']
    sys.argv += ['--metric_for_best_model', 'overall_f1']
    sys.argv += ['--save_total_limit', '1']

    sys.argv += ['--do_train', '--do_eval']
    if 'linear_probe' in config and config['linear_probe']==True:
        sys.argv += ['--linear_probe']
        
    if task == 'stanza_ner':
        train_file = os.path.join(STANZA_DIR, 'train.json')
        validation_file = os.path.join(STANZA_DIR, 'dev.json')
        sys.argv += ['--train_file', train_file]
        sys.argv += ['--validation_file', validation_file]
        
    if task == 'stanza_ner_10pct':
        train_file = os.path.join(STANZA_DIR, 'train_10pct.json')
        validation_file = os.path.join(STANZA_DIR, 'dev_10pct.json')
        sys.argv += ['--train_file', train_file]
        sys.argv += ['--validation_file', validation_file]
                
    if task == 'stanza_ner_1pct':
        train_file = os.path.join(STANZA_DIR, 'train_1pct.json')
        validation_file = os.path.join(STANZA_DIR, 'dev_1pct.json')
        sys.argv += ['--train_file', train_file]
        sys.argv += ['--validation_file', validation_file]
        
    run_ner(eval_name=config['eval_name'], task=task)
if __name__ == "__main__":
    run_ner()