run_wtq.py

#!/usr/bin/env python
# coding=utf-8
# Copyright 2022 The Microsoft and The HuggingFace Inc. 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.

"""
Fine-tuning the library models for tapex on table-based question answering tasks.
Adapted from script: https://github.com/huggingface/transformers/blob/master/examples/pytorch/summarization/run_summarization.py
"""

import logging
import os
import sys
from collections import defaultdict
from dataclasses import dataclass, field
from functools import partial
from typing import List, Optional

import nltk  # Here to have a nice missing dependency error message early on
import numpy as np
import pandas as pd
import json
from datasets import load_dataset

import transformers
from filelock import FileLock
from transformers import (
    AutoConfig,
    BartForConditionalGeneration,
    DataCollatorForSeq2Seq,
    HfArgumentParser,
    Seq2SeqTrainer,
    Seq2SeqTrainingArguments,
    TapexTokenizer,
    set_seed,
)
from transformers.file_utils import is_offline_mode
from transformers.trainer_utils import get_last_checkpoint, is_main_process
from transformers.utils import check_min_version


# Will error if the minimal version of Transformers is not installed. Remove at your own risks.
check_min_version("4.17.0.dev0")

logger = logging.getLogger(__name__)
os.environ["WANDB_PROJECT"] = "reastap_wtq_march"

try:
    nltk.data.find("tokenizers/punkt")
except (LookupError, OSError):
    if is_offline_mode():
        raise LookupError(
            "Offline mode: run this script without TRANSFORMERS_OFFLINE first to download nltk data files"
        )
    with FileLock(".lock") as lock:
        nltk.download("punkt", quiet=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. "
                "By default we use BART-large tokenizer for TAPEX-large."
            )
        },
    )
    cache_dir: Optional[str] = field(
        default=None,
        metadata={"help": "Where to store the pretrained models downloaded from huggingface.co"},
    )
    use_fast_tokenizer: bool = field(
        default=True,
        metadata={"help": "Whether to use one of the fast tokenizer (backed by the tokenizers library) or not."},
    )
    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)."
            )
        },
    )


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

    dataset_name: Optional[str] = field(
        default="wikitablequestions", 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 jsonlines or csv file)."}
    )
    validation_file: Optional[str] = field(
        default=None,
        metadata={
            "help": (
                "An optional input evaluation data file to evaluate the metrics (rouge) on (a jsonlines or csv file)."
            )
        },
    )
    test_file: Optional[str] = field(
        default=None,
        metadata={
            "help": "An optional input test data file to evaluate the metrics (rouge) on (a jsonlines or csv 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_source_length: Optional[int] = field(
        default=1024,
        metadata={
            "help": (
                "The maximum total input sequence length after tokenization. Sequences longer "
                "than this will be truncated, sequences shorter will be padded."
            )
        },
    )
    max_target_length: Optional[int] = field(
        default=128,
        metadata={
            "help": (
                "The maximum total sequence length for target text after tokenization. Sequences longer "
                "than this will be truncated, sequences shorter will be padded."
            )
        },
    )
    val_max_target_length: Optional[int] = field(
        default=None,
        metadata={
            "help": (
                "The maximum total sequence length for validation target text after tokenization. Sequences longer "
                "than this will be truncated, sequences shorter will be padded. Will default to `max_target_length`."
                "This argument is also used to override the ``max_length`` param of ``model.generate``, which is used "
                "during ``evaluate`` and ``predict``."
            )
        },
    )
    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."
            )
        },
    )
    num_beams: Optional[int] = field(
        default=None,
        metadata={
            "help": (
                "Number of beams to use for evaluation. This argument will be passed to ``model.generate``, "
                "which is used during ``evaluate`` and ``predict``."
            )
        },
    )
    ignore_pad_token_for_loss: bool = field(
        default=True,
        metadata={
            "help": "Whether to ignore the tokens corresponding to padded labels in the loss computation or not."
        },
    )
    inference_set: Optional[str] = field(
        default="validation",
        metadata={
            "help": "Use which set for inference."
        },
    )

    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."
        if self.val_max_target_length is None:
            self.val_max_target_length = self.max_target_length


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, Seq2SeqTrainingArguments))
    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()

    # 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."
            )

    # 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)],
    )
    logger.setLevel(logging.INFO if is_main_process(training_args.local_rank) else logging.WARN)

    # 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}"
    )
    # 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(f"Training/evaluation parameters {training_args}")

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

    # Get the datasets: you can either provide your own CSV/JSON 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 JSON files, this script will use the `question` column for the input question and `table` column for the corresponding table.
    #
    # 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, cache_dir=model_args.cache_dir)
    else:
        data_files = {}
        if data_args.train_file is not None:
            data_files["train"] = data_args.train_file
            extension = data_args.train_file.split(".")[-1]
        if data_args.validation_file is not None:
            data_files["validation"] = data_args.validation_file
            extension = data_args.validation_file.split(".")[-1]
        if data_args.test_file is not None:
            data_files["test"] = data_args.test_file
            extension = data_args.test_file.split(".")[-1]
        datasets = load_dataset(extension, data_files=data_files, cache_dir=model_args.cache_dir)

    # 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.

    # 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,
        cache_dir=model_args.cache_dir,
        revision=model_args.model_revision,
        use_auth_token=True if model_args.use_auth_token else None,
    )

    config.max_length = 1024
    config.early_stopping = False

    # load tapex tokenizer
    tokenizer = TapexTokenizer.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_tokenizer,
        revision=model_args.model_revision,
        use_auth_token=True if model_args.use_auth_token else None,
        add_prefix_space=True,
    )

    # load Bart based Tapex model (default tapex-large)
    model = BartForConditionalGeneration.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,
    )

    if model.config.decoder_start_token_id is None:
        raise ValueError("Make sure that `config.decoder_start_token_id` is correctly defined")

    # Preprocessing the datasets.
    # We need to tokenize inputs and targets.
    if training_args.do_train:
        column_names = datasets["train"].column_names
    elif training_args.do_eval:
        column_names = datasets["validation"].column_names
    elif training_args.do_predict:
        column_names = datasets["test"].column_names
    else:
        logger.info("There is nothing to do. Please pass `do_train`, `do_eval` and/or `do_predict`.")
        return

    # Temporarily set max_target_length for training.
    max_target_length = data_args.max_target_length
    padding = "max_length" if data_args.pad_to_max_length else False

    if training_args.label_smoothing_factor > 0 and not hasattr(model, "prepare_decoder_input_ids_from_labels"):
        logger.warning(
            "label_smoothing is enabled but the `prepare_decoder_input_ids_from_labels` method is not defined for"
            f"`{model.__class__.__name__}`. This will lead to loss being calculated twice and will take up more memory"
        )

    def preprocess_tableqa_function(examples, is_training=False):
        """
        The is_training FLAG is used to identify if we could use the supervision
        to truncate the table content if it is required.
        """

        questions = [question.lower() for question in examples["question"]]
        example_tables = examples["table"]
        tables = [
            pd.DataFrame.from_records(example_table["rows"], columns=example_table["header"])
            for example_table in example_tables
        ]

        # using wikitablequestion's answer set
        answers = examples["answers"]

        # IMPORTANT: we cannot pass by answers during evaluation, answers passed during training are used to
        # truncate large tables in the train set!
        if is_training:
            model_inputs = tokenizer(
                table=tables,
                query=questions,
                answer=answers,
                max_length=data_args.max_source_length,
                padding=padding,
                truncation=True,
            )
        else:
            model_inputs = tokenizer(
                table=tables, query=questions, max_length=data_args.max_source_length, padding=padding, truncation=True
            )

        labels = tokenizer(
            answer=[", ".join(answer) for answer in answers],
            max_length=max_target_length,
            padding=padding,
            truncation=True,
        )

        # If we are padding here, replace all tokenizer.pad_token_id in the labels by -100 when we want to ignore
        # padding in the loss.
        if padding == "max_length" and data_args.ignore_pad_token_for_loss:
            labels["input_ids"] = [
                [(l if l != tokenizer.pad_token_id else -100) for l in label] for label in labels["input_ids"]
            ]

        model_inputs["labels"] = labels["input_ids"]

        return model_inputs

    # in training, we can use the answer as extra information to truncate large tables
    preprocess_tableqa_function_training = partial(preprocess_tableqa_function, is_training=True)

    if training_args.do_train:
        if "train" not in datasets:
            raise ValueError("--do_train requires a train dataset")
        train_dataset = datasets["train"]
        if data_args.max_train_samples is not None:
            train_dataset = train_dataset.select(range(data_args.max_train_samples))
        train_dataset = train_dataset.map(
            preprocess_tableqa_function_training,
            batched=True,
            num_proc=data_args.preprocessing_num_workers,
            remove_columns=column_names,
            load_from_cache_file=not data_args.overwrite_cache,
        )

    if training_args.do_eval:
        max_target_length = data_args.val_max_target_length

        inference_set = data_args.inference_set
        eval_dataset = datasets[inference_set]
        if data_args.max_eval_samples is not None:
            eval_dataset = eval_dataset.select(range(data_args.max_eval_samples))
        eval_dataset = eval_dataset.map(
            preprocess_tableqa_function,
            batched=True,
            num_proc=data_args.preprocessing_num_workers,
            remove_columns=column_names,
            load_from_cache_file=not data_args.overwrite_cache,
        )

    if training_args.do_predict:
        max_target_length = data_args.val_max_target_length

        inference_set = data_args.inference_set
        predict_dataset = datasets[inference_set]
        raw_predict_dataset = datasets[inference_set]
        if data_args.max_predict_samples is not None:
            predict_dataset = predict_dataset.select(range(data_args.max_predict_samples))
        predict_dataset = predict_dataset.map(
            preprocess_tableqa_function,
            batched=True,
            num_proc=data_args.preprocessing_num_workers,
            remove_columns=column_names,
            load_from_cache_file=not data_args.overwrite_cache,
        )

    # Data collator
    label_pad_token_id = -100 if data_args.ignore_pad_token_for_loss else tokenizer.pad_token_id
    data_collator = DataCollatorForSeq2Seq(
        tokenizer,
        model=model,
        label_pad_token_id=label_pad_token_id,
        pad_to_multiple_of=8 if training_args.fp16 else None,
    )

    def postprocess_text(preds, labels):
        preds = [pred.strip() for pred in preds]
        labels = [label.strip() for label in labels]

        return preds, labels

    def compute_metrics(eval_preds):
        preds, labels = eval_preds
        if isinstance(preds, tuple):
            preds = preds[0]
        decoded_preds = tokenizer.batch_decode(preds, skip_special_tokens=True)
        if data_args.ignore_pad_token_for_loss:
            # Replace -100 in the labels as we can't decode them.
            labels = np.where(labels != -100, labels, tokenizer.pad_token_id)
        decoded_labels = tokenizer.batch_decode(labels, skip_special_tokens=True)

        # Some simple post-processing
        decoded_preds, decoded_labels = postprocess_text(decoded_preds, decoded_labels)

        delimiter = ", "

        # define example evaluation
        def evaluate_example(predict_str: str, ground_str: str):
            predict_spans = predict_str.split(delimiter)
            ground_spans = ground_str.split(delimiter)
            predict_values = defaultdict(lambda: 0)
            ground_values = defaultdict(lambda: 0)
            for span in predict_spans:
                try:
                    predict_values[float(span)] += 1
                except ValueError:
                    predict_values[span.strip()] += 1
            for span in ground_spans:
                try:
                    ground_values[float(span)] += 1
                except ValueError:
                    ground_values[span.strip()] += 1
            _is_correct = predict_values == ground_values
            return _is_correct

        def get_denotation_accuracy(predictions: List[str], references: List[str]):
            assert len(predictions) == len(references)
            correct_num = 0
            for predict_str, ground_str in zip(predictions, references):
                is_correct = evaluate_example(predict_str.lower(), ground_str.lower())
                if is_correct:
                    correct_num += 1
            return correct_num / len(predictions)

        accuracy = get_denotation_accuracy(decoded_preds, decoded_labels)
        result = {"denotation_accuracy": accuracy}

        return result

    # Initialize our Trainer
    trainer = Seq2SeqTrainer(
        model=model,
        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 if training_args.predict_with_generate else None,
    )

    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.train(resume_from_checkpoint=checkpoint)
        trainer.save_model()  # Saves the tokenizer too for easy upload

        metrics = train_result.metrics
        max_train_samples = (
            data_args.max_train_samples if data_args.max_train_samples is not None else len(train_dataset)
        )
        metrics["train_samples"] = min(max_train_samples, len(train_dataset))

        trainer.log_metrics("train", metrics)
        trainer.save_metrics("train", metrics)
        trainer.save_state()

    # Evaluation
    results = {}
    if training_args.do_eval:
        logger.info("*** Evaluate ***")

        print(data_args.inference_set)
        metrics = trainer.evaluate(
            max_length=data_args.val_max_target_length, num_beams=data_args.num_beams, metric_key_prefix="eval"
        )
        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)
        

    if training_args.do_predict:
        logger.info("*** Predict ***")

        predict_results = trainer.predict(
            predict_dataset,
            metric_key_prefix="predict",
            max_length=data_args.val_max_target_length,
            num_beams=data_args.num_beams,
        )
        metrics = predict_results.metrics
        max_predict_samples = (
            data_args.max_predict_samples if data_args.max_predict_samples is not None else len(predict_dataset)
        )
        metrics["predict_samples"] = min(max_predict_samples, len(predict_dataset))

        trainer.log_metrics("predict", metrics)

        predictions = tokenizer.batch_decode(
            predict_results.predictions, skip_special_tokens=True, clean_up_tokenization_spaces=True
        )
        predictions = [pred.strip() for pred in predictions]
        
        outputs = []
        for i, pred in enumerate(predictions):
            example = raw_predict_dataset[i]
            answer = ", ".join([i.lower() for i in example["answers"]])
            example_id = example["id"]
            outputs.append({"id": example_id, "prediction": pred, "answers": answer})

        model_name = model_args.model_name_or_path.split("/")[-1].split("-")[0]
        output_prediction_file = os.path.join(training_args.output_dir, f"{model_name}_{data_args.inference_set}_predictions.json")
        json.dump(outputs, open(output_prediction_file, "w"), indent=4)

    return results


def _mp_fn(index):
    # For xla_spawn (TPUs)
    main()


if __name__ == "__main__":
    main()