examples/pytorch/token-classification/run_ner.py/compute_metrics
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()

    # 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)
    datasets.utils.logging.set_verbosity(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)

    # 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.
        raw_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
        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]
        raw_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.

    if training_args.do_train:
        column_names = raw_datasets["train"].column_names
        features = raw_datasets["train"].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"
    else:
        label_column_name = column_names[1]

    # In the event the labels are not a `Sequence[ClassLabel]`, we will need to go through the dataset to get the
    # unique labels.
    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

    if isinstance(features[label_column_name].feature, ClassLabel):
        label_list = features[label_column_name].feature.names
        # No need to convert the labels since they are already ints.
        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
    #
    # 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,
        label2id=label_to_id,
        id2label={i: l for l, i in label_to_id.items()},
        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 {"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,
        )

    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,
    )

    # 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"
        )

    # 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,
            # 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,
        )
        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]])
                # 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(label_to_id[label[word_idx]] if data_args.label_all_tokens else -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:
            train_dataset = train_dataset.select(range(data_args.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:
            eval_dataset = eval_dataset.select(range(data_args.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:
            predict_dataset = predict_dataset.select(range(data_args.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 = load_metric("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=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,
    )

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

        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
    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)

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

        predictions, labels, metrics = trainer.predict(predict_dataset, metric_key_prefix="predict")
        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)
        ]

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

        # Save predictions
        output_predictions_file = os.path.join(training_args.output_dir, "predictions.txt")
        if trainer.is_world_process_zero():
            with open(output_predictions_file, "w") as writer:
                for prediction in true_predictions:
                    writer.write(" ".join(prediction) + "\n")

    if training_args.push_to_hub:
        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.push_to_hub(**kwargs)