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>

examples/README.md

@@ -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)

examples/test_examples.py

@@ -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)

examples/token-classification/README.md

-## 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
 

examples/token-classification/run.sh

-## 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

examples/token-classification/run_chunk.sh

@@ -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 \

examples/token-classification/run_ner.py

 # 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)."}
+    )
+    dataset_config_name: Optional[str] = field(
+        default=None, metadata={"help": "The configuration name of the dataset to use (via the datasets library)."}
     )
-    labels: Optional[str] = field(
+    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
+        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,
     )
-    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
+    # Data collator
+    data_collator = DataCollatorForTokenClassification(tokenizer)
 
-        out_label_list = [[] for _ in range(batch_size)]
-        preds_list = [[] for _ in range(batch_size)]
+    # Metrics
+    def compute_metrics(p):
+        predictions, labels = p
+        predictions = np.argmax(predictions, axis=2)
 
-        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]])
+        # 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)
+        ]
 
-        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 ***")
+
+        test_dataset = datasets["test"]
+        predictions, labels, metrics = trainer.predict(test_dataset)
+        predictions = np.argmax(predictions, axis=2)
 
-        predictions, label_ids, metrics = trainer.predict(test_dataset)
-        preds_list, _ = align_predictions(predictions, label_ids)
+        # 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
 

examples/token-classification/run_ner_old.py

+# 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()

examples/token-classification/run_old.sh

+## 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

examples/token-classification/run_pos.sh

@@ -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 \

examples/token-classification/test_ner_examples.py

@@ -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
 
 

model_cards/mrm8488/RuPERTa-base-finetuned-ner/README.md

@@ -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:
 

model_cards/mrm8488/RuPERTa-base-finetuned-pos/README.md

@@ -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:
 

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

@@ -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:
 

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

@@ -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):

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

@@ -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 📋
 

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

@@ -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:
 

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

@@ -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:
 

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

@@ -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:
 

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

@@ -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 📋
 

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

@@ -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 \