NER: Add new WNUT’17 example (#4681)

* ner: add preprocessing script for examples that splits longer sentences

* ner: example shell scripts use local preprocessing now

* ner: add new example section for WNUT’17 NER task. Remove old English CoNLL-03 results

* ner: satisfy black and isort

examples/token-classification/README.md

@@ -2,10 +2,17 @@
 
 Based on the scripts [`run_ner.py`](https://github.com/huggingface/transformers/blob/master/examples/token-classification/run_ner.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.
-This example fine-tune Bert Multilingual on GermEval 2014 (German NER).
+
+The following examples are covered in this section:
+
+* NER on the GermEval 2014 (German NER) dataset
+* Emerging and Rare Entities task: WNUT’17 (English NER) dataset
+
 Details and results for the fine-tuning provided by @stefan-it.
 
-### Data (Download and pre-processing steps)
+### GermEval 2014 (German NER) dataset
+
+#### Data (Download and pre-processing steps)
 
 Data can be obtained from the [GermEval 2014](https://sites.google.com/site/germeval2014ner/data) shared task page.
 
@@ -20,11 +27,10 @@ curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-test.tsv?attr
 | grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > test.txt.tmp
 ```
 
-The GermEval 2014 dataset contains some strange "control character" tokens like `'\x96', '\u200e', '\x95', '\xad' or '\x80'`. One problem with these tokens is, that `BertTokenizer` returns an empty token for them, resulting in misaligned `InputExample`s. I wrote a script that a) filters these tokens and b) splits longer sentences into smaller ones (once the max. subtoken length is reached).
+The GermEval 2014 dataset contains some strange "control character" tokens like `'\x96', '\u200e', '\x95', '\xad' or '\x80'`.
+One problem with these tokens is, that `BertTokenizer` returns an empty token for them, resulting in misaligned `InputExample`s.
+The `preprocess.py` script located in the `scripts` folder a) filters these tokens and b) splits longer sentences into smaller ones (once the max. subtoken length is reached).
 
-```bash
-wget "https://raw.githubusercontent.com/stefan-it/fine-tuned-berts-seq/master/scripts/preprocess.py"
-```
 Let's define some variables that we need for further pre-processing steps and training the model:
 
 ```bash
@@ -35,9 +41,9 @@ export BERT_MODEL=bert-base-multilingual-cased
 Run the pre-processing script on training, dev and test datasets:
 
 ```bash
-python3 preprocess.py train.txt.tmp $BERT_MODEL $MAX_LENGTH > train.txt
-python3 preprocess.py dev.txt.tmp $BERT_MODEL $MAX_LENGTH > dev.txt
-python3 preprocess.py test.txt.tmp $BERT_MODEL $MAX_LENGTH > test.txt
+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
 ```
 
 The GermEval 2014 dataset has much more labels than CoNLL-2002/2003 datasets, so an own set of labels must be used:
@@ -46,7 +52,7 @@ The GermEval 2014 dataset has much more labels than CoNLL-2002/2003 datasets, so
 cat train.txt dev.txt test.txt | cut -d " " -f 2 | grep -v "^$"| sort | uniq > labels.txt
 ```
 
-### Prepare the run
+#### Prepare the run
 
 Additional environment variables must be set:
 
@@ -58,7 +64,7 @@ export SAVE_STEPS=750
 export SEED=1
 ```
 
-### Run the Pytorch version
+#### Run the Pytorch version
 
 To start training, just run:
 
@@ -79,7 +85,7 @@ python3 run_ner.py --data_dir ./ \
 
 If your GPU supports half-precision training, just add the `--fp16` flag. After training, the model will be both evaluated on development and test datasets.
 
-### JSON-based configuration file
+#### 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:
 
@@ -124,16 +130,6 @@ On the test dataset the following results could be achieved:
 10/04/2019 00:42:42 - INFO - __main__ -     recall = 0.8624150210424085
 ```
 
-#### Comparing BERT (large, cased), RoBERTa (large, cased) and DistilBERT (base, uncased)
-
-Here is a small comparison between BERT (large, cased), RoBERTa (large, cased) and DistilBERT (base, uncased) with the same hyperparameters as specified in the [example documentation](https://huggingface.co/transformers/examples.html#named-entity-recognition) (one run):
-
-| Model | F-Score Dev | F-Score Test
-| --------------------------------- | ------- | --------
-| `bert-large-cased`            | 95.59 | 91.70
-| `roberta-large`                  | 95.96 | 91.87
-| `distilbert-base-uncased` | 94.34 | 90.32
-
 #### Run PyTorch version using PyTorch-Lightning
 
 Run `bash run_pl.sh` from the `ner` directory. This would also install `pytorch-lightning` and the `examples/requirements.txt`. It is a shell pipeline which would automatically download, pre-process the data and run the models in `germeval-model` directory. Logs are saved in `lightning_logs` directory.
@@ -141,7 +137,7 @@ Run `bash run_pl.sh` from the `ner` directory. This would also install `pytorch-
 Pass `--n_gpu` flag to change the number of GPUs. Default uses 1. At the end, the expected results are: `TEST RESULTS {'val_loss': tensor(0.0707), 'precision': 0.852427800698191, 'recall': 0.869537067011978, 'f1': 0.8608974358974358}`
 
 
-### Run the Tensorflow 2 version
+#### Run the Tensorflow 2 version
 
 To start training, just run:
 
@@ -205,3 +201,102 @@ On the test dataset the following results could be achieved:
 micro avg     0.8722    0.8774    0.8748     13869
 macro avg     0.8712    0.8774    0.8740     13869
 ```
+
+### Emerging and Rare Entities task: WNUT’17 (English NER) dataset
+
+Description of the WNUT’17 task from the [shared task website](http://noisy-text.github.io/2017/index.html):
+
+> The WNUT’17 shared task focuses on identifying unusual, previously-unseen entities in the context of emerging discussions.
+> Named entities form the basis of many modern approaches to other tasks (like event clustering and summarization), but recall on
+> them is a real problem in noisy text - even among annotators. This drop tends to be due to novel entities and surface forms.
+
+Six labels are available in the dataset. An overview can be found on this [page](http://noisy-text.github.io/2017/files/).
+
+#### Data (Download and pre-processing steps)
+
+The dataset can be downloaded from the [official GitHub](https://github.com/leondz/emerging_entities_17) repository.
+
+The following commands show how to prepare the dataset for fine-tuning:
+
+```bash
+mkdir -p data_wnut_17
+
+curl -L 'https://github.com/leondz/emerging_entities_17/raw/master/wnut17train.conll'  | tr '\t' ' ' > data_wnut_17/train.txt.tmp
+curl -L 'https://github.com/leondz/emerging_entities_17/raw/master/emerging.dev.conll' | tr '\t' ' ' > data_wnut_17/dev.txt.tmp
+curl -L 'https://raw.githubusercontent.com/leondz/emerging_entities_17/master/emerging.test.annotated' | tr '\t' ' ' > data_wnut_17/test.txt.tmp
+```
+
+Let's define some variables that we need for further pre-processing steps:
+
+```bash
+export MAX_LENGTH=128
+export BERT_MODEL=bert-large-cased
+```
+
+Here we use the English BERT large model for fine-tuning.
+The `preprocess.py` scripts splits longer sentences into smaller ones (once the max. subtoken length is reached):
+
+```bash
+python3 scripts/preprocess.py data_wnut_17/train.txt.tmp $BERT_MODEL $MAX_LENGTH > data_wnut_17/train.txt
+python3 scripts/preprocess.py data_wnut_17/dev.txt.tmp $BERT_MODEL $MAX_LENGTH > data_wnut_17/dev.txt
+python3 scripts/preprocess.py data_wnut_17/test.txt.tmp $BERT_MODEL $MAX_LENGTH > data_wnut_17/test.txt
+```
+
+In the last pre-processing step, the `labels.txt` file needs to be generated. This file contains all available labels:
+
+```bash
+cat data_wnut_17/train.txt data_wnut_17/dev.txt data_wnut_17/test.txt | cut -d " " -f 2 | grep -v "^$"| sort | uniq > data_wnut_17/labels.txt
+```
+
+#### 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.
+
+This configuration file looks like:
+
+```json
+{
+    "data_dir": "./data_wnut_17",
+    "labels": "./data_wnut_17/labels.txt",
+    "model_name_or_path": "bert-large-cased",
+    "output_dir": "wnut-17-model-1",
+    "max_seq_length": 128,
+    "num_train_epochs": 3,
+    "per_device_train_batch_size": 32,
+    "save_steps": 425,
+    "seed": 1,
+    "do_train": true,
+    "do_eval": true,
+    "do_predict": true,
+    "fp16": false
+}
+```
+
+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`.
+
+#### Evaluation
+
+Evaluation on development dataset outputs the following:
+
+```bash
+05/29/2020 23:33:44 - INFO - __main__ -   ***** Eval results *****
+05/29/2020 23:33:44 - INFO - __main__ -     eval_loss = 0.26505235286212275
+05/29/2020 23:33:44 - INFO - __main__ -     eval_precision = 0.7008264462809918
+05/29/2020 23:33:44 - INFO - __main__ -     eval_recall = 0.507177033492823
+05/29/2020 23:33:44 - INFO - __main__ -     eval_f1 = 0.5884802220680084
+05/29/2020 23:33:44 - INFO - __main__ -     epoch = 3.0
+```
+
+On the test dataset the following results could be achieved:
+
+```bash
+05/29/2020 23:33:44 - INFO - transformers.trainer -   ***** Running Prediction *****
+05/29/2020 23:34:02 - INFO - __main__ -     eval_loss = 0.30948806500973547
+05/29/2020 23:34:02 - INFO - __main__ -     eval_precision = 0.5840108401084011
+05/29/2020 23:34:02 - INFO - __main__ -     eval_recall = 0.3994439295644115
+05/29/2020 23:34:02 - INFO - __main__ -     eval_f1 = 0.47440836543753434
+```
+
+WNUT’17 is a very difficult task. Current state-of-the-art results on this dataset can be found [here](http://nlpprogress.com/english/named_entity_recognition.html).

examples/token-classification/run.sh

@@ -4,12 +4,12 @@ curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-dev.tsv?attre
 | grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > dev.txt.tmp
 curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-test.tsv?attredirects=0&d=1' \
 | grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > test.txt.tmp
-wget "https://raw.githubusercontent.com/stefan-it/fine-tuned-berts-seq/master/scripts/preprocess.py"
+
 export MAX_LENGTH=128
 export BERT_MODEL=bert-base-multilingual-cased
-python3 preprocess.py train.txt.tmp $BERT_MODEL $MAX_LENGTH > train.txt
-python3 preprocess.py dev.txt.tmp $BERT_MODEL $MAX_LENGTH > dev.txt
-python3 preprocess.py test.txt.tmp $BERT_MODEL $MAX_LENGTH > test.txt
+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

examples/token-classification/run_pl.sh

@@ -11,12 +11,12 @@ curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-dev.tsv?attre
 | grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > dev.txt.tmp
 curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-test.tsv?attredirects=0&d=1' \
 | grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > test.txt.tmp
-wget "https://raw.githubusercontent.com/stefan-it/fine-tuned-berts-seq/master/scripts/preprocess.py"
+
 export MAX_LENGTH=128
 export BERT_MODEL=bert-base-multilingual-cased
-python3 preprocess.py train.txt.tmp $BERT_MODEL $MAX_LENGTH > train.txt
-python3 preprocess.py dev.txt.tmp $BERT_MODEL $MAX_LENGTH > dev.txt
-python3 preprocess.py test.txt.tmp $BERT_MODEL $MAX_LENGTH > test.txt
+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 BATCH_SIZE=32
 export NUM_EPOCHS=3

examples/token-classification/scripts/preprocess.py

+import sys
+
+from transformers import AutoTokenizer
+
+
+dataset = sys.argv[1]
+model_name_or_path = sys.argv[2]
+max_len = int(sys.argv[3])
+
+subword_len_counter = 0
+
+tokenizer = AutoTokenizer.from_pretrained(model_name_or_path)
+max_len -= tokenizer.num_special_tokens_to_add()
+
+with open(dataset, "rt") as f_p:
+    for line in f_p:
+        line = line.rstrip()
+
+        if not line:
+            print(line)
+            subword_len_counter = 0
+            continue
+
+        token = line.split()[0]
+
+        current_subwords_len = len(tokenizer.tokenize(token))
+
+        # Token contains strange control characters like \x96 or \x95
+        # Just filter out the complete line
+        if current_subwords_len == 0:
+            continue
+
+        if (subword_len_counter + current_subwords_len) > max_len:
+            print("")
+            print(line)
+            subword_len_counter = current_subwords_len
+            continue
+
+        subword_len_counter += current_subwords_len
+
+        print(line)