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Support for torch-lightning in NER examples (#2890)

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* initial pytorch lightning commit

* tested multigpu

* Fix learning rate schedule

* black formatting

* fix flake8

* isort

* isort

* .

Co-authored-by: Check your git settings! <chris@chris-laptop>
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213
examples/README.md
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@ -3,7 +3,7 @@
In this section a few examples are put together. All of these examples work for several models, making use of the very
similar API between the different models.
**Important**
**Important**
To run the latest versions of the examples, you have to install from source and install some specific requirements for the examples.
Execute the following steps in a new virtual environment:
@ -15,8 +15,8 @@ pip install -r ./examples/requirements.txt
```
| Section | Description |
|----------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------|
| [TensorFlow 2.0 models on GLUE](#TensorFlow-2.0-Bert-models-on-GLUE) | Examples running BERT TensorFlow 2.0 model on the GLUE tasks.
|----------------------------|------------------------------------------------------------------------------------------------------------------------------------------
| [TensorFlow 2.0 models on GLUE](#TensorFlow-2.0-Bert-models-on-GLUE) | Examples running BERT TensorFlow 2.0 model on the GLUE tasks. |
| [Language Model training](#language-model-training) | Fine-tuning (or training from scratch) the library models for language modeling on a text dataset. Causal language modeling for GPT/GPT-2, masked language modeling for BERT/RoBERTa. |
| [Language Generation](#language-generation) | Conditional text generation using the auto-regressive models of the library: GPT, GPT-2, Transformer-XL and XLNet. |
| [GLUE](#glue) | Examples running BERT/XLM/XLNet/RoBERTa on the 9 GLUE tasks. Examples feature distributed training as well as half-precision. |
@ -88,7 +88,7 @@ a score of ~20 perplexity once fine-tuned on the dataset.
The following example fine-tunes RoBERTa on WikiText-2. Here too, we're using the raw WikiText-2. The loss is different
as BERT/RoBERTa have a bidirectional mechanism; we're therefore using the same loss that was used during their
pre-training: masked language modeling.
pre-training: masked language modeling.
In accordance to the RoBERTa paper, we use dynamic masking rather than static masking. The model may, therefore, converge
slightly slower (over-fitting takes more epochs).
@ -130,8 +130,8 @@ python run_generation.py \
Based on the script [`run_glue.py`](https://github.com/huggingface/transformers/blob/master/examples/run_glue.py).
Fine-tuning the library models for sequence classification on the GLUE benchmark: [General Language Understanding
Evaluation](https://gluebenchmark.com/). This script can fine-tune the following models: BERT, XLM, XLNet and RoBERTa.
Fine-tuning the library models for sequence classification on the GLUE benchmark: [General Language Understanding
Evaluation](https://gluebenchmark.com/). This script can fine-tune the following models: BERT, XLM, XLNet and RoBERTa.
GLUE is made up of a total of 9 different tasks. We get the following results on the dev set of the benchmark with an
uncased BERT base model (the checkpoint `bert-base-uncased`). All experiments ran single V100 GPUs with a total train
@ -179,20 +179,20 @@ python run_glue.py \
where task name can be one of CoLA, SST-2, MRPC, STS-B, QQP, MNLI, QNLI, RTE, WNLI.
The dev set results will be present within the text file `eval_results.txt` in the specified output_dir.
In case of MNLI, since there are two separate dev sets (matched and mismatched), there will be a separate
The dev set results will be present within the text file `eval_results.txt` in the specified output_dir.
In case of MNLI, since there are two separate dev sets (matched and mismatched), there will be a separate
output folder called `/tmp/MNLI-MM/` in addition to `/tmp/MNLI/`.
The code has not been tested with half-precision training with apex on any GLUE task apart from MRPC, MNLI,
CoLA, SST-2. The following section provides details on how to run half-precision training with MRPC. With that being
said, there shouldn’t be any issues in running half-precision training with the remaining GLUE tasks as well,
The code has not been tested with half-precision training with apex on any GLUE task apart from MRPC, MNLI,
CoLA, SST-2. The following section provides details on how to run half-precision training with MRPC. With that being
said, there shouldn’t be any issues in running half-precision training with the remaining GLUE tasks as well,
since the data processor for each task inherits from the base class DataProcessor.
### MRPC
#### Fine-tuning example
The following examples fine-tune BERT on the Microsoft Research Paraphrase Corpus (MRPC) corpus and runs in less
The following examples fine-tune BERT on the Microsoft Research Paraphrase Corpus (MRPC) corpus and runs in less
than 10 minutes on a single K-80 and in 27 seconds (!) on single tesla V100 16GB with apex installed.
Before running any one of these GLUE tasks you should download the
@ -219,12 +219,12 @@ python run_glue.py \
```
Our test ran on a few seeds with [the original implementation hyper-
parameters](https://github.com/google-research/bert#sentence-and-sentence-pair-classification-tasks) gave evaluation
parameters](https://github.com/google-research/bert#sentence-and-sentence-pair-classification-tasks) gave evaluation
results between 84% and 88%.
#### Using Apex and mixed-precision
Using Apex and 16 bit precision, the fine-tuning on MRPC only takes 27 seconds. First install
Using Apex and 16 bit precision, the fine-tuning on MRPC only takes 27 seconds. First install
[apex](https://github.com/NVIDIA/apex), then run the following example:
```bash
@ -360,8 +360,8 @@ Based on the script [`run_squad.py`](https://github.com/huggingface/transformers
#### Fine-tuning BERT on SQuAD1.0
This example code fine-tunes BERT on the SQuAD1.0 dataset. It runs in 24 min (with BERT-base) or 68 min (with BERT-large)
on a single tesla V100 16GB. The data for SQuAD can be downloaded with the following links and should be saved in a
This example code fine-tunes BERT on the SQuAD1.0 dataset. It runs in 24 min (with BERT-base) or 68 min (with BERT-large)
on a single tesla V100 16GB. The data for SQuAD can be downloaded with the following links and should be saved in a
$SQUAD_DIR directory.
* [train-v1.1.json](https://rajpurkar.github.io/SQuAD-explorer/dataset/train-v1.1.json)
@ -516,185 +516,6 @@ Larger batch size may improve the performance while costing more memory.
## Named Entity Recognition
Based on the scripts [`run_ner.py`](https://github.com/huggingface/transformers/blob/master/examples/run_ner.py) for Pytorch and
[`run_tf_ner.py`](https://github.com/huggingface/transformers/blob/master/examples/run_tf_ner.py) for Tensorflow 2.
This example fine-tune Bert Multilingual on GermEval 2014 (German NER).
Details and results for the fine-tuning provided by @stefan-it.
### Data (Download and pre-processing steps)
Data can be obtained from the [GermEval 2014](https://sites.google.com/site/germeval2014ner/data) shared task page.
Here are the commands for downloading and pre-processing train, dev and test datasets. The original data format has four (tab-separated) columns, in a pre-processing step only the two relevant columns (token and outer span NER annotation) are extracted:
```bash
curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-train.tsv?attredirects=0&d=1' \
| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > train.txt.tmp
curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-dev.tsv?attredirects=0&d=1' \
| 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
```
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).
```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
export MAX_LENGTH=128
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 $MAX_LENGTH > test.txt
```
The GermEval 2014 dataset has much more labels than CoNLL-2002/2003 datasets, so an own set of labels must be used:
```bash
cat train.txt dev.txt test.txt | cut -d " " -f 2 | grep -v "^$"| sort | uniq > labels.txt
```
### Prepare the run
Additional environment variables must be set:
```bash
export OUTPUT_DIR=germeval-model
export BATCH_SIZE=32
export NUM_EPOCHS=3
export SAVE_STEPS=750
export SEED=1
```
### Run the Pytorch version
To start training, just run:
```bash
python3 run_ner.py --data_dir ./ \
--model_type bert \
--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
```
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.
#### Evaluation
Evaluation on development dataset outputs the following for our example:
```bash
10/04/2019 00:42:06 - INFO - __main__ - ***** Eval results *****
10/04/2019 00:42:06 - INFO - __main__ - f1 = 0.8623348017621146
10/04/2019 00:42:06 - INFO - __main__ - loss = 0.07183869666975543
10/04/2019 00:42:06 - INFO - __main__ - precision = 0.8467916366258111
10/04/2019 00:42:06 - INFO - __main__ - recall = 0.8784592370979806
```
On the test dataset the following results could be achieved:
```bash
10/04/2019 00:42:42 - INFO - __main__ - ***** Eval results *****
10/04/2019 00:42:42 - INFO - __main__ - f1 = 0.8614389652384803
10/04/2019 00:42:42 - INFO - __main__ - loss = 0.07064602487454782
10/04/2019 00:42:42 - INFO - __main__ - precision = 0.8604651162790697
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 the Tensorflow 2 version
To start training, just run:
```bash
python3 run_tf_ner.py --data_dir ./ \
--model_type bert \
--labels ./labels.txt \
--model_name_or_path $BERT_MODEL \
--output_dir $OUTPUT_DIR \
--max_seq_length $MAX_LENGTH \
--num_train_epochs $NUM_EPOCHS \
--per_device_train_batch_size $BATCH_SIZE \
--save_steps $SAVE_STEPS \
--seed $SEED \
--do_train \
--do_eval \
--do_predict
```
Such as the Pytorch version, if your GPU supports half-precision training, just add the `--fp16` flag. After training, the model will be both evaluated on development and test datasets.
#### Evaluation
Evaluation on development dataset outputs the following for our example:
```bash
precision recall f1-score support
LOCderiv 0.7619 0.6154 0.6809 52
PERpart 0.8724 0.8997 0.8858 4057
OTHpart 0.9360 0.9466 0.9413 711
ORGpart 0.7015 0.6989 0.7002 269
LOCpart 0.7668 0.8488 0.8057 496
LOC 0.8745 0.9191 0.8963 235
ORGderiv 0.7723 0.8571 0.8125 91
OTHderiv 0.4800 0.6667 0.5581 18
OTH 0.5789 0.6875 0.6286 16
PERderiv 0.5385 0.3889 0.4516 18
PER 0.5000 0.5000 0.5000 2
ORG 0.0000 0.0000 0.0000 3
micro avg 0.8574 0.8862 0.8715 5968
macro avg 0.8575 0.8862 0.8713 5968
```
On the test dataset the following results could be achieved:
```bash
precision recall f1-score support
PERpart 0.8847 0.8944 0.8896 9397
OTHpart 0.9376 0.9353 0.9365 1639
ORGpart 0.7307 0.7044 0.7173 697
LOC 0.9133 0.9394 0.9262 561
LOCpart 0.8058 0.8157 0.8107 1150
ORG 0.0000 0.0000 0.0000 8
OTHderiv 0.5882 0.4762 0.5263 42
PERderiv 0.6571 0.5227 0.5823 44
OTH 0.4906 0.6667 0.5652 39
ORGderiv 0.7016 0.7791 0.7383 172
LOCderiv 0.8256 0.6514 0.7282 109
PER 0.0000 0.0000 0.0000 11
micro avg 0.8722 0.8774 0.8748 13869
macro avg 0.8712 0.8774 0.8740 13869
```
## XNLI
@ -705,7 +526,7 @@ Based on the script [`run_xnli.py`](https://github.com/huggingface/transformers/
#### Fine-tuning on XNLI
This example code fine-tunes mBERT (multi-lingual BERT) on the XNLI dataset. It runs in 106 mins
on a single tesla V100 16GB. The data for XNLI can be downloaded with the following links and should be both saved (and un-zipped) in a
on a single tesla V100 16GB. The data for XNLI can be downloaded with the following links and should be both saved (and un-zipped) in a
`$XNLI_DIR` directory.
* [XNLI 1.0](https://www.nyu.edu/projects/bowman/xnli/XNLI-1.0.zip)

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@ -0,0 +1,179 @@
## Named Entity Recognition
Based on the scripts [`run_ner.py`](https://github.com/huggingface/transformers/blob/master/examples/ner/run_ner.py) for Pytorch and
[`run_tf_ner.py`](https://github.com/huggingface/transformers/blob/master/examples/ner/run_tf_ner.py) for Tensorflow 2.
This example fine-tune Bert Multilingual on GermEval 2014 (German NER).
Details and results for the fine-tuning provided by @stefan-it.
### Data (Download and pre-processing steps)
Data can be obtained from the [GermEval 2014](https://sites.google.com/site/germeval2014ner/data) shared task page.
Here are the commands for downloading and pre-processing train, dev and test datasets. The original data format has four (tab-separated) columns, in a pre-processing step only the two relevant columns (token and outer span NER annotation) are extracted:
```bash
curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-train.tsv?attredirects=0&d=1' \
| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > train.txt.tmp
curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-dev.tsv?attredirects=0&d=1' \
| 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
```
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).
```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
export MAX_LENGTH=128
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 $MAX_LENGTH > test.txt
```
The GermEval 2014 dataset has much more labels than CoNLL-2002/2003 datasets, so an own set of labels must be used:
```bash
cat train.txt dev.txt test.txt | cut -d " " -f 2 | grep -v "^$"| sort | uniq > labels.txt
```
### Prepare the run
Additional environment variables must be set:
```bash
export OUTPUT_DIR=germeval-model
export BATCH_SIZE=32
export NUM_EPOCHS=3
export SAVE_STEPS=750
export SEED=1
```
### Run the Pytorch version
To start training, just run:
```bash
python3 run_ner.py --data_dir ./ \
--model_type bert \
--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
```
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.
#### Evaluation
Evaluation on development dataset outputs the following for our example:
```bash
10/04/2019 00:42:06 - INFO - __main__ - ***** Eval results *****
10/04/2019 00:42:06 - INFO - __main__ - f1 = 0.8623348017621146
10/04/2019 00:42:06 - INFO - __main__ - loss = 0.07183869666975543
10/04/2019 00:42:06 - INFO - __main__ - precision = 0.8467916366258111
10/04/2019 00:42:06 - INFO - __main__ - recall = 0.8784592370979806
```
On the test dataset the following results could be achieved:
```bash
10/04/2019 00:42:42 - INFO - __main__ - ***** Eval results *****
10/04/2019 00:42:42 - INFO - __main__ - f1 = 0.8614389652384803
10/04/2019 00:42:42 - INFO - __main__ - loss = 0.07064602487454782
10/04/2019 00:42:42 - INFO - __main__ - precision = 0.8604651162790697
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 the Tensorflow 2 version
To start training, just run:
```bash
python3 run_tf_ner.py --data_dir ./ \
--model_type bert \
--labels ./labels.txt \
--model_name_or_path $BERT_MODEL \
--output_dir $OUTPUT_DIR \
--max_seq_length $MAX_LENGTH \
--num_train_epochs $NUM_EPOCHS \
--per_device_train_batch_size $BATCH_SIZE \
--save_steps $SAVE_STEPS \
--seed $SEED \
--do_train \
--do_eval \
--do_predict
```
Such as the Pytorch version, 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.
#### Evaluation
Evaluation on development dataset outputs the following for our example:
```bash
precision recall f1-score support
LOCderiv 0.7619 0.6154 0.6809 52
PERpart 0.8724 0.8997 0.8858 4057
OTHpart 0.9360 0.9466 0.9413 711
ORGpart 0.7015 0.6989 0.7002 269
LOCpart 0.7668 0.8488 0.8057 496
LOC 0.8745 0.9191 0.8963 235
ORGderiv 0.7723 0.8571 0.8125 91
OTHderiv 0.4800 0.6667 0.5581 18
OTH 0.5789 0.6875 0.6286 16
PERderiv 0.5385 0.3889 0.4516 18
PER 0.5000 0.5000 0.5000 2
ORG 0.0000 0.0000 0.0000 3
micro avg 0.8574 0.8862 0.8715 5968
macro avg 0.8575 0.8862 0.8713 5968
```
On the test dataset the following results could be achieved:
```bash
precision recall f1-score support
PERpart 0.8847 0.8944 0.8896 9397
OTHpart 0.9376 0.9353 0.9365 1639
ORGpart 0.7307 0.7044 0.7173 697
LOC 0.9133 0.9394 0.9262 561
LOCpart 0.8058 0.8157 0.8107 1150
ORG 0.0000 0.0000 0.0000 8
OTHderiv 0.5882 0.4762 0.5263 42
PERderiv 0.6571 0.5227 0.5823 44
OTH 0.4906 0.6667 0.5652 39
ORGderiv 0.7016 0.7791 0.7383 172
LOCderiv 0.8256 0.6514 0.7282 109
PER 0.0000 0.0000 0.0000 11
micro avg 0.8722 0.8774 0.8748 13869
macro avg 0.8712 0.8774 0.8740 13869
```

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@ -0,0 +1,32 @@
curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-train.tsv?attredirects=0&d=1' \
| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > train.txt.tmp
curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-dev.tsv?attredirects=0&d=1' \
| 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 $MAX_LENGTH > test.txt
cat train.txt dev.txt test.txt | cut -d " " -f 2 | grep -v "^$"| 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 --data_dir ./ \
--model_type bert \
--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

0
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@ -0,0 +1,21 @@
# Require pytorch-lightning=0.6
export MAX_LENGTH=128
export BERT_MODEL=bert-base-multilingual-cased
export OUTPUT_DIR=germeval-model
export BATCH_SIZE=32
export NUM_EPOCHS=3
export SAVE_STEPS=750
export SEED=1
python3 run_pl_ner.py --data_dir ./ \
--model_type bert \
--labels ./labels.txt \
--model_name_or_path $BERT_MODEL \
--output_dir $OUTPUT_DIR \
--max_seq_length $MAX_LENGTH \
--num_train_epochs $NUM_EPOCHS \
--train_batch_size 32 \
--save_steps $SAVE_STEPS \
--seed $SEED \
--do_train \
--do_predict

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@ -0,0 +1,238 @@
import argparse
import glob
import logging
import os
import numpy as np
import torch
from seqeval.metrics import f1_score, precision_score, recall_score
from torch.nn import CrossEntropyLoss
from torch.utils.data import DataLoader, RandomSampler, SequentialSampler, TensorDataset
from torch.utils.data.distributed import DistributedSampler
from transformer_base import BaseTransformer, add_generic_args, generic_train
from utils_ner import convert_examples_to_features, get_labels, read_examples_from_file
logger = logging.getLogger(__name__)
class NERTransformer(BaseTransformer):
"""
A training module for NER. See BaseTransformer for the core options.
"""
def __init__(self, hparams):
self.labels = get_labels(hparams.labels)
num_labels = len(self.labels)
super(NERTransformer, self).__init__(hparams, num_labels)
def forward(self, **inputs):
return self.model(**inputs)
def training_step(self, batch, batch_num):
"Compute loss"
inputs = {"input_ids": batch[0], "attention_mask": batch[1], "labels": batch[3]}
if self.hparams.model_type != "distilbert":
inputs["token_type_ids"] = (
batch[2] if self.hparams.model_type in ["bert", "xlnet"] else None
) # XLM and RoBERTa don"t use segment_ids
outputs = self.forward(**inputs)
loss = outputs[0]
tensorboard_logs = {"loss": loss, "rate": self.lr_scheduler.get_last_lr()[-1]}
return {"loss": loss, "log": tensorboard_logs}
def load_dataset(self, mode, batch_size):
labels = get_labels(self.hparams.labels)
self.pad_token_label_id = CrossEntropyLoss().ignore_index
dataset = self.load_and_cache_examples(labels, self.pad_token_label_id, mode)
if mode == "train":
if self.hparams.n_gpu > 1:
sampler = DistributedSampler(dataset)
else:
sampler = RandomSampler(dataset)
else:
sampler = SequentialSampler(dataset)
dataloader = DataLoader(dataset, sampler=sampler, batch_size=batch_size)
return dataloader
def validation_step(self, batch, batch_nb):
inputs = {"input_ids": batch[0], "attention_mask": batch[1], "labels": batch[3]}
if self.hparams.model_type != "distilbert":
inputs["token_type_ids"] = (
batch[2] if self.hparams.model_type in ["bert", "xlnet"] else None
) # XLM and RoBERTa don"t use segment_ids
outputs = self.forward(**inputs)
tmp_eval_loss, logits = outputs[:2]
preds = logits.detach().cpu().numpy()
out_label_ids = inputs["labels"].detach().cpu().numpy()
return {"val_loss": tmp_eval_loss, "pred": preds, "target": out_label_ids}
def _eval_end(self, outputs):
"Task specific validation"
val_loss_mean = torch.stack([x["val_loss"] for x in outputs]).mean()
preds = np.concatenate([x["pred"] for x in outputs], axis=0)
preds = np.argmax(preds, axis=2)
out_label_ids = np.concatenate([x["target"] for x in outputs], axis=0)
label_map = {i: label for i, label in enumerate(self.labels)}
out_label_list = [[] for _ in range(out_label_ids.shape[0])]
preds_list = [[] for _ in range(out_label_ids.shape[0])]
for i in range(out_label_ids.shape[0]):
for j in range(out_label_ids.shape[1]):
if out_label_ids[i, j] != self.pad_token_label_id:
out_label_list[i].append(label_map[out_label_ids[i][j]])
preds_list[i].append(label_map[preds[i][j]])
results = {
"val_loss": val_loss_mean,
"precision": precision_score(out_label_list, preds_list),
"recall": recall_score(out_label_list, preds_list),
"f1": f1_score(out_label_list, preds_list),
}
if self.is_logger():
logger.info(self.proc_rank)
logger.info("***** Eval results *****")
for key in sorted(results.keys()):
logger.info(" %s = %s", key, str(results[key]))
tensorboard_logs = results
ret = {k: v for k, v in results.items()}
ret["log"] = tensorboard_logs
return ret, preds_list, out_label_list
def validation_end(self, outputs):
ret, preds, targets = self._eval_end(outputs)
return ret
def test_end(self, outputs):
ret, predictions, targets = self._eval_end(outputs)
if self.is_logger():
# Write output to a file:
# Save results
output_test_results_file = os.path.join(self.hparams.output_dir, "test_results.txt")
with open(output_test_results_file, "w") as writer:
for key in sorted(ret.keys()):
if key != "log":
writer.write("{} = {}\n".format(key, str(ret[key])))
# Save predictions
output_test_predictions_file = os.path.join(self.hparams.output_dir, "test_predictions.txt")
with open(output_test_predictions_file, "w") as writer:
with open(os.path.join(self.hparams.data_dir, "test.txt"), "r") as f:
example_id = 0
for line in f:
if line.startswith("-DOCSTART-") or line == "" or line == "\n":
writer.write(line)
if not predictions[example_id]:
example_id += 1
elif predictions[example_id]:
output_line = line.split()[0] + " " + predictions[example_id].pop(0) + "\n"
writer.write(output_line)
else:
logger.warning(
"Maximum sequence length exceeded: No prediction for '%s'.", line.split()[0]
)
return ret
def load_and_cache_examples(self, labels, pad_token_label_id, mode):
args = self.hparams
tokenizer = self.tokenizer
if self.proc_rank not in [-1, 0] and mode == "train":
torch.distributed.barrier() # Make sure only the first process in distributed training process the dataset, and the others will use the cache
# Load data features from cache or dataset file
cached_features_file = os.path.join(
args.data_dir,
"cached_{}_{}_{}".format(
mode, list(filter(None, args.model_name_or_path.split("/"))).pop(), str(args.max_seq_length)
),
)
if os.path.exists(cached_features_file) and not args.overwrite_cache:
logger.info("Loading features from cached file %s", cached_features_file)
features = torch.load(cached_features_file)
else:
logger.info("Creating features from dataset file at %s", args.data_dir)
examples = read_examples_from_file(args.data_dir, mode)
features = convert_examples_to_features(
examples,
labels,
args.max_seq_length,
tokenizer,
cls_token_at_end=bool(args.model_type in ["xlnet"]),
cls_token=tokenizer.cls_token,
cls_token_segment_id=2 if args.model_type in ["xlnet"] else 0,
sep_token=tokenizer.sep_token,
sep_token_extra=bool(args.model_type in ["roberta"]),
pad_on_left=bool(args.model_type in ["xlnet"]),
pad_token=tokenizer.convert_tokens_to_ids([tokenizer.pad_token])[0],
pad_token_segment_id=4 if args.model_type in ["xlnet"] else 0,
pad_token_label_id=pad_token_label_id,
)
if self.proc_rank in [-1, 0]:
logger.info("Saving features into cached file %s", cached_features_file)
torch.save(features, cached_features_file)
if self.proc_rank == 0 and mode == "train":
torch.distributed.barrier() # Make sure only the first process in distributed training process the dataset, and the others will use the cache
# Convert to Tensors and build dataset
all_input_ids = torch.tensor([f.input_ids for f in features], dtype=torch.long)
all_input_mask = torch.tensor([f.input_mask for f in features], dtype=torch.long)
all_segment_ids = torch.tensor([f.segment_ids for f in features], dtype=torch.long)
all_label_ids = torch.tensor([f.label_ids for f in features], dtype=torch.long)
dataset = TensorDataset(all_input_ids, all_input_mask, all_segment_ids, all_label_ids)
return dataset
@staticmethod
def add_model_specific_args(parser, root_dir):
# Add NER specific options
BaseTransformer.add_model_specific_args(parser, root_dir)
parser.add_argument(
"--max_seq_length",
default=128,
type=int,
help="The maximum total input sequence length after tokenization. Sequences longer "
"than this will be truncated, sequences shorter will be padded.",
)
parser.add_argument(
"--labels",
default="",
type=str,
help="Path to a file containing all labels. If not specified, CoNLL-2003 labels are used.",
)
parser.add_argument(
"--data_dir",
default=None,
type=str,
required=True,
help="The input data dir. Should contain the training files for the CoNLL-2003 NER task.",
)
parser.add_argument(
"--overwrite_cache", action="store_true", help="Overwrite the cached training and evaluation sets"
)
return parser
if __name__ == "__main__":
parser = argparse.ArgumentParser()
add_generic_args(parser, os.getcwd())
parser = NERTransformer.add_model_specific_args(parser, os.getcwd())
args = parser.parse_args()
model = NERTransformer(args)
trainer = generic_train(model, args)
if args.do_predict:
checkpoints = list(sorted(glob.glob(args.output_dir + "/checkpoint_*.ckpt", recursive=True)))
NERTransformer.load_from_checkpoint(checkpoints[-1])
trainer.test(model)

0
examples/run_tf_ner.py → examples/ner/run_tf_ner.py
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264
examples/ner/transformer_base.py Normal file
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@ -0,0 +1,264 @@
import os
import random
import numpy as np
import pytorch_lightning as pl
import torch
from transformers import (
AdamW,
BertConfig,
BertForTokenClassification,
BertTokenizer,
CamembertConfig,
CamembertForTokenClassification,
CamembertTokenizer,
DistilBertConfig,
DistilBertForTokenClassification,
DistilBertTokenizer,
RobertaConfig,
RobertaForTokenClassification,
RobertaTokenizer,
XLMRobertaConfig,
XLMRobertaForTokenClassification,
XLMRobertaTokenizer,
get_linear_schedule_with_warmup,
)
ALL_MODELS = sum(
(
tuple(conf.pretrained_config_archive_map.keys())
for conf in (BertConfig, RobertaConfig, DistilBertConfig, CamembertConfig, XLMRobertaConfig)
),
(),
)
MODEL_CLASSES = {
"bert": (BertConfig, BertForTokenClassification, BertTokenizer),
"roberta": (RobertaConfig, RobertaForTokenClassification, RobertaTokenizer),
"distilbert": (DistilBertConfig, DistilBertForTokenClassification, DistilBertTokenizer),
"camembert": (CamembertConfig, CamembertForTokenClassification, CamembertTokenizer),
"xlmroberta": (XLMRobertaConfig, XLMRobertaForTokenClassification, XLMRobertaTokenizer),
}
def set_seed(args):
random.seed(args.seed)
np.random.seed(args.seed)
torch.manual_seed(args.seed)
if args.n_gpu > 0:
torch.cuda.manual_seed_all(args.seed)
class BaseTransformer(pl.LightningModule):
def __init__(self, hparams, num_labels=None):
"Initialize a model."
super(BaseTransformer, self).__init__()
self.hparams = hparams
self.hparams.model_type = self.hparams.model_type.lower()
config_class, model_class, tokenizer_class = MODEL_CLASSES[self.hparams.model_type]
config = config_class.from_pretrained(
self.hparams.config_name if self.hparams.config_name else self.hparams.model_name_or_path,
num_labels=num_labels,
cache_dir=self.hparams.cache_dir if self.hparams.cache_dir else None,
)
tokenizer = tokenizer_class.from_pretrained(
self.hparams.tokenizer_name if self.hparams.tokenizer_name else self.hparams.model_name_or_path,
do_lower_case=self.hparams.do_lower_case,
cache_dir=self.hparams.cache_dir if self.hparams.cache_dir else None,
)
model = model_class.from_pretrained(
self.hparams.model_name_or_path,
from_tf=bool(".ckpt" in self.hparams.model_name_or_path),
config=config,
cache_dir=self.hparams.cache_dir if self.hparams.cache_dir else None,
)
self.config, self.tokenizer, self.model = config, tokenizer, model
self.proc_rank = -1
def is_logger(self):
return self.proc_rank <= 0
def configure_optimizers(self):
"Prepare optimizer and schedule (linear warmup and decay)"
model = self.model
t_total = (
len(self.train_dataloader())
// self.hparams.gradient_accumulation_steps
* float(self.hparams.num_train_epochs)
)
no_decay = ["bias", "LayerNorm.weight"]
optimizer_grouped_parameters = [
{
"params": [p for n, p in model.named_parameters() if not any(nd in n for nd in no_decay)],
"weight_decay": self.hparams.weight_decay,
},
{
"params": [p for n, p in model.named_parameters() if any(nd in n for nd in no_decay)],
"weight_decay": 0.0,
},
]
optimizer = AdamW(optimizer_grouped_parameters, lr=self.hparams.learning_rate, eps=self.hparams.adam_epsilon)
scheduler = get_linear_schedule_with_warmup(
optimizer, num_warmup_steps=self.hparams.warmup_steps, num_training_steps=t_total
)
self.lr_scheduler = scheduler
return [optimizer]
def optimizer_step(self, epoch, batch_idx, optimizer, optimizer_idx, second_order_closure=None):
# Step each time.
optimizer.step()
self.lr_scheduler.step()
optimizer.zero_grad()
def get_tqdm_dict(self):
tqdm_dict = {"loss": "{:.3f}".format(self.trainer.avg_loss), "lr": self.lr_scheduler.get_last_lr()[-1]}
return tqdm_dict
def test_step(self, batch, batch_nb):
return self.validation_step(batch, batch_nb)
def test_end(self, outputs):
return self.validation_end(outputs)
@pl.data_loader
def train_dataloader(self):
return self.load_dataset("train", self.hparams.train_batch_size)
@pl.data_loader
def val_dataloader(self):
return self.load_dataset("dev", self.hparams.eval_batch_size)
@pl.data_loader
def test_dataloader(self):
return self.load_dataset("test", self.hparams.eval_batch_size)
def init_ddp_connection(self, proc_rank, world_size):
self.proc_rank = proc_rank
super(BaseTransformer, self).init_ddp_connection(proc_rank, world_size)
@staticmethod
def add_model_specific_args(parser, root_dir):
parser.add_argument(
"--model_type",
default=None,
type=str,
required=True,
help="Model type selected in the list: " + ", ".join(MODEL_CLASSES.keys()),
)
parser.add_argument(
"--model_name_or_path",
default=None,
type=str,
required=True,
help="Path to pre-trained model or shortcut name selected in the list: " + ", ".join(ALL_MODELS),
)
parser.add_argument(
"--config_name", default="", type=str, help="Pretrained config name or path if not the same as model_name"
)
parser.add_argument(
"--tokenizer_name",
default="",
type=str,
help="Pretrained tokenizer name or path if not the same as model_name",
)
parser.add_argument(
"--cache_dir",
default="",
type=str,
help="Where do you want to store the pre-trained models downloaded from s3",
)
parser.add_argument(
"--do_lower_case", action="store_true", help="Set this flag if you are using an uncased model."
)
parser.add_argument("--learning_rate", default=5e-5, type=float, help="The initial learning rate for Adam.")
parser.add_argument("--weight_decay", default=0.0, type=float, help="Weight decay if we apply some.")
parser.add_argument("--adam_epsilon", default=1e-8, type=float, help="Epsilon for Adam optimizer.")
parser.add_argument("--warmup_steps", default=0, type=int, help="Linear warmup over warmup_steps.")
parser.add_argument(
"--num_train_epochs", default=3, type=int, help="Total number of training epochs to perform."
)
parser.add_argument("--train_batch_size", default=32, type=int)
parser.add_argument("--eval_batch_size", default=32, type=int)
def add_generic_args(parser, root_dir):
parser.add_argument(
"--output_dir",
default=None,
type=str,
required=True,
help="The output directory where the model predictions and checkpoints will be written.",
)
parser.add_argument(
"--fp16",
action="store_true",
help="Whether to use 16-bit (mixed) precision (through NVIDIA apex) instead of 32-bit",
)
parser.add_argument(
"--fp16_opt_level",
type=str,
default="O1",
help="For fp16: Apex AMP optimization level selected in ['O0', 'O1', 'O2', and 'O3']."
"See details at https://nvidia.github.io/apex/amp.html",
)
parser.add_argument("--n_gpu", type=int, default=1)
parser.add_argument("--max_grad_norm", default=1.0, type=float, help="Max gradient norm.")
parser.add_argument("--do_train", action="store_true", help="Whether to run training.")
parser.add_argument("--do_predict", action="store_true", help="Whether to run predictions on the test set.")
parser.add_argument(
"--gradient_accumulation_steps",
type=int,
default=1,
help="Number of updates steps to accumulate before performing a backward/update pass.",
)
parser.add_argument("--server_ip", type=str, default="", help="For distant debugging.")
parser.add_argument("--server_port", type=str, default="", help="For distant debugging.")
parser.add_argument("--seed", type=int, default=42, help="random seed for initialization")
def generic_train(model, args):
# init model
set_seed(args)
# Setup distant debugging if needed
if args.server_ip and args.server_port:
# Distant debugging - see https://code.visualstudio.com/docs/python/debugging#_attach-to-a-local-script
import ptvsd
print("Waiting for debugger attach")
ptvsd.enable_attach(address=(args.server_ip, args.server_port), redirect_output=True)
ptvsd.wait_for_attach()
if os.path.exists(args.output_dir) and os.listdir(args.output_dir) and args.do_train:
raise ValueError("Output directory ({}) already exists and is not empty.".format(args.output_dir))
checkpoint_callback = pl.callbacks.ModelCheckpoint(
filepath=args.output_dir, prefix="checkpoint", monitor="val_loss", mode="min", save_top_k=5
)
trainer = pl.Trainer(
accumulate_grad_batches=args.gradient_accumulation_steps,
gpus=args.n_gpu,
max_epochs=args.num_train_epochs,
use_amp=args.fp16,
amp_level=args.fp16_opt_level,
distributed_backend="ddp",
gradient_clip_val=args.max_grad_norm,
checkpoint_callback=checkpoint_callback,
)
if args.do_train:
trainer.fit(model)
return trainer

0
examples/utils_ner.py → examples/ner/utils_ner.py
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2
setup.cfg
View File

@ -15,6 +15,7 @@ known_third_party =
packaging
PIL
psutil
pytorch_lightning
seqeval
sklearn
tensorboardX
@ -23,6 +24,7 @@ known_third_party =
torch
torchtext
torchvision
torch_xla
line_length = 119
lines_after_imports = 2