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https://github.com/dmis-lab/biobert

Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining
https://github.com/dmis-lab/biobert

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Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining

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# BioBERT

This repository provides the code for fine-tuning BioBERT, a biomedical language representation model designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc.

Please refer to our paper [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](http://doi.org/10.1093/bioinformatics/btz682) for more details.

This project is done by [DMIS-Lab](https://dmis.korea.ac.kr).



## Download

We provide five versions of pre-trained weights. Pre-training was based on the [original BERT code](https://github.com/google-research/bert) provided by Google, and training details are described in our paper. Currently available versions of pre-trained weights are as follows ([SHA1SUM](http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/sha1sum.html)):



* **[BioBERT-Base v1.2 (+ PubMed 1M)](https://huggingface.co/dmis-lab/biobert-base-cased-v1.2)** - trained in the same way as BioBERT-Base v1.1 but includes LM head, which can be useful for probing (available in PyTorch)

* **[BioBERT-Large v1.1 (+ PubMed 1M)](http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/biobert_large_v1.1_pubmed.tar.gz)** - based on BERT-large-Cased (custom 30k vocabulary), [NER/QA Results](https://github.com/dmis-lab/biobert/wiki/BioBERT-Large-Results)

* **[BioBERT-Base v1.1 (+ PubMed 1M)](http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/biobert_v1.1_pubmed.tar.gz)** - based on BERT-base-Cased (same vocabulary), [Results in the Paper](http://doi.org/10.1093/bioinformatics/btz682)

* **[BioBERT-Base v1.0 (+ PubMed 200K)](http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/biobert_v1.0_pubmed.tar.gz)** - based on BERT-base-Cased (same vocabulary), [Results in the Paper](http://doi.org/10.1093/bioinformatics/btz682)

* **[BioBERT-Base v1.0 (+ PMC 270K)](http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/biobert_v1.0_pmc.tar.gz)** - based on BERT-base-Cased (same vocabulary), [Results in the Paper](http://doi.org/10.1093/bioinformatics/btz682)

* **[BioBERT-Base v1.0 (+ PubMed 200K + PMC 270K)](http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/biobert_v1.0_pubmed_pmc.tar.gz)** - based on BERT-base-Cased (same vocabulary), [Results in the Paper](http://doi.org/10.1093/bioinformatics/btz682)



Note that the performances of v1.0 and v1.1 base models (BioBERT-Base v1.0, BioBERT-Base v1.1) are reported in the paper.

Alternately, you can download pre-trained weights from [here](https://github.com/naver/biobert-pretrained/releases)



## Installation

Sections below describe the installation and the fine-tuning process of BioBERT based on Tensorflow 1 (python version <= 3.7).

For PyTorch version of BioBERT, you can check out [this repository](https://github.com/dmis-lab/biobert-pytorch).

If you are not familiar with coding and just want to recognize biomedical entities in your text using BioBERT, please use [this tool](https://bern.korea.ac.kr) which uses BioBERT for multi-type NER and normalization.



To fine-tune BioBERT, you need to download the [pre-trained weights of BioBERT](https://github.com/naver/biobert-pretrained).

After downloading the pre-trained weights, use `requirements.txt` to install BioBERT as follows:

```bash

$ git clone https://github.com/dmis-lab/biobert.git

$ cd biobert; pip install -r requirements.txt

```

Note that this repository is based on the [BERT repository](https://github.com/google-research/bert) by Google.

All the fine-tuning experiments were conducted on a single TITAN Xp GPU machine which has 12GB of RAM.

You might want to install `java` to use the official evaluation script of BioASQ. See `requirements.txt` for other details.



## Quick Links

Link | Detail

------------- | -------------

[BioBERT-PyTorch](https://github.com/dmis-lab/biobert-pytorch) | PyTorch-based BioBERT implementation

[BERN](http://bern.korea.ac.kr) | Web-based biomedical NER + normalization using BioBERT

[BERN2](http://bern2.korea.ac.kr) | Advanced version of BERN (web-based biomedical NER) w/ NER from BioLM + NEN from PubMedBERT

[covidAsk](https://covidask.korea.ac.kr) | BioBERT based real-time question answering model for COVID-19

[7th BioASQ](https://github.com/dmis-lab/bioasq-biobert) | Code for the seventh BioASQ challenge winning model (factoid/yesno/list)

[Paper](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz682/5566506) | Paper link with [BibTeX](https://github.com/dmis-lab/biobert#citation) (Bioinformatics)



## FAQs

*   [How can I use BioBERT with PyTorch?](https://github.com/dmis-lab/biobert-pytorch)

*   [Can I get word/sentence embeddings using BioBERT?](https://github.com/dmis-lab/biobert/issues/23)

*   [How can I pre-train QA models on SQuAD?](https://github.com/dmis-lab/biobert/issues/10)

*   [What vocabulary does BioBERT use?](https://github.com/naver/biobert-pretrained/issues/1)



## Datasets

We provide a pre-processed version of benchmark datasets for each task as follows:

*   **[`Named Entity Recognition`](http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/NERdata.zip)**: (17.3 MB), 8 datasets on biomedical named entity recognition

*   **[`Relation Extraction`](http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/REdata.zip)**: (2.5 MB), 2 datasets on biomedical relation extraction

*   **[`Question Answering`](http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/QA.zip)**: (5.23 MB), 3 datasets on biomedical question answering task.



You can simply run `download.sh` to download all the datasets at once.

```bash

$ ./download.sh

```

This will download the datasets under the folder `datasets`.

Due to the copyright issue of other datasets, we provide links of those datasets instead: **[`2010 i2b2/VA`](https://www.i2b2.org/NLP/DataSets/Main.php)**, **[`ChemProt`](http://www.biocreative.org/)**.



## Fine-tuning BioBERT

After downloading one of the pre-trained weights, unpack it to any directory you want, and we will denote this as `$BIOBERT_DIR`.

For instance, when using BioBERT-Base v1.1 (+ PubMed 1M), set `BIOBERT_DIR` environment variable as:

```bash

$ export BIOBERT_DIR=./biobert_v1.1_pubmed

$ echo $BIOBERT_DIR

>>> ./biobert_v1.1_pubmed

```



### Named Entity Recognition (NER)

Let `$NER_DIR` indicate a folder for a single NER dataset which contains `train_dev.tsv`, `train.tsv`, `devel.tsv` and `test.tsv`. Also, set `$OUTPUT_DIR` as a directory for NER outputs (trained models, test predictions, etc). For example, when fine-tuning on the NCBI disease corpus,

```bash

$ export NER_DIR=./datasets/NER/NCBI-disease

$ export OUTPUT_DIR=./ner_outputs

```

Following command runs fine-tuning code on NER with default arguments.

```bash

$ mkdir -p $OUTPUT_DIR

$ python run_ner.py --do_train=true --do_eval=true --vocab_file=$BIOBERT_DIR/vocab.txt --bert_config_file=$BIOBERT_DIR/bert_config.json --init_checkpoint=$BIOBERT_DIR/model.ckpt-1000000 --num_train_epochs=10.0 --data_dir=$NER_DIR --output_dir=$OUTPUT_DIR

```

You can change the arguments as you want. Once you have trained your model, you can use it in inference mode by using `--do_train=false --do_predict=true` for evaluating `test.tsv`.

The token-level evaluation result will be printed as stdout format.

For example, the result for NCBI-disease dataset will be like this:

```

INFO:tensorflow:***** token-level evaluation results *****

INFO:tensorflow:  eval_f = 0.8972311

INFO:tensorflow:  eval_precision = 0.88150835

INFO:tensorflow:  eval_recall = 0.9136615

INFO:tensorflow:  global_step = 2571

INFO:tensorflow:  loss = 28.247158

```

(tips : You should go up a few lines to find the result. It comes before `INFO:tensorflow:**** Trainable Variables ****` )



Note that this result is the token-level evaluation measure while the official evaluation should use the entity-level evaluation measure. 

The results of `python run_ner.py` will be recorded as two files: `token_test.txt` and `label_test.txt` in `$OUTPUT_DIR`.

Use `./biocodes/ner_detokenize.py` to obtain word level prediction file.

```bash

$ python biocodes/ner_detokenize.py --token_test_path=$OUTPUT_DIR/token_test.txt --label_test_path=$OUTPUT_DIR/label_test.txt --answer_path=$NER_DIR/test.tsv --output_dir=$OUTPUT_DIR

```

This will generate `NER_result_conll.txt` in `$OUTPUT_DIR`.

Use `./biocodes/conlleval.pl` for entity-level exact match evaluation results.

```bash

$ perl biocodes/conlleval.pl < $OUTPUT_DIR/NER_result_conll.txt

```



The entity-level results for the NCBI disease corpus will be like:

```

processed 24497 tokens with 960 phrases; found: 983 phrases; correct: 852.

accuracy:  98.49%; precision:  86.67%; recall:  88.75%; FB1:  87.70

             MISC: precision:  86.67%; recall:  88.75%; FB1:  87.70  983

``` 

Note that this is a sample run of an NER model.

The performance of NER models usually converges at more than 50 epochs (learning rate = 1e-5 is recommended).



### Relation Extraction (RE)

Let `$RE_DIR` indicate a folder for a single RE dataset, `$TASK_NAME` denote the name of task (two possible options: {gad, euadr}), and `$OUTPUT_DIR` denote a directory for RE outputs:

```bash

$ export RE_DIR=./datasets/RE/GAD/1

$ export TASK_NAME=gad

$ export OUTPUT_DIR=./re_outputs_1

```

Following command runs fine-tuning code on RE with default arguments.

```bash

$ python run_re.py --task_name=$TASK_NAME --do_train=true --do_eval=true --do_predict=true --vocab_file=$BIOBERT_DIR/vocab.txt --bert_config_file=$BIOBERT_DIR/bert_config.json --init_checkpoint=$BIOBERT_DIR/model.ckpt-1000000 --max_seq_length=128 --train_batch_size=32 --learning_rate=2e-5 --num_train_epochs=3.0 --do_lower_case=false --data_dir=$RE_DIR --output_dir=$OUTPUT_DIR

```

The predictions will be saved into a file called `test_results.tsv` in the `$OUTPUT_DIR`.

Use `./biocodes/re_eval.py` for the evaluation.

Note that the CHEMPROT dataset is a multi-class classification dataset and to evaluate the CHEMPROT result, you should run `re_eval.py` with additional `--task=chemprot` flag.

```bash

$ python ./biocodes/re_eval.py --output_path=$OUTPUT_DIR/test_results.tsv --answer_path=$RE_DIR/test.tsv

```

The result for GAD dataset will be like this:

```

f1 score    : 83.74%

recall      : 90.75%

precision   : 77.74%

specificity : 71.15%

```

Please be aware that you have to change `$OUTPUT_DIR` to train/test a new model.

For instance, as most RE datasets are in 10-fold, you have to make a different output directory to train/test a model for a different fold (e.g., `$ export OUTPUT_DIR=./re_outputs_2`).



### Question Answering (QA)

To use the BioASQ dataset, you need to register in the [BioASQ website](http://participants-area.bioasq.org/general_information/general_information_registration/) which authorizes the use of the dataset.

Please unpack the pre-processed BioASQ dataset provided above to a directory `$QA_DIR`.

For example, with `$OUTPUT_DIR` for QA outputs, set as:

```bash

$ export QA_DIR=./datasets/QA/BioASQ

$ export OUTPUT_DIR=./qa_outputs

```

Files named as `BioASQ-*.json` are used for training and testing the model which are the pre-processed format for BioBERT.

Note that we pre-trained our model on SQuAD dataset to get state-of-the-art performance (see [here](https://github.com/dmis-lab/bioasq-biobert) to get BioBERT pre-trained on SQuAD), and you might have to change `$BIOBERT_DIR` accordingly.

Following command runs fine-tuning code on QA with default arguments.

```bash

$ python run_qa.py --do_train=True --do_predict=True --vocab_file=$BIOBERT_DIR/vocab.txt --bert_config_file=$BIOBERT_DIR/bert_config.json --init_checkpoint=$BIOBERT_DIR/model.ckpt-1000000 --max_seq_length=384 --train_batch_size=12 --learning_rate=5e-6 --doc_stride=128 --num_train_epochs=5.0 --do_lower_case=False --train_file=$QA_DIR/BioASQ-train-factoid-4b.json --predict_file=$QA_DIR/BioASQ-test-factoid-4b-1.json --output_dir=$OUTPUT_DIR

```

The predictions will be saved into a file called `predictions.json` and `nbest_predictions.json` in `$OUTPUT_DIR`.

Run `./biocodes/transform_nbset2bioasqform.py` to convert `nbest_predictions.json` to the BioASQ JSON format, which will be used for the official evaluation.

```bash

$ python ./biocodes/transform_nbset2bioasqform.py --nbest_path=$OUTPUT_DIR/nbest_predictions.json --output_path=$OUTPUT_DIR

```

This will generate `BioASQform_BioASQ-answer.json` in `$OUTPUT_DIR`.

Clone **[`evaluation code`](https://github.com/BioASQ/Evaluation-Measures)** from BioASQ github and run evaluation code on `Evaluation-Measures` directory. Please note that you should always put 5 as parameter for -e.

```bash

$ git clone https://github.com/BioASQ/Evaluation-Measures.git

$ cd Evaluation-Measures

$ java -Xmx10G -cp $CLASSPATH:./flat/BioASQEvaluation/dist/BioASQEvaluation.jar evaluation.EvaluatorTask1b -phaseB -e 5 ../$QA_DIR/4B1_golden.json ../$OUTPUT_DIR/BioASQform_BioASQ-answer.json

```

As our model is only on factoid questions, the result will be like,

```

0.0 0.3076923076923077 0.5384615384615384 0.394017094017094 0.0 0.0 0.0 0.0 0.0 0.0

```

where the second, third and fourth numbers will be SAcc, LAcc, and MRR of factoid questions respectively.

For list and yes/no type questions, please refer to our repository for [BioBERT at the 7th BioASQ Challenge](https://github.com/dmis-lab/bioasq-biobert).



## License and Disclaimer

Please see the LICENSE file for details. Downloading data indicates your acceptance of our disclaimer.



## Citation

```bibtex

@article{lee2020biobert,

  title={BioBERT: a pre-trained biomedical language representation model for biomedical text mining},

  author={Lee, Jinhyuk and Yoon, Wonjin and Kim, Sungdong and Kim, Donghyeon and Kim, Sunkyu and So, Chan Ho and Kang, Jaewoo},

  journal={Bioinformatics},

  volume={36},

  number={4},

  pages={1234--1240},

  year={2020},

  publisher={Oxford University Press}

}

```



## Contact Information

For help or issues using BioBERT, please submit a GitHub issue. Please contact Jinhyuk Lee

(`lee.jnhk (at) gmail.com`), or Wonjin Yoon (`wonjin.info (at) gmail.com`) for communication related to BioBERT.