gem-hunter

Repository for Publicly Available Clinical BERT Embeddings (NAACL Clinical NLP Workshop 2019)

UPDATE: You can now use ClinicalBERT directly through the transformers library. Check out the Bio+Clinical BERT and Bio+Discharge Summary BERT model pages for instructions on how to use the models within the Transformers library.

The Clinical BERT models can also be downloaded here, or via

wget -O pretrained_bert_tf.tar.gz https://www.dropbox.com/s/8armk04fu16algz/pretrained_bert_tf.tar.gz?dl=1

biobert_pretrain_output_all_notes_150000 corresponds to Bio+Clinical BERT, and biobert_pretrain_output_disch_100000 corresponds to Bio+Discharge Summary BERT. Both models are finetuned from BioBERT. We specifically use the BioBERT-Base v1.0 (+ PubMed 200K + PMC 270K) version of BioBERT.

bert_pretrain_output_all_notes_150000 corresponds to Clinical BERT, and bert_pretrain_output_disch_100000 corresponds to Discharge Summary BERT. Both models are finetuned from the cased version of BERT, specifically cased_L-12_H-768_A-12.

To reproduce the steps necessary to finetune BERT or BioBERT on MIMIC data, follow the following steps:

1. Run format_mimic_for_BERT.py - Note you'll need to change the file paths at the top of the file.
2. Run create_pretrain_data.sh
3. Run finetune_lm_tf.sh

Note: See issue #4 for ways to improve section splitting code.

To see an example of how to use clinical BERT for the Med NLI tasks, go to the run_classifier.sh script in the downstream_tasks folder. To see an example for NER tasks, go to the run_i2b2.sh script.

Please post a Github issue or contact emilya@mit.edu if you have any questions.

Please acknowledge the following work in papers or derivative software:

Emily Alsentzer, John Murphy, William Boag, Wei-Hung Weng, Di Jin, Tristan Naumann, and Matthew McDermott. 2019. Publicly available clinical BERT embeddings. In Proceedings of the 2nd Clinical Natural Language Processing Workshop, pages 72-78, Minneapolis, Minnesota, USA. Association for Computational Linguistics.

@inproceedings{alsentzer-etal-2019-publicly,
    title = "Publicly Available Clinical {BERT} Embeddings",
    author = "Alsentzer, Emily  and
      Murphy, John  and
      Boag, William  and
      Weng, Wei-Hung  and
      Jin, Di  and
      Naumann, Tristan  and
      McDermott, Matthew",
    booktitle = "Proceedings of the 2nd Clinical Natural Language Processing Workshop",
    month = jun,
    year = "2019",
    address = "Minneapolis, Minnesota, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/W19-1909",
    doi = "10.18653/v1/W19-1909",
    pages = "72--78"
}