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

Download Clinical BERT

The Clinical BERT models can be downloaded here, or via

wget -O pretrained_bert_tf.tar.gz

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.

Reproduce Clinical BERT


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

  1. Run - Note you'll need to change the file paths at the top of the file.
  2. Run
  3. Run

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

Downstream Tasks

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


Please post a Github issue or contact 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.

    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 = "",
    doi = "10.18653/v1/W19-1909",
    pages = "72--78"
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