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BlueBert-Base, Uncased, PubMed and MIMIC-III

Model description

A BERT model pre-trained on PubMed abstracts and clinical notes (MIMIC-III).

Intended uses & limitations

How to use

Please see https://github.com/ncbi-nlp/bluebert

Training data

We provide preprocessed PubMed texts that were used to pre-train the BlueBERT models. The corpus contains ~4000M words extracted from the PubMed ASCII code version.

Pre-trained model: https://huggingface.co/bert-base-uncased

Training procedure

Below is a code snippet for more details.

value = value.lower()
value = re.sub(r'[\r\n]+', ' ', value)
value = re.sub(r'[^\x00-\x7F]+', ' ', value)

tokenized = TreebankWordTokenizer().tokenize(value)
sentence = ' '.join(tokenized)
sentence = re.sub(r"\s's\b", "'s", sentence)

BibTeX entry and citation info

  author    = {Yifan Peng and Shankai Yan and Zhiyong Lu},
  title     = {Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets},
  booktitle = {Proceedings of the 2019 Workshop on Biomedical Natural Language Processing (BioNLP 2019)},
  year      = {2019},
  pages     = {58--65},


This work was supported by the Intramural Research Programs of the National Institutes of Health, National Library of Medicine and Clinical Center. This work was supported by the National Library of Medicine of the National Institutes of Health under award number 4R00LM013001-01.

We are also grateful to the authors of BERT and ELMo to make the data and codes publicly available.

We would like to thank Dr Sun Kim for processing the PubMed texts.


This tool shows the results of research conducted in the Computational Biology Branch, NCBI. The information produced on this website is not intended for direct diagnostic use or medical decision-making without review and oversight by a clinical professional. Individuals should not change their health behavior solely on the basis of information produced on this website. NIH does not independently verify the validity or utility of the information produced by this tool. If you have questions about the information produced on this website, please see a health care professional. More information about NCBI's disclaimer policy is available.

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