roberttinn's picture
language: en
  - exbert
license: mit
  - text: '[MASK] is a tyrosine kinase inhibitor.'

PubMedBERT-large (abstracts only)

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. Recent work shows that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. Followup work explores larger model sizes and the impact of these on performance on the BLURB benchmark.

This PubMedBERT is pretrained from scratch using abstracts from PubMed.


If you find PubMedBERT useful in your research, please cite the following paper:

  doi = {10.48550/ARXIV.2112.07869},
  url = {},
  author = {Tinn, Robert and Cheng, Hao and Gu, Yu and Usuyama, Naoto and Liu, Xiaodong and Naumann, Tristan and Gao, Jianfeng and Poon, Hoifung},
  keywords = {Computation and Language (cs.CL), Machine Learning (cs.LG), FOS: Computer and information sciences, FOS: Computer and information sciences},
  title = {Fine-Tuning Large Neural Language Models for Biomedical Natural Language Processing},
  publisher = {arXiv},
  year = {2021},
  copyright = { perpetual, non-exclusive license}