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BigBio: A Framework for Data-Centric Biomedical Natural Language Processing

Jason Fries · Leon Weber · Natasha Seelam · Gabriel Altay · Debajyoti Datta · Samuele Garda · Sunny Kang · Rosaline Su · Wojciech Kusa · Samuel Cahyawijaya · Fabio Barth · Simon Ott · Matthias Samwald · Stephen Bach · Stella Biderman · Mario Sänger · Bo Wang · Alison Callahan · Daniel León Periñán · Théo Gigant · Patrick Haller · Jenny Chim · Jose Posada · John Giorgi · Karthik Rangasai Sivaraman · Marc Pàmies · Marianna Nezhurina · Robert Martin · Michael Cullan · Moritz Freidank · Nathan Dahlberg · Shubhanshu Mishra · Shamik Bose · Nicholas Broad · Yanis Labrak · Shlok Deshmukh · Sid Kiblawi · Ayush Singh · Minh Chien Vu · Trishala Neeraj · Jonas Golde · Albert Villanova del Moral · Benjamin Beilharz

Hall J (level 1) #1012

Keywords: [ Language Modeling ] [ Natural Language Processing ] [ biomedical ] [ Data-centric AI ]


Training and evaluating language models increasingly requires the construction of meta-datasets -- diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a variety of novel instruction tuning tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBio a community library of 126+ biomedical NLP datasets, currently covering 13 task categories and 10+ languages. BigBio facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBio is an ongoing community effort and is available at

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