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

30 June 2022
Jason Alan Fries
Leon Weber
Natasha Seelam
Gabriel Altay
Debajyoti Datta
Samuele Garda
Myungsun Kang
Ruisi Su
Wojciech Kusa
Samuel Cahyawijaya
Fabio Barth
Simon Ott
Matthias Samwald
Stephen H. Bach
Stella Biderman
Mario Sanger
Bo Wang
A. Callahan
Daniel León Perinán
Théo Gigant
Patrick Haller
Jenny Chim
J. Posada
John Giorgi
Karthi Sivaraman
Marc Pàmies
Marianna Nezhurina
Robert Martin
Michael Cullan
M. Freidank
N. Dahlberg
Shubhanshu Mishra
Shamik Bose
N. Broad
Yanis Labrak
Shlok S Deshmukh
Sid Kiblawi
Ayush Singh
Minh Chien Vu
Trishala Neeraj
Jonas Golde
Albert Villanova del Moral
Benjamin Beilharz
    LM&MA
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Abstract

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 diversity of novel pretraining 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 12 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 https://github.com/bigscience-workshop/biomedical

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