Bigbio: A framework for data-centric biomedical natural language processing

J Fries, L Weber, N Seelam, G Altay… - Advances in …, 2022 - proceedings.neurips.cc
J Fries, L Weber, N Seelam, G Altay, D Datta, S Garda, S Kang, R Su, W Kusa
Advances in Neural Information Processing Systems, 2022proceedings.neurips.cc
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 …
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 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 https://github. com/bigscience-workshop/biomedical
proceedings.neurips.cc