BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature

Abstract

The development of vision-language models (VLMs) is driven by large-scale and diverse multi-modal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are limited to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA: a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset. Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are additionally provided.We demonstrate the utility and accessibility of our resource by releasing BMC-CLIP, a suite of CLIP-style models continuously pre-trained on BIOMEDICA dataset via streaming (eliminating the need to download 27 TB of data locally). On average, our models achieve state-of-the-art performance across 40 tasks — spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology — excelling in zero-shot classification with 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively) and stronger image-text retrieval while using 10x less compute. To foster reproducibility and collaboration, we release our codebase1, 2 and dataset3 to the broader research community.