{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/biobridge-bridging-biomedical-foundation","title":"BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs","arxiv_id":"2310.03320","date":"2023-10-05","proceeding":null,"authors":["Zifeng Wang","Zichen Wang","Balasubramaniam Srinivasan","Vassilis N. Ioannidis","Huzefa Rangwala","Rishita Anubhai"],"abstract":"Foundation models (FMs) are able to leverage large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation of biomedical FMs, we present BioBridge, a novel parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our empirical results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by around 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs.","url_abs":"https://arxiv.org/abs/2310.03320v4","url_pdf":"https://arxiv.org/pdf/2310.03320v4.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"biobridge-bridging-biomedical-foundation","repo_url":"https://github.com/ryanwangzf/biobridge","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"cross-modal-retrieval","task_name":"Cross-Modal Retrieval"},{"task_slug":"domain-generalization","task_name":"Domain Generalization"},{"task_slug":"knowledge-graphs","task_name":"Knowledge Graphs"},{"task_slug":"question-answering","task_name":"Question Answering"},{"task_slug":"retrieval","task_name":"Retrieval"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2310.03320","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2310.03320"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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