Aligning Biomedical Texts and Knowledge Graphs: A Systematic Comparison of Lightweight Alignment Strategies

The paper introduces a unified framework for aligning biomedical text with knowledge graphs using a lightweight projection learned via contrastive learning, keeping the text encoder and KG embedding model frozen. It evaluates six design choices—text encoder, KG embedding, projection head, triple composition, training direction, and hard‑negative sampling—on a newly created CTD‑Align corpus of 22K chemical‑gene interaction pairs linked to PubMed passages. The study finds that triple composition and training direction have the largest impact, while simpler linear projections over concatenated subject, predicate, and object embeddings yield the best performance.

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