A Systematic Study of Biomedical Retrieval Pipeline Trade-offs in Performance and Efficiency

Abstract

Retrieval systems are increasingly used in biomedical and clinical natural language processing applications, yet practical guidance for researchers building such systems is limited. In this work, we provide such guidance through an empirical study of how retrieval pipeline design choices affect performance and efficiency at scale. In particular, we examine retrieval over a variety of existing, public biomedical text datasets, leveraging a variety of disparate types of queries, including exam-style questions, conversational medical queries, community-asked questions, and non-question formulations across various retrieval pipeline settings spanning corpus selection, chunk granularity, and vector index configuration. Retrieval results are judged using a robust, win-rate comparison assessment via an LLM-as-a-judge setting with human validation. Across these experiments, we identify several points of concrete guidance for reviewers, including the superiority of corpus aggregation for absolute retrieval quality, and the emergence of MedRAG/pubmed as the Pareto-optimal singleton corpus under graph-based (HNSW) indexing, appropriate chunking strategies, and FAISS indexing choices that offer the best trade-offs in speed and efficiency.