Beyond Retrieval: Ensembling Cross-encoders And GPT Rerankers With Llms For Biomedical QA
2025 · Shashank Verma, Fengyi Jiang, Xiangning Xue
Abstract
Biomedical semantic question answering rooted in information retrieval can play a crucial role in keeping up to date with vast, rapidly evolving and ever-growing biomedical literature. A robust system can help researchers, healthcare professionals and even layman users access relevant knowledge grounded in evidence. The BioASQ 2025 Task13b Challenge serves as an important benchmark, offering a competitive platform for advancement of this space. This paper presents the methodologies and results from our participation in this challenge where we built a Retrieval-Augmented Generation (RAG) system that can answer biomedical questions by retrieving relevant PubMed documents and snippets to generate answers. For the retrieval task, we generated dense embeddings from biomedical articles for initial retrieval, and applied an ensemble of finetuned cross-encoders and large language models (LLMs) for re-ranking to identify top relevant documents. Our solution achieved an MAP@10 of 0.1581, placing
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