# Beyond Retrieval: Ensembling Cross-Encoders and GPT Rerankers with LLMs for Biomedical QA

arXiv: https://arxiv.org/abs/2507.05577 · HTML: https://mlsanity.com/paper/2507.05577/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 27 references that are in the map.
- First posted on arXiv 8 Jul 2025.

## Builds on (most cited first, 19 of 19)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Billion-scale similarity search with GPUs](https://mlsanity.com/paper/1702.08734/) (2017)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [MiniLM: Deep Self-Attention Distillation for Task-Agnostic Compression of Pre-Trained Transformers](https://mlsanity.com/paper/2002.10957/) (2020)
- [BEIR: A Heterogenous Benchmark for Zero-shot Evaluation of Information Retrieval Models](https://mlsanity.com/paper/2104.08663/) (2021)
- [Leveraging Passage Retrieval with Generative Models for Open Domain Question Answering](https://mlsanity.com/paper/2007.01282/) (2020)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Efficient and robust approximate nearest neighbor search using Hierarchical Navigable Small World graphs](https://mlsanity.com/paper/1603.09320/) (2016)
- [AdapterFusion: Non-Destructive Task Composition for Transfer Learning](https://mlsanity.com/paper/2005.00247/) (2020)
- [Passage Re-ranking with BERT](https://mlsanity.com/paper/1901.04085/) (2019)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Zero-Shot Listwise Document Reranking with a Large Language Model](https://mlsanity.com/paper/2305.02156/) (2023)
- [RankVicuna: Zero-Shot Listwise Document Reranking with Open-Source Large Language Models](https://mlsanity.com/paper/2309.15088/) (2023)
- [In Defense of Cross-Encoders for Zero-Shot Retrieval](https://mlsanity.com/paper/2212.06121/) (2022)
- [Can Open-Source LLMs Compete with Commercial Models? Exploring the Few-Shot Performance of Current GPT Models in Biomedical Tasks](https://mlsanity.com/paper/2407.13511/) (2024)

## Built on by (most cited first, 2 of 2)

- [Overview of BioASQ 2025: The Thirteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering](https://mlsanity.com/paper/2508.20554/) (2025)
- [Self-MedRAG: a Self-Reflective Hybrid Retrieval-Augmented Generation Framework for Reliable Medical Question Answering](https://mlsanity.com/paper/2601.04531/) (2026)

## Abstract (arXiv)

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 10th on the leaderboard for the retrieval task. For answer generation, we employed few-shot prompting of instruction-tuned LLMs. Our system achieved macro-F1 score of 0.95 for yes/no questions (rank 12), Mean Reciprocal Rank (MRR) of 0.64 for factoid questions (rank 1), mean-F1 score of 0.63 for list questions (rank 5), and ROUGE-SU4 F1 score of 0.29 for ideal answers (rank 11).