# Overview of the MedHopQA track at BioCreative IX: track description, participation and evaluation of systems for multi-hop medical question answering

arXiv: https://arxiv.org/abs/2605.12313 · HTML: https://mlsanity.com/paper/2605.12313/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 41 references that are in the map.
- First posted on arXiv 12 May 2026.

## Builds on (most cited first, 14 of 14)

- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Efficient Memory Management for Large Language Model Serving with PagedAttention](https://mlsanity.com/paper/2309.06180/) (2023)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Constructing Datasets for Multi-hop Reading Comprehension Across Documents](https://mlsanity.com/paper/1710.06481/) (2017)
- [MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval](https://mlsanity.com/paper/2307.00589/) (2023)
- [emrQA: A Large Corpus for Question Answering on Electronic Medical Records](https://mlsanity.com/paper/1809.00732/) (2018)
- [Med42-v2: A Suite of Clinical LLMs](https://mlsanity.com/paper/2408.06142/) (2024)
- [BM25S: Orders of magnitude faster lexical search via eager sparse scoring](https://mlsanity.com/paper/2407.03618/) (2024)
- [Rationale-Guided Retrieval Augmented Generation for Medical Question Answering](https://mlsanity.com/paper/2411.00300/) (2024)
- [DeepRAG: Integrating Hierarchical Reasoning and Process Supervision for Biomedical Multi-Hop QA](https://mlsanity.com/paper/2506.00671/) (2025)
- [CaresAI at BioCreative IX Track 1 -- LLM for Biomedical QA](https://mlsanity.com/paper/2509.00806/) (2025)
- [Evaluating Advanced Prompting on Gemini Flash for Multi-Hop Biomedical QA](https://mlsanity.com/paper/2606.07548/) (2026)

## Abstract (arXiv)

Multi-hop question answering (QA) remains a significant challenge in the biomedical domain, requiring systems to integrate information across multiple sources to answer complex questions. To address this problem, the BioCreative IX MedHopQA shared task was designed to benchmark in multi-hop reasoning for large language models (LLMs). We developed a novel dataset of 1,000 challenging QA pairs spanning diseases, genes, and chemicals, with particular emphasis on rare diseases. Each question was constructed to require two-hop reasoning through the integration of information from two distinct Wikipedia pages. The challenge attracted 48 submissions from 13 teams. Systems were evaluated using both surface string comparison and conceptual accuracy (MedCPT score). The results showed a substantial performance gap between baseline LLMs and enhanced systems. The top-ranked submission achieved an 89.30% F1 score on the MedCPT metric and an 87.30% exact match (EM) score, compared with 67.40% and 60.20%, respectively, for the zero-shot baseline. A central finding of the challenge was that retrieval-augmented generation (RAG) and related retrieval-based strategies were critical for strong performance. In addition, concept-level evaluation improved answer assessment when correct responses differed in surface form. The MedHopQA dataset is publicly available to support continued progress in this important area. Challenge materials: https://www.ncbi.nlm.nih.gov/research/bionlp/medhopqa and benchmark https://www.codabench.org/competitions/7609/