1 National Library of Medicine (NLM), National Institutes of Health (NIH), MD, 20894, Bethesda, USA.
2 University of Illinois at Urbana Champaign.
3 Korea University.
4 VNU University of Engineering and Technology, Hanoi, Vietnam.
5 Concordia University, Montreal, QC, CA.
6 Institute of Biomedical Chemistry (IBMC), 10 bld. 8, Pogodinskaya str., 119121 Moscow, Russia.
7 LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
8 Faculty of Engineering, Computer Engineering Department Cairo University.
9 CaresAI, Australia.
10 Menzies School of Health Research, Charles Darwin University, NT, Australia.

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/.