@inproceedings{kim-etal-2025-biohopr,
    title = "{B}io{H}op{R}: A Benchmark for Multi-Hop, Multi-Answer Reasoning in Biomedical Domain",
    author = "Kim, Yunsoo  and
      Abdulle, Yusuf  and
      Wu, Honghan",
    editor = "Che, Wanxiang  and
      Nabende, Joyce  and
      Shutova, Ekaterina  and
      Pilehvar, Mohammad Taher",
    booktitle = "Findings of the Association for Computational Linguistics: ACL 2025",
    month = jul,
    year = "2025",
    address = "Vienna, Austria",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/display_plenaries/2025.findings-acl.668/",
    pages = "12894--12908",
    ISBN = "979-8-89176-256-5",
    abstract = "Biomedical reasoning often requires traversing interconnected relationships across entities such as drugs, diseases, and proteins. Despite the increasing prominence of large language models (LLMs), existing benchmarks lack the ability to evaluate multi-hop reasoning in the biomedical domain, particularly for queries involving one-to-many and many-to-many relationships. This gap leaves the critical challenges of biomedical multi-hop reasoning underexplored. To address this, we introduce BioHopR, a novel benchmark designed to evaluate multi-hop, multi-answer reasoning in structured biomedical knowledge graphs. Built from the comprehensive PrimeKG, BioHopR includes 1-hop and 2-hop reasoning tasks that reflect real-world biomedical complexities.Evaluations of state-of-the-art models reveal that O3-mini, a proprietary reasoning-focused model, achieves 37.93{\%} precision on 1-hop tasks and 14.57{\%} on 2-hop tasks, outperforming proprietary models such as GPT4O and open-source biomedical models including HuatuoGPT-o1-70B and Llama-3.3-70B. However, all models exhibit significant declines in multi-hop performance, underscoring the challenges of resolving implicit reasoning steps in the biomedical domain. By addressing the lack of benchmarks for multi-hop reasoning in biomedical domain, BioHopR sets a new standard for evaluating reasoning capabilities and highlights critical gaps between proprietary and open-source models while paving the way for future advancements in biomedical LLMs. BioHopR is available at https://huggingface.co/datasets/knowlab-research/BioHopR."
}