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Hyper-RAG: combating LLM hallucinations using hypergraph-driven retrieval-augmented generation

  • Yifan Feng
  • , Hao Hu
  • , Shihui Ying
  • , Xingliang Hou
  • , Shiquan Liu
  • , Mingyuan Yang
  • , Junchang Li
  • , Shaoyi Du*
  • , Nanning Zheng*
  • , Han Hu*
  • , Yue Gao*
  • *Corresponding author for this work
  • Tsinghua University
  • Xi'an Jiaotong University
  • The Second Affiliated Hospital of Xi’an Jiaotong University
  • Shanghai University
  • Xi'an Jiaotong University
  • Newchase (Shanghai) Pharmaceutical Technology Co. Ltd.
  • Shenzhen University
  • Beijing Institute of Technology

Research output: Contribution to journalArticlepeer-review

Abstract

Large language models (LLMs) have transformed various sectors, including education, finance, and medicine, by enhancing content generation and decision-making processes. However, their integration into the medical field is cautious due to hallucinations, instances where generated content deviates from factual accuracy, potentially leading to adverse outcomes. To address this, we introduce Hyper-RAG, a hypergraph-driven Retrieval-Augmented Generation method that comprehensively captures both pairwise and beyond-pairwise correlations in domain-specific knowledge, thereby mitigating hallucinations. Experiments on the NeurologyCrop dataset with six prominent LLMs demonstrated that Hyper-RAG improves accuracy by an average of 12.3% over direct LLM use and outperforms GraphRAG and LightRAG by 6.3% and 6.0%, respectively. Additionally, Hyper-RAG maintained stable performance with increasing query complexity, unlike existing methods which declined. Further validation across nine diverse datasets showed a 35.5% performance improvement over LightRAG using a selection-based assessment. The lightweight variant, Hyper-RAG-Lite, achieved twice the retrieval speed and a 3.3% performance boost compared with LightRAG. These results confirm Hyper-RAG’s effectiveness in enhancing LLM reliability and reducing hallucinations, making it a robust solution for high-stakes applications like medical diagnostics.

Original languageEnglish
Article number5778
JournalNature Communications
Volume17
Issue number1
DOIs
Publication statusPublished - Dec 2026
Externally publishedYes

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