MedKGent: A Large Language Model Agent Framework for Constructing Temporally Evolving Medical Knowledge Graph

Duzhen Zhang; Zixiao Wang; Zhong-Zhi Li; Yahan Yu; Shuncheng Jia; Jiahua Dong; Haotian Xu; Xing Wu; Yingying Zhang; Tielin Zhang; Jie Yang; Xiuying Chen; Le Song

arXiv · 2508.12393

MedKGent: A Large Language Model Agent Framework for Constructing Temporally Evolving Medical Knowledge Graph

Duzhen Zhang·Zixiao Wang·Zhong-Zhi Li·Yahan Yu·Shuncheng Jia·Jiahua Dong·Haotian Xu·Xing Wu·Yingying Zhang·Tielin Zhang·Jie Yang·Xiuying Chen·Le Song

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Abstract

The rapid expansion of medical literature challenges the scalable structuring of domain knowledge. Knowledge Graphs (KGs) offer a solution, yet current construction methods lack generalizability and ignore the temporal dynamics of evolving knowledge. To address this, we introduce MedKGent, a Large Language Model (LLM) agent framework for building temporally evolving medical KGs. Using over 10 million PubMed abstracts from 1975 to 2023, MedKGent incrementally constructs a KG daily via two specialized agents. The Extractor Agent identifies knowledge triples and assigns confidence scores, while the Constructor Agent integrates these triples into a temporal graph, reinforcing recurring knowledge and resolving conflicts. The resulting KG contains 156,275 entities and 2,971,384 triples, making it, to our knowledge, the largest LLM-derived medical KG to date. Automated and expert assessments showed triple-validity rates approaching 90%. In downstream evaluations, MedKGent-KG significantly improved retrieval-augmented generation for five LLMs across seven medical question-answering benchmarks. Together, these results position MedKGent as a scalable and temporally aware infrastructure for medical knowledge representation and literature-grounded AI research.

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Duzhen Zhang, Zixiao Wang, Zhong-Zhi Li, Yahan Yu, Shuncheng Jia, Jiahua Dong, Haotian Xu, Xing Wu, Yingying Zhang, Tielin Zhang, Jie Yang, Xiuying Chen, Le Song. 2025-08-17. MedKGent: A Large Language Model Agent Framework for Constructing Temporally Evolving Medical Knowledge Graph. https://arxiv.org/abs/2508.12393

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