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MedKGent represents a significant advancement in medical AI by utilizing LLM agents to construct the largest temporally evolving knowledge graph directly from PubMed literature. This framework addresses critical scalability issues and improves retrieval-augmented generation for downstream clinical question-answering tasks with high validity rates. The work establishes new infrastructure standards for integrating vast, time-sensitive biomedical data into robust machine learning pipelines.
MedKGent: A Large Language Model Agent Framework for Constructing Temporally Evolving Medical Knowledge Graph
arXiv:2508.12393v3 Announce Type: replace-cross 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.
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.
Computation and Language (cs.CL); Artificial Intelligence (cs.AI)
arXiv:2508.12393 [cs.CL]
(or arXiv:2508.12393v3 [cs.CL] for this version)
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