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arXiv · 2510.06742

MultiCNKG: Integrating Cognitive Neuroscience, Gene, and Disease Knowledge Graphs Using Large Language Models

Ali Sarabadani·Kheirolah Rahsepar Fard
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Abstract

The advent of large language models (LLMs) has revolutionized the integration of knowledge graphs (KGs) in biomedical and cognitive sciences, overcoming limitations in traditional machine learning methods for capturing intricate semantic links among genes, diseases, and cognitive processes. We introduce MultiCNKG, an innovative framework that merges three key knowledge sources: the Cognitive Neuroscience Knowledge Graph (CNKG) with 2.9K nodes and 4.3K edges across 9 node types and 20 edge types; Gene Ontology (GO) featuring 43K nodes and 75K edges in 3 node types and 4 edge types; and Disease Ontology (DO) comprising 11.2K nodes and 8.8K edges with 1 node type and 2 edge types. Leveraging LLMs like GPT-4, we conduct entity alignment, semantic similarity computation, and graph augmentation to create a cohesive KG that interconnects genetic mechanisms, neurological disorders, and cognitive functions. The resulting MultiCNKG encompasses 6.9K nodes across 5 types (e.g., Genes, Diseases, Cognitive Processes) and 11.3K edges spanning 7 types (e.g., Causes, Associated with, Regulates), facilitating a multi-layered view from molecular to behavioral domains. Assessments using metrics such as precision (85.20%), recall (87.30%), coverage (92.18%), graph consistency (82.50%), novelty detection (40.28%), and expert validation (89.50%) affirm its robustness and coherence. Link prediction evaluations with models like TransE (MR: 391, MRR: 0.411) and RotatE (MR: 263, MRR: 0.395) show competitive performance against benchmarks like FB15k-237 and WN18RR. This KG advances applications in personalized medicine, cognitive disorder diagnostics, and hypothesis formulation in cognitive neuroscience.

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Ali Sarabadani, Kheirolah Rahsepar Fard. 2025-10-08. MultiCNKG: Integrating Cognitive Neuroscience, Gene, and Disease Knowledge Graphs Using Large Language Models. https://doi.org/10.22034/tmi.2026.244943

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