Adaptive multi-view learning method for enhanced drug repurposing using chemical-induced transcriptional profiles,knowledge graphs,and large language models
10.1016/j.jpha.2025.101275
- Author:
Yudong YAN
1
;
Yinqi YANG
;
Zhuohao TONG
;
Yu WANG
;
Fan YANG
;
Zupeng PAN
;
Chuan LIU
;
Mingze BAI
;
Yongfang XIE
;
Yuefei LI
;
Kunxian SHU
;
Yinghong LI
Author Information
1. Chongqing Key Laboratory of Big Data for Bio Intelligence,Chongqing University of Posts and Telecommunications,Chongqing,400065,China
- Publication Type:Journal Article
- Keywords:
Drug repurposing;
Multi-view learning;
Chemical-induced transcriptional profile;
Knowledge graph;
Large language model;
Heterogeneous network
- From:
Journal of Pharmaceutical Analysis
2025;15(6):1354-1369
- CountryChina
- Language:English
-
Abstract:
Drug repurposing offers a promising alternative to traditional drug development and significantly re-duces costs and timelines by identifying new therapeutic uses for existing drugs.However,the current approaches often rely on limited data sources and simplistic hypotheses,which restrict their ability to capture the multi-faceted nature of biological systems.This study introduces adaptive multi-view learning(AMVL),a novel methodology that integrates chemical-induced transcriptional profiles(CTPs),knowledge graph(KG)embeddings,and large language model(LLM)representations,to enhance drug repurposing predictions.AMVL incorporates an innovative similarity matrix expansion strategy and leverages multi-view learning(MVL),matrix factorization,and ensemble optimization techniques to integrate heterogeneous multi-source data.Comprehensive evaluations on benchmark datasets(Fdata-set,Cdataset,and Ydataset)and the large-scale iDrug dataset demonstrate that AMVL outperforms state-of-the-art(SOTA)methods,achieving superior accuracy in predicting drug-disease associations across multiple metrics.Literature-based validation further confirmed the model's predictive capabilities,with seven out of the top ten predictions corroborated by post-2011 evidence.To promote transparency and reproducibility,all data and codes used in this study were open-sourced,providing resources for pro-cessing CTPs,KG,and LLM-based similarity calculations,along with the complete AMVL algorithm and benchmarking procedures.By unifying diverse data modalities,AMVL offers a robust and scalable so-lution for accelerating drug discovery,fostering advancements in translational medicine and integrating multi-omics data.We aim to inspire further innovations in multi-source data integration and support the development of more precise and efficient strategies for advancing drug discovery and translational medicine.
