Factor graph-aggregated heterogeneous network embedding for disease-gene association prediction

• Main Authors: Ming He, Chen Huang, Bo Liu, Yadong Wang, Junyi Li
• Format: Article
• Language: English
• Published: BMC 2021-03-01
• Series: BMC Bioinformatics
• Subjects: Disease-gene association prediction; Heterogeneous network; Graph neural network; Factorization
• Online Access: https://doi.org/10.1186/s12859-021-04099-3

Abstract Background Exploring the relationship between disease and gene is of great significance for understanding the pathogenesis of disease and developing corresponding therapeutic measures. The prediction of disease-gene association by computational methods accelerates the process. Results Many existing methods cannot fully utilize the multi-dimensional biological entity relationship to predict disease-gene association due to multi-source heterogeneous data. This paper proposes FactorHNE, a factor graph-aggregated heterogeneous network embedding method for disease-gene association prediction, which captures a variety of semantic relationships between the heterogeneous nodes by factorization. It produces different semantic factor graphs and effectively aggregates a variety of semantic relationships, by using end-to-end multi-perspectives loss function to optimize model. Then it produces good nodes embedding to prediction disease-gene association. Conclusions Experimental verification and analysis show FactorHNE has better performance and scalability than the existing models. It also has good interpretability and can be extended to large-scale biomedical network data analysis.