Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks

Cen Wan, Domenico Cozzetto, Rui Fa and David T Jones

PLOS ONE, 2019, vol. 14, issue 7, 1-21

Abstract: Protein-protein interaction network data provides valuable information that infers direct links between genes and their biological roles. This information brings a fundamental hypothesis for protein function prediction that interacting proteins tend to have similar functions. With the help of recently-developed network embedding feature generation methods and deep maxout neural networks, it is possible to extract functional representations that encode direct links between protein-protein interactions information and protein function. Our novel method, STRING2GO, successfully adopts deep maxout neural networks to learn functional representations simultaneously encoding both protein-protein interactions and functional predictive information. The experimental results show that STRING2GO outperforms other protein-protein interaction network-based prediction methods and one benchmark method adopted in a recent large scale protein function prediction competition.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0209958

DOI: 10.1371/journal.pone.0209958

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