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Journal Articles Journal of Computational Biology Year : 2022

DeepVir, Graphical Deep Matrix Factorization for In Silico Antiviral Repositioning. Application to COVID19.

Abstract

This study formulates antiviral repositioning as a matrix completion problem wherein the antiviral drugs are along the rows and the viruses are along the columns. The input matrix is partially filled, with ones in positions where the antiviral drug has been known to be effective against a virus. The curated metadata for antivirals (chemical structure and pathways) and viruses (genomic structure and symptoms) are encoded into our matrix completion framework as graph Laplacian regularization. We then frame the resulting multiple graph regularized matrix completion (GRMC) problem as deep matrix factorization. This is solved by using a novel optimization method called HyPALM (Hybrid Proximal Alternating Linearized Minimization). Results of our curated RNA drug–virus association data set show that the proposed approach excels over state-of-the-art GRMC techniques. When applied to in silico prediction of antivirals for COVID-19, our approach returns antivirals that are either used for treating patients or are under trials for the same.
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Dates and versions

hal-02946338 , version 1 (23-09-2020)

Identifiers

Cite

Aanchal Mongia, Stuti Jain, Emilie Chouzenoux, Angshul Majumdar. DeepVir, Graphical Deep Matrix Factorization for In Silico Antiviral Repositioning. Application to COVID19.. Journal of Computational Biology, 2022, 29 (5), pp.441-452. ⟨10.36227/techrxiv.12987497.v1⟩. ⟨hal-02946338⟩
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