DeepVir -- Graphical Deep Matrix Factorization for "In Silico" Antiviral Repositioning: Application to COVID-19

This work formulates antiviral repositioning as a matrix completion problem where the antiviral drugs are along the rows and the viruses along the columns. The input matrix is partially filled, with ones in positions where the antiviral has been known to be effective against a virus. The curated metadata for antivirals (chemical structure and pathways) and viruses (genomic structure and symptoms) is encoded into our matrix completion framework as graph Laplacian regularization. We then frame the resulting multiple graph regularized matrix completion problem as deep matrix factorization. This is solved by using a novel optimization method called HyPALM (Hybrid Proximal Alternating Linearized Minimization). Results on our curated RNA drug virus association (DVA) dataset shows that the proposed approach excels over state-of-the-art graph regularized matrix completion 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 for trials for the same.

Deep Latent Factor Model for Collaborative Filtering

Latent factor models have been used widely in collaborative filtering based recommender systems. In recent years, deep learning has been successful in solving a wide variety of machine learning problems. Motivated by the success of deep learning, we propose a deeper version of latent factor model. Experiments on benchmark datasets shows that our proposed technique significantly outperforms all state-of-the-art collaborative filtering techniques.