Fast Dual-Regularized Autoencoder for Sparse Biological Data

Algorithms for sparse matrix completion are used in recommender systems to predict user preferences to items such as news, movies, or songs [1]. The same methods can be successfully applied in other fields, for instance in systems biology to predict gene-disease associations or in computational systems pharmacology to predict adverse drug reactions [2] and to repurpose FDA approved drugs [3]. Matrix completion is the task of filling out missing entries in an observed sparse matrix. A low rank solution to matrix completion problem can be obtained via matrix factorization, a technique that approximates the input sparse matrix as a product of two lower dimensional matrices of users' and items' latent vectors [4]. Despite efforts to develop more sophisticated techniques, such as the methods based on artificial neural networks [5], matrix factorization remains the method of choice in recommender systems due to its efficiency and high accuracy [6].