Graph regularized non-negative matrix factorization with [Formula: see text] norm regularization terms for drug–target interactions prediction

BACKGROUND: Identifying drug–target interactions (DTIs) plays a key role in drug development. Traditional wet experiments to identify DTIs are costly and time consuming. Effective computational methods to predict DTIs are useful to speed up the process of drug discovery. A variety of non-negativity matrix factorization based methods are proposed to predict DTIs, but most of them overlooked the sparsity of feature matrices and the convergence of adopted matrix factorization algorithms, therefore their performances can be further improved. RESULTS: In order to predict DTIs more accurately, we propose a novel method iPALM-DLMF. iPALM-DLMF models DTIs prediction as a problem of non-negative matrix factorization with graph dual regularization terms and [Formula: see text] norm regularization terms. The graph dual regularization terms are used to integrate the information from the drug similarity matrix and the target similarity matrix, and [Formula: see text] norm regularization terms are used to ensure the sparsity of the feature matrices obtained by non-negative matrix factorization. To solve the model, iPALM-DLMF adopts non-negative double singular value decomposition to initialize the nonnegative matrix factorization, and an inertial Proximal Alternating Linearized Minimization iterating process, which has been proved to converge to a KKT point, to obtain the final result of the matrix factorization. Extensive experimental results show that iPALM-DLMF has better performance than other state-of-the-art methods. In case studies, in 50 highest-scoring proteins targeted by the drug gabapentin predicted by iPALM-DLMF, 46 have been validated, and in 50 highest-scoring drugs targeting prostaglandin-endoperoxide synthase 2 predicted by iPALM-DLMF, 47 have been validated. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05496-6.