Integrative graph regularized matrix factorization for drug-pathway associations analysis

Abstract

Pathway-based drug discovery can give full consideration to the efficacy of compounds in the systemic physiological environment. The recently emerged drug-pathway association identification approaches gain popularity due to its potential to decipher the mechanism of action and the targets of compounds. In this study, we propose a novel drug-pathway association identification method: Integrative Graph regularized Matrix Factorization (IGMF). It employs graph regularization to encode data geometrical information and prevent possible overfitting in prediction. Furthermore, it achieves parts-based and sparse data representation by imposing L₁-norm regularization on the objective function. Empirical studies demonstrate that IGMF has strong advantages in identifying more new drug-pathway associations compared to its peer methods. It further shows a good capability to unveil the intrinsic structures of data. As an effective drug-pathway discovery method, it will inspire new analytics methods in this subfield.

Keywords: Drug-pathway associations; Graph regularized; Integrative matrix factorization; Pathway-based.