Multi-Domain Manifold Learning for Drug-Target Interaction Prediction

Abstract

Drug-target interaction (DTI) provides novel insights about the genomic drug discovery, and is a critical technique to drug discovery. Recently, researchers try to incorporate different information about drugs and targets for prediction. However, the heterogeneous and high-dimensional data poses huge challenge to existing machine learning methods. In the last few years, extensive research efforts have been devoted to the utilization of manifold property on high dimensional data, e.g. dimension reduction methods preserving local structures of the manifolds. Motivated by the successes of these studies, we propose a general framework incorporating both manifold structures and known interaction/non-interaction information to predict the drug-target interactions. To overcome the challenges of domain scaling and information inconsistency, we formulate the problem with Semidefinite Programming (SDP), including new constraints to improve the robustness of the learning procedure. A variety of optimization techniques are also designed to enhance the scalability of the problem solver. Effectiveness of the method is evaluated by experiments on the benchmark dataset. Compared with state-of-the-art methods, the proposed methods generate much more accurate drug-target interaction prediction.