Background and Objective: In silico prediction of drug-target interactions (DTI) could provide valuable information and speed-up the process of drug repositioning -finding novel usage for existing drugs. In our work, we focus on machine learning algorithms supporting drug-centric repositioning approach, which aims to find novel usage for existing or abandoned drugs. We aim at proposing a per-drug ranking-based method, which reflects the needs of drug-centric repositioning research better than conventional drug-target prediction approaches. Methods: We propose Bayesian Ranking Prediction of Drug-Target Interactions(BRDTI). The method is based on Bayesian Personalized Ranking matrix factorization (BPR) which has been shown to be an excellent approach for various preference learning tasks, however, it has not been used for DTI prediction previously. In order to successfully deal with DTI challenges, we extended BPR by proposing: (i) the incorporation of target bias, (ii) a technique to handle new drugs and (iii) content alignment to take structural similarities of drugs and targets into account. Conclusions:Based on the evaluation, we can conclude that BRDTI is an appropriate choice for researchers looking for an in silico DTI prediction technique to be used in drugcentric repositioning scenarios. BRDTI Software and supplementary materials are available online at www.ksi.mff.cuni.cz/~peska/BRDTI.

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