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Virus–human protein–protein interaction prediction using Bayesian matrix factorization and projection techniques

Nourani E., Khunjush F., Sevilgen F. E.

Biocybernetics and Biomedical Engineering

2018

Vol. 38, no. 3

574--585

Pathogens infect host organisms by exploiting host cellular mechanisms and evading host defence mechanisms through molecular pathogen–host interactions (PHIs). Discovering new interactions between pathogen and human proteins is very crucial in understanding the infection mechanisms. By analysing interaction networks, the interactions responsible for infectious diseases can be detected and new drugs disabling these interactions can be delivered. In this paper, we propose a method based on Bayesian matrix factorization for predicting PHIs along with a projection-based technique and combine the results by employing an ensemble method. Furthermore, two features, target similarity and attacker similarity, are utilized for the first time in the literature for PHI prediction. The advantages of the proposed methods are two folds. Firstly, they relieve the need for negative samples which is significant since there is no available dataset providing negative samples for most of the pathogenic systems. Secondly, the experiments demonstrate that the proposed approach outperforms state-of-the-art methods; roughly 20% of top 50 predictions are among recently validated interactions. So, the search space for wet-lab experiments to obtain validated interactions can be considerably narrowed down from a huge number of possible interactions.