Protein-Protein Interaction Prediction via Graph Signal Processing

Abstract

This paper tackles the problem of predicting the protein-protein interactions that arise in all living systems. Inference of protein-protein interactions is of paramount importance for understanding fundamental biological phenomena, including cross-species protein-protein interactions, such as those causing the 2020-21 pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Furthermore, it is relevant also for applications such as drug repurposing, where a known authorized drug is applied to novel diseases. On the other hand, a large fraction of existing protein interactions are not known, and their experimental measurement is resource consuming. To this purpose, we adopt a Graph Signal Processing based approach modeling the protein-protein interaction (PPI) network (a.k.a. the interactome) as a graph and some connectivity related node features as a signal on the graph. We then leverage the signal on graph features to infer links between graph nodes, corresponding to interactions between proteins. Specifically, we develop a Markovian model of the signal on graph that enables the representation of connectivity properties of the nodes, and exploit it to derive an algorithm to infer the graph edges. Performance assessment by several metrics recognized in the literature proves that the proposed approach, named GRAph signal processing Based PPI prediction (GRABP), effectively captures underlying biologically grounded properties of the PPI network.

Keywords

• Protein-protein interaction
• Markov random field
• graph signal processing