Discovery of pathways in protein-protein interaction networks using a genetic algorithm

Biological pathways have played an important role in understanding cell activities and evolution. In order to find these pathways, it is necessary to orient protein-protein interactions, which are usually given in forms of undirected networks or graphs. Previous findings indicate that orienting protein interactions can improve the process of pathway discovery. However, assigning orientation for protein interactions is a combinatorial optimization problem which has been proved to be NP-hard, making it critical to develop efficient algorithms. This paper proposes a method for orienting protein-protein interaction networks (PPIs) and discovering pathways. For our proposal, the mathematical model of the problem is given and then a genetic algorithm is designed to find the solution for the problem taking into account the problem's characteristics. We conducted multiple runs on the data of yeast PPI networks to test the best option for the problem. The obtained results were compared with a well-known algorithm (ROLS), which was shown to be the best in dealing with this problem, in terms of the run time, fitness function values, and especially the ratio of matching gold standard pathways. The results show the good performance of our approach in addressing this problem. (C) 2015 Elsevier B.V. All rights reserved.