Predicting protein-protein interactions as a one-class classification problem

Abstract

Protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been used to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. While it is easy to get a dataset of interacting protein as positive example, there is no experimentally confirmed non-interacting protein to be considered as a negative set. Therefore, in this paper we solve this problem as a one-class classification problem using One-Class SVM (OCSVM). Using only positive examples (interacting protein pairs) for training, the OCSVM achieves accuracy of 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with reliable accuracy.