Correlated Protein Function Prediction with Robust Feature Selection

Abstract

Determining the functional roles of proteins is a vital task to understand life at molecular level and has great biomedical and pharmaceutical implications. With the development of novel high-throughput techniques, enormous amounts of protein-protein interaction (PPI) data are collected and provide an important and feasible way for studying protein function predictions. According to this, many approaches assign biological functions to all proteins using PPI networks directly. However, due to the extreme complexity of the topology structure of real PPI networks, it is very difficult and time consuming to seek the global optimization or clustering on the networks. In addition, biological functions are often highly correlated, which makes functions assigned to proteins are not independent. To address these challenges, in this paper we propose a two-stage function annotation method with robust feature selection. First, we transform the network into the low-dimensional representations of nodes via manifold learning. Then, we integrate the functional correlation into the framework of multi-label linear regression, and introduce robust sparse penalty to achieve the function assignment and representative feature selection simultaneously. For the optimization, we design an efficient algorithm to iteratively solve several subproblems with closed-form solutions. Extensive experiments against other baseline methods on Saccharomyces cerevisiae data demonstrate the effectiveness of the proposed approach.