Predicting Protein–Protein Interactions via Gated Graph Attention Signed Network

Abstract

Protein–protein interactions (PPIs) play a key role in signal transduction and pharmacogenomics, and hence, accurate PPI prediction is crucial. Graph structures have received increasing attention owing to their outstanding performance in machine learning. In practice, PPIs can be expressed as a signed network (i.e., graph structure), wherein the nodes in the network represent proteins, and edges represent the interactions (positive or negative effects) of protein nodes. PPI predictions can be realized by predicting the links of the signed network; therefore, the use of gated graph attention for signed networks (SN-GGAT) is proposed herein. First, the concept of graph attention network (GAT) is applied to signed networks, in which “attention” represents the weight of neighbor nodes, and GAT updates the node features through the weighted aggregation of neighbor nodes. Then, the gating mechanism is defined and combined with the balance theory to obtain the high-order relations of protein nodes to improve the attention effect, making the attention mechanism follow the principle of “low-order high attention, high-order low attention, different signs opposite”. PPIs are subsequently predicted on the Saccharomyces cerevisiae core dataset and the Human dataset. The test results demonstrate that the proposed method exhibits strong competitiveness.