MSE-CapsPPISP: Spatial Hierarchical Protein-Protein Interaction Sites Prediction Using Squeeze-and-Excitation Capsule Networks

The discovery of protein-protein interaction sites (PPIs) is vital for exploring the principle of PPI and understanding the nature of life activities. Developing computational approaches to predict PPIs can effectively compensate for the shortcomings of biological experiments, which are mostly time-consuming and vulnerable to noise. In recent years, deep learning has been used to develop PPIs prediction models. Most of them consider the contextual information of the target amino acid residues and use a local protein sequence to represent the targets. However, the traditional deep-learning techniques, e.g., deep neural networks (DNNs) and convolutional neural networks (CNNs), disregard the important spatial hierarchies contained in the features of protein sequences, leading to their failure to effectively distinguish the interaction sites from different residue regions. In this work, we design MSE-CapsPPISP, a new deep-learning model to address the PPIs prediction with spatial hierarchies. The key idea of MSE-CapsPPISP is to take into account the hierarchical relationships between the features of protein sequences. We characterize the hierarchical relationships by designing a tailored Capsule Network (CapsNet) model, which is a novel type of neural network with vector neurons. Moreover, to make the network representation more robust, MSE-CapsPPISP uses multi-scale CNNs to extract multi-scale features of protein sequences and Squeeze-and-Excitation blocks to recalibrate the features. The validation results show that our MSE-CapsPPISP outperforms the baseline CNNs-based architecture DeepPPISP and other competing schemes in the PPIs prediction task.