HGLA: Biomolecular Interaction Prediction Based on Mixed High-Order Graph Convolution With Filter Network via LSTM and Channel Attention.
Journal:
IEEE/ACM transactions on computational biology and bioinformatics
Published Date:
Dec 10, 2024
Abstract
Predicting biomolecular interactions is significant for understanding biological systems. Most existing methods for link prediction are based on graph convolution. Although graph convolution methods are advantageous in extracting structure information of biomolecular interactions, two key challenges still remain. One is how to consider both the immediate and high-order neighbors. Another is how to reduce noise when aggregating high-order neighbors. To address these challenges, we propose a novel method, called mixed high-order graph convolution with filter network via LSTM and channel attention (HGLA), to predict biomolecular interactions. Firstly, the basic and high-order features are extracted respectively through the traditional graph convolutional network (GCN) and the two-layer Higher-Order Graph Convolutional Architectures via Sparsified Neighborhood Mixing (MixHop). Secondly, these features are mixed and input into the filter network composed of LayerNorm, SENet and LSTM to generate filtered features, which are concatenated and used for link prediction. The advantages of HGLA are: 1) HGLA processes high-order features separately, rather than simply concatenating them; 2) HGLA better balances the basic features and high-order features; 3) HGLA effectively filters the noise from high-order neighbors. It outperforms state-of-the-art networks on four benchmark datasets.