Junyu Chen

Junyu Chen, Long Shi, Badong Chen

Graph Neural Networks (GNNs) have exhibited remarkable efficacy in learning from multi-view graph data. In the framework of multi-view graph neural networks, a critical challenge lies in effectively combining diverse views, where each view has distinct graph structure features (GSFs). Existing approaches to this challenge primarily focus on two aspects: 1) prioritizing the most important GSFs, 2) utilizing GNNs for feature aggregation. However, prioritizing the most important GSFs can lead to limited feature diversity, and existing GNN-based aggregation strategies equally treat each view without considering view quality. To address these issues, we propose a novel Multi-View Graph Neural Network with Reliable Structural Enhancement and Aggregation (RSEA-MVGNN). Firstly, we estimate view-specific uncertainty employing subjective logic. Based on this uncertainty, we design reliable structural enhancement by feature de-correlation algorithm. This approach enables each enhancement to focus on different GSFs, thereby achieving diverse feature representation in the enhanced structure. Secondly, the model learns view-specific beliefs and uncertainty as opinions, which are utilized to evaluate view quality. Based on these opinions, the model enables high-quality views to dominate GNN aggregation, thereby facilitating representation learning. Experimental results conducted on five real-world datasets demonstrate that RSEA-MVGNN outperforms several state-of-the-art GNN-based methods.

Kexuan Xin, Qingyun Wang, Junyu Chen et al.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.