Related papers: Building explainable graph neural network by spars…

Graph Neural Networks (GNNs) have received considerable attention since its introduction. It has been widely applied in various fields due to its ability to represent graph structured data. However, the application of GNNs is constrained by…

Graph neural networks (GNNs) demonstrate outstanding performance in a broad range of applications. While the majority of GNN applications assume that a graph structure is given, some recent methods substantially expanded the applicability…

Graph Neural Networks (GNNs) have become essential tools for analyzing graph-structured data in domains such as drug discovery and financial analysis, leading to growing demands for model transparency. Recent advances in explainable GNNs…

Malware detection in modern computing environments demands models that are not only accurate but also interpretable and robust to evasive techniques. Graph neural networks (GNNs) have shown promise in this domain by modeling rich structural…

Graphs are naturally used to describe the structures of various real-world systems in biology, society, computer science etc., where subgraphs or motifs as basic blocks play an important role in function expression and information…

Omics data, such as transcriptomics, proteomics, and metabolomics, provide critical insights into disease mechanisms and clinical outcomes. However, their high dimensionality, small sample sizes, and intricate biological networks pose major…

Graph neural networks (GNNs) work well when the graph structure is provided. However, this structure may not always be available in real-world applications. One solution to this problem is to infer a task-specific latent structure and then…

In this work, we provide a new formulation for Graph Convolutional Neural Networks (GCNNs) for link prediction on graph data that addresses common challenges for biomedical knowledge graphs (KGs). We introduce a regularized attention…

Subgraph GNNs enhance message-passing GNNs expressivity by representing graphs as sets of subgraphs, demonstrating impressive performance across various tasks. However, their scalability is hindered by the need to process large numbers of…

Accurately reconstructing Gene Regulatory Networks (GRNs) is crucial for understanding gene functions and disease mechanisms. Single-cell RNA sequencing (scRNA-seq) technology provides vast data for computational GRN reconstruction. Since…

Representation learning over graph structure data has been widely studied due to its wide application prospects. However, previous methods mainly focus on static graphs while many real-world graphs evolve over time. Modeling such evolution…

We explore different strategies to integrate prior domain knowledge into the design of a deep neural network (DNN). We focus on graph neural networks (GNN), with a use case of estimating the potential energy of chemical systems (molecules…

Binding affinity prediction of three-dimensional (3D) protein ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and…

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their…

Drug combination therapy is a powerful solution for the treatment of complex disease such as cancers due to its capability of therapeutic efficacy and reducing side effects. Nevertheless, it is very difficult to screen all drug combinations…

Graph classification is essential for understanding complex biological systems, where molecular structures and interactions are naturally represented as graphs. Traditional graph neural networks (GNNs) perform well on static tasks but…

Graph Neural Networks (GNNs) are exemplary deep models designed for graph data. Message passing mechanism enables GNNs to effectively capture graph topology and push the performance boundaries across various graph tasks. However, the trend…

Graph self-supervised learning (GSSL) has demonstrated strong potential for generating expressive graph embeddings without the need for human annotations, making it particularly valuable in domains with high labeling costs such as molecular…

Accurate prediction of blood-brain barrier permeability (BBBP) is essential for central nervous system (CNS) drug development. While graph neural networks (GNNs) have advanced molecular property prediction, they often rely on molecular…

Molecular interaction networks are powerful resources for the discovery. They are increasingly used with machine learning methods to predict biologically meaningful interactions. While deep learning on graphs has dramatically advanced the…