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Gaussian processes (GPs) are an attractive class of machine learning models because of their simplicity and flexibility as building blocks of more complex Bayesian models. Meanwhile, graph neural networks (GNNs) emerged recently as a…
In recent years, graph neural networks (GNNs) have gained significant attention for node classification tasks on graph-structured data. However, traditional GNNs primarily focus on adjacency relationships between nodes, often overlooking…
Graph Neural Networks (GNNs) are characterized by their capacity of processing graph-structured data. However, due to the sparsity of labels under semi-supervised learning, they have been found to exhibit biased performance on specific…
Graph neural networks (GNNs) are a class of deep models that operate on data with arbitrary topology represented as graphs. We introduce an efficient memory layer for GNNs that can jointly learn node representations and coarsen the graph.…
We present a systematic investigation using graph neural networks (GNNs) to model organic chemical reactions. To do so, we prepared a dataset collection of four ubiquitous reactions from the organic chemistry literature. We evaluate seven…
Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive…
Recommendation models utilizing Graph Convolutional Networks (GCNs) have achieved state-of-the-art performance, as they can integrate both the node information and the topological structure of the user-item interaction graph. However, these…
Since multidrug combination is widely applied, the accurate prediction of drug-drug interaction (DDI) is becoming more and more critical. In our method, we use graph to represent drug-drug interaction: nodes represent drug; edges represent…
Graph Neural Networks have emerged as the most popular architecture for graph-level learning, including graph classification and regression tasks, which frequently arise in areas such as biochemistry and drug discovery. Achieving good…
Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect…
Graph convolutional network (GCN) based approaches have achieved significant progress for solving complex, graph-structured problems. GCNs incorporate the graph structure information and the node (or edge) features through message passing…
This paper explores the ability of Graph Neural Networks (GNNs) in learning various forms of information for link prediction, alongside a brief review of existing link prediction methods. Our analysis reveals that GNNs cannot effectively…
Graph Neural Networks (GNN) are reshaping our understanding of biomedicine and diseases by revealing the deep connections among genes and cells. As both algorithmic and biomedical technologies have advanced significantly, we're entering a…
Insomnia affects a vast population of the world and can have a wide range of causes. Existing treatments for insomnia have been linked with many side effects like headaches, dizziness, etc. As such, there is a clear need for improved…
Biomarker discovery from high-throughput transcriptomic data is crucial for advancing precision medicine. However, existing methods often neglect gene-gene regulatory relationships and lack stability across datasets, leading to conflation…
The ongoing need for effective epidemic modeling has driven advancements in capturing the complex dynamics of infectious diseases. Traditional models, such as Susceptible-Infected-Recovered, and graph-based approaches often fail to account…
Deep graph neural networks (GNNs) have achieved excellent results on various tasks on increasingly large graph datasets with millions of nodes and edges. However, memory complexity has become a major obstacle when training deep GNNs for…
The integration of multi-omic data is pivotal for understanding complex diseases, but its high dimensionality and noise present significant challenges. Graph Neural Networks (GNNs) offer a robust framework for analyzing large-scale…
Learning graph convolutional networks (GCNs) is an emerging field which aims at generalizing convolutional operations to arbitrary non-regular domains. In particular, GCNs operating on spatial domains show superior performances compared to…
Unraveling the complexities of Gene Regulatory Networks (GRNs) is crucial for understanding cellular processes and disease mechanisms. Traditional computational methods often struggle with the dynamic nature of these networks. This study…