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Graph neural networks (GNNs), which are capable of learning representations from graphical data, are naturally suitable for modeling molecular systems. This review introduces GNNs and their various applications for small organic molecules.…

Graph Convolutional Neural Networks (GCNNs) are the most recent exciting advancement in deep learning field and their applications are quickly spreading in multi-cross-domains including bioinformatics, chemoinformatics, social networks,…

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.…

Recently, graph-based models designed for downstream tasks have significantly advanced research on graph neural networks (GNNs). GNN baselines based on neural message-passing mechanisms such as GCN and GAT perform worse as the network…

Graph Neural Networks (GNNs) and Transformers share significant similarities in their encoding strategies for interacting with features from nodes of interest, where Transformers use query-key scores and GNNs use edges. Compared to GNNs,…

Convolutional neural networks (CNNs) are usually used as a backbone to design methods in biomedical image segmentation. However, the limitation of receptive field and large number of parameters limit the performance of these methods. In…

Graph Neural Networks (GNN) have shown a strong potential to be integrated into commercial products for network control and management. Early works using GNN have demonstrated an unprecedented capability to learn from different network…

Deep learning's performance has been extensively recognized recently. Graph neural networks (GNNs) are designed to deal with graph-structural data that classical deep learning does not easily manage. Since most GNNs were created using…

Recent years have witnessed fast developments of graph neural networks (GNNs) that have benefited myriad graph analytic tasks and applications. Most GNNs rely on the homophily assumption that nodes belonging to the same class are more…

Graph neural networks (GNNs) have received much attention recently because of their excellent performance on graph-based tasks. However, existing research on GNNs focuses on designing more effective models without considering much about the…

In the last decade or so, we have witnessed deep learning reinvigorating the machine learning field. It has solved many problems in the domains of computer vision, speech recognition, natural language processing, and various other tasks…

As large-scale graphs become more widespread, more and more computational challenges with extracting, processing, and interpreting large graph data are being exposed. It is therefore natural to search for ways to summarize these expansive…

Graph neural networks (GNNs) demonstrate a robust capability for representation learning on graphs with complex structures, showcasing superior performance in various applications. The majority of existing GNNs employ a graph convolution…

Graph neural networks (GNNs) have attracted much attention due to their ability to leverage the intrinsic geometries of the underlying data. Although many different types of GNN models have been developed, with many benchmarking procedures…

Graph Neural Networks (GNNs) are becoming central in the study of time series, coupled with existing algorithms as Temporal Convolutional Networks and Recurrent Neural Networks. In this paper, we see time series themselves as directed…

Graph Neural Networks (GNNs) have emerged as a powerful tool to learn from graph-structured data. A paramount example of such data is the brain, which operates as a network, from the micro-scale of neurons, to the macro-scale of regions.…

Important advances have been made using convolutional neural network (CNN) approaches to solve complicated problems in areas that rely on grid structured data such as image processing and object classification. Recently, research on graph…

Graph Neural Networks (GNNs) have emerged as powerful representation learning tools for capturing complex dependencies within diverse graph-structured data. Despite their success in a wide range of graph mining tasks, GNNs have raised…

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats…

In this work, we benchmark a variety of single- and multi-task graph neural network (GNN) models against lower-bar and higher-bar traditional machine learning approaches employing human engineered molecular features. We consider four GNN…