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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 Neural Networks (GNNs) are key tools for graph representation learning, demonstrating strong results across diverse prediction tasks. In this paper, we present Convexified Message-Passing Graph Neural Networks (CGNNs), a novel and…

Machine learning frameworks such as graph neural networks typically rely on a given, fixed graph to exploit relational inductive biases and thus effectively learn from network data. However, when said graphs are (partially) unobserved,…

Constructing appropriate representations of molecules lies at the core of numerous tasks such as material science, chemistry and drug designs. Recent researches abstract molecules as attributed graphs and employ graph neural networks (GNN)…

Graph Neural Networks (GNNs) have been proposed as a tool for learning sparse matrix preconditioners, which are key components in accelerating linear solvers. We present theoretical and empirical evidence that message-passing GNNs are…

Graph neural networks (GNNs) are widely applied in graph data modeling. However, existing GNNs are often trained in a task-driven manner that fails to fully capture the intrinsic nature of the graph structure, resulting in sub-optimal node…

Graph neural networks (GNNs) achieve strong performance on graph learning tasks, but training on large-scale networks remains computationally challenging. Transferability results show that GNNs with fixed weights can generalize from smaller…

We explore the use of graph neural networks (GNNs) to model spatial processes in which there is no a priori graphical structure. Similar to finite element analysis, we assign nodes of a GNN to spatial locations and use a computational…

Recent advances in equivariant graph neural networks (GNNs) have made deep learning amenable to developing fast surrogate models to expensive ab initio quantum mechanics (QM) approaches for molecular potential predictions. However, building…

Graph neural networks (GNNs) have been widely adopted in engineering applications such as social network analysis, chemical research and computer vision. However, their efficacy is severely compromised by the inherent homophily assumption,…

Accurate prediction of physical properties is critical for discovering and designing novel materials. Machine learning technologies have attracted significant attention in the materials science community for their potential for large-scale…

Graph Neural Networks (GNN) can capture the geometric properties of neural representations in EEG data. Here we utilise those to study how reinforcement-based motor learning affects neural activity patterns during motor planning, leveraging…

Graph Neural Networks (GNNs) are powerful and flexible neural networks that use the naturally sparse connectivity information of the data. GNNs represent this connectivity as sparse matrices, which have lower arithmetic intensity and thus…

Graph neural networks (GNNs) have been predominantly driven by message-passing, where node representations are iteratively updated via local neighborhood aggregation. Despite their success, message-passing suffers from fundamental…

Neural Networks (GNNs) have revolutionized the molecular discovery to understand patterns and identify unknown features that can aid in predicting biophysical properties and protein-ligand interactions. However, current models typically…

The representation learning on textual graph is to generate low-dimensional embeddings for the nodes based on the individual textual features and the neighbourhood information. Recent breakthroughs on pretrained language models and graph…

As more deep learning models are being applied in real-world applications, there is a growing need for modeling and learning the representations of neural networks themselves. An efficient representation can be used to predict target…

Despite much research, Graph Neural Networks (GNNs) still do not display the favorable scaling properties of other deep neural networks such as Convolutional Neural Networks and Transformers. Previous work has identified issues such as…

Graph neural networks (GNNs) have demonstrated great success in representation learning for graph-structured data. The layer-wise graph convolution in GNNs is shown to be powerful at capturing graph topology. During this process, GNNs are…

Convolution Neural Networks on Graphs are important generalization and extension of classical CNNs. While previous works generally assumed that the graph structures of samples are regular with unified dimensions, in many applications, they…