Related papers: DualEquiNet: A Dual-Space Hierarchical Equivariant…

Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making…

Geometric Graph Neural Networks (GNNs) and Transformers have become state-of-the-art for learning from 3D protein structures. However, their reliance on message passing prevents them from capturing the hierarchical interactions that govern…

Geometric deep learning has been revolutionizing the molecular modeling field. Despite the state-of-the-art neural network models are approaching ab initio accuracy for molecular property prediction, their applications, such as drug…

Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…

Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these…

Effectively predicting molecular interactions has the potential to accelerate molecular dynamics by multiple orders of magnitude and thus revolutionize chemical simulations. Graph neural networks (GNNs) have recently shown great successes…

Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale…

Predicting the binding sites of target proteins plays a fundamental role in drug discovery. Most existing deep-learning methods consider a protein as a 3D image by spatially clustering its atoms into voxels and then feed the voxelized…

Recent advances in applying Graph Neural Networks (GNNs) to molecular science have showcased the power of learning three-dimensional (3D) structure representations with GNNs. However, most existing GNNs suffer from the limitations of…

The prediction of physicochemical properties from molecular structures is a crucial task for artificial intelligence aided molecular design. A growing number of Graph Neural Networks (GNNs) have been proposed to address this challenge.…

Graph Neural Networks (GNNs) with equivariant properties have achieved significant success in modeling complex dynamic systems and molecular properties. However, their expressiveness ability is limited by: (1) Existing methods often…

Graph neural networks (GNNs) have gained traction in high-energy physics (HEP) for their potential to improve accuracy and scalability. However, their resource-intensive nature and complex operations have motivated the development of…

Equivariant Graph Neural Networks (GNNs) have achieved remarkable success across diverse scientific applications. However, existing approaches face critical efficiency challenges when scaling to large geometric graphs and suffer significant…

Graph Neural Networks (GNNs) have proven effective in various medical imaging applications, such as automated disease diagnosis. However, due to the local neighborhood aggregation paradigm in message passing which characterizes these…

Graph neural networks (GNNs) based on message passing between neighboring nodes are known to be insufficient for capturing long-range interactions in graphs. In this project we study hierarchical message passing models that leverage a…

Graph neural networks excel at modeling pairwise interactions, but they cannot flexibly accommodate higher-order interactions and features. Topological deep learning (TDL) has emerged recently as a promising tool for addressing this issue.…

Recent advances in computational modelling of atomic systems, spanning molecules, proteins, and materials, represent them as geometric graphs with atoms embedded as nodes in 3D Euclidean space. In these graphs, the geometric attributes…

Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics…

Learning to reason about relations and dynamics over multiple interacting objects is a challenging topic in machine learning. The challenges mainly stem from that the interacting systems are exponentially-compositional, symmetrical, and…

Molecular sciences address a wide range of problems involving molecules of different types and sizes and their complexes. Recently, geometric deep learning, especially Graph Neural Networks, has shown promising performance in molecular…