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Learning continuous-time dynamics on complex networks is crucial for understanding, predicting and controlling complex systems in science and engineering. However, this task is very challenging due to the combinatorial complexities in the…

Social and Information Networks · Computer Science 2020-06-19 Chengxi Zang , Fei Wang

Data assimilation presents computational challenges because many high-fidelity models must be simulated. Various deep-learning-based surrogate modeling techniques have been developed to reduce the simulation costs associated with these…

Machine Learning · Computer Science 2022-12-28 Su Jiang , Louis J. Durlofsky

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…

This paper proposes a Fast Graph Convolutional Neural Network (FGRNN) architecture to predict sequences with an underlying graph structure. The proposed architecture addresses the limitations of the standard recurrent neural network (RNN),…

Signal Processing · Electrical Eng. & Systems 2020-01-28 Sai Kiran Kadambari , Sundeep Prabhakar Chepuri

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…

Biomolecules · Quantitative Biology 2023-11-21 Shuo Zhang , Yang Liu , Lei Xie

Accurate prediction of wind flow fields in urban canopies is crucial for ensuring pedestrian comfort, safety, and sustainable urban design. Traditional methods using wind tunnels and Computational Fluid Dynamics, such as Large-Eddy…

Computational Physics · Physics 2025-07-10 Themistoklis Vargiemezis , Catherine Gorlé

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such…

Machine Learning · Computer Science 2020-06-22 Luca Franceschi , Mathias Niepert , Massimiliano Pontil , Xiao He

It has been observed that message-passing graph neural networks (GNN) sometimes struggle to maintain a healthy balance between the efficient/scalable modeling of long-range dependencies across nodes while avoiding unintended consequences…

Machine Learning · Computer Science 2025-05-21 Yongyi Yang , Tang Liu , Yangkun Wang , Zengfeng Huang , David Wipf

Graph Neural Networks (GNNs) have been widely applied to various fields due to their powerful representations of graph-structured data. Despite the success of GNNs, most existing GNNs are designed to learn node representations on the fixed…

Machine Learning · Computer Science 2021-06-14 Seongjun Yun , Minbyul Jeong , Sungdong Yoo , Seunghun Lee , Sean S. Yi , Raehyun Kim , Jaewoo Kang , Hyunwoo J. Kim

Recent years have seen the vast potential of Graph Neural Networks (GNN) in many fields where data is structured as graphs (e.g., chemistry, recommender systems). In particular, GNNs are becoming increasingly popular in the field of…

The graph neural network (GNN) has demonstrated its superior performance in various applications. The working mechanism behind it, however, remains mysterious. GNN models are designed to learn effective representations for graph-structured…

Machine Learning · Computer Science 2022-06-10 Zepeng Zhang , Ziping Zhao

Graph convolutional networks (GCNs) have been employed as a kind of significant tool on many graph-based applications recently. Inspired by convolutional neural networks (CNNs), GCNs generate the embeddings of nodes by aggregating the…

Machine Learning · Computer Science 2020-11-20 Tao Huang , Yihan Zhang , Jiajing Wu , Junyuan Fang , Zibin Zheng

Accurately forecasting dynamic processes on graphs, such as traffic flow or disease spread, remains a challenge. While Graph Neural Networks (GNNs) excel at modeling and forecasting spatio-temporal data, they often lack the ability to…

Machine Learning · Computer Science 2024-08-30 Zakaria Elabid , Lena Sasal , Daniel Busby , Abdenour Hadid

Many scientific and engineering processes produce spatially unstructured data. However, most data-driven models require a feature matrix that enforces both a set number and order of features for each sample. They thus cannot be easily…

Machine Learning · Computer Science 2021-09-30 Francis Ogoke , Kazem Meidani , Amirreza Hashemi , Amir Barati Farimani

Network models are an essential block of modern networks. For example, they are widely used in network planning and optimization. However, as networks increase in scale and complexity, some models present limitations, such as the assumption…

Graphs are essential for modeling complex relationships and capturing structured interactions in data. Graph Neural Networks (GNNs) are particularly effective when such relational structure is explicitly available, but many real-world…

Graphics · Computer Science 2026-03-02 Haozhe Chen , Soheila Farokhi , Kelvyn Bladen , Hamid Karimi , Kevin R. Moon

Accurate and efficient physical simulations are essential in science and engineering, yet traditional numerical solvers face significant challenges in computational cost when handling simulations across dynamic scenarios involving complex…

Computational Engineering, Finance, and Science · Computer Science 2025-12-12 Pengwei Liu , Xingyu Ren , Pengkai Wang , Hangjie Yuan , Zhongkai Hao , Guanyu Chen , Chao Xu , Dong Ni , Shengze Cai

Molecular dynamics (MD) simulations are a central tool in science and engineering enabling the study of dynamical behavior and the link between microscopic structure and macroscopic function. Their high computational cost, however, has…

Chemical Physics · Physics 2026-01-22 Salman N. Salman , Sergey A. Shteingolts , Ron Levie , Dan Mendels

Graph Neural Networks (GNNs) are a form of deep learning that enable a wide range of machine learning applications on graph-structured data. The learning of GNNs, however, is known to pose challenges for memory-constrained devices such as…

Machine Learning · Computer Science 2023-05-01 Jeroen Bollen , Jasper Steegmans , Jan Van den Bussche , Stijn Vansummeren

We present MeshGraphNet-Transformer (MGN-T), a novel architecture that combines the global modeling capabilities of Transformers with the geometric inductive bias of MeshGraphNets, while preserving a mesh-based graph representation. MGN-T…

Machine Learning · Computer Science 2026-02-06 Mikel M. Iparraguirre , Iciar Alfaro , David Gonzalez , Elias Cueto