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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

Molecular graph neural networks (GNNs) often focus exclusively on XYZ-based geometric representations and thus overlook valuable chemical context available in public databases like PubChem. This work introduces a multimodal framework that…

Machine Learning · Computer Science 2025-05-20 Can Polat , Hasan Kurban , Erchin Serpedin , Mustafa Kurban

Interacting particle systems play a key role in science and engineering. Access to the governing particle interaction law is fundamental for a complete understanding of such systems. However, the inherent system complexity keeps the…

Machine Learning · Computer Science 2022-10-25 Zhichao Han , David S. Kammer , Olga Fink

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

The determination of charged particle trajectories in collisions at the CERN Large Hadron Collider (LHC) is an important but challenging problem, especially in the high interaction density conditions expected during the future…

Graph neural networks (GNNs) are designed to process data associated with graphs. They are finding an increasing range of applications; however, as with other modern machine learning techniques, their theoretical understanding is limited.…

Disordered Systems and Neural Networks · Physics 2026-02-23 O. Duranthon , L. Zdeborová

The simulation of microcirculatory blood flow in realistic vascular architectures poses significant challenges due to the multiscale nature of the problem and the topological complexity of capillary networks. In this work, we propose a…

Numerical Analysis · Mathematics 2025-12-12 Paolo Botta , Piermario Vitullo , Thomas Ventimiglia , Andreas Linninger , Paolo Zunino

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…

Machine Learning · Computer Science 2019-11-19 Ferran Alet , Adarsh K. Jeewajee , Maria Bauza , Alberto Rodriguez , Tomas Lozano-Perez , Leslie Pack Kaelbling

Gaussian processes (GPs) are widely used as surrogate models for emulating computer code, which simulate complex physical phenomena. In many problems, additional boundary information (i.e., the behavior of the phenomena along input…

Methodology · Statistics 2019-08-26 Liang Ding , Simon Mak , C. F. Jeff Wu

This study aims to predict the spatio-temporal evolution of physical quantities observed in multi-layered display panels subjected to the drop impact of a ball. To model these complex interactions, graph neural networks have emerged as…

Computational Physics · Physics 2024-11-05 Jiyong Kim , Jangseop Park , Nayong Kim , Younyeol Yu , Kiseok Chang , Chang-Seung Woo , Sunwoong Yang , Namwoo Kang

In engineering design, surrogate models are widely employed to replace computationally expensive simulations by leveraging design variables and geometric parameters from computer-aided design (CAD) models. However, these models often lose…

Machine Learning · Computer Science 2024-06-05 Jangseop Park , Namwoo Kang

Simulation of the dynamics of physical systems is essential to the development of both science and engineering. Recently there is an increasing interest in learning to simulate the dynamics of physical systems using neural networks.…

Machine Learning · Computer Science 2022-01-31 Ce Yang , Weihao Gao , Di Wu , Chong Wang

Neural representations of 3D data have been widely adopted across various applications, particularly in recent work leveraging coordinate-based networks to model scalar or vector fields. However, these approaches face inherent challenges,…

Computer Vision and Pattern Recognition · Computer Science 2026-02-24 Biao Zhang , Jing Ren , Peter Wonka

We develop and implement two realizations of quantum graph neural networks (QGNN), applied to the task of particle interaction simulation. The first QGNN is a speculative quantum-classical hybrid learning model that relies on the ability to…

Geometric data acquired from real-world scenes, e.g., 2D depth images, 3D point clouds, and 4D dynamic point clouds, have found a wide range of applications including immersive telepresence, autonomous driving, surveillance, etc. Due to…

Computer Vision and Pattern Recognition · Computer Science 2021-09-07 Wei Hu , Jiahao Pang , Xianming Liu , Dong Tian , Chia-Wen Lin , Anthony Vetro

Recently, techniques for applying convolutional neural networks to graph-structured data have emerged. Graph convolutional neural networks (GCNNs) have been used to address node and graph classification and matrix completion. Although the…

Machine Learning · Statistics 2018-11-28 Yingxue Zhang , Soumyasundar Pal , Mark Coates , Deniz Üstebay

Mesh-based Graph Neural Networks (GNNs) have recently shown capabilities to simulate complex multiphysics problems with accelerated performance times. However, mesh-based GNNs require a large number of message-passing (MP) steps and suffer…

Computational Engineering, Finance, and Science · Computer Science 2024-02-15 Roberto Perera , Vinamra Agrawal

Modeling human trajectories in crowded environments is challenging due to the complex nature of pedestrian behavior and interactions. This paper proposes a geometric graph neural network (GNN) architecture that integrates domain knowledge…

Machine Learning · Computer Science 2024-10-24 Sara Honarvar , Yancy Diaz-Mercado

Mesh-based simulations play a key role when modeling complex physical systems that, in many disciplines across science and engineering, require the solution of parametrized time-dependent nonlinear partial differential equations (PDEs). In…

Numerical Analysis · Mathematics 2023-08-04 Nicola Rares Franco , Stefania Fresca , Filippo Tombari , Andrea Manzoni

Learning from graph-structured data is an important task in machine learning and artificial intelligence, for which Graph Neural Networks (GNNs) have shown great promise. Motivated by recent advances in geometric representation learning, we…

Machine Learning · Computer Science 2019-10-30 Qi Liu , Maximilian Nickel , Douwe Kiela
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