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Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Biomolecules · Quantitative Biology 2023-10-10 Apakorn Kengkanna , Masahito Ohue

Triangular meshes are widely used to represent three-dimensional objects. As a result, many recent works have address the need for geometric deep learning on 3D mesh. However, we observe that the complexities in many of these architectures…

Machine Learning · Computer Science 2024-02-20 Thuan Trang , Nhat Khang Ngo , Daniel Levy , Thieu N. Vo , Siamak Ravanbakhsh , Truong Son Hy

The accurate description of electrostatic interactions remains a challenging problem for fitted potential-energy functions. The commonly used fixed partial-charge approximation fails to reproduce the electrostatic potential at short range…

Chemical Physics · Physics 2022-04-05 Moritz Thürlemann , Lennard Böselt , Sereina Riniker

With many frameworks based on message passing neural networks proposed to predict molecular and bulk properties, machine learning methods have tremendously shifted the paradigms of computational sciences underpinning physics, material…

Machine Learning · Computer Science 2021-09-03 Zun Wang , Chong Wang , Sibo Zhao , Yong Xu , Shaogang Hao , Chang Yu Hsieh , Bing-Lin Gu , Wenhui Duan

Graph neural networks (GNNs) have shown promise in learning unstructured mesh-based simulations of physical systems, including fluid dynamics. In tandem, geometric deep learning principles have informed the development of equivariant…

Predicting electronic energies, densities, and related chemical properties can facilitate the discovery of novel catalysts, medicines, and battery materials. By developing a physics-inspired equivariant neural network, we introduce a method…

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

Recent work has shown deep learning can accelerate the prediction of physical dynamics relative to numerical solvers. However, limited physical accuracy and an inability to generalize under distributional shift limit its applicability to…

Machine Learning · Computer Science 2021-03-17 Rui Wang , Robin Walters , Rose Yu

We describe N-body networks, a neural network architecture for learning the behavior and properties of complex many body physical systems. Our specific application is to learn atomic potential energy surfaces for use in molecular dynamics…

Machine Learning · Computer Science 2018-03-06 Risi Kondor

As they carry great potential for modeling complex interactions, graph neural network (GNN)-based methods have been widely used to predict quantum mechanical properties of molecules. Most of the existing methods treat molecules as molecular…

Machine Learning · Computer Science 2020-09-29 Zeren Shui , George Karypis

Incorporating symmetry as an inductive bias into neural network architecture has led to improvements in generalization, data efficiency, and physical consistency in dynamics modeling. Methods such as CNNs or equivariant neural networks use…

Machine Learning · Computer Science 2022-06-17 Rui Wang , Robin Walters , Rose Yu

Data over non-Euclidean manifolds, often discretized as surface meshes, naturally arise in computer graphics and biological and physical systems. In particular, solutions to partial differential equations (PDEs) over manifolds depend…

Machine Learning · Computer Science 2023-11-06 Jung Yeon Park , Lawson L. S. Wong , Robin Walters

In this paper, we develop SE3Set, an SE(3) equivariant hypergraph neural network architecture tailored for advanced molecular representation learning. Hypergraphs are not merely an extension of traditional graphs; they are pivotal for…

Machine Learning · Computer Science 2024-05-28 Hongfei Wu , Lijun Wu , Guoqing Liu , Zhirong Liu , Bin Shao , Zun Wang

Invariant and equivariant networks have been successfully used for learning images, sets, point clouds, and graphs. A basic challenge in developing such networks is finding the maximal collection of invariant and equivariant linear layers.…

Machine Learning · Computer Science 2019-05-01 Haggai Maron , Heli Ben-Hamu , Nadav Shamir , Yaron Lipman

The crucial role played by the underlying symmetries of high energy physics and lattice field theories calls for the implementation of such symmetries in the neural network architectures that are applied to the physical system under…

High Energy Physics - Lattice · Physics 2022-02-16 Srinath Bulusu , Matteo Favoni , Andreas Ipp , David I. Müller , Daniel Schuh

Deep neural networks have demonstrated remarkable efficacy in extracting meaningful representations from complex datasets. This has propelled representation learning as a compelling area of research across diverse fields. One interesting…

Quantum Physics · Physics 2024-05-28 Philipp Schmidt , Florian Marquardt , Naeimeh Mohseni

Equivariant Graph Neural Networks (GNNs) have demonstrated significant success across various applications. To achieve completeness -- that is, the universal approximation property over the space of equivariant functions -- the network must…

Machine Learning · Computer Science 2025-10-16 Jiacheng Cen , Anyi Li , Ning Lin , Tingyang Xu , Yu Rong , Deli Zhao , Zihe Wang , Wenbing Huang

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.…

Machine Learning · Computer Science 2025-02-07 Claudio Battiloro , Ege Karaismailoğlu , Mauricio Tec , George Dasoulas , Michelle Audirac , Francesca Dominici

Two-body interactions of elementary particles are useful in particle and nuclear physics to describe qualitatively and quantitatively few- and many-body systems. We are extending for this purpose the quantum inversion approach for systems…

Nuclear Theory · Physics 2016-09-08 M. Sander , H. V. von Geramb

In recent years, deep learning techniques have shown great success in various tasks related to inverse problems, where a target quantity of interest can only be observed through indirect measurements by a forward operator. Common approaches…

Numerical Analysis · Mathematics 2024-03-18 Matthias Beckmann , Nick Heilenkötter