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We apply a temporal edge prediction model for weighted dynamic graphs to predict time-dependent changes in molecular structure. Each molecule is represented as a complete graph in which each atom is a vertex and all vertex pairs are…

机器学习 · 计算机科学 2021-06-28 Michael Hunter Ashby , Jenna A. Bilbrey

We present a systematic investigation using graph neural networks (GNNs) to model organic chemical reactions. To do so, we prepared a dataset collection of four ubiquitous reactions from the organic chemistry literature. We evaluate seven…

机器学习 · 计算机科学 2020-07-10 Serim Ryou , Michael R. Maser , Alexander Y. Cui , Travis J. DeLano , Yisong Yue , Sarah E. Reisman

Graph neural networks have recently become a standard method for analysing chemical compounds. In the field of molecular property prediction, the emphasis is now put on designing new model architectures, and the importance of atom…

化学物理 · 物理学 2021-02-15 Agnieszka Pocha , Tomasz Danel , Łukasz Maziarka

Data-driven prediction of molecular properties presents unique challenges to the design of machine learning methods concerning data structure/dimensionality, symmetry adaption, and confidence management. In this paper, we present a…

机器学习 · 计算机科学 2019-01-31 Yu-Hang Tang , Wibe A. de Jong

Neural message passing on molecular graphs is one of the most promising methods for predicting formation energy and other properties of molecules and materials. In this work we extend the neural message passing model with an edge update…

机器学习 · 统计学 2018-06-11 Peter Bjørn Jørgensen , Karsten Wedel Jacobsen , Mikkel N. Schmidt

According to density functional theory, any chemical property can be inferred from the electron density, making it the most informative attribute of an atomic structure. In this work, we demonstrate the use of established physical methods…

材料科学 · 物理学 2023-09-12 Ethan M. Sunshine , Muhammed Shuaibi , Zachary W. Ulissi , John R. Kitchin

The increasing CO2 level is a critical concern and suitable materials are needed to capture such gases from the environment. While experimental and conventional computational methods are useful in finding such materials, they are usually…

This study presents a deep learning approach to predicting structural and electronic properties of materials using Graph Neural Networks (GNNs). Leveraging data from the Materials Project database, we construct graph representations of…

无序系统与神经网络 · 物理学 2024-12-20 Selva Chandrasekaran Selvaraj

Forecasting electricity demand is increasingly challenging as energy systems become more decentralized and intertwined with renewable sources. Graph Neural Networks (GNNs) have recently emerged as a powerful paradigm to model spatial…

机器学习 · 计算机科学 2025-11-04 Eloi Campagne , Yvenn Amara-Ouali , Yannig Goude , Itai Zehavi , Argyris Kalogeratos

Energy-based models for discrete domains, such as graphs, explicitly capture relative likelihoods, naturally enabling composable probabilistic inference tasks like conditional generation or enforcing constraints at test-time. However,…

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…

生物大分子 · 定量生物学 2023-10-10 Apakorn Kengkanna , Masahito Ohue

This work presents the use of graph learning for the prediction of multi-step experimental outcomes for applications across experimental research, including material science, chemistry, and biology. The viability of geometric learning for…

机器学习 · 计算机科学 2024-08-13 Amanda A. Volk , Robert W. Epps , Jeffrey G. Ethier , Luke A. Baldwin

Molecular property calculations are the bedrock of chemical physics. High-fidelity \textit{ab initio} modeling techniques for computing the molecular properties can be prohibitively expensive, and motivate the development of…

Graphs can model real-world, complex systems by representing entities and their interactions in terms of nodes and edges. To better exploit the graph structure, graph neural networks have been developed, which learn entity and edge…

机器学习 · 计算机科学 2022-06-06 Tong Liu , Yushan Liu , Marcel Hildebrandt , Mitchell Joblin , Hang Li , Volker Tresp

Predicting relaxed atomic structures of chemically complex materials remains a major computational challenge, particularly for high-entropy systems where traditional first-principles methods become prohibitively expensive. We introduce the…

无序系统与神经网络 · 物理学 2025-12-09 Neethu Mohan Mangalassery , Abhishek Kumar Singh

Modeling molecular potential energy surface is of pivotal importance in science. Graph Neural Networks have shown great success in this field. However, their message passing schemes need special designs to capture geometric information and…

机器学习 · 计算机科学 2023-04-24 Xiyuan Wang , Muhan Zhang

We refine the OrbNet model to accurately predict energy, forces, and other response properties for molecules using a graph neural-network architecture based on features from low-cost approximated quantum operators in the symmetry-adapted…

Recommender systems play a crucial role in alleviating information overload by providing personalized recommendations tailored to users' preferences and interests. Recently, Graph Neural Networks (GNNs) have emerged as a promising approach…

信息检索 · 计算机科学 2026-03-24 Antonio Purificato , Fabrizio Silvestri

Electron charge density distribution of materials is one of the key quantities in computational materials science as theoretically it determines the ground state energy and practically it is used in many materials analyses. However, the…

计算物理 · 物理学 2019-11-13 Sheng Gong , Tian Xie , Taishan Zhu , Shuo Wang , Eric R. Fadel , Yawei Li , Jeffrey C. Grossman

Machine learning (ML) methods have drawn significant interest in material design and discovery. Graph neural networks (GNNs), in particular, have demonstrated strong potential for predicting material properties. The present study proposes a…

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