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The past decade has witnessed a surge of interest in exploring emergent particles in condensed matter systems. Novel particles, emerged as excitations around exotic band degeneracy points, continue to be reported in real materials and…

Mesoscale and Nanoscale Physics · Physics 2021-12-28 Zhi-Ming Yu , Zeying Zhang , Gui-Bin Liu , Weikang Wu , Xiao-Ping Li , Run-Wu Zhang , Shengyuan A Yang , Yugui Yao

We introduce Equivariant Neural Diffusion (END), a novel diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Compared to current state-of-the-art equivariant diffusion models, the key innovation…

Machine Learning · Computer Science 2025-06-13 François Cornet , Grigory Bartosh , Mikkel N. Schmidt , Christian A. Naesseth

A range of generative machine learning models for the design of novel molecules and materials have been proposed in recent years. Models that can generate three-dimensional structures are particularly suitable for quantum chemistry…

Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology. Previous methods usually first predict the interatomic distances,…

Artificial Intelligence · Computer Science 2023-01-02 Jinhua Zhu , Yingce Xia , Chang Liu , Lijun Wu , Shufang Xie , Yusong Wang , Tong Wang , Tao Qin , Wengang Zhou , Houqiang Li , Haiguang Liu , Tie-Yan Liu

We introduce a novel equivariant graph neural network (GNN) architecture designed to predict the tensorial response properties of molecules. Unlike traditional frameworks that focus on regressing scalar quantities and derive tensorial…

Machine Learning · Computer Science 2025-11-11 Jean Philip Filling , Felix Post , Michael Wand , Denis Andrienko

Recent advances in machine learning for molecules exhibit great potential for facilitating drug discovery from in silico predictions. Most models for molecule generation rely on the decomposition of molecules into frequently occurring…

Chemical Physics · Physics 2023-11-08 Leon Hetzel , Johanna Sommer , Bastian Rieck , Fabian Theis , Stephan Günnemann

Many generative applications, such as synthesis-based 3D molecular design, involve constructing compositional objects with continuous features. Here, we introduce Compositional Generative Flows (CGFlow), a novel framework that extends flow…

Machine Learning · Computer Science 2025-07-16 Tony Shen , Seonghwan Seo , Ross Irwin , Kieran Didi , Simon Olsson , Woo Youn Kim , Martin Ester

In this work, we utilize thin dielectric meta-atoms placed on a silver substrate to efficiently enhance and manipulate the third harmonic generation. We theoretically and experimentally reveal that when the structural symmetry of the…

Molecules in equilibrium follow a Boltzmann distribution, making the underlying energy landscape a physically grounded modeling objective. However, such landscapes are difficult to learn from data and, once learned, hard to sample from.…

Machine Learning · Computer Science 2026-05-19 Christoph Griesbacher , Lea Bogensperger , Andreas Habring , Thomas Pock

Learning 3D representations that generalize well to arbitrarily oriented inputs is a challenge of practical importance in applications varying from computer vision to physics and chemistry. We propose a novel multi-resolution convolutional…

Machine Learning · Computer Science 2021-03-22 James Fox , Bo Zhao , Sivasankaran Rajamanickam , Rampi Ramprasad , Le Song

Generating desirable molecular structures in 3D is a fundamental problem for drug discovery. Despite the considerable progress we have achieved, existing methods usually generate molecules in atom resolution and ignore intrinsic local…

Biomolecules · Quantitative Biology 2023-05-29 Bo Qiang , Yuxuan Song , Minkai Xu , Jingjing Gong , Bowen Gao , Hao Zhou , Weiying Ma , Yanyan Lan

Diffusion-based generative models represent the current state-of-the-art for image generation. However, standard diffusion models are based on Euclidean geometry and do not translate directly to manifold-valued data. In this work, we…

Machine Learning · Computer Science 2023-12-20 Yesukhei Jagvaral , Francois Lanusse , Rachel Mandelbaum

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…

Machine Learning · Computer Science 2022-03-03 Tuan Le , Frank Noé , Djork-Arné Clevert

Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in…

Machine Learning · Computer Science 2025-07-29 Zian Li , Cai Zhou , Xiyuan Wang , Xingang Peng , Muhan Zhang

Structure-informed protein representation learning is essential for effective protein function annotation and \textit{de novo} design. However, the presence of inherent noise in both crystal and AlphaFold-predicted structures poses…

Biomolecules · Quantitative Biology 2025-03-25 Zhongyue Zhang , Runze Ma , Yanjie Huang , Shuangjia Zheng

Generative models show great promise for the inverse design of molecules and inorganic crystals, but remain largely ineffective within more complex structures such as amorphous materials. Here, we present a diffusion model that reliably…

Disordered Systems and Neural Networks · Physics 2026-01-21 Kai Yang , Daniel Schwalbe-Koda

Despite recent advancement in 3D molecule conformation generation driven by diffusion models, its high computational cost in iterative diffusion/denoising process limits its application. In this paper, an equivariant consistency model…

Biomolecules · Quantitative Biology 2023-11-27 Zhiguang Fan , Yuedong Yang , Mingyuan Xu , Hongming Chen

Machine learning has recently emerged as a powerful tool for generating new molecular and material structures. The success of state-of-the-art models stems from their ability to incorporate physical symmetries, such as translation,…

Machine Learning · Computer Science 2024-05-16 Bingqing Cheng

A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…

Machine Learning · Computer Science 2020-01-01 Elman Mansimov , Omar Mahmood , Seokho Kang , Kyunghyun Cho

A general machine learning architecture is introduced that uses wavelet scattering coefficients of an inputted three dimensional signal as features. Solid harmonic wavelet scattering transforms of three dimensional signals were previously…

Computational Physics · Physics 2019-01-30 Xavier Brumwell , Paul Sinz , Kwang Jin Kim , Yue Qi , Matthew Hirn