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Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…

Machine Learning · Computer Science 2025-08-27 Wenyin Zhou , Christopher Iliffe Sprague , Vsevolod Viliuga , Matteo Tadiello , Arne Elofsson , Hossein Azizpour

Diffusion models offer stable training and state-of-the-art performance for deep generative modeling tasks. Here, we consider their use in the context of multivariate subsurface modeling and probabilistic inversion. We first demonstrate…

Computer Vision and Pattern Recognition · Computer Science 2026-01-28 Roberto Miele , Niklas Linde

One of the main drawback of diffusion models is the slow inference time for image generation. Among the most successful approaches to addressing this problem are distillation methods. However, these methods require considerable…

Computer Vision and Pattern Recognition · Computer Science 2024-10-16 Senmao Li , Taihang Hu , Joost van de Weijer , Fahad Shahbaz Khan , Tao Liu , Linxuan Li , Shiqi Yang , Yaxing Wang , Ming-Ming Cheng , Jian Yang

Pore-scale simulations accurately describe transport properties of fluids in the subsurface. These simulations enhance our understanding of applications such as assessing hydrogen storage efficiency and forecasting CO$_2$ sequestration…

Understanding the structure of real data is paramount in advancing modern deep-learning methodologies. Natural data such as images are believed to be composed of features organized in a hierarchical and combinatorial manner, which neural…

Machine Learning · Statistics 2024-12-25 Antonio Sclocchi , Alessandro Favero , Matthieu Wyart

Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…

Tissues and Organs · Quantitative Biology 2017-07-27 Richard J. McMurtrey

The predominant success of diffusion models in generative modeling has spurred significant interest in understanding their theoretical foundations. In this work, we propose a feature learning framework aimed at analyzing and comparing the…

Machine Learning · Statistics 2025-03-04 Andi Han , Wei Huang , Yuan Cao , Difan Zou

Diffusion Models (DMs) have demonstrated state-of-the-art performance in content generation without requiring adversarial training. These models are trained using a two-step process. First, a forward - diffusion - process gradually adds…

Computer Vision and Pattern Recognition · Computer Science 2024-03-13 Anwaar Ulhaq , Naveed Akhtar

Efficient exploration of the vast chemical space is a fundamental challenge in materials design and discovery, particularly for designing functional inorganic crystalline materials with targeted properties. Diffusion-based generative models…

Materials Science · Physics 2026-03-20 Sourav Mal , Nehad Ahmed , Junaid Jami , Subhankar Mishra , Prasenjit Sen

Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a…

Chemical Physics · Physics 2023-03-02 Bowen Jing , Gabriele Corso , Jeffrey Chang , Regina Barzilay , Tommi Jaakkola

Deep generative models such as diffusion and flow matching are powerful machine learning tools capable of learning and sampling from high-dimensional distributions. They are particularly useful when the training data appears to be…

High Energy Physics - Phenomenology · Physics 2026-04-30 Zachary Bogorad , Ibrahim Elsharkawy , Yonatan Kahn , Andrew J. Larkoski , Noam Levi

Generative models have made significant impacts across various domains, largely due to their ability to scale during training by increasing data, computational resources, and model size, a phenomenon characterized by the scaling laws.…

Computer Vision and Pattern Recognition · Computer Science 2025-01-17 Nanye Ma , Shangyuan Tong , Haolin Jia , Hexiang Hu , Yu-Chuan Su , Mingda Zhang , Xuan Yang , Yandong Li , Tommi Jaakkola , Xuhui Jia , Saining Xie

Diffusion models, a family of generative models based on deep learning, have become increasingly prominent in cutting-edge machine learning research. With a distinguished performance in generating samples that resemble the observed data,…

Machine Learning · Computer Science 2023-05-02 Lequan Lin , Zhengkun Li , Ruikun Li , Xuliang Li , Junbin Gao

Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…

Computational Physics · Physics 2023-10-10 Zihan Zhou , Ruiying Liu , Chaolong Ying , Ruimao Zhang , Tianshu Yu

We present a generative diffusion model specifically tailored to the discovery of surface structures. The generative model takes into account substrate registry and periodicity by including masked atoms and $z$-directional confinement.…

Computational Physics · Physics 2025-01-22 Nikolaj Rønne , Alán Aspuru-Guzik , Bjørk Hammer

Diffusion models generate high-dimensional data such as images by learning a process that gradually removes noise from corrupted data. Recent studies have shown that the backward dynamics of diffusion models exhibit two characteristic…

Statistical Mechanics · Physics 2026-04-14 Tomoei Takahashi , Takashi Takahashi , Yoshiyuki Kabashima

Diffusion Models have become a cornerstone of modern generative AI for their exceptional generation quality and controllability. However, their inherent \textit{multi-step iterations} and \textit{complex backbone networks} lead to…

Generating physically realistic 3D molecular structures remains a core challenge in molecular generative modeling. While diffusion models equipped with equivariant neural networks have made progress in capturing molecular geometries, they…

Machine Learning · Computer Science 2025-08-25 Zhijian Zhou , Junyi An , Zongkai Liu , Yunfei Shi , Xuan Zhang , Fenglei Cao , Chao Qu , Yuan Qi

In a convergence of machine learning and biology, we reveal that diffusion models are evolutionary algorithms. By considering evolution as a denoising process and reversed evolution as diffusion, we mathematically demonstrate that diffusion…

Neural and Evolutionary Computing · Computer Science 2026-05-12 Yanbo Zhang , Benedikt Hartl , Hananel Hazan , Michael Levin

Generative AI is a fast-growing area of research offering various avenues for exploration in high-energy nuclear physics. In this work, we explore the use of generative models for simulating electron-proton collisions relevant to…

High Energy Physics - Phenomenology · Physics 2024-08-14 Peter Devlin , Jian-Wei Qiu , Felix Ringer , Nobuo Sato