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Generative modeling of peptide sequences requires navigating a discrete and highly constrained space in which many intermediate states are chemically implausible or unstable. Existing discrete diffusion and flow-based methods rely on…

Biomolecules · Quantitative Biology 2026-02-02 Shrey Goel , Pranam Chatterjee

Scalable sampling of molecular states in thermodynamic equilibrium is a long-standing challenge in statistical physics. Boltzmann generators tackle this problem by pairing normalizing flows with importance sampling to obtain uncorrelated…

Machine Learning · Computer Science 2026-01-21 Charlie B. Tan , Avishek Joey Bose , Chen Lin , Leon Klein , Michael M. Bronstein , Alexander Tong

Geophysical inverse problems are often ill-posed and admit multiple solutions. Conventional discriminative methods typically yield a single deterministic solution, which fails to model the posterior distribution, cannot generate diverse…

Reconstructing dynamics using samples from sparsely time-resolved snapshots is an important problem in both natural sciences and machine learning. Here, we introduce a new deep learning approach for solving regularized unbalanced optimal…

Machine Learning · Computer Science 2025-05-09 Zhenyi Zhang , Tiejun Li , Peijie Zhou

This paper introduces a new approach to generating sample paths of unknown Markovian stochastic differential equations (SDEs) using diffusion models, a class of generative AI methods commonly employed in image and video applications. Unlike…

Machine Learning · Computer Science 2026-03-17 Xuefeng Gao , Jiale Zha , Xun Yu Zhou

Markov chains are fundamental models for stochastic dynamics, with applications in a wide range of areas such as population dynamics, queueing systems, reinforcement learning, and Monte Carlo methods. Estimating the transition matrix and…

Statistics Theory · Mathematics 2026-01-26 Lasse Leskelä , Maximilien Dreveton

Posterior sampling in high-dimensional spaces using generative models holds significant promise for various applications, including but not limited to inverse problems and guided generation tasks. Despite many recent developments,…

Machine Learning · Statistics 2024-10-04 Vishal Purohit , Matthew Repasky , Jianfeng Lu , Qiang Qiu , Yao Xie , Xiuyuan Cheng

We provide a new convergence analysis of stochastic gradient Langevin dynamics (SGLD) for sampling from a class of distributions that can be non-log-concave. At the core of our approach is a novel conductance analysis of SGLD using an…

Machine Learning · Computer Science 2021-02-24 Difan Zou , Pan Xu , Quanquan Gu

Diffusion and Schr\"{o}dinger Bridge models have established state-of-the-art performance in generative modeling but are often hampered by significant computational costs and complex training procedures. While continuous-time bridges…

Machine Learning · Computer Science 2025-12-16 Maria Khilchuk , Vladimir Latypov , Pavel Kleshchev , Alexander Hvatov

We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…

Biomolecules · Quantitative Biology 2023-07-19 Lars Holdijk , Yuanqi Du , Ferry Hooft , Priyank Jaini , Bernd Ensing , Max Welling

In this paper we introduce and analyse Langevin samplers that consist of perturbations of the standard underdamped Langevin dynamics. The perturbed dynamics is such that its invariant measure is the same as that of the unperturbed dynamics.…

Probability · Mathematics 2017-12-06 A. B. Duncan , N. Nuesken , G. A. Pavliotis

Chaotic dynamical systems exhibit strong sensitivity to initial conditions and often contain unresolved multiscale processes, making deterministic forecasting fundamentally limited. Generative models offer an appealing alternative by…

Machine Learning · Computer Science 2026-01-01 Patrick Wyrod , Ashesh Chattopadhyay , Daniele Venturi

Diffusion models (DMs) have become the dominant paradigm of generative modeling in a variety of domains by learning stochastic processes from noise to data. Recently, diffusion denoising bridge models (DDBMs), a new formulation of…

Machine Learning · Computer Science 2024-11-01 Guande He , Kaiwen Zheng , Jianfei Chen , Fan Bao , Jun Zhu

We present Fractional Diffusion Bridge Models (FDBM), a novel generative diffusion bridge framework driven by an approximation of the rich and non-Markovian fractional Brownian motion (fBM). Real stochastic processes exhibit a degree of…

The rise of artificial intelligence (AI) hinges on the efficient training of modern deep neural networks (DNNs) for non-convex optimization and uncertainty quantification, which boils down to a non-convex Bayesian learning problem. A…

Computation · Statistics 2023-06-01 Wei Deng

A Schr\"odinger bridge is the most probable time-dependent probability distribution that connects an initial probability distribution $w_{i}$ to a final one $w_{f}$. The problem has been solved and widely used for the case of simple…

Statistical Mechanics · Physics 2025-07-02 Henri Orland

Stochastic-gradient sampling methods are often used to perform Bayesian inference on neural networks. It has been observed that the methods in which notions of differential geometry are included tend to have better performances, with the…

Machine Learning · Computer Science 2024-04-02 Hanlin Yu , Marcelo Hartmann , Bernardo Williams , Arto Klami

Modeling the dynamics from sparsely time-resolved snapshot data is crucial for understanding complex cellular processes and behavior. Existing methods leverage optimal transport, Schr\"odinger bridge theory, or their variants to…

Machine Learning · Computer Science 2025-10-28 Zhenyi Zhang , Zihan Wang , Yuhao Sun , Tiejun Li , Peijie Zhou

We propose a new Stein self-repulsive dynamics for obtaining diversified samples from intractable un-normalized distributions. Our idea is to introduce Stein variational gradient as a repulsive force to push the samples of Langevin dynamics…

Machine Learning · Computer Science 2020-12-16 Mao Ye , Tongzheng Ren , Qiang Liu

In this study, we introduce a novel method for generating new synthetic samples that are independent and identically distributed (i.i.d.) from high-dimensional real-valued probability distributions, as defined implicitly by a set of Ground…

Machine Learning · Statistics 2024-07-09 Hamidreza Behjoo , Michael Chertkov