The paper introduces a data-driven effective model for stochastic chemical reaction networks that bypasses the high computational cost of the Stochastic Simulation Algorithm (SSA). By approximating the finite-time transition kernel of the SSA-induced continuous-time Markov chain with a generative machine learning model, the method operates on a user-defined coarse time step independent of microscopic reaction events. Using a conditional normalizing flow as the stochastic propagator, the trained model recursively generates statistically consistent trajectories, achieving significant computational savings while maintaining accuracy, as demonstrated through numerous numerical examples.
arXiv:2609.17736v1 Announce Type: cross Abstract: Most molecular transitions occur on timescales far beyond direct molecular dynamics simulations. The committor, the probability that a configuration...
arXiv:2606. 01086v1 Announce Type: cross Abstract: Flow and diffusion models generate high-quality samples in many modalities; however, many network evaluations are required during inference due to numerical integration of an underlying differential equation.
arXiv:2606. 27737v1 Announce Type: new Abstract: Programming adaptive behaviors at the cellular level is a long-standing goal that raises the question of how probabilistic computation can be implemented in biochemical systems.
arXiv:2606. 11156v1 Announce Type: cross Abstract: Recent one-step generative models accelerate sampling by learning deterministic flow maps of the underlying dynamics.
arXiv:2608.25631v1 Announce Type: cross Abstract: Continuous-time Markov chains (CTMCs) provide the backbone for modeling discrete stochastic dynamics across applied, physical, and biological science...
arXiv:2608. 07648v1 Announce Type: cross Abstract: Sampling high-dimensional probability distributions is a central task in scientific computing, with applications ranging from Bayesian inference to statistical physics and molecular simulation.
arXiv:2606. 09434v1 Announce Type: new Abstract: The Fokker-Planck equation (FPE) plays a pivotal role in describing the time evolution of probability density functions (PDFs) for systems governed by stochastic dynamics.
arXiv:2606. 15793v1 Announce Type: cross Abstract: This paper explores policy gradient algorithms for training stochastic policies to sample from structured discrete probability distributions under the Generative Flow Network (GFlowNet) framework.
ReCurveflow is a flow‑matching framework that learns to predict transition state geometries by training on continuously curved reference paths derived from full NEB bands, rather than straight linear paths. It introduces an off‑path correction mechanism that generates corrective velocity fields when the model encounters geometries off the training path, improving resistance to exposure bias and TS prediction accuracy. Across multiple data splits and evaluation metrics, ReCurveflow outperforms seven baselines and produces reaction trajectories whose energy profiles closely follow the reference NEB path, aiding NEB optimization and demonstrating effective corrective behavior.
arXiv:2603. 18907v2 Announce Type: replace Abstract: We propose a new Neural Galerkin Normalizing Flow framework to approximate the transition probability density function of a diffusion process by solving the corresponding Fokker-Planck equation with an atomic initial distribution, parametrically with respect to the location of the initial mass.
arXiv:2606. 23757v1 Announce Type: cross Abstract: Extracting interpretable governing equations from sparse, noisy chemical time-series data remains difficult because discrete reaction topology and continuous kinetic parameters are tightly coupled.
arXiv:2604. 13213v2 Announce Type: replace-cross Abstract: Rare events such as conformational changes in biomolecules, phase transitions, and chemical reactions are central to the behavior of many physical systems, yet they are extremely difficult to study computationally because unbiased simulations seldom produce them.