arXiv:2604. 02121v2 Announce Type: replace-cross Abstract: Stochastic kinetic models are ubiquitous in physics, yet inferring their parameters from experimental data remains challenging.
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.
arXiv:2607. 12922v1 Announce Type: cross Abstract: Stochastic-process models are, as a rule, far easier to simulate than to condition.
arXiv:2607. 15682v1 Announce Type: new Abstract: Sampling from an unnormalized Boltzmann density requires proposals that move probability mass globally while retaining enough path-probability information for statistical correction.
Stochastic-process models are, as a rule, far easier to simulate than to condition. Non-linear observations, non-Gaussian likelihoods, black-box information, and global constraints all induce intractable conditional laws, requiring bespoke, model-specific constructions.
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:2607. 27077v1 Announce Type: new Abstract: Energy-Based Models (EBMs) provide an interpretable framework for generative modeling of scientific data, but poor Markov Chain Monte Carlo mixing often limits their reliability.
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:2608. 11544v1 Announce Type: cross Abstract: We propose CVaR-penalized Generative Particle Algorithm (CVaR-GPA), a robust, tail-agnostic algorithm for fine-tuning generative models to learn heavy-tailed distributions and capture extreme events, requiring no prior knowledge or estimation of the target's tail characteristics.
The paper investigates the relationship between discrete gradient descent (GD) and its continuous-time gradient-flow counterpart in the context of ReLU neural networks. It shows that while GD states converge over a finite horizon, the exact discrete derivatives obtained via automatic differentiation do not necessarily match the derivative of the limiting flow, due to singular curvature at activation events. The authors provide a Stieltjes representation that separates continuous regional Hessians from atomic interface curvature, revealing rank-one discrepancies at activation jumps and demonstrating that even globally strongly convex residual-ReLU losses can exhibit large sensitivity ratios on certain initialization sets.
arXiv:2608. 13800v1 Announce Type: new Abstract: Transition path sampling (TPS) aims to efficiently generate rare molecular transition trajectories between metastable states and is essential for understanding biomolecular mechanisms.
The paper introduces GRAS, a method that improves training‑free reward alignment for discrete diffusion models by reducing variance in guided proposals and adapting the resampling temperature during search. It achieves this without adding denoiser cost, using Rao‑Blackwellized estimates for differentiable rewards and a leave‑one‑out baseline for non‑differentiable ones. Experiments on regulatory DNA and protein design show GRAS outperforms existing training‑free techniques and rivals reward‑fine‑tuned models.