The ISOKANN (Invariant Subspaces of Koopman Operators Learned by Artificial Neural Networks) framework provides a data-driven route to extract collective variables (CVs) and effective dynamics from complex molecular systems. In this work, we integrate the theoretical foundation of Koopman operators with Krylov-like subspace algorithms, and reduced dynamical modeling to build a coherent picture of how to describe metastable transitions in high-dimensional systems based on CVs. Starting from the identification of CVs based on dominant invariant subspaces, we derive the corresponding effective dynamics on the latent space and connect these to transition rates and times, committor functions, and transition pathways. The combination of Koopman-based learning and reduced-dimensional effective dynamics yields a principled framework for computing transition rates and pathways from simulation data. Numerical experiments on one-, two-, and three-dimensional benchmark potentials illustrate the ability of ISOKANN to reconstruct the coarse-grained kinetics and reproduce transition times across enthalpic and entropic barriers.

These processes find wide application in the natural sciences and machine learning, but their inference is known to be far from trivial.

Learning discrete neural samplers is challenging due to the lack of gradients and combinatorial complexity. While stochastic optimal control (SOC) and Schrödinger bridge (SB) provide principled solutions, efficient SOC solvers like adjoint matching (AM), which excel in continuous domains, remain unexplored for discrete spaces. We bridge this gap by revealing that the core mechanism of AM is $\mathit{state}\text{-}\mathit{space~agnostic}$, and introduce $\mathbf{discrete~ASBS}$, a unified framework that extends AM and adjoint Schrödinger bridge sampler (ASBS) to discrete spaces. Theoretically, we analyze the optimality conditions of the discrete SB problem and its connection to SOC, identifying a necessary cyclic group structure on the state space to enable this extension. Empirically, discrete ASBS achieves competitive sample quality with significant advantages in training efficiency and scalability.

Masked diffusion models have emerged as a powerful framework for text and multimodal generation. However, their sampling procedure updates multiple tokens simultaneously and treats generated tokens as immutable, which may lead to error accumulation when early mistakes cannot be revised. In this work, we revisit existing self-correction methods and identify limitations stemming from additional training requirements or reliance on misaligned likelihood estimates. We propose a training-free self-correction framework that exploits the inductive biases of pre-trained masked diffusion models. Without modifying model parameters or introducing auxiliary evaluators, our method significantly improves generation quality on text-to-image generation and multimodal understanding tasks with reduced sampling steps. Moreover, the proposed framework generalizes across different masked diffusion architectures, highlighting its robustness and practical applicability. Code can be found in https://github.com/huge123/FreeCorrection.

Discrete flow models (DFMs) have been proposed to learn the data distribution on a finite state space, offering a flexible framework as an alternative to discrete diffusion models. A line of recent work has studied samplers for discrete diffusion models, such as tau-leaping and Euler solver. However, these samplers require a large number of iterations to control discretization error, since the transition rates are frozen in time and evaluated at the initial state within each time interval. Moreover, theoretical results for these samplers often require boundedness conditions of the transition rate or they focus on a specific type of source distributions. To address those limitations, we establish non-asymptotic discretization error bounds for those samplers without any restriction on transition rates and source distributions, under the framework of discrete flow models. Furthermore, by analyzing a one-step lower bound of the Euler sampler, we propose two corrected samplers: \textit{time-corrected sampler} and \textit{location-corrected sampler}, which can reduce the discretization error of tau-leaping and Euler solver with almost no additional computational cost. We rigorously show that the location-corrected sampler has a lower iteration complexity than existing parallel samplers. We validate the effectiveness of the proposed method by demonstrating improved generation quality and reduced inference time on both simulation and text-to-image generation tasks. Code can be found in https://github.com/WanZhengyan/Corrected-Samplers-for-Discrete-Flow-Models.

For a transition between two stable states, the committor is the probability that the dynamics leads to one stable state before the other. It can be estimated from trajectory data by minimizing an expression for the transition rate that depends on a lag time. We show that an existing such expression is minimized by the exact committor only when the lag time is a single time step, resulting in a biased estimate in practical applications. We introduce an alternative expression that is minimized by the exact committor at any lag time. The key idea is that, when trajectories enter the stable states, the times that they enter (stopping times) must be used for estimating the committor and transition rate instead of the lag time. Numerical tests on benchmark systems demonstrate that our committor and transition rate estimates are much less sensitive to the choice of lag time. We show how further accuracy for the transition rate can be achieved by combining results from two lag times. We also relate the transition rate expression to a variational approach for kinetic statistics based on the mean-squared residual and discuss further numerical considerations with the aid of a decomposition of the error into dynamic modes.

First provide a summary of the paper, and then address the following criteria: Quality, clarity, originality and significance. In reply to the author's feedback Our description of uniformization might be misleading, because the problems we describe do not occur in all of its applications. For the SGCP model discussed in our paper, however, the uniformization really is over the rate, which is lambda in our model. There is no MJP in the SGCP model, because the rate is continuous. After rereading the relevant sections of the paper, I am sure that this is incorrect.

We show that the maximum-likelihood (ML) estimate of models derived from Luce's choice axiom (e.g., the Plackett-Luce model) can be expressed as the

Guidance provides a simple and effective framework for posterior sampling by steering the generation process towards the desired distribution. When modeling discrete data, existing approaches mostly focus on guidance with the first-order Taylor approximation to improve the sampling efficiency. However, such an approximation is inappropriate in discrete state spaces since the approximation error could be large. A novel guidance framework for discrete data is proposed to address this problem: We derive the exact transition rate for the desired distribution given a learned discrete flow matching model, leading to guidance that only requires a single forward pass in each sampling step, significantly improving efficiency. This unified novel framework is general enough, encompassing existing guidance methods as special cases, and it can also be seamlessly applied to the masked diffusion model. We demonstrate the effectiveness of our proposed guidance on energy-guided simulations and preference alignment on text-to-image generation and multimodal understanding tasks. The code is available through https://github.com/WanZhengyan/Discrete-Guidance-Matching/tree/main.