Sampling from unnormalised discrete distributions is a fundamental problem across various domains. While Markov chain Monte Carlo offers a principled approach, it often suffers from slow mixing and poor convergence. In this paper, we propose Discrete Neural Flow Samplers (DNFS), a trainable and efficient framework for discrete sampling. DNFS learns the rate matrix of a continuous-time Markov chain such that the resulting dynamics satisfy the Kolmogorov equation. As this objective involves the intractable partition function, we then employ control variates to reduce the variance of its Monte Carlo estimation, leading to a coordinate descent learning algorithm. To further facilitate computational efficiency, we propose locally equivaraint Transformer, a novel parameterisation of the rate matrix that significantly improves training efficiency while preserving powerful network expressiveness. Empirically, we demonstrate the efficacy of DNFS in a wide range of applications, including sampling from unnormalised distributions, training discrete energy-based models, and solving combinatorial optimisation problems.

Discrete state space diffusion models have shown significant advantages in applications involving discrete data, such as text and image generation. It has also been observed that their performance is highly sensitive to the choice of rate matrices, particularly between uniform and absorbing rate matrices. While empirical results suggest that absorbing rate matrices often yield better generation quality compared to uniform rate matrices, existing theoretical works have largely focused on the uniform rate matrices case. Notably, convergence guarantees and error analyses for absorbing diffusion models are still missing. In this work, we provide the first finite-time error bounds and convergence rate analysis for discrete diffusion models using absorbing rate matrices.

Sampling from unnormalised discrete distributions is a fundamental problem across various domains. While Markov chain Monte Carlo offers a principled approach, it often suffers from slow mixing and poor convergence. In this paper, we propose Discrete Neural Flow Samplers (DNFS), a trainable and efficient framework for discrete sampling. DNFS learns the rate matrix of a continuous-time Markov chain such that the resulting dynamics satisfy the Kolmogorov equation. As this objective involves the intractable partition function, we then employ control variates to reduce the variance of its Monte Carlo estimation, leading to a coordinate descent learning algorithm. To further facilitate computational efficiency, we propose locally equivaraint Transformer, a novel parameterisation of the rate matrix that significantly improves training efficiency while preserving powerful network expressiveness. Empirically, we demonstrate the efficacy of DNFS in a wide range of applications, including sampling from unnormalised distributions, training discrete energy-based models, and solving combinatorial optimisation problems.

Discrete state space diffusion models have shown significant advantages in applications involving discrete data, such as text and image generation. It has also been observed that their performance is highly sensitive to the choice of rate matrices, particularly between uniform and absorbing rate matrices. While empirical results suggest that absorbing rate matrices often yield better generation quality compared to uniform rate matrices, existing theoretical works have largely focused on the uniform rate matrices case. Notably, convergence guarantees and error analyses for absorbing diffusion models are still missing. In this work, we provide the first finite-time error bounds and convergence rate analysis for discrete diffusion models using absorbing rate matrices.

Discrete diffusion has become a leading framework for generative modeling in various applications including language, vision, and biology. Existing convergence theory, however, exhibits fundamental limitations. KL-based analyses diverge under singular priors such as the masked distribution, while bounds in total variation (TV) depend on the state space size $S$ and become vacuous for modern language tasks, where vocabularies contain hundreds of thousands of tokens. We develop a unified adjoint-equation-based framework that establishes dimension-free convergence guarantees in any integral probability metric (IPM). To the best of our knowledge, our bounds are the first to be entirely free of $S$ and applicable to both masked and uniform priors. Importantly, our theory relies only on a single standard rate-matrix regularity assumption and is compatible with time-inhomogeneous schedules. Four novel techniques drive our improvements: working in the space of observables via adjoint equations rather than directly with probability measures, a regularity analysis that yields bounds on any IPM, a coupling argument that removes $S$-dependence under uniform transitions, and a score-marginal cancellation technique that removes $S$-dependence under masked transitions. Our framework thus sharply departs from prior analyses and avoids the shortcomings of pathspace-KL and existing TV-based approaches. Beyond convergence bounds, our framework provides a versatile toolkit for further theoretical study of discrete diffusion models.

Amino acid substitution rate matrices are fundamental to statistical phylogenetics and evolutionary biology. Estimating them typically requires reconstructed trees for massive amounts of aligned proteins, which poses a major computational bottleneck. In this paper, we develop a near-linear time method to estimate these rate matrices from multiple sequence alignments (MSAs) alone, thereby speeding up computation by orders of magnitude. Our method relies on a near-linear time cherry reconstruction algorithm which we call FastCherries and it can be easily applied to MSAs with millions of sequences. On both simulated and real data, we demonstrate the speed and accuracy of our method as applied to the classical model of protein evolution. By leveraging the unprecedented scalability of our method, we develop a new, rich phylogenetic model called SiteRM, which can estimate a general site-specific rate matrix for each column of an MSA. Remarkably, in variant effect prediction for both clinical and deep mutational scanning data in ProteinGym, we show that despite being an independent-sites model, our SiteRM model outperforms large protein language models that learn complex residue-residue interactions between different sites. We attribute our increased performance to conceptual advances in our probabilistic treatment of evolutionary data and our ability to handle extremely large MSAs. We anticipate that our work will have a lasting impact across both statistical phylogenetics and computational variant effect prediction.

Discrete diffusion models have achieved strong empirical performance in text and other symbolic domains, with masked (absorbing-rate) variants emerging as competitive alternatives to autoregressive models. Among existing samplers, the Euler method remains the standard choice in many applications, and more recently, the First-Hitting Sampler (FHS) has shown considerable promise for masked diffusion models. Despite their practical success, the theoretical understanding of these samplers remains limited. Existing analyses are conducted in Kullback-Leibler (KL) divergence, which often yields loose parameter dependencies and requires strong assumptions on score estimation. Moreover, these guarantees do not cover recently developed high-performance sampler of FHS. In this work, we first develop a direct total-variation (TV) based analysis for the Euler method that overcomes these limitations. Our results relax assumptions on score estimation, improve parameter dependencies, and establish convergence guarantees without requiring any surrogate initialization. Also for this setting, we provide the first convergence lower bound for the Euler sampler, establishing tightness with respect to both the data dimension $d$ and the target accuracy $\varepsilon$. Finally, we analyze the FHS sampler and show that it incurs no sampling error beyond that induced by score estimation, which we show to be tight with a matching lower error bound. Overall, our analysis introduces a direct TV-based error decomposition along the CTMC trajectory and a decoupling-based path-wise analysis for FHS, which may be of independent interest.

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

Diffusion generative models, as an emerging research focus, have been applied to graph generation tasks.