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.

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.

We present a systematic theoretical framework that interprets masked diffusion models (MDMs) as solutions to energy minimization problems in discrete optimal transport. Specifically, we prove that three distinct energy formulations--kinetic, conditional kinetic, and geodesic energy--are mathematically equivalent under the structure of MDMs, and that MDMs minimize all three when the mask schedule satisfies a closed-form optimality condition. This unification not only clarifies the theoretical foundations of MDMs, but also motivates practical improvements in sampling. By parameterizing interpolation schedules via Beta distributions, we reduce the schedule design space to a tractable 2D search, enabling efficient post-training tuning without model modification. Experiments on synthetic and real-world benchmarks demonstrate that our energy-inspired schedules outperform hand-crafted baselines, particularly in low-step sampling settings.

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. We begin by deriving an upper bound on the KL divergence of the forward process, introducing a surrogate initialization distribution to address the challenge posed by the absorbing stationary distribution, which is a singleton and causes the KL divergence to be ill-defined. We then establish the first convergence guarantees for both the $τ$-leaping and uniformization samplers under absorbing rate matrices, demonstrating improved rates over their counterparts using uniform rate matrices. Furthermore, under suitable assumptions, we provide convergence guarantees without early stopping. Our analysis introduces several new technical tools to address challenges unique to absorbing rate matrices. These include a Jensen-type argument for bounding forward process convergence, novel techniques for bounding absorbing score functions, and a non-divergent upper bound on the score near initialization that removes the need of early-stopping.

Discrete diffusion models have recently gained significant prominence in applications involving natural language and graph data. A key factor influencing their effectiveness is the efficiency of discretized samplers. Among these, $τ$-leaping samplers have become particularly popular due to their theoretical and empirical success. However, existing theoretical analyses of $τ$-leaping often rely on somewhat restrictive and difficult-to-verify regularity assumptions, and their convergence bounds contain quadratic dependence on the vocabulary size. In this work, we introduce a new analytical approach for discrete diffusion models that removes the need for such assumptions. For the standard $τ$-leaping method, we establish convergence guarantees in KL divergence that scale linearly with vocabulary size, improving upon prior results with quadratic dependence. Our approach is also more broadly applicable: it provides the first convergence guarantees for other widely used samplers, including the Euler method and Tweedie $τ$-leaping. Central to our approach is a novel technique based on differential inequalities, offering a more flexible alternative to the traditional Girsanov change-of-measure methods. This technique may also be of independent interest for the analysis of other stochastic processes.