Jumping up and down: Denoiser diffusion models for discrete ordinal data

Flow-based generative modeling in continuous spaces exploit Tweedie's formula to express the denoiser (learned in training) as a score function (used in sampling). In contrast, this relation has been largely missing in the discrete setting where common approaches focus on learning discrete scores and rates. In this work we close this gap for discrete non-negative ordinal data by introducing Binomial flows. Our framework provides a simple recipe for training a discrete diffusion model which simultaneously denoises, samples, and estimates exact likelihoods. We verify our methodology on synthetic examples and obtain competitive results on real-world data sets.

Diffusion models have excelled at generative tasks for both continuous and token-based domains, but their application to discrete ordinal data remains underdeveloped. We present CountsDiff, a diffusion framework designed to model distributions on the natural numbers. CountsDiff extends the Blackout diffusion framework by simplifying its formulation through a direct parameterization in terms of a survival probability schedule and an explicit loss weighting. This introduces flexibility through design parameters with direct analogues in existing diffusion modeling frameworks. Beyond this reparameterization, CountsDiff introduces features from modern diffusion models, previously absent in counts-based domains, including continuous-time training, classifier-free guidance, and churn/remasking reverse dynamics that allow non-monotone reverse trajectories. We propose an initial instantiation of CountsDiff and validate it on natural image datasets (CIFAR-10, CelebA), exploring the effects of the introduced design parameters in a complex, well-studied, and interpretable data domain. We then highlight biological count assays as a natural use case, evaluating CountsDiff on single-cell RNA-seq imputation in fetal and heart cell atlases. Remarkably, we find that even this simple instantiation matches or surpasses the performance of a state-of-the-art discrete generative model and leading scRNA-seq imputation methods, while leaving substantial headroom for further gains through optimized design choices in future work.

What does a discrete diffusion model actually learn? The literature trains denoisers, bridge plug-ins, and concrete scores, each deriving its own ELBO objective under different conventions. This fragmentation makes the object being learned unclear and ELBO values difficult to interpret and compare. All three methods learn the same object in different coordinates: the exact time-reversal of the noising process. We first prove the Oracle Distance identity: for any noising process, the negative ELBO is not just a bound on the likelihood; it equals the data entropy plus the path KL divergence from the reversed noising process to the learned one. Next, for token-factorizing noise, we show that denoiser, bridge plug-in, and concrete score are three coordinates of this reverse process, derive exact conversions between them, and identify the probability distribution learned by each. In particular, contrary to its standard interpretation, the bridge plug-in learns not a denoiser but the cavity distribution: the clean token given the noisy sequence excluding its own position. We confirm the theory by training all three coordinates with masked, uniform, and GIDD kernels on OpenWebText under a shared recipe, and by training uniform-diffusion solvers on four logic tasks. The learned coordinates agree after conversion, while confusing the cavity with the denoiser can severely degrade sampling quality. Together with exact boundary-term formulas, closed-form NELBO calibrations at initialization, and a clock interpretation of time schedules, these results provide a conceptual framework and a mechanical recipe for deriving, implementing, and comparing discrete diffusion processes.