# CountsDiff: A Diffusion Model on the Natural Numbers for Generation and Imputation of Count-Based Data

arXiv: https://arxiv.org/abs/2604.03779 · HTML: https://mlsanity.com/paper/2604.03779/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 45 of its 93 references that are in the map.
- First posted on arXiv 4 Apr 2026.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 30 of 45)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Photorealistic Text-to-Image Diffusion Models with Deep Language Understanding](https://mlsanity.com/paper/2205.11487/) (2022)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Improved Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2102.09672/) (2021)
- [Deep Learning Face Attributes in the Wild](https://mlsanity.com/paper/1411.7766/) (2014)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [Improved Techniques for Training GANs](https://mlsanity.com/paper/1606.03498/) (2016)
- [Video Diffusion Models](https://mlsanity.com/paper/2204.03458/) (2022)
- [Consistency Models](https://mlsanity.com/paper/2303.01469/) (2023)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Variational Diffusion Models](https://mlsanity.com/paper/2107.00630/) (2021)
- [FLUX.1 Kontext: Flow Matching for In-Context Image Generation and Editing in Latent Space](https://mlsanity.com/paper/2506.15742/) (2025)
- [Simple and Effective Masked Diffusion Language Models](https://mlsanity.com/paper/2406.07524/) (2024)
- [Modeling Tabular data using Conditional GAN](https://mlsanity.com/paper/1907.00503/) (2019)
- [Simplified and Generalized Masked Diffusion for Discrete Data](https://mlsanity.com/paper/2406.04329/) (2024)
- [CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation](https://mlsanity.com/paper/2107.03502/) (2021)
- [Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions](https://mlsanity.com/paper/2102.05379/) (2021)
- [Mean Flows for One-step Generative Modeling](https://mlsanity.com/paper/2505.13447/) (2025)
- [Importance Weighted Autoencoders](https://mlsanity.com/paper/1509.00519/) (2015)
- [A Continuous Time Framework for Discrete Denoising Models](https://mlsanity.com/paper/2205.14987/) (2022)
- [TabDDPM: Modelling Tabular Data with Diffusion Models](https://mlsanity.com/paper/2209.15421/) (2022)
- [GAIN: Missing Data Imputation using Generative Adversarial Nets](https://mlsanity.com/paper/1806.02920/) (2018)
- [Understanding Diffusion Objectives as the ELBO with Simple Data Augmentation](https://mlsanity.com/paper/2303.00848/) (2023)
- [Diffusion-based Time Series Imputation and Forecasting with Structured State Space Models](https://mlsanity.com/paper/2208.09399/) (2022)
- [Remasking Discrete Diffusion Models with Inference-Time Scaling](https://mlsanity.com/paper/2503.00307/) (2025)
- [Simple Guidance Mechanisms for Discrete Diffusion Models](https://mlsanity.com/paper/2412.10193/) (2024)

## Built on by (most cited first, 2 of 2)

- [Stochastic Flow Map for Count Data](https://mlsanity.com/paper/2609.23290/) (2026)
- [CRNDiff: Count-Native Diffusion Framework via Chemical Reaction Networks](https://mlsanity.com/paper/2609.31149/) (2026)

## Abstract (arXiv)

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.