# A Unification of Discrete, Gaussian, and Simplicial Diffusion

arXiv: https://arxiv.org/abs/2512.15923 · HTML: https://mlsanity.com/paper/2512.15923/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Diffusion foundations and sampling, one of 14 directions in Diffusion models.
- Builds on 34 of its 59 references that are in the map.
- First posted on arXiv 17 Dec 2025.

## Placed in

- Diffusion models / [Diffusion foundations and sampling](https://mlsanity.com/diffusion/diffusion-foundations-and-sampling/)

## Builds on (most cited first, 30 of 34)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Simple and Effective Masked Diffusion Language Models](https://mlsanity.com/paper/2406.07524/) (2024)
- [Discrete Diffusion Modeling by Estimating the Ratios of the Data Distribution](https://mlsanity.com/paper/2310.16834/) (2023)
- [Simplified and Generalized Masked Diffusion for Discrete Data](https://mlsanity.com/paper/2406.04329/) (2024)
- [A Continuous Time Framework for Discrete Denoising Models](https://mlsanity.com/paper/2205.14987/) (2022)
- [Your Absorbing Discrete Diffusion Secretly Models the Conditional Distributions of Clean Data](https://mlsanity.com/paper/2406.03736/) (2024)
- [Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design](https://mlsanity.com/paper/2402.04997/) (2024)
- [Continuous diffusion for categorical data](https://mlsanity.com/paper/2211.15089/) (2022)
- [Masked Diffusion Models are Secretly Time-Agnostic Masked Models and Exploit Inaccurate Categorical Sampling](https://mlsanity.com/paper/2409.02908/) (2024)
- [SSD-LM: Semi-autoregressive Simplex-based Diffusion Language Model for Text Generation and Modular Control](https://mlsanity.com/paper/2210.17432/) (2022)
- [Protein Design with Guided Discrete Diffusion](https://mlsanity.com/paper/2305.20009/) (2023)
- [The Diffusion Duality](https://mlsanity.com/paper/2506.10892/) (2025)
- [Dirichlet Flow Matching with Applications to DNA Sequence Design](https://mlsanity.com/paper/2402.05841/) (2024)
- [Diffusion Language Models Are Versatile Protein Learners](https://mlsanity.com/paper/2402.18567/) (2024)
- [Reflected Diffusion Models](https://mlsanity.com/paper/2304.04740/) (2023)
- [Variational Flow Matching for Graph Generation](https://mlsanity.com/paper/2406.04843/) (2024)
- [Dirichlet Diffusion Score Model for Biological Sequence Generation](https://mlsanity.com/paper/2305.10699/) (2023)
- [Fisher Flow Matching for Generative Modeling over Discrete Data](https://mlsanity.com/paper/2405.14664/) (2024)
- [TESS: Text-to-Text Self-Conditioned Simplex Diffusion](https://mlsanity.com/paper/2305.08379/) (2023)
- [DPLM-2: A Multimodal Diffusion Protein Language Model](https://mlsanity.com/paper/2410.13782/) (2024)
- [From Denoising Diffusions to Denoising Markov Models](https://mlsanity.com/paper/2211.03595/) (2022)
- [Categorical SDEs with Simplex Diffusion](https://mlsanity.com/paper/2210.14784/) (2022)
- [Beyond In-Place Corruption: Insertion and Deletion In Denoising Probabilistic Models](https://mlsanity.com/paper/2107.07675/) (2021)
- [Diffusion Models are Evolutionary Algorithms](https://mlsanity.com/paper/2410.02543/) (2024)
- [Why Masking Diffusion Works: Condition on the Jump Schedule for Improved Discrete Diffusion](https://mlsanity.com/paper/2506.08316/) (2025)
- [Diffusion on the Probability Simplex](https://mlsanity.com/paper/2309.02530/) (2023)
- [Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation](https://mlsanity.com/paper/2503.17361/) (2025)
- [Bridging discrete and continuous state spaces: Exploring the Ehrenfest process in time-continuous diffusion models](https://mlsanity.com/paper/2405.03549/) (2024)
- [Smoothie: Smoothing Diffusion on Token Embeddings for Text Generation](https://mlsanity.com/paper/2505.18853/) (2025)

## Built on by (most cited first, 1 of 1)

- [Simplex Relaxation for Discrete Diffusion](https://mlsanity.com/paper/2608.10615/) (2026)

## Abstract (arXiv)

To model discrete sequences such as DNA, proteins, and language using diffusion, practitioners must choose between three major methods: diffusion in discrete space, Gaussian diffusion in Euclidean space, or diffusion on the simplex. Despite their shared goal, these models have disparate algorithms, theoretical structures, and tradeoffs: discrete diffusion has the most natural domain, Gaussian diffusion has more mature algorithms, and diffusion on the simplex in principle combines the strengths of the other two but in practice suffers from a numerically unstable stochastic processes. Ideally we could see each of these models as instances of the same underlying framework, and enable practitioners to switch between models for downstream applications. However previous theories have only considered connections in special cases. Here we build a theory unifying all three methods of discrete diffusion as different parameterizations of the same underlying process: the Wright-Fisher population genetics model. In particular, we find simplicial and Gaussian diffusion as two large-population limits. Our theory formally connects the likelihoods and hyperparameters of these models and leverages decades of mathematical genetics literature to unlock stable simplicial diffusion. Finally, we relieve the practitioner of balancing model trade-offs by demonstrating it is possible to train a single model that can perform diffusion in any of these three domains at test time. Our experiments show that Wright-Fisher simplicial diffusion is more stable and outperforms previous simplicial diffusion models on conditional DNA generation. We also show that we can train models on multiple domains at once that are competitive with models trained on any individual domain.