# Quotient-Space Diffusion Models

arXiv: https://arxiv.org/abs/2604.21809 · HTML: https://mlsanity.com/paper/2604.21809/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 33 of its 47 references that are in the map.
- First posted on arXiv 23 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 33)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [Imagen Video: High Definition Video Generation with Diffusion Models](https://mlsanity.com/paper/2210.02303/) (2022)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [DiffWave: A Versatile Diffusion Model for Audio Synthesis](https://mlsanity.com/paper/2009.09761/) (2020)
- [Stochastic Interpolants: A Unifying Framework for Flows and Diffusions](https://mlsanity.com/paper/2303.08797/) (2023)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Flow Matching on General Geometries](https://mlsanity.com/paper/2302.03660/) (2023)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (2022)
- [Equivariant Flows: Exact Likelihood Generative Learning for Symmetric Densities](https://mlsanity.com/paper/2006.02425/) (2020)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [Riemannian Score-Based Generative Modelling](https://mlsanity.com/paper/2202.02763/) (2022)
- [SE(3) diffusion model with application to protein backbone generation](https://mlsanity.com/paper/2302.02277/) (2023)
- [Structure-based Drug Design with Equivariant Diffusion Models](https://mlsanity.com/paper/2210.13695/) (2022)
- [Geometric Latent Diffusion Models for 3D Molecule Generation](https://mlsanity.com/paper/2305.01140/) (2023)
- [Fast Timing-Conditioned Latent Audio Diffusion](https://mlsanity.com/paper/2402.04825/) (2024)
- [Riemannian Diffusion Models](https://mlsanity.com/paper/2208.07949/) (2022)
- [GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles](https://mlsanity.com/paper/2106.07802/) (2021)
- [Diffusion-based Molecule Generation with Informative Prior Bridges](https://mlsanity.com/paper/2209.00865/) (2022)
- [Physics-Informed Diffusion Models](https://mlsanity.com/paper/2403.14404/) (2024)
- [VideoGen: A Reference-Guided Latent Diffusion Approach for High Definition Text-to-Video Generation](https://mlsanity.com/paper/2309.00398/) (2023)
- [Proteina: Scaling Flow-based Protein Structure Generative Models](https://mlsanity.com/paper/2503.00710/) (2025)
- [Swallowing the Bitter Pill: Simplified Scalable Conformer Generation](https://mlsanity.com/paper/2311.17932/) (2023)
- [ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation](https://mlsanity.com/paper/2410.22388/) (2024)
- [MUDiff: Unified Diffusion for Complete Molecule Generation](https://mlsanity.com/paper/2304.14621/) (2023)
- [Trivialized Momentum Facilitates Diffusion Generative Modeling on Lie Groups](https://mlsanity.com/paper/2405.16381/) (2024)

## Abstract (arXiv)

Diffusion-based generative models have reformed generative AI, and also enabled new capabilities in the science domain, e.g., fast generation of 3D structures of molecules. In such tasks, there is often a symmetry in the system, identifying elements that can be converted by certain transformations as equivalent. Equivariant diffusion models guarantee a symmetric distribution, but miss the opportunity to make learning easier, while alignment-based simplification attempts fail to preserve the target distribution. In this work, we develop quotient-space diffusion models, a principled generative framework to fully handle and leverage symmetry. By viewing the intrinsic generation process on the quotient space, the exact construction that removes symmetry redundancy, the framework simplifies learning by allowing model output to have an arbitrary intra-equivalence-class movement, while generating the correct symmetric target distribution with guarantee. We instantiate the framework for molecular structure generation which follows SE(3) (rigid-body movement) symmetry. It improves the performance over equivariant diffusion models and outperforms alignment-based methods universally for small molecules and proteins, representing a new framework that surpasses previous symmetry treatments in generative models.