# Crystal Structure Prediction by Joint Equivariant Diffusion

arXiv: https://arxiv.org/abs/2309.04475 · HTML: https://mlsanity.com/paper/2309.04475/

## Key facts

- Cited by 148 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 39 of its 75 references that are in the map.
- First posted on arXiv 30 Jul 2023.

## 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 39)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Hierarchical Text-Conditional Image Generation with CLIP Latents](https://mlsanity.com/paper/2204.06125/) (2022)
- [Improved Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2102.09672/) (2021)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Improved Techniques for Training Score-Based Generative Models](https://mlsanity.com/paper/2006.09011/) (2020)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions](https://mlsanity.com/paper/2102.05379/) (2021)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking](https://mlsanity.com/paper/2210.01776/) (2022)
- [Crystal Diffusion Variational Autoencoder for Periodic Material Generation](https://mlsanity.com/paper/2110.06197/) (2021)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (2022)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [The Open Catalyst 2020 (OC20) Dataset and Community Challenges](https://mlsanity.com/paper/2010.09990/) (2020)
- [Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem](https://mlsanity.com/paper/2206.04119/) (2022)
- [Riemannian Score-Based Generative Modelling](https://mlsanity.com/paper/2202.02763/) (2022)
- [TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials](https://mlsanity.com/paper/2202.02541/) (2022)
- [Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules](https://mlsanity.com/paper/1906.00957/) (2019)
- [EGSDE: Unpaired Image-to-Image Translation via Energy-Guided Stochastic Differential Equations](https://mlsanity.com/paper/2207.06635/) (2022)
- [Learning Gradient Fields for Molecular Conformation Generation](https://mlsanity.com/paper/2105.03902/) (2021)
- [Riemannian Diffusion Models](https://mlsanity.com/paper/2208.07949/) (2022)

## Built on by (most cited first, 30 of 148)

- [FlowMM: Generating Materials with Riemannian Flow Matching](https://mlsanity.com/paper/2406.04713/) (2024)
- [MatterGen: a generative model for inorganic materials design](https://mlsanity.com/paper/2312.03687/) (2023)
- [All-atom Diffusion Transformers: Unified generative modelling of molecules and materials](https://mlsanity.com/paper/2503.03965/) (2025)
- [A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems](https://mlsanity.com/paper/2312.07511/) (2023)
- [Flow Matching with General Discrete Paths: A Kinetic-Optimal Perspective](https://mlsanity.com/paper/2412.03487/) (2024)
- [FlowLLM: Flow Matching for Material Generation with Large Language Models as Base Distributions](https://mlsanity.com/paper/2410.23405/) (2024)
- [SymmCD: Symmetry-Preserving Crystal Generation with Diffusion Models](https://mlsanity.com/paper/2502.03638/) (2025)
- [Space Group Informed Transformer for Crystalline Materials Generation](https://mlsanity.com/paper/2403.15734/) (2024)
- [Are LLMs Ready for Real-World Materials Discovery?](https://mlsanity.com/paper/2402.05200/) (2024)
- [A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications](https://mlsanity.com/paper/2403.00485/) (2024)
- [Open Materials Generation with Stochastic Interpolants](https://mlsanity.com/paper/2502.02582/) (2025)
- [Wyckoff Transformer: Generation of Symmetric Crystals](https://mlsanity.com/paper/2503.02407/) (2025)
- [WyckoffDiff -- A Generative Diffusion Model for Crystal Symmetry](https://mlsanity.com/paper/2502.06485/) (2025)
- [MOFDiff: Coarse-grained Diffusion for Metal-Organic Framework Design](https://mlsanity.com/paper/2310.10732/) (2023)
- [LeMat-GenBench: A Unified Evaluation Framework for Crystal Generative Models](https://mlsanity.com/paper/2512.04562/) (2025)
- [Guiding Generative Models to Uncover Diverse and Novel Crystals via Reinforcement Learning](https://mlsanity.com/paper/2511.07158/) (2025)
- [Are High-Degree Representations Really Unnecessary in Equivariant Graph Neural Networks?](https://mlsanity.com/paper/2410.11443/) (2024)
- [MatExpert: Decomposing Materials Discovery by Mimicking Human Experts](https://mlsanity.com/paper/2410.21317/) (2024)
- [Foundational Large Language Models for Materials Research](https://mlsanity.com/paper/2412.09560/) (2024)
- [MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks](https://mlsanity.com/paper/2410.17270/) (2024)
- [Periodic Materials Generation using Text-Guided Joint Diffusion Model](https://mlsanity.com/paper/2503.00522/) (2025)
- [Space Group Equivariant Crystal Diffusion](https://mlsanity.com/paper/2505.10994/) (2025)
- [PLaID++: A Preference Aligned Language Model for Targeted Inorganic Materials Design](https://mlsanity.com/paper/2509.07150/) (2025)
- [LLEMA: Evolutionary Search with LLMs for Multi-Objective Materials Discovery](https://mlsanity.com/paper/2510.22503/) (2025)
- [LLM Meets Diffusion: A Hybrid Framework for Crystal Material Generation](https://mlsanity.com/paper/2510.23040/) (2025)
- [Ab Initio Structure Solutions from Nanocrystalline Powder Diffraction Data](https://mlsanity.com/paper/2406.10796/) (2024)
- [Invariant Tokenization of Crystalline Materials for Language Model Enabled Generation](https://mlsanity.com/paper/2503.00152/) (2025)
- [All that structure matches does not glitter](https://mlsanity.com/paper/2509.12178/) (2025)
- [Riemannian Variational Flow Matching for Material and Protein Design](https://mlsanity.com/paper/2502.12981/) (2025)
- [AI-driven inverse design of materials: Past, present and future](https://mlsanity.com/paper/2411.09429/) (2024)

## Abstract (arXiv)

Crystal Structure Prediction (CSP) is crucial in various scientific disciplines. While CSP can be addressed by employing currently-prevailing generative models (e.g. diffusion models), this task encounters unique challenges owing to the symmetric geometry of crystal structures -- the invariance of translation, rotation, and periodicity. To incorporate the above symmetries, this paper proposes DiffCSP, a novel diffusion model to learn the structure distribution from stable crystals. To be specific, DiffCSP jointly generates the lattice and atom coordinates for each crystal by employing a periodic-E(3)-equivariant denoising model, to better model the crystal geometry. Notably, different from related equivariant generative approaches, DiffCSP leverages fractional coordinates other than Cartesian coordinates to represent crystals, remarkably promoting the diffusion and the generation process of atom positions. Extensive experiments verify that our DiffCSP significantly outperforms existing CSP methods, with a much lower computation cost in contrast to DFT-based methods. Moreover, the superiority of DiffCSP is also observed when it is extended for ab initio crystal generation.