# All-atom Diffusion Transformers: Unified generative modelling of molecules and materials

arXiv: https://arxiv.org/abs/2503.03965 · HTML: https://mlsanity.com/paper/2503.03965/

## Key facts

- Cited by 75 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 67 references that are in the map.
- First posted on arXiv 5 Mar 2025.

## 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)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [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)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [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)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Adding Conditional Control to Text-to-Image Diffusion Models](https://mlsanity.com/paper/2302.05543/) (2023)
- [Scaling Rectified Flow Transformers for High-Resolution Image Synthesis](https://mlsanity.com/paper/2403.03206/) (2024)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [WorldSimBench: Towards Video Generation Models as World Simulators](https://mlsanity.com/paper/2410.18072/) (2024)
- [SiT: Exploring Flow and Diffusion-based Generative Models with Scalable Interpolant Transformers](https://mlsanity.com/paper/2401.08740/) (2024)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Score-based Generative Modeling in Latent Space](https://mlsanity.com/paper/2106.05931/) (2021)
- [DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking](https://mlsanity.com/paper/2210.01776/) (2022)
- [Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design](https://mlsanity.com/paper/2402.04997/) (2024)
- [Emu: Enhancing Image Generation Models Using Photogenic Needles in a Haystack](https://mlsanity.com/paper/2309.15807/) (2023)
- [Crystal Diffusion Variational Autoencoder for Periodic Material Generation](https://mlsanity.com/paper/2110.06197/) (2021)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [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)
- [EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations](https://mlsanity.com/paper/2306.12059/) (2023)
- [Geometric Latent Diffusion Models for 3D Molecule Generation](https://mlsanity.com/paper/2305.01140/) (2023)
- [Crystal Structure Prediction by Joint Equivariant Diffusion](https://mlsanity.com/paper/2309.04475/) (2023)
- [FlowMM: Generating Materials with Riemannian Flow Matching](https://mlsanity.com/paper/2406.04713/) (2024)
- [MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation](https://mlsanity.com/paper/2302.09048/) (2023)

## Built on by (most cited first, 30 of 75)

- [LeMat-GenBench: A Unified Evaluation Framework for Crystal Generative Models](https://mlsanity.com/paper/2512.04562/) (2025)
- [FlowMol3: Flow Matching for 3D De Novo Small-Molecule Generation](https://mlsanity.com/paper/2508.12629/) (2025)
- [Guiding Generative Models to Uncover Diverse and Novel Crystals via Reinforcement Learning](https://mlsanity.com/paper/2511.07158/) (2025)
- [SimpleFold: Folding Proteins is Simpler than You Think](https://mlsanity.com/paper/2509.18480/) (2025)
- [PLaID++: A Preference Aligned Language Model for Targeted Inorganic Materials Design](https://mlsanity.com/paper/2509.07150/) (2025)
- [LLM Meets Diffusion: A Hybrid Framework for Crystal Material Generation](https://mlsanity.com/paper/2510.23040/) (2025)
- [TABASCO: A Fast, Simplified Model for Molecular Generation with Improved Physical Quality](https://mlsanity.com/paper/2507.00899/) (2025)
- [All that structure matches does not glitter](https://mlsanity.com/paper/2509.12178/) (2025)
- [Towards Unified and Lossless Latent Space for 3D Molecular Latent Diffusion Modeling](https://mlsanity.com/paper/2503.15567/) (2025)
- [Materials Generation in the Era of Artificial Intelligence: A Comprehensive Survey](https://mlsanity.com/paper/2505.16379/) (2025)
- [Flexible MOF Generation with Torsion-Aware Flow Matching](https://mlsanity.com/paper/2505.17914/) (2025)
- [Platonic Transformers: A Solid Choice For Equivariance](https://mlsanity.com/paper/2510.03511/) (2025)
- [Crystalite: A Lightweight Transformer for Efficient Crystal Modeling](https://mlsanity.com/paper/2604.02270/) (2026)
- [Scalable Autoregressive 3D Molecule Generation](https://mlsanity.com/paper/2505.13791/) (2025)
- [Open Materials Generation with Inference-Time Reinforcement Learning](https://mlsanity.com/paper/2602.00424/) (2026)
- [Space Group Conditional Flow Matching](https://mlsanity.com/paper/2509.23822/) (2025)
- [Transformers Discover Molecular Structure Without Graph Priors](https://mlsanity.com/paper/2510.02259/) (2025)
- [Multimodal Crystal Flow: Any-to-Any Modality Generation for Unified Crystal Modeling](https://mlsanity.com/paper/2602.20210/) (2026)
- [Sampling 3D Molecular Conformers with Diffusion Transformers](https://mlsanity.com/paper/2506.15378/) (2025)
- [TopoMAS: Large Language Model Driven Topological Materials Multiagent System](https://mlsanity.com/paper/2507.04053/) (2025)
- [CrystalDiT: A Diffusion Transformer for Crystal Generation](https://mlsanity.com/paper/2508.16614/) (2025)
- [Continuous SUN (Stable, Unique, and Novel) Metric for Generative Modeling of Inorganic Crystals](https://mlsanity.com/paper/2510.12405/) (2025)
- [Boltzmann generators for amorphous particle systems](https://mlsanity.com/paper/2512.16607/) (2025)
- [End-to-End Training for Unified Tokenization and Latent Denoising](https://mlsanity.com/paper/2603.22283/) (2026)
- [Learning Inter-Atomic Potentials without Explicit Equivariance](https://mlsanity.com/paper/2510.00027/) (2025)
- [Branching Flows: Discrete, Continuous, and Manifold Flow Matching with Splits and Deletions](https://mlsanity.com/paper/2511.09465/) (2025)
- [Mofasa: A Step Change in Metal-Organic Framework Generation](https://mlsanity.com/paper/2512.01756/) (2025)
- [Zatom-1: Towards a Multimodal Foundation Model for 3D Molecules and Materials](https://mlsanity.com/paper/2602.22251/) (2026)
- [Building-Block Aware Generative Modeling for 3D Crystals of Metal Organic Frameworks](https://mlsanity.com/paper/2505.08531/) (2025)
- [MiAD: Mirage Atom Diffusion for De Novo Crystal Generation](https://mlsanity.com/paper/2511.14426/) (2025)

## Abstract (arXiv)

Diffusion models are the standard toolkit for generative modelling of 3D atomic systems. However, for different types of atomic systems -- such as molecules and materials -- the generative processes are usually highly specific to the target system despite the underlying physics being the same. We introduce the All-atom Diffusion Transformer (ADiT), a unified latent diffusion framework for jointly generating both periodic materials and non-periodic molecular systems using the same model: (1) An autoencoder maps a unified, all-atom representations of molecules and materials to a shared latent embedding space; and (2) A diffusion model is trained to generate new latent embeddings that the autoencoder can decode to sample new molecules or materials. Experiments on MP20, QM9 and GEOM-DRUGS datasets demonstrate that jointly trained ADiT generates realistic and valid molecules as well as materials, obtaining state-of-the-art results on par with molecule and crystal-specific models. ADiT uses standard Transformers with minimal inductive biases for both the autoencoder and diffusion model, resulting in significant speedups during training and inference compared to equivariant diffusion models. Scaling ADiT up to half a billion parameters predictably improves performance, representing a step towards broadly generalizable foundation models for generative chemistry. Open source code: https://github.com/facebookresearch/all-atom-diffusion-transformer