# Sampling 3D Molecular Conformers with Diffusion Transformers

arXiv: https://arxiv.org/abs/2506.15378 · HTML: https://mlsanity.com/paper/2506.15378/

## Key facts

- Cited by 6 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 64 of its 87 references that are in the map.
- First posted on arXiv 18 Jun 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 64)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [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)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Training Compute-Optimal Large Language Models](https://mlsanity.com/paper/2203.15556/) (2022)
- [Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges](https://mlsanity.com/paper/2104.13478/) (2021)
- [Variational Diffusion Models](https://mlsanity.com/paper/2107.00630/) (2021)
- [Building Normalizing Flows with Stochastic Interpolants](https://mlsanity.com/paper/2209.15571/) (2022)
- [Stochastic Interpolants: A Unifying Framework for Flows and Diffusions](https://mlsanity.com/paper/2303.08797/) (2023)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [Learning Mesh-Based Simulation with Graph Networks](https://mlsanity.com/paper/2010.03409/) (2020)
- [Vector Quantized Diffusion Model for Text-to-Image Synthesis](https://mlsanity.com/paper/2111.14822/) (2021)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Latte: Latent Diffusion Transformer for Video Generation](https://mlsanity.com/paper/2401.03048/) (2024)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [All are Worth Words: A ViT Backbone for Diffusion Models](https://mlsanity.com/paper/2209.12152/) (2022)
- [Sora: A Review on Background, Technology, Limitations, and Opportunities of Large Vision Models](https://mlsanity.com/paper/2402.17177/) (2024)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [MolGAN: An implicit generative model for small molecular graphs](https://mlsanity.com/paper/1805.11973/) (2018)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data](https://mlsanity.com/paper/1807.02547/) (2018)
- [Understanding Diffusion Objectives as the ELBO with Simple Data Augmentation](https://mlsanity.com/paper/2303.00848/) (2023)
- [Guiding a Diffusion Model with a Bad Version of Itself](https://mlsanity.com/paper/2406.02507/) (2024)

## Built on by (most cited first, 6 of 6)

- [Learning Hamiltonian Flow Maps: Mean Flow Consistency for Large-Timestep Molecular Dynamics](https://mlsanity.com/paper/2601.22123/) (2026)
- [Multimodal Crystal Flow: Any-to-Any Modality Generation for Unified Crystal Modeling](https://mlsanity.com/paper/2602.20210/) (2026)
- [Generative Pseudo-Force Fields for Molecular Generation](https://mlsanity.com/paper/2605.19050/) (2026)
- [Recurrent Equivariant Constraint Modulation: Learning Per-Layer Symmetry Relaxation from Data](https://mlsanity.com/paper/2602.02853/) (2026)
- [SymDrift: One-Shot Generative Modeling under Symmetries](https://mlsanity.com/paper/2605.06140/) (2026)
- [ManifoldCache: Training-Free Diffusion Acceleration via Constraint Manifold Caching](https://mlsanity.com/paper/2610.04510/) (2026)

## Abstract (arXiv)

Diffusion Transformers (DiTs) have demonstrated strong performance in generative modeling, particularly in image synthesis, making them a compelling choice for molecular conformer generation. However, applying DiTs to molecules introduces novel challenges, such as integrating discrete molecular graph information with continuous 3D geometry, handling Euclidean symmetries, and designing conditioning mechanisms that generalize across molecules of varying sizes and structures. We propose DiTMC, a framework that adapts DiTs to address these challenges through a modular architecture that separates the processing of 3D coordinates from conditioning on atomic connectivity. To this end, we introduce two complementary graph-based conditioning strategies that integrate seamlessly with the DiT architecture. These are combined with different attention mechanisms, including both standard non-equivariant and SO(3)-equivariant formulations, enabling flexible control over the trade-off between between accuracy and computational efficiency. Experiments on standard conformer generation benchmarks (GEOM-QM9, -DRUGS, -XL) demonstrate that DiTMC achieves state-of-the-art precision and physical validity. Our results highlight how architectural choices and symmetry priors affect sample quality and efficiency, suggesting promising directions for large-scale generative modeling of molecular structures. Code is available at https://github.com/ML4MolSim/dit_mc.