# Generative Modeling Enables Molecular Structure Retrieval from Coulomb Explosion Imaging

arXiv: https://arxiv.org/abs/2511.00179 · HTML: https://mlsanity.com/paper/2511.00179/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 52 references that are in the map.
- First posted on arXiv 31 Oct 2025.

## Builds on (most cited first, 8 of 8)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [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)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [Exact solutions to the nonlinear dynamics of learning in deep linear neural networks](https://mlsanity.com/paper/1312.6120/) (2013)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Deep Learning Techniques for Inverse Problems in Imaging](https://mlsanity.com/paper/2005.06001/) (2020)

## Abstract (arXiv)

Capturing the structural changes that molecules undergo during chemical reactions in real space and time is a long-standing dream and an essential prerequisite for understanding and ultimately controlling femtochemistry. A key approach to tackle this challenging task is Coulomb explosion imaging, which benefited decisively from recently emerging high-repetition-rate X-ray free-electron laser sources. With this technique, information on the molecular structure is inferred from the momentum distributions of the ions produced by the rapid Coulomb explosion of molecules. Retrieving molecular structures from these distributions poses a highly non-linear inverse problem that remains unsolved for molecules consisting of more than a few atoms. Here, we address this challenge using a diffusion-based Transformer neural network. We show that the network reconstructs unknown molecular geometries from ion-momentum distributions with a mean absolute error below one Bohr radius, which is half the length of a typical chemical bond.