# Stiefel Flow Matching for Moment-Constrained Structure Elucidation

arXiv: https://arxiv.org/abs/2412.12540 · HTML: https://mlsanity.com/paper/2412.12540/

## Key facts

- Cited by 5 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 50 of its 110 references that are in the map.
- First posted on arXiv 17 Dec 2024.

## 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 50)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Scaling Rectified Flow Transformers for High-Resolution Image Synthesis](https://mlsanity.com/paper/2403.03206/) (2024)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Diffusion Posterior Sampling for General Noisy Inverse Problems](https://mlsanity.com/paper/2209.14687/) (2022)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Solving Inverse Problems in Medical Imaging with Score-Based Generative Models](https://mlsanity.com/paper/2111.08005/) (2021)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Discrete Flow Matching](https://mlsanity.com/paper/2407.15595/) (2024)
- [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)
- [Multisample Flow Matching: Straightening Flows with Minibatch Couplings](https://mlsanity.com/paper/2304.14772/) (2023)
- [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)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [A Variational Perspective on Solving Inverse Problems with Diffusion Models](https://mlsanity.com/paper/2305.04391/) (2023)
- [Reduce, Reuse, Recycle: Compositional Generation with Energy-Based Diffusion Models and MCMC](https://mlsanity.com/paper/2302.11552/) (2023)
- [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)
- [Continuous diffusion for categorical data](https://mlsanity.com/paper/2211.15089/) (2022)
- [Frame Averaging for Invariant and Equivariant Network Design](https://mlsanity.com/paper/2110.03336/) (2021)
- [SE(3)-Stochastic Flow Matching for Protein Backbone Generation](https://mlsanity.com/paper/2310.02391/) (2023)
- [Crystal Structure Prediction by Joint Equivariant Diffusion](https://mlsanity.com/paper/2309.04475/) (2023)
- [Equivariant flow matching](https://mlsanity.com/paper/2306.15030/) (2023)

## Built on by (most cited first, 5 of 5)

- [Diffuse Everything: Multimodal Diffusion Models on Arbitrary State Spaces](https://mlsanity.com/paper/2506.07903/) (2025)
- [Flow Matching Meets Biology and Life Science: A Survey](https://mlsanity.com/paper/2507.17731/) (2025)
- [Energy-Based Flow Matching for Generating 3D Molecular Structure](https://mlsanity.com/paper/2508.18949/) (2025)
- [InertialAR: Autoregressive 3D Molecule Generation with Inertial Frames](https://mlsanity.com/paper/2510.27497/) (2025)
- [Graph Generation with Spectral Geodesic Flow Matching](https://mlsanity.com/paper/2510.02520/) (2025)

## Abstract (arXiv)

Molecular structure elucidation is a fundamental step in understanding chemical phenomena, with applications in identifying molecules in natural products, lab syntheses, forensic samples, and the interstellar medium. We consider the task of predicting a molecule's all-atom 3D structure given only its molecular formula and moments of inertia, motivated by the ability of rotational spectroscopy to measure these moments. While existing generative models can conditionally sample 3D structures with approximately correct moments, this soft conditioning fails to leverage the many digits of precision afforded by experimental rotational spectroscopy. To address this, we first show that the space of n-atom point clouds with a fixed set of moments of inertia is embedded in the Stiefel manifold St(n, 4). We then propose Stiefel Flow Matching as a generative model for elucidating 3D structure under exact moment constraints. Additionally, we learn simpler and shorter flows by finding approximate solutions for equivariant optimal transport on the Stiefel manifold. Empirically, enforcing exact moment constraints allows Stiefel Flow Matching to achieve higher success rates and faster sampling than Euclidean diffusion models, even on high-dimensional manifolds corresponding to large molecules in the GEOM dataset.