# A survey of probabilistic generative frameworks for molecular simulations

arXiv: https://arxiv.org/abs/2411.09388 · HTML: https://mlsanity.com/paper/2411.09388/

## Key facts

- Cited by 1 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 16 of its 53 references that are in the map.
- First posted on arXiv 14 Nov 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, 16 of 16)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Neural Ordinary Differential Equations](https://mlsanity.com/paper/1806.07366/) (2018)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Density estimation using Real NVP](https://mlsanity.com/paper/1605.08803/) (2016)
- [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)
- [DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking](https://mlsanity.com/paper/2210.01776/) (2022)
- [A survey of the Schr"odinger problem and some of its connections with optimal transport](https://mlsanity.com/paper/1308.0215/) (2013)
- [Stochastic interpolants with data-dependent couplings](https://mlsanity.com/paper/2310.03725/) (2023)
- [Simulation-free Schr"odinger bridges via score and flow matching](https://mlsanity.com/paper/2307.03672/) (2023)
- [Boltzmann Generators -- Sampling Equilibrium States of Many-Body Systems with Deep Learning](https://mlsanity.com/paper/1812.01729/) (2018)
- [Generative artificial intelligence for computational chemistry: a roadmap to predicting emergent phenomena](https://mlsanity.com/paper/2409.03118/) (2024)
- [Efficient Sound Field Reconstruction with Conditional Invertible Neural Networks](https://mlsanity.com/paper/2404.06928/) (2024)

## Built on by (most cited first, 1 of 1)

- [Operator Flow Matching for Timeseries Forecasting](https://mlsanity.com/paper/2510.15101/) (2025)

## Abstract (arXiv)

Generative artificial intelligence is now a widely used tool in molecular science. Despite the popularity of probabilistic generative models, numerical experiments benchmarking their performance on molecular data are lacking. In this work, we introduce and explain several classes of generative models, broadly sorted into two categories: flow-based models and diffusion models. We select three representative models: Neural Spline Flows, Conditional Flow Matching, and Denoising Diffusion Probabilistic Models, and examine their accuracy, computational cost, and generation speed across datasets with tunable dimensionality, complexity, and modal asymmetry. Our findings are varied, with no one framework being the best for all purposes. In a nutshell, (i) Neural Spline Flows do best at capturing mode asymmetry present in low-dimensional data, (ii) Conditional Flow Matching outperforms other models for high-dimensional data with low complexity, and (iii) Denoising Diffusion Probabilistic Models appears the best for low-dimensional data with high complexity. Our datasets include a Gaussian mixture model and the dihedral torsion angle distribution of the Aibtextsubscript9 peptide, generated via a molecular dynamics simulation. We hope our taxonomy of probabilistic generative frameworks and numerical results may guide model selection for a wide range of molecular tasks.