# Training-Free Guidance for Discrete Diffusion Models for Molecular Generation

arXiv: https://arxiv.org/abs/2409.07359 · HTML: https://mlsanity.com/paper/2409.07359/

## 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 9 of its 13 references that are in the map.
- First posted on arXiv 11 Sep 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, 9 of 9)

- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Discrete Diffusion Modeling by Estimating the Ratios of the Data Distribution](https://mlsanity.com/paper/2310.16834/) (2023)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [Universal Guidance for Diffusion Models](https://mlsanity.com/paper/2302.07121/) (2023)
- [FreeDoM: Training-Free Energy-Guided Conditional Diffusion Model](https://mlsanity.com/paper/2303.09833/) (2023)
- [Understanding and Improving Training-free Loss-based Diffusion Guidance](https://mlsanity.com/paper/2403.12404/) (2024)
- [Classifier-free graph diffusion for molecular property targeting](https://mlsanity.com/paper/2312.17397/) (2023)

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

- [How Discrete and Continuous Diffusion Meet: Comprehensive Analysis of Discrete Diffusion Models via a Stochastic Integral Framework](https://mlsanity.com/paper/2410.03601/) (2024)
- [Fast Solvers for Discrete Diffusion Models: Theory and Applications of High-Order Algorithms](https://mlsanity.com/paper/2502.00234/) (2025)
- [Debiasing Guidance for Discrete Diffusion with Sequential Monte Carlo](https://mlsanity.com/paper/2502.06079/) (2025)
- [Learning Flexible Forward Trajectories for Masked Molecular Diffusion](https://mlsanity.com/paper/2505.16790/) (2025)
- [FluxLite: Inference-Time Proposal Control for Discrete Diffusion Models](https://mlsanity.com/paper/2609.35947/) (2026)
- [Generating time-consistent dynamics with discriminator-guided image diffusion models](https://mlsanity.com/paper/2505.09089/) (2025)

## Abstract (arXiv)

Training-free guidance methods for continuous data have seen an explosion of interest due to the fact that they enable foundation diffusion models to be paired with interchangable guidance models. Currently, equivalent guidance methods for discrete diffusion models are unknown. We present a framework for applying training-free guidance to discrete data and demonstrate its utility on molecular graph generation tasks using the discrete diffusion model architecture of DiGress. We pair this model with guidance functions that return the proportion of heavy atoms that are a specific atom type and the molecular weight of the heavy atoms and demonstrate our method's ability to guide the data generation.