# Conditional Synthesis of 3D Molecules with Time Correction Sampler

arXiv: https://arxiv.org/abs/2411.00551 · HTML: https://mlsanity.com/paper/2411.00551/

## 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 40 of its 64 references that are in the map.
- First posted on arXiv 1 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, 30 of 40)

- [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)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Video Diffusion Models](https://mlsanity.com/paper/2204.03458/) (2022)
- [Diffusion Posterior Sampling for General Noisy Inverse Problems](https://mlsanity.com/paper/2209.14687/) (2022)
- [DiffWave: A Versatile Diffusion Model for Audio Synthesis](https://mlsanity.com/paper/2009.09761/) (2020)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Diffusion Probabilistic Models for 3D Point Cloud Generation](https://mlsanity.com/paper/2103.01458/) (2021)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Movie Gen: A Cast of Media Foundation Models](https://mlsanity.com/paper/2410.13720/) (2024)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Sora: A Review on Background, Technology, Limitations, and Opportunities of Large Vision Models](https://mlsanity.com/paper/2402.17177/) (2024)
- [DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking](https://mlsanity.com/paper/2210.01776/) (2022)
- [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations](https://mlsanity.com/paper/2202.02514/) (2022)
- [Cormorant: Covariant Molecular Neural Networks](https://mlsanity.com/paper/1906.04015/) (2019)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (2022)
- [Equivariant Flows: Exact Likelihood Generative Learning for Symmetric Densities](https://mlsanity.com/paper/2006.02425/) (2020)
- [Learning Gradient Fields for Shape Generation](https://mlsanity.com/paper/2008.06520/) (2020)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [Nearly d-Linear Convergence Bounds for Diffusion Models via Stochastic Localization](https://mlsanity.com/paper/2308.03686/) (2023)
- [Diffusion models as plug-and-play priors](https://mlsanity.com/paper/2206.09012/) (2022)
- [Geometric Latent Diffusion Models for 3D Molecule Generation](https://mlsanity.com/paper/2305.01140/) (2023)
- [Convergence for score-based generative modeling with polynomial complexity](https://mlsanity.com/paper/2206.06227/) (2022)
- [Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules](https://mlsanity.com/paper/1906.00957/) (2019)
- [A Primer on Zeroth-Order Optimization in Signal Processing and Machine Learning](https://mlsanity.com/paper/2006.06224/) (2020)
- [Diffusion-based Molecule Generation with Informative Prior Bridges](https://mlsanity.com/paper/2209.00865/) (2022)

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

- [Continuous Diffusion Model for Language Modeling](https://mlsanity.com/paper/2502.11564/) (2025)
- [Schedule On the Fly: Diffusion Time Prediction for Faster and Better Image Generation](https://mlsanity.com/paper/2412.01243/) (2024)
- [Equivariant Neural Diffusion for Molecule Generation](https://mlsanity.com/paper/2506.10532/) (2025)
- [Improved Constrained Generation by Bridging Pretrained Generative Models](https://mlsanity.com/paper/2603.06742/) (2026)
- [MolHIT: Advancing Molecular-Graph Generation with Hierarchical Discrete Diffusion Models](https://mlsanity.com/paper/2602.17602/) (2026)

## Abstract (arXiv)

Diffusion models have demonstrated remarkable success in various domains, including molecular generation. However, conditional molecular generation remains a fundamental challenge due to an intrinsic trade-off between targeting specific chemical properties and generating meaningful samples from the data distribution. In this work, we present Time-Aware Conditional Synthesis (TACS), a novel approach to conditional generation on diffusion models. It integrates adaptively controlled plug-and-play "online" guidance into a diffusion model, driving samples toward the desired properties while maintaining validity and stability. A key component of our algorithm is our new type of diffusion sampler, Time Correction Sampler (TCS), which is used to control guidance and ensure that the generated molecules remain on the correct manifold at each reverse step of the diffusion process at the same time. Our proposed method demonstrates significant performance in conditional 3D molecular generation and offers a promising approach towards inverse molecular design, potentially facilitating advancements in drug discovery, materials science, and other related fields.