# Property-Guided Molecular Generation and Optimization via Latent Flows

arXiv: https://arxiv.org/abs/2603.26889 · HTML: https://mlsanity.com/paper/2603.26889/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 34 of its 52 references that are in the map.
- First posted on arXiv 27 Mar 2026.

## Builds on (most cited first, 30 of 34)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [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)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (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)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Optuna: A Next-generation Hyperparameter Optimization Framework](https://mlsanity.com/paper/1907.10902/) (2019)
- [Variational Inference with Normalizing Flows](https://mlsanity.com/paper/1505.05770/) (2015)
- [Diffusion Posterior Sampling for General Noisy Inverse Problems](https://mlsanity.com/paper/2209.14687/) (2022)
- [Normalizing Flows for Probabilistic Modeling and Inference](https://mlsanity.com/paper/1912.02762/) (2019)
- [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)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [FFJORD: Free-form Continuous Dynamics for Scalable Reversible Generative Models](https://mlsanity.com/paper/1810.01367/) (2018)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation](https://mlsanity.com/paper/1806.02473/) (2018)
- [Molecular De Novo Design through Deep Reinforcement Learning](https://mlsanity.com/paper/1704.07555/) (2017)
- [Optimization of Molecules via Deep Reinforcement Learning](https://mlsanity.com/paper/1810.08678/) (2018)
- [pymoo: Multi-objective Optimization in Python](https://mlsanity.com/paper/2002.04504/) (2020)
- [MoFlow: An Invertible Flow Model for Generating Molecular Graphs](https://mlsanity.com/paper/2006.10137/) (2020)
- [Flow Matching in Latent Space](https://mlsanity.com/paper/2307.08698/) (2023)
- [Sample-Efficient Optimization in the Latent Space of Deep Generative Models via Weighted Retraining](https://mlsanity.com/paper/2006.09191/) (2020)
- [Parallel Bayesian Optimization of Multiple Noisy Objectives with Expected Hypervolume Improvement](https://mlsanity.com/paper/2105.08195/) (2021)
- [Align Your Flow: Scaling Continuous-Time Flow Map Distillation](https://mlsanity.com/paper/2506.14603/) (2025)
- [Local Latent Space Bayesian Optimization over Structured Inputs](https://mlsanity.com/paper/2201.11872/) (2022)
- [Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation](https://mlsanity.com/paper/2404.19739/) (2024)

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

- [PhAME: Phenotype-Aware Molecular Editing via Latent Diffusion](https://mlsanity.com/paper/2605.28226/) (2026)

## Abstract (arXiv)

Molecular discovery is increasingly framed as an inverse design problem: identifying molecular structures that satisfy desired property profiles under feasibility constraints. While recent generative models provide continuous latent representations of chemical space, targeted optimization within these representations often leads to degraded validity, loss of structural fidelity, or unstable behavior. We introduce MoltenFlow, a modular framework that combines property-organized latent representations with flow-matching generative priors and gradient-based guidance. This formulation supports both conditioned generation and local optimization within a single latent-space framework. We show that guided latent flows enable efficient multi-objective molecular optimization under fixed oracle budgets with controllable trade-offs, while a learned flow prior improves unconditional generation quality.