# A Genetic Algorithm for Navigating Synthesizable Molecular Spaces

arXiv: https://arxiv.org/abs/2509.20719 · HTML: https://mlsanity.com/paper/2509.20719/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 40 of its 79 references that are in the map.
- First posted on arXiv 25 Sep 2025.

## Builds on (most cited first, 30 of 40)

- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Contrastive Learning with Hard Negative Samples](https://mlsanity.com/paper/2010.04592/) (2020)
- [GPyTorch: Blackbox Matrix-Matrix Gaussian Process Inference with GPU Acceleration](https://mlsanity.com/paper/1809.11165/) (2018)
- [Flow Network based Generative Models for Non-Iterative Diverse Candidate Generation](https://mlsanity.com/paper/2106.04399/) (2021)
- [Neural Additive Models: Interpretable Machine Learning with Neural Nets](https://mlsanity.com/paper/2004.13912/) (2020)
- [GuacaMol: Benchmarking Models for De Novo Molecular Design](https://mlsanity.com/paper/1811.09621/) (2018)
- [Molecular De Novo Design through Deep Reinforcement Learning](https://mlsanity.com/paper/1704.07555/) (2017)
- [Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development](https://mlsanity.com/paper/2102.09548/) (2021)
- [Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets](https://mlsanity.com/paper/2205.07249/) (2022)
- [Sample Efficiency Matters: A Benchmark for Practical Molecular Optimization](https://mlsanity.com/paper/2206.12411/) (2022)
- [Multi-Objective De Novo Drug Design with Conditional Graph Generative Model](https://mlsanity.com/paper/1801.07299/) (2018)
- [The Synthesizability of Molecules Proposed by Generative Models](https://mlsanity.com/paper/2002.07007/) (2020)
- [Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space](https://mlsanity.com/paper/1909.11655/) (2019)
- [Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning](https://mlsanity.com/paper/2004.12485/) (2020)
- [Guiding Deep Molecular Optimization with Genetic Exploration](https://mlsanity.com/paper/2007.04897/) (2020)
- [Reinforced Genetic Algorithm for Structure-based Drug Design](https://mlsanity.com/paper/2211.16508/) (2022)
- [Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design](https://mlsanity.com/paper/2110.06389/) (2021)
- [GAUCHE: A Library for Gaussian Processes in Chemistry](https://mlsanity.com/paper/2212.04450/) (2022)
- [RGFN: Synthesizable Molecular Generation Using GFlowNets](https://mlsanity.com/paper/2406.08506/) (2024)
- [Genetic-guided GFlowNets for Sample Efficient Molecular Optimization](https://mlsanity.com/paper/2402.05961/) (2024)
- [A Model to Search for Synthesizable Molecules](https://mlsanity.com/paper/1906.05221/) (2019)
- [Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement Learning](https://mlsanity.com/paper/2004.14308/) (2020)
- [JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design](https://mlsanity.com/paper/2106.04011/) (2021)
- [Barking up the right tree: an approach to search over molecule synthesis DAGs](https://mlsanity.com/paper/2012.11522/) (2020)
- [Genetic algorithms are strong baselines for molecule generation](https://mlsanity.com/paper/2310.09267/) (2023)
- [SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints](https://mlsanity.com/paper/2405.01155/) (2024)
- [Molecule Generation with Fragment Retrieval Augmentation](https://mlsanity.com/paper/2411.12078/) (2024)
- [Generative Flows on Synthetic Pathway for Drug Design](https://mlsanity.com/paper/2410.04542/) (2024)
- [Generative Artificial Intelligence for Navigating Synthesizable Chemical Space](https://mlsanity.com/paper/2410.03494/) (2024)

## Built on by (most cited first, 4 of 4)

- [Synthesizable Molecular Generation via Soft-constrained GFlowNets with Rich Chemical Priors](https://mlsanity.com/paper/2602.04119/) (2026)
- [MolLIBRA: Genetic Molecular Optimization with Multi-Fingerprint Surrogates and Text-Molecule Aligned Critic](https://mlsanity.com/paper/2602.07002/) (2026)
- [Amortized Molecular Optimization via Group Relative Policy Optimization](https://mlsanity.com/paper/2602.12162/) (2026)
- [SynLaD: Latent Diffusion for Generating Synthesizable Molecules Conditioned on 3D Pharmacophore Profiles](https://mlsanity.com/paper/2607.01105/) (2026)

## Abstract (arXiv)

Inspired by the effectiveness of genetic algorithms and the importance of synthesizability in molecular design, we present SynGA, a simple genetic algorithm that operates directly over synthesis routes. Our method features custom crossover and mutation operators that explicitly constrain it to synthesizable molecular space. By modifying the fitness function, we demonstrate the effectiveness of SynGA on a variety of design tasks, including synthesizable analog search and sample-efficient property optimization, for both 2D and 3D objectives. Furthermore, by coupling SynGA with a machine learning-based filter that focuses the building block set, we boost SynGA to state-of-the-art performance. For property optimization, this manifests as a model-based variant SynGBO, which employs SynGA and block filtering in the inner loop of Bayesian optimization. Since SynGA is lightweight and enforces synthesizability by construction, our hope is that SynGA can not only serve as a strong standalone baseline but also as a versatile module that can be incorporated into larger synthesis-aware workflows in the future.