mlsanityData to 7 Oct 2026

A Genetic Algorithm for Navigating Synthesizable Molecular Spaces

arXiv 2509.20719 ↗First posted 25 Sep 2025cs.LG q-bio.QMcited by 4

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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.

Key facts. Cited by 4 papers in the map (data through 7 Oct 2026). Builds on 40 of its 79 references that are in the map. First posted on arXiv 25 Sep 2025.

Builds on

40 of 79 references.

References · 40

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  12. 2018Multi-Objective De Novo Drug Design with Conditional Graph Generative Modelcited by 101
28 more
  1. 2020The Synthesizability of Molecules Proposed by Generative Modelscited by 67
  2. 2019Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Spacecited by 66
  3. 2020Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learningcited by 57
  4. 2020Guiding Deep Molecular Optimization with Genetic Explorationcited by 51
  5. 2022Reinforced Genetic Algorithm for Structure-based Drug Designcited by 46
  6. 2021Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Designcited by 44
  7. 2022GAUCHE: A Library for Gaussian Processes in Chemistrycited by 40
  8. 2024RGFN: Synthesizable Molecular Generation Using GFlowNetscited by 39
  9. 2019A Model to Search for Synthesizable Moleculescited by 37
  10. 2024Genetic-guided GFlowNets for Sample Efficient Molecular Optimizationcited by 36
  11. 2020Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement Learningcited by 32
  12. 2020Barking up the right tree: an approach to search over molecule synthesis DAGscited by 31
  13. 2021JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Designcited by 31
  14. 2023Genetic algorithms are strong baselines for molecule generationcited by 31
  15. 2024SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraintscited by 26
  16. 2024Molecule Generation with Fragment Retrieval Augmentationcited by 22
  17. 2024Generative Flows on Synthetic Pathway for Drug Designcited by 20
  18. 2024Generative Artificial Intelligence for Navigating Synthesizable Chemical Spacecited by 18
  19. 2024Projecting Molecules into Synthesizable Chemical Spacescited by 17
  20. 2022Tartarus: A Benchmarking Platform for Realistic And Practical Inverse Molecular Designcited by 16
  21. 2024Saturn: Sample-efficient Generative Molecular Design using Memory Manipulationcited by 14
  22. 2025LLM-Augmented Chemical Synthesis and Design Decision Programscited by 13
  23. 2024Diagnosing and fixing common problems in Bayesian optimization for molecule designcited by 9
  24. 2025SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Modelscited by 9
  25. 2023Recent advances in the Self-Referencing Embedding Strings (SELFIES) librarycited by 8
  26. 2024Procedural Synthesis of Synthesizable Moleculescited by 6
  27. 2025Compositional Flows for 3D Molecule and Synthesis Pathway Co-designcited by 6
  28. 2025Neural Genetic Search in Discrete Spacescited by 5

Built on by

Cited by year (2026 to 7 Oct)

Citing papers per year: 2026: 4.

4 papers.

  1. 2026Synthesizable Molecular Generation via Soft-constrained GFlowNets with Rich Chemical Priorscited by 0
  2. 2026MolLIBRA: Genetic Molecular Optimization with Multi-Fingerprint Surrogates and Text-Molecule Aligned Criticcited by 0
  3. 2026Amortized Molecular Optimization via Group Relative Policy Optimizationcited by 0
  4. 2026SynLaD: Latent Diffusion for Generating Synthesizable Molecules Conditioned on 3D Pharmacophore Profilescited by 0