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用机器学习增强遗传算法进行逆分子设计。

Augmenting genetic algorithms with machine learning for inverse molecular design.

作者信息

Kneiding Hannes, Balcells David

机构信息

Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo P.O. Box 1033, Blindern 0315 Oslo Norway

出版信息

Chem Sci. 2024 Sep 11;15(38):15522-39. doi: 10.1039/d4sc02934h.

Abstract

Evolutionary and machine learning methods have been successfully applied to the generation of molecules and materials exhibiting desired properties. The combination of these two paradigms in inverse design tasks can yield powerful methods that explore massive chemical spaces more efficiently, improving the quality of the generated compounds. However, such synergistic approaches are still an incipient area of research and appear underexplored in the literature. This perspective covers different ways of incorporating machine learning approaches into evolutionary learning frameworks, with the overall goal of increasing the optimization efficiency of genetic algorithms. In particular, machine learning surrogate models for faster fitness function evaluation, discriminator models to control population diversity on-the-fly, machine learning based crossover operations, and evolution in latent space are discussed. The further potential of these synergistic approaches in generative tasks is also assessed, outlining promising directions for future developments.

摘要

进化方法和机器学习方法已成功应用于生成具有所需特性的分子和材料。在逆设计任务中,将这两种范式相结合可以产生强大的方法,更有效地探索巨大的化学空间,提高生成化合物的质量。然而,这种协同方法仍是一个新兴的研究领域,在文献中似乎未得到充分探索。本视角涵盖了将机器学习方法纳入进化学习框架的不同方式,总体目标是提高遗传算法的优化效率。特别讨论了用于更快适应度函数评估的机器学习代理模型、实时控制种群多样性的判别模型、基于机器学习的交叉操作以及潜在空间中的进化。还评估了这些协同方法在生成任务中的进一步潜力,概述了未来发展的有前景的方向。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e466/11445739/53a1332a8a43/d4sc02934h-f1.jpg

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本文引用的文献

1
Directional multiobjective optimization of metal complexes at the billion-system scale.
Nat Comput Sci. 2024 Apr;4(4):263-273. doi: 10.1038/s43588-024-00616-5. Epub 2024 Mar 29.
2
A genetic optimization strategy with generality in asymmetric organocatalysis as a primary target.
Chem Sci. 2024 Jan 31;15(10):3640-3660. doi: 10.1039/d3sc06208b. eCollection 2024 Mar 6.
3
Artificial design of organic emitters a genetic algorithm enhanced by a deep neural network.
Chem Sci. 2024 Jan 11;15(7):2618-2639. doi: 10.1039/d3sc05306g. eCollection 2024 Feb 14.
4
Recent advances in the self-referencing embedded strings (SELFIES) library.
Digit Discov. 2023 Jul 1;2(4):897-908. doi: 10.1039/d3dd00044c. eCollection 2023 Aug 8.
5
Toward De Novo Catalyst Discovery: Fast Identification of New Catalyst Candidates for Alcohol-Mediated Morita-Baylis-Hillman Reactions.
Angew Chem Int Ed Engl. 2023 Dec 4;62(49):e202310580. doi: 10.1002/anie.202310580. Epub 2023 Oct 31.
6
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design.
J Chem Inf Model. 2023 Aug 28;63(16):5107-5119. doi: 10.1021/acs.jcim.3c00963. Epub 2023 Aug 9.
8
Generative Models Should at Least Be Able to Design Molecules That Dock Well: A New Benchmark.
J Chem Inf Model. 2023 Jun 12;63(11):3238-3247. doi: 10.1021/acs.jcim.2c01355. Epub 2023 May 24.
9
Generative Models as an Emerging Paradigm in the Chemical Sciences.
J Am Chem Soc. 2023 Apr 26;145(16):8736-8750. doi: 10.1021/jacs.2c13467. Epub 2023 Apr 13.

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