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Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space

About

Challenges in natural sciences can often be phrased as optimization problems. Machine learning techniques have recently been applied to solve such problems. One example in chemistry is the design of tailor-made organic materials and molecules, which requires efficient methods to explore the chemical space. We present a genetic algorithm (GA) that is enhanced with a neural network (DNN) based discriminator model to improve the diversity of generated molecules and at the same time steer the GA. We show that our algorithm outperforms other generative models in optimization tasks. We furthermore present a way to increase interpretability of genetic algorithms, which helped us to derive design principles.

AkshatKumar Nigam, Pascal Friederich, Mario Krenn, Al\'an Aspuru-Guzik• 2019

Related benchmarks

TaskDatasetResultRank
Property optimizationZINC250k (test)
1st Order Metric0.946
33
Constrained Property OptimizationZINC250K
Improvement3.04
27
Molecular Generationjak2
Top-Hit 5% Docking Score (kcal/mol)-8.61
27
Molecular Generation5ht1b
Docking Score (Top-Hit 5%, kcal/mol)-8.567
27
Molecular Generationfa7
Top-Hit 5% Docking Score (kcal/mol)-6.539
27
Molecular Generationparp1
Top-Hit 5% Docking Score (kcal/mol)-8.365
27
Molecular Generationbraf
Top-Hit 5% Docking Score (kcal/mol)-9.371
26
Molecular Dockingjak2
Mean Docking Score-8.61
18
Molecular Docking5ht1b
Mean Docking Score-8.567
18
Molecular Dockingfa7
Mean Docking Score-6.539
18
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