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

In this experiment, we follow the experimental setup proposed by You et al. (2018). We optimize the penalized logP score of 800 low-scoring molecules from the ZINC data set. Our genetic algorithm is initiated with a molecule from the data set, and we run each experiment for 20 generations and a population size of 500 without the discriminator. For each run, we report the molecule m that increases the penalized logP the greatest, while possessing a similarity sim(m,m′) δ with the respective reference molecules m′. We calculate molecular similarity based on Morgan Fingerprints of radius 2. To ensure generation of molecules possessing a certain similarity, for molecule m we modify the fitness to: Here, SimilarityPenalty(m) is 0 if sim(m,m′) δ and 106 otherwise.