Evolutionary design of molecules based on deep learning and a genetic algorithm

Abstract

Abstract Evolutionary design has gained significant attention as a useful tool to accelerate the design process by automatically modifying molecular structures to obtain molecules with the target properties. However, its methodology presents a practical challenge—devising a way in which to rapidly evolve molecules while maintaining their chemical validity. In this study, we address this limitation by developing an evolutionary design method. The method employs deep learning models to extract the inherent knowledge from a database of materials and is used to effectively guide the evolutionary design. In the proposed method, the Morgan fingerprint vectors of seed molecules are evolved using the techniques of mutation and crossover within the genetic algorithm. Then, a recurrent neural network is used to reconstruct the final fingerprints into actual molecular structures while maintaining their chemical validity. The use of deep neural network models to predict the properties of these molecules enabled more versatile and efficient molecular evaluations to be conducted by using the proposed method repeatedly. Four design tasks were performed to modify the light-absorbing wavelengths of organic molecules from the PubChem library.