Variational autoencoders and evolutionary algorithms for targeted novel enzyme design

Abstract

Recent developments in Generative Deep Learning have fostered new engineering methods for protein design. Although deep generative models trained on protein sequence can learn biologically meaningful representations, the design of proteins with optimised properties remains a challenge. We combined deep learning architectures with evolutionary computation to steer the protein generative process towards specific sets of properties to address this problem. The latent space of a Variational Autoencoder is explored by evolutionary algorithms to find the best candidates. A set of single-objective and multi-objective problems were conceived to evaluate the algorithms' capacity to optimise proteins. The optimisation tasks consider the average proteins' hydrophobicity, their solubility and the probability of being generated by a defined functional Hidden Markov Model profile. The results show that Evolutionary Algorithms can achieve good results while allowing for more variability in the design of the experiment, thus resulting in a much greater set of possibly functional novel proteins.