Towards AI-designed genomes using a variational autoencoder

Abstract

Genomes encode elaborate networks of genes whose products must seamlessly interact to support living organisms. Humans capacity to understand these biological systems is limited by their sheer size and complexity. In this work, we develop a proof of concept framework for training a machine learning algorithm to model bacterial genome composition. To achieve this, we create simplified representations of genomes in the form of binary vectors that indicate the encoded genes, henceforth referred to as genome vectors. A denoising variational autoencoder was trained to accept corrupted genome vectors, in which most genes had been masked, and reconstruct the original. The resulting model, DeepGenomeVector, effectively captures complex dependencies in genomic networks, as evaluated by both qualitative and quantitative metrics. An in-depth functional analysis of a generated genome vector shows that its encoded pathways are interconnected, near complete, and ecologically cohesive. On the test set, where the models ability to reconstruct uncorrupted genome vectors was evaluated, AUC and F1 scores of 0.98 and 0.83, respectively, support the models strong performance. This work showcases the power of machine learning approaches for synthetic biology and highlights the possibility that AI agents may one day be able to design genomes that animate carbon-based cells.