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In G3 (Bethesda, Md.)

Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here we explore the utility of variational autoencoders (VAEs)-generative machine learning models in which a pair of neural networks seek to first compress and then recreate the input data-for visualizing population genetic variation. VAEs incorporate nonlinear relationships, allow users to define the dimensionality of the latent space, and in our tests preserve global geometry better than t-SNE and UMAP. Our implementation, which we call popvae, is available as a command-line python program at The approach yields latent embeddings that capture subtle aspects of population structure in humans and Anopheles mosquitoes, and can generate artificial genotypes characteristic of a given sample or population.

Battey C J, Coffing Gabrielle C, Kern Andrew D


data visualization, deep learning, machine learning, neural network, pca, population genetics, population structure, variational autoencoder