A variational autoencoder (VAE) is used to learn a reduced representation of the SNP dataset by minimizing the difference between the input SNPs and the reconstructed SNPs.
Link to code on Google Colab: https://colab.research.google.com/github/sokrypton/sp_deli/blob/master/sp_deli_final.ipynb
The mean (μ) and standard deviation (σ) are used for plotting. The black circles indicate the μ. The transparent colors show the σ (100 sampled "Z" or latent variables for each organism). For the following animation, we show the change of μ and σ during optimization (1 frame per 10 epoches). Each color represents a different species.
For more info, see pre-print here: https://www.biorxiv.org/content/early/2018/09/28/429662