LAI-Net: Local-Ancestry Inference with Neural Networks

Local-ancestry inference (LAI), also referred to as ancestry deconvolution, provides high-resolution ancestry estimation along the human genome. In both research and industry, LAI is emerging as a critical step in DNA sequence analysis with applications extending from polygenic risk scores (used to predict traits in embryos and disease risk in adults) to genome-wide association studies, and from pharmacogenomics to inference of human population history. While many LAI methods have been developed, advances in computing hardware (GPUs) combined with machine learning techniques, such as neural networks, are enabling the development of new methods that are fast, robust and easily shared and stored. In this paper we develop the first neural network based LAI method, named LAI-Net, providing competitive accuracy with state-of-the-art methods and robustness to missing or noisy data, while having a small number of layers.