Genomes

Positive natural selection leaves detectable, distinctive patterns in the genome in the form of a selective sweep. Identifying areas of the genome that have undergone selective sweeps is an area of high interest as it enables understanding of species and population evolution. Previous work has accomplished this by evaluating patterns within summary statistics computed across the genome and through application of machine learning techniques to raw population genomic data. When using raw population genomic data, convolutional neural networks have most recently been employed as they can handle large input arrays and maintain correlations among elements. Yet, such models often require massive amounts of training data and can be computationally expensive to train for a given problem. Instead, transfer learning has recently been used in the image analysis literature to improve machine learning models by learning the important features of images from large unrelated datasets beforehand, and then refining these models through subsequent application on smaller and more relevant datasets. We combine transfer learning with convolutional neural networks to improve classification of selective sweeps from raw population genomic data. We show that the combination of transfer learning with convolutional neural networks allows for accurate classification of selective sweeps.