Interpreting Convolutional Neural Networks in Population Genetics

Abstract

Machine learning approaches have become a powerful alternative to traditional methods in population genetics. Convolutional neural networks (CNNs) in particular have been successful in inferring natural selection, recombination rates, introgression, dispersal distances, and effective population size changes. One limitation of CNNs and other deep learning methods is that they can be difficult to interpret. When they have been shown to be as or more successful than summary-statistic-based methods, what are they learning? Here we investigate CNNs from two different methods: the pg-gan discriminator for identifying real vs.∼simulated data, and two networks trained to detect selective sweeps. We first compute correlations between learned network features and traditional summary statistics, then assess whether summary statistics can be predicted from the learned features. To understand the learned features, we compute feature importance through SHAP values and feature groupings through dimensionality reduction. Finally we use decision trees and random forests to build an interpretable "model-of-the-model". Our results reveal that some CNN architectures can implicitly compute summary statistics such as pairwise heterozygosity, while statistics such as the site frequency spectrum are less similar to the network's learned features. We find that long-range linkage disequilibrium is readily approximated by the networks and may be more efficiently computed by CNNs than traditional methods (which are quadratic in the number of sites). Overall, this work contributes to the interpretability of deep learning methods in population genetics by clarifying the relationships between model architecture, learned network features, established summary statistics, and predicted evolutionary parameters.

The authors' abstract, as published at the source. Molecular Biology and Evolution, 2026 · DOI ↗