On convolutional neural networks for selection inference: Revealing the effect of preprocessing on model learning and the capacity to discover novel patterns

DOI

10.1371/journal.pcbi.1010979

Document Type

Journal Article

Publication Date

11-1-2023

Publication Title

PLoS computational biology

Volume

19

Issue

11

First Page

e1010979

Abstract

A central challenge in population genetics is the detection of genomic footprints of selection. As machine learning tools including convolutional neural networks (CNNs) have become more sophisticated and applied more broadly, these provide a logical next step for increasing our power to learn and detect such patterns; indeed, CNNs trained on simulated genome sequences have recently been shown to be highly effective at this task. Unlike previous approaches, which rely upon human-crafted summary statistics, these methods are able to be applied directly to raw genomic data, allowing them to potentially learn new signatures that, if well-understood, could improve the current theory surrounding selective sweeps. Towards this end, we examine a representative CNN from the literature, paring it down to the minimal complexity needed to maintain comparable performance; this low-complexity CNN allows us to directly interpret the learned evolutionary signatures. We then validate these patterns in more complex models using metrics that evaluate feature importance. Our findings reveal that preprocessing steps, which determine how the population genetic data is presented to the model, play a central role in the learned prediction method. This results in models that mimic previously-defined summary statistics; in one case, the summary statistic itself achieves similarly high accuracy. For evolutionary processes that are less well understood than selective sweeps, we hope this provides an initial framework for using CNNs in ways that go beyond simply achieving high classification performance. Instead, we propose that CNNs might be useful as tools for learning novel patterns that can translate to easy-to-implement summary statistics available to a wider community of researchers.

Open Access

38011281 (pubmed); PMC10703409 (pmc); 10.1371/journal.pcbi.1010979 (doi); PCOMPBIOL-D-23-00312 (pii)

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