The unreasonable effectiveness of convolutional neural networks in population genetic inference

Lex Flagel, Yaniv Brandvain, Daniel R. Schrider

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

Population-scale genomic data sets have given researchers incredible amounts of information from which to infer evolutionary histories. Concomitant with this flood of data, theoretical and methodological advances have sought to extract information from genomic sequences to infer demographic events such as population size changes and gene flow among closely related populations/species, construct recombination maps, and uncover loci underlying recent adaptation. To date, most methods make use of only one or a few summaries of the input sequences and therefore ignore potentially useful information encoded in the data. The most sophisticated of these approaches involve likelihood calculations, which require theoretical advances for each new problem, and often focus on a single aspect of the data (e.g., only allele frequency information) in the interest of mathematical and computational tractability. Directly interrogating the entirety of the input sequence data in a likelihood-free manner would thus offer a fruitful alternative. Here, we accomplish this by representing DNA sequence alignments as images and using a class of deep learning methods called convolutional neural networks (CNNs) to make population genetic inferences from these images. We apply CNNs to a number of evolutionary questions and find that they frequently match or exceed the accuracy of current methods. Importantly, we show that CNNs perform accurate evolutionary model selection and parameter estimation, even on problems that have not received detailed theoretical treatments. Thus, when applied to population genetic alignments, CNNs are capable of outperforming expert-derived statistical methods and offer a new path forward in cases where no likelihood approach exists.

Original languageEnglish (US)
Pages (from-to)220-238
Number of pages19
JournalMolecular biology and evolution
Volume36
Issue number2
DOIs
StatePublished - Feb 1 2019

Bibliographical note

Funding Information:
We thank Matt Hahn for comments on the manuscript D.R.S. was funded by the National Institutes of Health under award number R00HG008696. Y.B. would like to acknowledge the Minnesota Supercomputing Institute for computational resources.

Funding Information:
We thank Matt Hahn for comments on the manuscript. D.R.S. was funded by the National Institutes of Health under award number R00HG008696. Y.B. would like to acknowledge the Minnesota Supercomputing Institute for computational resources.

Keywords

  • Demographic inference
  • Introgression
  • Machine learning
  • Population genetics
  • Recombination
  • Selective sweeps

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