On the Fourier transform of a quantitative trait: implications for compressive sensing

DOI10.1016/J.JTBI.2021.110985zbMATH Open1489.92105arXiv2101.01234OpenAlexW3189454515WikidataQ113869619 ScholiaQ113869619MaRDI QIDQ2137407FDOQ2137407

Authors: Stephen Doro, Matthew A. Herman 

Publication date: 16 May 2022

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: This paper explores the genotype-phenotype relationship. It outlines conditions under which the dependence of a quantitative trait on the genome might be predictable, based on measurement of a limited subset of genotypes. It uses the theory of real-valued Boolean functions in a systematic way to translate trait data into the Fourier domain. Important trait features, such as the roughness of the trait landscape or the modularity of a trait have a simple Fourier interpretation. Ruggedness at a gene location corresponds to high sensitivity to mutation, while a modular organization of gene activity reduces such sensitivity. Traits where rugged loci are rare will naturally compress gene data in the Fourier domain, leading to a sparse representation of trait data, concentrated in identifiable, low-level coefficients. This Fourier representation of a trait organizes epistasis in a form which is isometric to the trait data. As Fourier matrices are known to be maximally incoherent with the standard basis, this permits employing compressive sensing techniques to work from data sets that are relatively small -- sometimes even of polynomial size -- compared to the exponentially large sets of possible genomes. This theory provides a theoretical underpinning for systematic use of Boolean function machinery to dissect the dependency of a trait on the genome and environment.

Full work available at URL: https://arxiv.org/abs/2101.01234

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zbMATH Keywords

Fourier transformcomputational biologygenomicshypergraphsBoolean functionsquantitative traits

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Systems biology, networks (92C42) Fourier and Fourier-Stieltjes transforms and other transforms of Fourier type (42A38) Boolean functions (06E30)

Cites Work

• Statistical mechanics of complex networks
• Near-Optimal Signal Recovery From Random Projections: Universal Encoding Strategies?
• Spectral redemption in clustering sparse networks
• Stable signal recovery from incomplete and inaccurate measurements
• Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information
• The book of why. The new science of cause and effect
• Compressed sensing
• A Probabilistic and RIPless Theory of Compressed Sensing
• Sparsity and incoherence in compressive sampling
• Title not available (Why is that?)
• Analysis of Boolean Functions
• Hadamard matrices and their applications
• Constant depth circuits, Fourier transform, and learnability
• Quantitative analyses of empirical fitness landscapes
• Title not available (Why is that?)
• Fourier and Taylor series on fitness landscapes
• Evolvability and robustness: a paradox restored

Cited In (3)

• Approximate location of relevant variables under the crossover distribution.
• Analysis of phenotype-genotype associations using genomic informational field theory (GIFT)
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Uses Software

• FASTA

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