On latent idealized models in symbolic datasets: unveiling signals in noisy sequencing data

DOI10.1007/S00285-023-01961-1MaRDI QIDQ6116337zbMATH OpenOpenAlexFDO

Authors A. Pearson, Manuel E. Lladser

Publication date 18 July 2023

Published in Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2002.05592

zbMATH Keywords

DNA methylationexchangeabilitysymbolic dataomicscategorical datacontaminationsequencing errors

Mathematics Subject Classification ID

Nonparametric hypothesis testing (62G10) Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Mathematical modeling or simulation for problems pertaining to biology (92-10) Computational methods for problems pertaining to biology (92-08) Research data for problems pertaining to biology (92-11)

Abstract: Data taking values on discrete sample spaces are the embodiment of modern biological research. "Omics" experiments produce millions of symbolic outcomes in the form of reads (i.e., DNA sequences of a few dozens to a few hundred nucleotides). Unfortunately, these intrinsically non-numerical datasets are often highly contaminated, and the possible sources of contamination are usually poorly characterized. This contrasts with numerical datasets where Gaussian-type noise is often well-justified. To overcome this hurdle, we introduce the notion of latent weight, which measures the largest expected fraction of samples from a contaminated probabilistic source that conform to a model in a well-structured class of desired models. We examine various properties of latent weights, which we specialize to the class of exchangeable probability distributions. As proof of concept, we analyze DNA methylation data from the 22 human autosome pairs. Contrary to what it is usually assumed, we provide strong evidence that highly specific methylation patterns are overrepresented at some genomic locations when contamination is taken into account.

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