Limit theorems for empirical Rényi entropy and divergence with applications to molecular diversity analysis

DOI10.1007/S11749-016-0489-ZMaRDI QIDQ2397985zbMATH OpenOpenAlexFDO

Authors Maciej Pietrzak, Michał T. Seweryn, Jacek Wesołowski, Grzegorz A. Rempala

Publication date 14 August 2017

Published in Test (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1505.03220

zbMATH Keywords

central limit theoremtriangular arraysnext-generation sequencingHill numberT-cell receptorsempirical Rényi entropy

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Problems related to evolution (92D15) Central limit and other weak theorems (60F05) Martingales with discrete parameter (60G42) Measures of information, entropy (94A17)

Abstract: Quantitative methods for studying biodiversity have been traditionally rooted in the classical theory of finite frequency tables analysis. However, with the help of modern experimental tools, like high throughput sequencing, we now begin to unlock the outstanding diversity of genomic data in plants and animals reflective of the long evolutionary history of our planet. This molecular data often defies the classical frequency/contingency tables assumptions and seems to require sparse tables with very large number of categories and highly unbalanced cell counts, e.g., following heavy tailed distributions (for instance, power laws). Motivated by the molecular diversity studies, we propose here a frequency-based framework for biodiversity analysis in the asymptotic regime where the number of categories grows with sample size (an infinite contingency table). Our approach is rooted in information theory and based on the Gaussian limit results for the effective number of species (the Hill numbers) and the empirical Renyi entropy and divergence. We argue that when applied to molecular biodiversity analysis our methods can properly account for the complicated data frequency patterns on one hand and the practical sample size limitations on the other. We illustrate this principle with two specific RNA sequencing examples: a comparative study of T-cell receptor populations and a validation of some preselected molecular hepatocellular carcinoma (HCC) markers.

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Cited in

(10)

• Entropy-based pivotal statistics for multi-sample problems in planar shape
• Mathematical bounds on Shannon entropy given the abundance of the \(i\)th most abundant taxon
• Rényi's divergence as a chemical similarity criterion
• The probabilities of large deviations for a certain class of statistics associated with multinomial distribution
• Defining diversity, specialization, and gene specificity in transcriptomes through information theory
• Poisson limit theorems for the Cressie-Read statistics
• The analysis of biodiversity using rank abundance distributions
• Methods for diversity and overlap analysis in T-cell receptor populations
• Double asymptotics for the chi-square statistic
• On the asymptotic properties of a certain class of goodness-of-fit tests associated with multinomial distributions

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