Structure learning for zero-inflated counts with an application to single-cell RNA sequencing data

DOI10.1214/23-AOAS1732OpenAlexW3110219854MaRDI QIDQ6138580FDOQ6138580

Authors Thi Kim Hue Nguyen, Monica Chiogna, Davide Risso

Publication date 16 January 2024

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2011.12044

zbMATH Keywords

graphical modelsstructure learningzero-inflated countssingle-cell RNA-seq

Mathematics Subject Classification ID

Applications of statistics (62Pxx)

Abstract: The problem of estimating the structure of a graph from observed data is of growing interest in the context of high-throughput genomic data, and single-cell RNA sequencing in particular. These, however, are challenging applications, since the data consist of high-dimensional counts with high variance and over-abundance of zeros. Here, we present a general framework for learning the structure of a graph from single-cell RNA-seq data, based on the zero-inflated negative binomial distribution. We demonstrate with simulations that our approach is able to retrieve the structure of a graph in a variety of settings and we show the utility of the approach on real data.

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Cited in

(1)

• Core-elements for large-scale least squares estimation

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