A Newℓ₀-Regularized Log-Linear Poisson Graphical Model with Applications to RNA Sequencing Data Article Swipe

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Caesar Z. Li , Eric S. Kawaguchi , Gang Li ·

YOU? · · 2021 · Open Access · · DOI: https://doi.org/10.1089/cmb.2020.0558

In this article, we develop a new ℓ ₀ -based sparse Poisson graphical model with applications to gene network inference from RNA-seq gene expression count data. Assuming a pair-wise Markov property, we propose to fit a separate broken adaptive ridge-regularized log-linear Poisson regression on each node to evaluate the conditional, instead of marginal, association between two genes in the presence of all other genes. The resulting sparse gene networks are generally more accurate than those generated by the ℓ ₁ -regularized Poisson graphical model as demonstrated by our empirical studies. A real data illustration is given on a kidney renal clear cell carcinoma micro-RNA-seq data from the Cancer Genome Atlas.

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Graphical model Poisson distribution Poisson regression Count data Inference Computer science Computational biology Node (physics) Markov chain Algorithm Mathematics Data mining Biology Statistics Artificial intelligence Machine learning Population Engineering Structural engineering Demography Sociology

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Type: article
Language: en
Landing Page: https://doi.org/10.1089/cmb.2020.0558
OA Status: green
Cited By: 1
References: 44
Related Works: 10
OpenAlex ID: https://openalex.org/W3189878693

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DOI: https://doi.org/10.1089/cmb.2020.0558

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Title: A Newℓ₀-Regularized Log-Linear Poisson Graphical Model with Applications to RNA Sequencing Data

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Language: en

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Publication year: 2021

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Publication date: 2021-08-10

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Authors: Caesar Z. Li, Eric S. Kawaguchi, Gang Li

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Landing page: https://doi.org/10.1089/cmb.2020.0558

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Concepts: Graphical model, Poisson distribution, Poisson regression, Count data, Inference, Computer science, Computational biology, Node (physics), Markov chain, Algorithm, Mathematics, Data mining, Biology, Statistics, Artificial intelligence, Machine learning, Population, Engineering, Structural engineering, Demography, Sociology

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A Newℓ0-Regularized Log-Linear Poisson Graphical Model with Applications to RNA Sequencing Data Article Swipe

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A Newℓ₀-Regularized Log-Linear Poisson Graphical Model with Applications to RNA Sequencing Data Article Swipe