Adaptive basis selection for exponential family smoothing splines with application in joint modeling of multiple sequencing samples

DOI10.5705/SS.202015.0423zbMATH Open1392.62324arXiv1702.01875OpenAlexW2963899355WikidataQ115479369 ScholiaQ115479369MaRDI QIDQ4601252FDOQ4601252

Authors: Ping Ma, Nan Zhang, Jianhua Z. Huang, Wenxuan Zhong 

Publication date: 12 January 2018

Published in: STATISTICA SINICA (Search for Journal in Brave)

Abstract: Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments in parallel. After the resulting sequences (short reads) are mapped to the genome, one gets a sequence of short read counts along the genome. Effective extraction of signals in these short read counts is the key to the success of sequencing technologies. Nonparametric methods, in particular smoothing splines, have been used extensively for modeling and processing single sequencing samples. However, nonparametric joint modeling of multiple second-generation sequencing samples is still lacking due to computational cost. In this article, we develop an adaptive basis selection method for efficient computation of exponential family smoothing splines for modeling multiple second-generation sequencing samples. Our adaptive basis selection gives a sparse approximation of smoothing splines, yielding a lower-dimensional effective model space for a more scalable computation. The asymptotic analysis shows that the effective model space is rich enough to retain essential features of the data. Moreover, exponential family smoothing spline models computed via adaptive basis selection are shown to have good statistical properties, e.g., convergence at the same rate as that of full basis exponential family smoothing splines. The empirical performance is demonstrated through simulation studies and two second-generation sequencing data examples.

Full work available at URL: https://arxiv.org/abs/1702.01875

Recommendations

• Bayesian adaptive smoothing splines using stochastic differential equations
• More efficient approximation of smoothing splines via space-filling basis selection
• Efficient computation of smoothing splines via adaptive basis sampling
• Component selection and smoothing for nonparametric regression in exponential families
• Adaptive empirical Bayesian smoothing splines

zbMATH Keywords

samplinggeneralized linear modelnonparametric regressionpenalized likelihoodRNA-seqbisulfite sequencing

Mathematics Subject Classification ID

Nonparametric regression and quantile regression (62G08) Applications of statistics to biology and medical sciences; meta analysis (62P10) Generalized linear models (logistic models) (62J12)

Cited In (4)

• Bayesian functional data analysis over dependent regions and its application for identification of differentially methylated regions
• Model-based quality assessment and base-calling for second-generation sequencing data
• Dynamical modeling for non-Gaussian data with high-dimensional sparse ordinary differential equations
• Smoothing Splines Approximation Using Hilbert Curve Basis Selection

This page was built for publication: Adaptive basis selection for exponential family smoothing splines with application in joint modeling of multiple sequencing samples

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q4601252)