Nonbifurcating Phylogenetic Tree Inference via the Adaptive LASSO

DOI10.1080/01621459.2020.1778481zbMath1464.62480arXiv1805.11073OpenAlexW3035455049WikidataQ112651981 ScholiaQ112651981MaRDI QIDQ4999164

Vu Dinh, Cheng Zhang, Frederick A. IV Matsen

Publication date: 6 July 2021

Published in: Journal of the American Statistical Association (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1805.11073

zbMATH Keywords

consistencymodel selectionsparsityphylogeneticsadaptive Lasso\(\ell_1\) regularization

Mathematics Subject Classification ID

Ridge regression; shrinkage estimators (Lasso) (62J07) Applications of statistics to biology and medical sciences; meta analysis (62P10) Robustness and adaptive procedures (parametric inference) (62F35)

Uses Software

• MrBayes
• RAxML
• sparsenet
• Nextstrain
• PhyloGeoTool

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• The Adaptive Lasso and Its Oracle Properties
• A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems
• Support recovery without incoherence: a case for nonconvex regularization
• One-step sparse estimates in nonconcave penalized likelihood models
• Discussion: One-step sparse estimates in nonconcave penalized likelihood models
• The sparsity and bias of the LASSO selection in high-dimensional linear regression
• Lasso-type recovery of sparse representations for high-dimensional data
• Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
• Relaxed sparse eigenvalue conditions for sparse estimation via non-convex regularized regression
• Least angle regression. (With discussion)
• Statistical consistency and asymptotic normality for high-dimensional robust \(M\)-estimators
• A molecular sequence metric and evolutionary trees
• Adaptive restart for accelerated gradient schemes
• Invariants of some probability models used in phylogenetic inference
• Simultaneous analysis of Lasso and Dantzig selector
• Consistency and convergence rate of phylogenetic inference via regularization
• Calibrating nonconvex penalized regression in ultra-high dimension
• Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites
• High-dimensional graphs and variable selection with the Lasso
• Strong oracle optimality of folded concave penalized estimation
• Variable selection using MM algorithms
• SparseNet: Coordinate Descent With Nonconvex Penalties
• A Global Lojasiewicz Inequality for Algebraic Varieties
• Variable Selection via Nonconcave Penalized Likelihood and its Oracle Properties
• Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
• Smoothly Clipped Absolute Deviation on High Dimensions
• Signal Recovery by Proximal Forward-Backward Splitting
• A unified framework for high-dimensional analysis of \(M\)-estimators with decomposable regularizers
• A general theory of concave regularization for high-dimensional sparse estimation problems

This page was built for publication: Nonbifurcating Phylogenetic Tree Inference via the Adaptive LASSO