Works (25)
Updated: January 2nd, 2024 14:02
2018 journal article
Algorithms for Fitting the Constrained Lasso
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS, 27(4), 861–871.
TL;DR:
This work employs the alternating direction method of multipliers (ADMM) and also derive an efficient solution path algorithm for solving the constrained lasso problem, and shows that, for an arbitrary penalty matrix, the generalized lasso can be transformed to a constrainedLasso, while the converse is not true.
(via Semantic Scholar)
open access via arxiv.org (repository)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: NC State University Libraries
Added: December 31, 2018
2018 journal article
MM ALGORITHMS FOR VARIANCE COMPONENT ESTIMATION AND SELECTION IN LOGISTIC LINEAR MIXED MODEL
STATISTICA SINICA, 29(3), 1585–1605.
author keywords: Generalized linear mixed model (GLMM); Laplace approximation; MM algorithm; variance components selection
TL;DR:
Two efficient and stable minorization-maximization algorithms for estimating variance components based on a Laplace approximation of the logistic model and a simple iterative soft-thresholding algorithm for variance component selection using the maximum penalized approximated likelihood.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 29, 2019
2018 journal article
MM Algorithms for Variance Components Models
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS, 28(2), 350–361.
author keywords: Global convergence; Linear mixed model (LMM); Matrix convexity; Maximum a posteriori (MAP) estimation; Minorization-maximization (MM); Multivariate response; Penalized estimation; Variance components model
TL;DR:
The global convergence of the MM algorithm to a Karush–Kuhn–Tucker point is established and it is demonstrated that it converges faster than the classical EM algorithm when the number of variance components is greater than two and all covariance matrices are positive definite.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 15, 2019
2018 journal article
TENSOR GENERALIZED ESTIMATING EQUATIONS FOR LONGITUDINAL IMAGING ANALYSIS
STATISTICA SINICA, 29(4), 1977–2005.
author keywords: Generalized estimating equations; longitudinal imaging; low rank tensor decomposition; magnetic resonance imaging; multidimensional array; tensor regression
TL;DR:
The proposed GEE approach accounts for intra-subject correlation, and an imposed low-rank structure on the coefficient tensor effectively reduces the dimensionality in several tensor generalized estimating equations (GEEs).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: September 30, 2019
2015 journal article
IsoDOT Detects Differential RNA-Isoform Expression/Usage With Respect to a Categorical or Continuous Covariate With High Sensitivity and Specificity
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 110(511), 975–986.
author keywords: Differential isoform expression; Differential isoform usage; Isoform; Penalized regression; RNA-seq
TL;DR:
A statistical method named IsoDOT is developed to assess differential isoform expression (DIE) and differentialisoform usage (DIU) using RNA-seq data and identifies a group of genes whose isoform usages respond to haloperidol treatment.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Path following in the exact penalty method of convex programming
COMPUTATIONAL OPTIMIZATION AND APPLICATIONS, 61(3), 609–634.
author keywords: Constrained convex optimization; Exact penalty; Geometric programming; Ordinary differential equation; Quadratically constrained quadratic programming; Regularization; Semidefinite programming
TL;DR:
Instead of performing optimization at a single penalty constant, the solution is traced as a continuous function of the penalty constant and path following starts at the unconstrained solution and follows the solution path as the penalty Constant increases.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test
AMERICAN JOURNAL OF HUMAN GENETICS, 96(5), 797–807.
MeSH headings : Computer Simulation; Genetics, Population; High-Throughput Nucleotide Sequencing; Humans; Microbiota / genetics; Models, Statistical; Phylogeny; Polymorphism, Single Nucleotide; Software
TL;DR:
The microbiome regression-based kernel association test (MiRKAT), which directly regresses the outcome on the microbiome profiles via the semi-parametric kernel machine regression framework, is proposed and applied to real microbiome datasets to show that microbial communities are associated with smoking and with fecal protease levels after confounders are controlled for.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
A Brief Survey of Modern Optimization for Statisticians
INTERNATIONAL STATISTICAL REVIEW, 82(1), 46–70.
author keywords: acceleration; augmented Lagrangian; penalization; MM algorithm; Newton's method; Block relaxation
TL;DR:
This broad survey stresses a few important principles in algorithm design, and suggests that it is more productive to mix and match them than view these principles in isolation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2014 journal article
ConvexLAR: An Extension of Least Angle Regression
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS, 24(3), 603–626.
author keywords: Solution path; Group lasso; Regularization; Ordinary differential equation (ODE); Lasso
TL;DR:
This article proposes a ConvexLAR algorithm that works for any convex loss function and naturally extends to group selection and data adaptive variable selection and yields new exact path algorithms for certain penalty methods such as a conveX loss function with lasso or group lasso penalty.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
A Generic Path Algorithm for Regularized Statistical Estimation
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 109(506), 686–699.
author keywords: Gaussian graphical model; Generalized linear model; Lasso; Log-concave density estimation; Ordinary differential equations; Quasi-likelihoods; Regularization; Shape restricted regression; Solution path
TL;DR:
This article proposes an exact path solver based on ordinary differential equations (EPSODE) that works for any convex loss function and can deal with generalized ℓ1 penalties as well as more complicated regularization such as inequality constraints encountered in shape-restricted regressions and nonparametric density estimation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2013 journal article
Distance majorization and its applications
MATHEMATICAL PROGRAMMING, 146(1-2), 409–436.
author keywords: Constrained optimization; Majorization-minimization (MM); Sequential unconstrained minimization; Projection
TL;DR:
This proposal is an instance of a sequential unconstrained minimization technique and revolves around three ideas: the majorization-minimization principle, the classical penalty method for constrained optimization, and quasi-Newton acceleration of fixed-point algorithms.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
Mendel: the Swiss army knife of genetic analysis programs
BIOINFORMATICS, 29(12), 1568–1570.
MeSH headings : Chromosome Mapping / methods; Data Interpretation, Statistical; Genetic Linkage; Genome-Wide Association Study; Humans; Pedigree; Software
TL;DR:
UNLABELLED Mendel is one of the few statistical genetics packages that provide a full spectrum of gene mapping methods, ranging from parametric linkage in large pedigrees to genome-wide association with rare variants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2013 journal article
Regularized matrix regression
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 76(2), 463–483.
TL;DR:
A class of regularized matrix regression methods based on spectral regularization is proposed, and a degrees‐of‐freedom formula is derived to facilitate model selection along the regularization path.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2013 journal article
Tensor Regression with Applications in Neuroimaging Data Analysis
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 108(502), 540–552.
author keywords: Brain imaging; Dimension reduction; Generalized linear model; Magnetic Resonance Imaging; Multidimensional array; Tensor regression
TL;DR:
A new family of Tensor regression models that efficiently exploit the special structure of tensor covariates are proposed and ultrahigh dimensionality is reduced to a manageable level, resulting in efficient estimation and prediction.
(via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018
2012 journal article
Determining duration of HER2-targeted therapy using stem cell extinction models
PLoS One, 7(12).
Source: NC State University Libraries
Added: August 6, 2018
2012 journal article
EM vs MM: A case study
COMPUTATIONAL STATISTICS & DATA ANALYSIS, 56(12), 3909–3920.
author keywords: Convergence rate; Dirichlet-multinomial distribution; EM algorithm; MM algorithm
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2012 conference paper
Fast genome-wide QTL association mapping with pedigrees
Genetic Epidemiology, 36(7), 771–772.
Source: NC State University Libraries
Added: August 6, 2018
2012 journal article
Genotype imputation via matrix completion
GENOME RESEARCH, 23(3), 509–518.
MeSH headings : Algorithms; Artificial Intelligence; Computer Simulation; Genome, Human; Genotype; HapMap Project; Humans; Microarray Analysis; Models, Genetic; Polymorphism, Single Nucleotide; Software
TL;DR:
Compared with leading imputation programs, the matrix completion algorithm embodied in the program MENDEL-IMPUTE achieves comparable imputation accuracy while reducing run times significantly.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2012 journal article
MM algorithms for geometric and signomial programming
MATHEMATICAL PROGRAMMING, 143(1-2), 339–356.
author keywords: Arithmetic-geometric mean inequality; Geometric programming; Global convergence; MM algorithm; Linearly constrained quadratic programming; Parameter separation; Penalty method; Signomial programming
TL;DR:
New algorithms for signomial programming, a generalization of geometric programming, are derived based on a generic principle for optimization called the MM algorithm, which can converge to a boundary point or to one point of a continuum of minimum points.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2012 article
Nonlinear dimension reduction with Wright-Fisher kernel for genotype aggregation and association mapping
Zhu, H., Li, L., & Zhou, H. (2012, September 15). BIOINFORMATICS, Vol. 28, pp. I375–I381.
MeSH headings : Algorithms; Genetic Association Studies; Genotype; High-Throughput Nucleotide Sequencing; Humans; Markov Chains; Polymorphism, Single Nucleotide
TL;DR:
This work proposes a joint association test strategy based on a nonlinear supervised dimension reduction approach for effective SNP information aggregation and a novel kernel specially designed for qualitative genotype data that demonstrates superior performance in identifying causal genes over existing methods across a large variety of disease models simulated from sequence data of real genes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2012 journal article
Path Algorithm for Constrained Estimation
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS, 22(2), 261–283.
author keywords: Exact penalty; l(1) regularization; Shape-restricted regression
TL;DR:
A new path-following algorithm for quadratic programming that replaces hard constraints by what are called exact penalties is proposed, which can be framed entirely in terms of the sweep operator of regression analysis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2011 journal article
Extinction models for cancer stem cell therapy
MATHEMATICAL BIOSCIENCES, 234(2), 132–146.
author keywords: Birth-death process; Cancer; Stem cells; Extinction probability; Finite Fourier transform; Stochastic simulation
MeSH headings : Cell Death / drug effects; Computer Simulation; Humans; Markov Chains; Models, Biological; Neoplasms / drug therapy; Neoplasms / pathology; Neoplastic Stem Cells / drug effects; Neoplastic Stem Cells / pathology; Stochastic Processes
TL;DR:
Borders are set on the killing differential (difference between death rates of cancer stem cells and normal stem cells) that must exist for the survival of an adequate number of normalstem cells and the impact of quiescence (the resting state) on stem cell dynamics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2010 journal article
Association screening of common and rare genetic variants by penalized regression
BIOINFORMATICS, 26(19), 2375–2382.
MeSH headings : Breast Neoplasms / genetics; Databases, Factual; Female; Genetic Predisposition to Disease; Genetic Variation; Genome-Wide Association Study / methods; Humans; Regression Analysis
TL;DR:
The latest research on penalized estimation methods in genome-wide association studies to the realm of rare variants and findings on breast cancer data replicate previous results and shed light on variant effects within genes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2010 journal article
Graphics Processing Units and High-Dimensional Optimization
STATISTICAL SCIENCE, 25(3), 311–324.
author keywords: Block relaxation; EM and MM algorithms; multidimensional scaling; nonnegative matrix factorization; parallel computing; PET scanning
TL;DR:
The utility of GPUs in nonnegative matrix factorization, PET image reconstruction, and multidimensional scaling is demonstrated and it is demonstrated that speedups of 100 fold can easily be attained.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
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