Updated: January 2nd, 2024 14:02

2019 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

2019 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

2019 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

2018 journal article

Algorithms for Fitting the Constrained Lasso

*JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS*, *27*(4), 861–871.

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

2015 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

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

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

2014 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

2014 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

2014 journal article

Regularized matrix regression

*JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY*, *76*(2), 463–483.

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

2014 journal article

Rejoinder

*INTERNATIONAL STATISTICAL REVIEW*, *82*(1), 81–89.

Contributors: K. Lange ^{*}, E. Chi & ^{ n}

Sources: Web Of Science, ORCID

Added: August 6, 2018

2013 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

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

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

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 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

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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