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Journal of the American Statistical Association

Jeffrey W Miller, Matthew T Harrison
A natural Bayesian approach for mixture models with an unknown number of components is to take the usual finite mixture model with symmetric Dirichlet weights, and put a prior on the number of components-that is, to use a mixture of finite mixtures (MFM). The most commonly-used method of inference for MFMs is reversible jump Markov chain Monte Carlo, but it can be nontrivial to design good reversible jump moves, especially in high-dimensional spaces. Meanwhile, there are samplers for Dirichlet process mixture (DPM) models that are relatively simple and are easily adapted to new applications...
2018: Journal of the American Statistical Association
Quefeng Li, Guang Cheng, Jianqing Fan, Yuyan Wang
Factor modeling is an essential tool for exploring intrinsic dependence structures among high-dimensional random variables. Much progress has been made for estimating the covariance matrix from a high-dimensional factor model. However, the blessing of dimensionality has not yet been fully embraced in the literature: much of the available data are often ignored in constructing covariance matrix estimates. If our goal is to accurately estimate a covariance matrix of a set of targeted variables, shall we employ additional data, which are beyond the variables of interest, in the estimation? In this article, we provide sufficient conditions for an affirmative answer, and further quantify its gain in terms of Fisher information and convergence rate...
2018: Journal of the American Statistical Association
Yin Xia, Tianxi Cai, T Tony Cai
Making accurate inference for gene regulatory networks, including inferring about pathway by pathway interactions, is an important and difficult task. Motivated by such genomic applications, we consider multiple testing for conditional dependence between subgroups of variables. Under a Gaussian graphical model framework, the problem is translated into simultaneous testing for a collection of submatrices of a high-dimensional precision matrix with each submatrix summarizing the dependence structure between two subgroups of variables...
2018: Journal of the American Statistical Association
David Rossell, Donatello Telesca
Jointly achieving parsimony and good predictive power in high dimensions is a main challenge in statistics. Non-local priors (NLPs) possess appealing properties for model choice, but their use for estimation has not been studied in detail. We show that for regular models NLP-based Bayesian model averaging (BMA) shrink spurious parameters either at fast polynomial or quasi-exponential rates as the sample size n increases, while non-spurious parameter estimates are not shrunk. We extend some results to linear models with dimension p growing with n ...
2017: Journal of the American Statistical Association
Valen E Johnson, Richard D Payne, Tianying Wang, Alex Asher, Soutrik Mandal
Investigators from a large consortium of scientists recently performed a multi-year study in which they replicated 100 psychology experiments. Although statistically significant results were reported in 97% of the original studies, statistical significance was achieved in only 36% of the replicated studies. This article presents a reanalysis of these data based on a formal statistical model that accounts for publication bias by treating outcomes from unpublished studies as missing data, while simultaneously estimating the distribution of effect sizes for those studies that tested nonnull effects...
2017: Journal of the American Statistical Association
Zihuai He, Min Zhang, Seunggeun Lee, Jennifer A Smith, Sharon L R Kardia, Ana V Diez Roux, Bhramar Mukherjee
We propose a generalized score type test for set-based inference for gene-environment interaction with longitudinally measured quantitative traits. The test is robust to misspecification of within subject correlation structure and has enhanced power compared to existing alternatives. Unlike tests for marginal genetic association, set-based tests for gene-environment interaction face the challenges of a potentially misspecified and high-dimensional main effect model under the null hypothesis. We show that our proposed test is robust to main effect misspecification of environmental exposure and genetic factors under the gene-environment independence condition...
2017: Journal of the American Statistical Association
Yifei Sun, Chiung-Yu Huang, Mei-Cheng Wang
Benefit-risk assessment is a crucial step in medical decision process. In many biomedical studies, both longitudinal marker measurements and time to a terminal event serve as important endpoints for benefit-risk assessment. The effect of an intervention or a treatment on the longitudinal marker process, however, can be in conflict with its effect on the time to the terminal event. Thus, questions arise on how to evaluate treatment effects based on the two endpoints, for the purpose of deciding on which treatment is most likely to benefit the patients...
2017: Journal of the American Statistical Association
Kyle R White, Leonard A Stefanski, Yichao Wu
This paper develops a nonparametric shrinkage and selection estimator via the measurement error selection likelihood approach recently proposed by Stefanski, Wu, and White. The Measurement Error Kernel Regression Operator (MEKRO) has the same form as the Nadaraya-Watson kernel estimator, but optimizes a measurement error model selection likelihood to estimate the kernel bandwidths. Much like LASSO or COSSO solution paths, MEKRO results in solution paths depending on a tuning parameter that controls shrinkage and selection via a bound on the harmonic mean of the pseudo-measurement error standard deviations...
2017: Journal of the American Statistical Association
Shizhe Chen, Ali Shojaie, Daniela M Witten
We consider the task of learning a dynamical system from high-dimensional time-course data. For instance, we might wish to estimate a gene regulatory network from gene expression data measured at discrete time points. We model the dynamical system nonparametrically as a system of additive ordinary differential equations. Most existing methods for parameter estimation in ordinary differential equations estimate the derivatives from noisy observations. This is known to be challenging and inefficient. We propose a novel approach that does not involve derivative estimation...
2017: Journal of the American Statistical Association
Yacine Aït-Sahalia, Jianqing Fan, Roger J A Laeven, Christina Dan Wang, Xiye Yang
This paper examines the leverage effect, or the generally negative covariation between asset returns and their changes in volatility, under a general setup that allows the log-price and volatility processes to be Itô semimartingales. We decompose the leverage effect into continuous and discontinuous parts and develop statistical methods to estimate them. We establish the asymptotic properties of these estimators. We also extend our methods and results (for the continuous leverage) to the situation where there is market microstructure noise in the observed returns...
2017: Journal of the American Statistical Association
Shujie Ma, Yanyuan Ma, Yanqing Wang, Eli S Kravitz, Raymond J Carroll
We consider a problem motivated by issues in nutritional epidemiology, across diseases and populations. In this area, it is becoming increasingly common for diseases to be modeled by a single diet score, such as the Healthy Eating Index, the Mediterranean Diet Score, etc. For each disease and for each population, a partially linear single-index model is fit. The partially linear aspect of the problem is allowed to differ in each population and disease. However, and crucially, the single-index itself, having to do with the diet score, is common to all diseases and populations, and the nonparametrically estimated functions of the single-index are the same up to a scale parameter...
2017: Journal of the American Statistical Association
Ran Tao, Donglin Zeng, Dan-Yu Lin
In modern epidemiological and clinical studies, the covariates of interest may involve genome sequencing, biomarker assay, or medical imaging and thus are prohibitively expensive to measure on a large number of subjects. A cost-effective solution is the two-phase design, under which the outcome and inexpensive covariates are observed for all subjects during the first phase and that information is used to select subjects for measurements of expensive covariates during the second phase. For example, subjects with extreme values of quantitative traits were selected for whole-exome sequencing in the National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP)...
2017: Journal of the American Statistical Association
Philip T Reiss, Jeff Goldsmith
No abstract text is available yet for this article.
2017: Journal of the American Statistical Association
Michalis K Titsias, Christopher Yau
We introduce the Hamming ball sampler, a novel Markov chain Monte Carlo algorithm, for efficient inference in statistical models involving high-dimensional discrete state spaces. The sampling scheme uses an auxiliary variable construction that adaptively truncates the model space allowing iterative exploration of the full model space. The approach generalizes conventional Gibbs sampling schemes for discrete spaces and provides an intuitive means for user-controlled balance between statistical efficiency and computational tractability...
2017: Journal of the American Statistical Association
Boyu Ren, Sergio Bacallado, Stefano Favaro, Susan Holmes, Lorenzo Trippa
Human microbiome studies use sequencing technologies to measure the abundance of bacterial species or Operational Taxonomic Units (OTUs) in samples of biological material. Typically the data are organized in contingency tables with OTU counts across heterogeneous biological samples. In the microbial ecology community, ordination methods are frequently used to investigate latent factors or clusters that capture and describe variations of OTU counts across biological samples. It remains important to evaluate how uncertainty in estimates of each biological sample's microbial distribution propagates to ordination analyses, including visualization of clusters and projections of biological samples on low dimensional spaces...
2017: Journal of the American Statistical Association
Robert T Krafty, Ori Rosen, David S Stoffer, Daniel J Buysse, Martica H Hall
This article considers the problem of analyzing associations between power spectra of multiple time series and cross-sectional outcomes when data are observed from multiple subjects. The motivating application comes from sleep medicine, where researchers are able to non-invasively record physiological time series signals during sleep. The frequency patterns of these signals, which can be quantified through the power spectrum, contain interpretable information about biological processes. An important problem in sleep research is drawing connections between power spectra of time series signals and clinical characteristics; these connections are key to understanding biological pathways through which sleep affects, and can be treated to improve, health...
2017: Journal of the American Statistical Association
Yijian Huang
Dynamic regression models, including the quantile regression model and Aalen's additive hazards model, are widely adopted to investigate evolving covariate effects. Yet lack of monotonicity respecting with standard estimation procedures remains an outstanding issue. Advances have recently been made, but none provides a complete resolution. In this article, we propose a novel adaptive interpolation method to restore monotonicity respecting, by successively identifying and then interpolating nearest monotonicity-respecting points of an original estimator...
2017: Journal of the American Statistical Association
Xinyu Zhang, Haiying Wang, Yanyuan Ma, Raymond J Carroll
Prediction precision is arguably the most relevant criterion of a model in practice and is often a sought after property. A common difficulty with covariates measured with errors is the impossibility of performing prediction evaluation on the data even if a model is completely given without any unknown parameters. We bypass this inherent difficulty by using special properties on moment relations in linear regression models with measurement errors. The end product is a model selection procedure that achieves the same optimality properties that are achieved in classical linear regression models without covariate measurement error...
2017: Journal of the American Statistical Association
Chuan Hong, Yong Chen, Yang Ning, Shuang Wang, Hao Wu, Raymond J Carroll
Motivated by analyses of DNA methylation data, we propose a semiparametric mixture model, namely the generalized exponential tilt mixture model, to account for heterogeneity between differentially methylated and non-differentially methylated subjects in the cancer group, and capture the differences in higher order moments (e.g. mean and variance) between subjects in cancer and normal groups. A pairwise pseudolikelihood is constructed to eliminate the unknown nuisance function. To circumvent boundary and non-identifiability problems as in parametric mixture models, we modify the pseudolikelihood by adding a penalty function...
2017: Journal of the American Statistical Association
Sihai Dave Zhao, T Tony Cai, Thomas P Cappola, Kenneth B Margulies, Hongzhe Li
Genome-wide association studies (GWAS) and differential expression analyses have had limited success in finding genes that cause complex diseases such as heart failure (HF), a leading cause of death in the United States. This paper proposes a new statistical approach that integrates GWAS and expression quantitative trait loci (eQTL) data to identify important HF genes. For such genes, genetic variations that perturb its expression are also likely to influence disease risk. The proposed method thus tests for the presence of simultaneous signals: SNPs that are associated with the gene's expression as well as with disease...
2017: Journal of the American Statistical Association
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