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Journal of the American Statistical Association

Nilanjan Chatterjee, Yi-Hau Chen, Paige Maas, Raymond J Carroll
Information from various public and private data sources of extremely large sample sizes are now increasingly available for research purposes. Statistical methods are needed for utilizing information from such big data sources while analyzing data from individual studies that may collect more detailed information required for addressing specific hypotheses of interest. In this article, we consider the problem of building regression models based on individual-level data from an "internal" study while utilizing summary-level information, such as information on parameters for reduced models, from an "external" big data source...
March 2016: Journal of the American Statistical Association
Mengjie Chen, Zhao Ren, Hongyu Zhao, Harrison Zhou
A tuning-free procedure is proposed to estimate the covariate-adjusted Gaussian graphical model. For each finite subgraph, this estimator is asymptotically normal and efficient. As a consequence, a confidence interval can be obtained for each edge. The procedure enjoys easy implementation and efficient computation through parallel estimation on subgraphs or edges. We further apply the asymptotic normality result to perform support recovery through edge-wise adaptive thresholding. This support recovery procedure is called ANTAC, standing for Asymptotically Normal estimation with Thresholding after Adjusting Covariates...
March 2016: Journal of the American Statistical Association
Michalis K Titsias, Christopher C Holmes, Christopher Yau
Hidden Markov models (HMMs) are one of the most widely used statistical methods for analyzing sequence data. However, the reporting of output from HMMs has largely been restricted to the presentation of the most-probable (MAP) hidden state sequence, found via the Viterbi algorithm, or the sequence of most probable marginals using the forward-backward algorithm. In this article, we expand the amount of information we could obtain from the posterior distribution of an HMM by introducing linear-time dynamic programming recursions that, conditional on a user-specified constraint in the number of segments, allow us to (i) find MAP sequences, (ii) compute posterior probabilities, and (iii) simulate sample paths...
January 2, 2016: Journal of the American Statistical Association
Ci-Ren Jiang, John A D Aston, Jane-Ling Wang
Positron emission tomography (PET) is an imaging technique which can be used to investigate chemical changes in human biological processes such as cancer development or neurochemical reactions. Most dynamic PET scans are currently analyzed based on the assumption that linear first-order kinetics can be used to adequately describe the system under observation. However, there has recently been strong evidence that this is not the case. To provide an analysis of PET data which is free from this compartmental assumption, we propose a nonparametric deconvolution and analysis model for dynamic PET data based on functional principal component analysis...
January 2, 2016: Journal of the American Statistical Association
Yize Zhao, Matthias Chung, Brent A Johnson, Carlos S Moreno, Qi Long
Our work is motivated by a prostate cancer study aimed at identifying mRNA and miRNA biomarkers that are predictive of cancer recurrence after prostatectomy. It has been shown in the literature that incorporating known biological information on pathway memberships and interactions among biomarkers improves feature selection of high-dimensional biomarkers in relation to disease risk. Biological information is often represented by graphs or networks, in which biomarkers are represented by nodes and interactions among them are represented by edges; however, biological information is often not fully known...
2016: Journal of the American Statistical Association
Fernando A Quintana, Wesley O Johnson, Elaine Waetjen, Ellen Gold
Practical Bayesian nonparametric methods have been developed across a wide variety of contexts. Here, we develop a novel statistical model that generalizes standard mixed models for longitudinal data that include flexible mean functions as well as combined compound symmetry (CS) and autoregressive (AR) covariance structures. AR structure is often specified through the use of a Gaussian process (GP) with covariance functions that allow longitudinal data to be more correlated if they are observed closer in time than if they are observed farther apart...
2016: Journal of the American Statistical Association
Emre Barut, Jianqing Fan, Anneleen Verhasselt
Independence screening is powerful for variable selection when the number of variables is massive. Commonly used independence screening methods are based on marginal correlations or its variants. When some prior knowledge on a certain important set of variables is available, a natural assessment on the relative importance of the other predictors is their conditional contributions to the response given the known set of variables. This results in conditional sure independence screening (CSIS). CSIS produces a rich family of alternative screening methods by different choices of the conditioning set and can help reduce the number of false positive and false negative selections when covariates are highly correlated...
2016: Journal of the American Statistical Association
Ritabrata Das, Moulinath Banerjee, Bin Nan, Huiyong Zheng
Estimation of change-point locations in the broken-stick model has significant applications in modeling important biological phenomena. In this article we present a computationally economical likelihood-based approach for estimating change-point(s) efficiently in both cross-sectional and longitudinal settings. Our method, based on local smoothing in a shrinking neighborhood of each change-point, is shown via simulations to be computationally more viable than existing methods that rely on search procedures, with dramatic gains in the multiple change-point case...
2016: Journal of the American Statistical Association
Kyu Ha Lee, Francesca Dominici, Deborah Schrag, Sebastien Haneuse
Readmission following discharge from an initial hospitalization is a key marker of quality of health care in the United States. For the most part, readmission has been studied among patients with 'acute' health conditions, such as pneumonia and heart failure, with analyses based on a logistic-Normal generalized linear mixed model (Normand et al., 1997). Naïve application of this model to the study of readmission among patients with 'advanced' health conditions such as pancreatic cancer, however, is problematic because it ignores death as a competing risk...
2016: Journal of the American Statistical Association
Jon Wakefield, Daniel Simpson, Jessica Godwin
No abstract text is available yet for this article.
2016: Journal of the American Statistical Association
Guanhua Chen, Donglin Zeng, Michael R Kosorok
In dose-finding clinical trials, it is becoming increasingly important to account for individual level heterogeneity while searching for optimal doses to ensure an optimal individualized dose rule (IDR) maximizes the expected beneficial clinical outcome for each individual. In this paper, we advocate a randomized trial design where candidate dose levels assigned to study subjects are randomly chosen from a continuous distribution within a safe range. To estimate the optimal IDR using such data, we propose an outcome weighted learning method based on a nonconvex loss function, which can be solved efficiently using a difference of convex functions algorithm...
2016: Journal of the American Statistical Association
Sung Won Han, Gong Chen, Myun-Seok Cheon, Hua Zhong
Graphical models are a popular approach to find dependence and conditional independence relationships between gene expressions. Directed acyclic graphs (DAGs) are a special class of directed graphical models, where all the edges are directed edges and contain no directed cycles. The DAGs are well known models for discovering causal relationships between genes in gene regulatory networks. However, estimating DAGs without assuming known ordering is challenging due to high dimensionality, the acyclic constraints, and the presence of equivalence class from observational data...
2016: Journal of the American Statistical Association
Zhe Yu, Raquel Prado, Erin B Quinlan, Steven C Cramer, Hernando Ombao
Stroke is a disturbance in blood supply to the brain resulting in the loss of brain functions, particularly motor function. A study was conducted by the UCI Neurorehabilitation Lab to investigate the impact of stroke on motor-related brain regions. Functional MRI (fMRI) data were collected from stroke patients and healthy controls while the subjects performed a simple motor task. In addition to affecting local neuronal activation strength, stroke might also alter communications (i.e., connectivity) between brain regions...
2016: Journal of the American Statistical Association
Rui Pan, Hansheng Wang, Runze Li
This paper is concerned with the problem of feature screening for multi-class linear discriminant analysis under ultrahigh dimensional setting. We allow the number of classes to be relatively large. As a result, the total number of relevant features is larger than usual. This makes the related classification problem much more challenging than the conventional one, where the number of classes is small (very often two). To solve the problem, we propose a novel pairwise sure independence screening method for linear discriminant analysis with an ultrahigh dimensional predictor...
2016: Journal of the American Statistical Association
Chen Yue, Vadim Zipunnikov, Pierre-Louis Bazin, Dzung Pham, Daniel Reich, Ciprian Crainiceanu, Brian Caffo
In this manuscript, we are concerned with data generated from a diffusion tensor imaging (DTI) experiment. The goal is to parameterize manifold-like white matter tracts, such as the corpus callosum, using principal surfaces. The problem is approached by finding a geometrically motivated surface-based representation of the corpus callosum and visualized fractional anisotropy (FA) values projected onto the surface. The method also applies to any other diffusion summary. An algorithm is proposed that 1) constructs the principal surface of a corpus callosum; 2) flattens the surface into a parametric 2D map; 3) projects associated FA values on the map...
2016: Journal of the American Statistical Association
Jacob Bien, Florentina Bunea, Luo Xiao
We introduce a new sparse estimator of the covariance matrix for high-dimensional models in which the variables have a known ordering. Our estimator, which is the solution to a convex optimization problem, is equivalently expressed as an estimator which tapers the sample covariance matrix by a Toeplitz, sparsely-banded, data-adaptive matrix. As a result of this adaptivity, the convex banding estimator enjoys theoretical optimality properties not attained by previous banding or tapered estimators. In particular, our convex banding estimator is minimax rate adaptive in Frobenius and operator norms, up to log factors, over commonly-studied classes of covariance matrices, and over more general classes...
2016: Journal of the American Statistical Association
Tianxi Cai, T Tony Cai, Anru Zhang
Matrix completion has attracted significant recent attention in many fields including statistics, applied mathematics and electrical engineering. Current literature on matrix completion focuses primarily on independent sampling models under which the individual observed entries are sampled independently. Motivated by applications in genomic data integration, we propose a new framework of structured matrix completion (SMC) to treat structured missingness by design. Specifically, our proposed method aims at efficient matrix recovery when a subset of the rows and columns of an approximately low-rank matrix are observed...
2016: Journal of the American Statistical Association
Yanxun Xu, Peter Müller, Abdus S Wahed, Peter F Thall
We analyze a dataset arising from a clinical trial involving multi-stage chemotherapy regimes for acute leukemia. The trial design was a 2 × 2 factorial for frontline therapies only. Motivated by the idea that subsequent salvage treatments affect survival time, we model therapy as a dynamic treatment regime (DTR), that is, an alternating sequence of adaptive treatments or other actions and transition times between disease states. These sequences may vary substantially between patients, depending on how the regime plays out...
2016: Journal of the American Statistical Association
Stanislav Minsker, Ying-Qi Zhao, Guang Cheng
Individualized treatment rules (ITRs) tailor treatments according to individual patient characteristics. They can significantly improve patient care and are thus becoming increasingly popular. The data collected during randomized clinical trials are often used to estimate the optimal ITRs. However, these trials are generally expensive to run, and, moreover, they are not designed to efficiently estimate ITRs. In this article, we propose a cost-effective estimation method from an active learning perspective. In particular, our method recruits only the "most informative" patients (in terms of learning the optimal ITRs) from an ongoing clinical trial...
2016: Journal of the American Statistical Association
Lin Zhang, Veerabhadran Baladandayuthapani, Hongxiao Zhu, Keith A Baggerly, Tadeusz Majewski, Bogdan A Czerniak, Jeffrey S Morris
We develop a functional conditional autoregressive (CAR) model for spatially correlated data for which functions are collected on areal units of a lattice. Our model performs functional response regression while accounting for spatial correlations with potentially nonseparable and nonstationary covariance structure, in both the space and functional domains. We show theoretically that our construction leads to a CAR model at each functional location, with spatial covariance parameters varying and borrowing strength across the functional domain...
2016: Journal of the American Statistical Association
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