Abstract:
:Motivated by the spatial modeling of aberrant crypt foci (ACF) in colon carcinogenesis, we consider binary data with probabilities modeled as the sum of a nonparametric mean plus a latent Gaussian spatial process that accounts for short-range dependencies. The mean is modeled in a general way using regression splines. The mean function can be viewed as a fixed effect and is estimated with a penalty for regularization. With the latent process viewed as another random effect, the model becomes a generalized linear mixed model. In our motivating data set and other applications, the sample size is too large to easily accommodate maximum likelihood or restricted maximum likelihood estimation (REML), so pairwise likelihood, a special case of composite likelihood, is used instead. We develop an asymptotic theory for models that are sufficiently general to be used in a wide variety of applications, including, but not limited to, the problem that motivated this work. The splines have penalty parameters that must converge to zero asymptotically: we derive theory for this along with a data-driven method for selecting the penalty parameter, a method that is shown in simulations to improve greatly upon standard devices, such as likelihood crossvalidation. Finally, we apply the methods to the data from our experiment ACF. We discover an unexpected location for peak formation of ACF.
journal_name
Biometricsjournal_title
Biometricsauthors
Apanasovich TV,Ruppert D,Lupton JR,Popovic N,Turner ND,Chapkin RS,Carroll RJdoi
10.1111/j.1541-0420.2007.00892.xsubject
Has Abstractpub_date
2008-06-01 00:00:00pages
490-500issue
2eissn
0006-341Xissn
1541-0420pii
BIOM892journal_volume
64pub_type
杂志文章相关文献
BIOMETRICS文献大全abstract::In controlled clinical trials there are usually several prognostic factors known or thought to influence the patient's ability to respond to treatment. Therefore, the method of sequential treatment assignment needs to be designed so that treatment balance is simultaneously achieved across all such patients factor. Tra...
journal_title:Biometrics
pub_type: 临床试验,杂志文章
doi:
更新日期:1975-03-01 00:00:00
abstract::Covariate-specific receiver operating characteristic (ROC) curves are often used to evaluate the classification accuracy of a medical diagnostic test or a biomarker, when the accuracy of the test is associated with certain covariates. In many large-scale screening tests, the gold standard is subject to missingness due...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2011.01562.x
更新日期:2011-09-01 00:00:00
abstract::This paper focuses on the methodology developed for analyzing a multivariate interval-censored data set from an AIDS observational study. A purpose of the study was to determine the natural history of the opportunistic infection cytomeglovirus (CMV) in an HIV-infected individual. For this observational study, laborato...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.2000.00940.x
更新日期:2000-09-01 00:00:00
abstract::Assuming a model of proportional failure rates, Cox (1972) presents a systematic study of the use of covariates in the analysis of life time. The treatment of tied observations is a particularly troublesome point in both theory and application. It appears that grouping rather than discrete time is the right way to han...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1977-09-01 00:00:00
abstract::Advances in sequencing technologies and bioinformatics tools have vastly improved our ability to collect and analyze data from complex microbial communities. A major goal of microbiome studies is to correlate the overall microbiome composition with clinical or environmental variables. La Rosa et al. recently proposed ...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.13154
更新日期:2020-06-01 00:00:00
abstract::Many statistical tests have been proposed for case-control data to detect disease association with multiple single nucleotide polymorphisms (SNPs) in linkage disequilibrium. The main reason for the existence of so many tests is that each test aims to detect one or two aspects of many possible distributional difference...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2011.01649.x
更新日期:2012-03-01 00:00:00
abstract::A broad approach to the design of Phase I clinical trials for the efficient estimation of the maximum tolerated dose is presented. The method is rooted in formal optimal design theory and involves the construction of constrained Bayesian c- and D-optimal designs. The imposed constraint incorporates the optimal design ...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/1541-0420.00069
更新日期:2003-09-01 00:00:00
abstract::Currently, the design of group sequential clinical trials requires choosing among several distinct design categories, design scales, and strategies for determining stopping rules. This approach can limit the design selection process so that clinical issues are not fully addressed. This paper describes a family of desi...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.1999.00874.x
更新日期:1999-09-01 00:00:00
abstract::Exposure to high levels of air pollution during the pregnancy is associated with increased probability of preterm birth (PTB), a major cause of infant morbidity and mortality. New statistical methodology is required to specifically determine when a particular pollutant impacts the PTB outcome, to determine the role of...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2012.01774.x
更新日期:2012-12-01 00:00:00
abstract::We consider Bayesian methodology for comparing two or more unlabeled point sets. Application of the technique to a set of steroid molecules illustrates its potential utility involving the comparison of molecules in chemoinformatics and bioinformatics. We initially match a pair of molecules, where one molecule is regar...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2006.00622.x
更新日期:2007-03-01 00:00:00
abstract::Directed acyclic graphical (DAG) models are increasingly employed in the study of physical and biological systems to model direct influences between variables. Identifying the graph from data is a challenging endeavor, which can be more reasonably tackled if the variables are assumed to satisfy a given ordering; in th...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.12018
更新日期:2013-06-01 00:00:00
abstract::In multivariate failure time data analysis, a marginal regression modeling approach is often preferred to avoid assumptions on the dependence structure among correlated failure times. In this paper, a marginal mixed baseline hazards model is introduced. Estimating equations are proposed for the estimation of the margi...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.1999.00805.x
更新日期:1999-09-01 00:00:00
abstract::Variable selection for recovering sparsity in nonadditive and nonparametric models with high-dimensional variables has been challenging. This problem becomes even more difficult due to complications in modeling unknown interaction terms among high-dimensional variables. There is currently no variable selection method ...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.12518
更新日期:2016-12-01 00:00:00
abstract::We consider methods for estimating the treatment effect and/or the covariate by treatment interaction effect in a randomized clinical trial under noncompliance with time-to-event outcome. As in Cuzick et al. (2007), assuming that the patient population consists of three (possibly latent) subgroups based on treatment p...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.12472
更新日期:2016-09-01 00:00:00
abstract::Spatial replication is a common theme in count surveys of animals. Such surveys often generate sparse count data from which it is difficult to estimate population size while formally accounting for detection probability. In this article, I describe a class of models (N-mixture models) which allow for estimation of pop...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341X.2004.00142.x
更新日期:2004-03-01 00:00:00
abstract::In spatial surveys for estimating the density of objects in a survey region, systematic designs will generally yield lower variance than random designs. However, estimating the systematic variance is well known to be a difficult problem. Existing methods tend to overestimate the variance, so although the variance is g...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2011.01604.x
更新日期:2011-12-01 00:00:00
abstract::We propose optimal choice of the design parameters for random discontinuation designs (RDD) using a Bayesian decision-theoretic approach. We consider applications of RDDs to oncology phase II studies evaluating activity of cytostatic agents. The design consists of two stages. The preliminary open-label stage treats al...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2011.01623.x
更新日期:2012-03-01 00:00:00
abstract::Brain connectivity analysis is now at the foreground of neuroscience research. A connectivity network is characterized by a graph, where nodes represent neural elements such as neurons and brain regions, and links represent statistical dependence that is often encoded in terms of partial correlation. Such a graph is i...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.12633
更新日期:2017-09-01 00:00:00
abstract::Diggle's tests of spatial randomness based on empirical distributions of interpoint distances can be performed with and without edge-effect correction. We present here numerical results illustrating that tests without the edge-effect correction proposed by Diggle (1979, Biometrics 35, 87-101) have a higher power for s...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.1999.00156.x
更新日期:1999-03-01 00:00:00
abstract::Ophthalmologic studies often compare several groups of subjects for the presence or absence of some ocular finding, where each subject may contribute two eyes to the analysis, the values from the two eyes being highly correlated. Rosner (1982, Biometrics 38, 105-114) and Dallal (1988, Biometrics 44, 253-257) proposed ...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1989-06-01 00:00:00
abstract::The distance between homologous DNA sequences of two species is proposed to be -1/4 ln[det(P)], where P is the conditional probability matrix specifying the proportions of the various nucleotides in the second sequence, corresponding to each of the four nucleotides in the first sequence. A probability model is describ...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1987-06-01 00:00:00
abstract::The variogram is a standard tool in the analysis of spatial data, and its shape provides useful information on the form of spatial correlation that may be present. However, it is also useful to be able to assess the evidence for the presence of any spatial correlation. A method of doing this, based on an assessment of...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.2001.00211.x
更新日期:2001-03-01 00:00:00
abstract::Development of HIV resistance mutations is a major cause for failure of antiretroviral treatment. This article proposes a method for jointly modeling the processes of viral genetic changes and treatment failure. Because the viral genome is measured with uncertainty, a hidden Markov model is used to fit the viral genet...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2006.00635.x
更新日期:2007-03-01 00:00:00
abstract::Capture-recapture models were originally developed to account for encounter probabilities that are less than 1 in free-ranging animal populations. Nowadays, these models can deal with the movement of animals between different locations and are also used to study transitions between different states. However, their use...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2005.00318.x
更新日期:2005-06-01 00:00:00
abstract::We propose a nonparametric Bayesian approach to estimate the natural direct and indirect effects through a mediator in the setting of a continuous mediator and a binary response. Several conditional independence assumptions are introduced (with corresponding sensitivity parameters) to make these effects identifiable f...
journal_title:Biometrics
pub_type: 杂志文章,随机对照试验
doi:10.1111/j.1541-0420.2012.01781.x
更新日期:2012-12-01 00:00:00
abstract::The distribution of health care payments to insurance plans has substantial consequences for social policy. Risk adjustment formulas predict spending in health insurance markets in order to provide fair benefits and health care coverage for all enrollees, regardless of their health status. Unfortunately, current risk ...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.13206
更新日期:2020-09-01 00:00:00
abstract::We develop a parameterization of the beta-binomial mixture that provides sensible inferences about the size of a closed population when probabilities of capture or detection vary among individuals. Three classes of mixture models (beta-binomial, logistic-normal, and latent-class) are fitted to recaptures of snowshoe h...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/1541-0420.00042
更新日期:2003-06-01 00:00:00
abstract::We extend the Mantel-Haenszel estimating function to estimate both the intra-cluster pairwise correlation and the main effects for sparse clustered binary data. We propose both a composite likelihood approach and an estimating function approach for the analysis of such data. The proposed estimators are consistent and ...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2005.00362.x
更新日期:2005-12-01 00:00:00
abstract::Long-term follow-up is common in many medical investigations where the interest lies in predicting patients' risks for a future adverse outcome using repeatedly measured predictors over time. A key quantity is the likelihood of developing an adverse outcome among individuals who survived up to time s given their covar...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.12562
更新日期:2017-03-01 00:00:00
abstract::Prognostic models in survival analysis typically aim to describe the association between patient covariates and future outcomes. More recently, efforts have been made to include covariate information that is updated over time. However, there exists as yet no standard approach to assess the predictive accuracy of such ...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2007.00889.x
更新日期:2008-06-01 00:00:00