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Articles 361 - 390 of 567
Full-Text Articles in Biostatistics
Diagnosing And Responding To Violations In The Positivity Assumption, Maya L. Petersen, Kristin Porter, Susan Gruber, Yue Wang, Mark J. Van Der Laan
Diagnosing And Responding To Violations In The Positivity Assumption, Maya L. Petersen, Kristin Porter, Susan Gruber, Yue Wang, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
The assumption of positivity or experimental treatment assignment requires that observed treatment levels vary within confounder strata. This article discusses the positivity assumption in the context of assessing model and parameter-specific identifiability of causal effects. Positivity violations occur when certain subgroups in a sample rarely or never receive some treatments of interest. The resulting sparsity in the data may increase bias with or without an increase in variance and can threaten valid inference. The parametric bootstrap is presented as a tool to assess the severity of such threats and its utility as a diagnostic is explored using simulated data. Several …
Stratifying Subjects For Treatment Selection With Censored Event Time Data From A Comparative Study, Lihui Zhao, Tianxi Cai, Lu Tian, Hajime Uno, Scott D. Solomon, L. J. Wei
Stratifying Subjects For Treatment Selection With Censored Event Time Data From A Comparative Study, Lihui Zhao, Tianxi Cai, Lu Tian, Hajime Uno, Scott D. Solomon, L. J. Wei
Harvard University Biostatistics Working Paper Series
No abstract provided.
Principled Sure Independence Screening For Cox Models With Ultra-High-Dimensional Covariates, Sihai Dave Zhao, Yi Li
Principled Sure Independence Screening For Cox Models With Ultra-High-Dimensional Covariates, Sihai Dave Zhao, Yi Li
Harvard University Biostatistics Working Paper Series
No abstract provided.
Estimation Of Causal Effects Of Community Based Interventions, Mark J. Van Der Laan
Estimation Of Causal Effects Of Community Based Interventions, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
Suppose one assigns two interventions to a small number K of different populations or communities, and one measures covariates and outcomes on a random sample of independent individuals from each of the K populations. We investigate the problem of identification and estimation of the causal effect of the choice of intervention assigned at the community level, and, if the intervention is time-dependent, the causal effect of the changes in the intervention at time t, on the outcome. The challenge one is confronted with is that different populations have different environmental factors and that the intervention and environment are assigned to …
Multi-State Life Tables, Equilibrium Prevalence, And Baseline Selection Bias, Paula Diehr, David Yanez
Multi-State Life Tables, Equilibrium Prevalence, And Baseline Selection Bias, Paula Diehr, David Yanez
UW Biostatistics Working Paper Series
Consider a 3-state system with one absorbing state, such as Healthy, Sick, and Dead. If the system satisfies the 1-step Markov conditions, the prevalence of the Healthy state will converge to a value that is independent of the initial distribution. This equilibrium prevalence and its variance are known under the assumption of time homogeneity, and provided reasonable estimates in the time non-homogeneous systems studied. Here, we derived the equilibrium prevalence for a system with more than three states. Under time homogeneity, the equilibrium prevalence distribution was shown to be an eigenvector of a partition of the matrix of transition probabilities. …
Powerful Snp Set Analysis For Case-Control Genome Wide Association Studies, Michael C. Wu, Peter Kraft, Michael P. Epstein, Deanne M. Taylor, Stephen J. Chanock, David J. Hunter, Xihong Lin
Powerful Snp Set Analysis For Case-Control Genome Wide Association Studies, Michael C. Wu, Peter Kraft, Michael P. Epstein, Deanne M. Taylor, Stephen J. Chanock, David J. Hunter, Xihong Lin
Harvard University Biostatistics Working Paper Series
No abstract provided.
Estimating Causal Effects In Trials Involving Multi-Treatment Arms Subject To Non-Compliance: A Bayesian Frame-Work, Qi Long, Roderick J. Little, Xihong Lin
Estimating Causal Effects In Trials Involving Multi-Treatment Arms Subject To Non-Compliance: A Bayesian Frame-Work, Qi Long, Roderick J. Little, Xihong Lin
Harvard University Biostatistics Working Paper Series
No abstract provided.
A Targeted Maximum Likelihood Estimator Of A Causal Effect On A Bounded Continuous Outcome, Susan Gruber, Mark J. Van Der Laan
A Targeted Maximum Likelihood Estimator Of A Causal Effect On A Bounded Continuous Outcome, Susan Gruber, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
Targeted maximum likelihood estimation of a parameter of a data generating distribution, known to be an element of a semiparametric model, involves constructing a parametric model through an initial density estimator with parameter epsilon representing an amount of fluctuation of the initial density estimator, where the score of this fluctuation model at epsilon=0 equals the efficient influence curve/canonical gradient. The latter constraint can be satisfied by many parametric fluctuation models, since it represents only a local constraint of its behavior at zero fluctuation. However, it is very important that the fluctuations stay within the semiparametric model for the observed data …
Super Learner In Prediction, Eric C. Polley, Mark J. Van Der Laan
Super Learner In Prediction, Eric C. Polley, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
Super learning is a general loss based learning method that has been proposed and analyzed theoretically in van der Laan et al. (2007). In this article we consider super learning for prediction. The super learner is a prediction method designed to find the optimal combination of a collection of prediction algorithms. The super learner algorithm finds the combination of algorithms minimizing the cross-validated risk. The super learner framework is built on the theory of cross-validation and allows for a general class of prediction algorithms to be considered for the ensemble. Due to the previously established oracle results for the cross-validation …
Assessing Noninferiority In A Three-Arm Trial Using The Bayesian Approach, Pulak Ghosh, Farouk S. Nathoo, Mithat Gonen, Ram C. Tiwari
Assessing Noninferiority In A Three-Arm Trial Using The Bayesian Approach, Pulak Ghosh, Farouk S. Nathoo, Mithat Gonen, Ram C. Tiwari
Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series
Non-inferiority trials, which aim to demonstrate that a test product is not worse than a competitor by more than a pre-specified small amount, are of great importance to the pharmaceutical community. As a result, methodology for designing and analyzing such trials is required, and developing new methods for such analysis is an important area of statistical research. The three-arm clinical trial is usually recommended for non-inferiority trials by the Food and Drug Administration (FDA). The three-arm trial consists of a placebo, a reference, and an experimental treatment, and simultaneously tests the superiority of the reference over the placebo along with …
Nonparametric Regression With Missing Outcomes Using Weighted Kernel Estimating Equations, Lu Wang, Andrea Rotnitzky, Xihong Lin
Nonparametric Regression With Missing Outcomes Using Weighted Kernel Estimating Equations, Lu Wang, Andrea Rotnitzky, Xihong Lin
Harvard University Biostatistics Working Paper Series
No abstract provided.
Utilizing The Integrated Difference Of Two Survival Functions To Quantify The Treatment Contrast For Designing, Monitoring And Analyzing A Comparative Clinical Study, Lihui Zhao, Lu Tian, Hajime Uno, Scott D. Solomon, Marc A. Pfeffer, J. S. Schindler, L. J. Wei
Utilizing The Integrated Difference Of Two Survival Functions To Quantify The Treatment Contrast For Designing, Monitoring And Analyzing A Comparative Clinical Study, Lihui Zhao, Lu Tian, Hajime Uno, Scott D. Solomon, Marc A. Pfeffer, J. S. Schindler, L. J. Wei
Harvard University Biostatistics Working Paper Series
No abstract provided.
Likelihood Ratio Testing For Admixture Models With Application To Genetic Linkage Analysis, Chong-Zhi Di, Kung-Yee Liang
Likelihood Ratio Testing For Admixture Models With Application To Genetic Linkage Analysis, Chong-Zhi Di, Kung-Yee Liang
Johns Hopkins University, Dept. of Biostatistics Working Papers
We consider likelihood ratio tests (LRT) and their modifications for homogeneity in admixture models. The admixture model is a special case of two component mixture model, where one component is indexed by an unknown parameter while the parameter value for the other component is known. It has been widely used in genetic linkage analysis under heterogeneity, in which the kernel distribution is binomial. For such models, it is long recognized that testing for homogeneity is nonstandard and the LRT statistic does not converge to a conventional 2 distribution. In this paper, we investigate the asymptotic behavior of the LRT for …
Targeted Maximum Likelihood Method For Repeated Measures Semiparametric Regression: Discovery For Transcription Factor Activity, Catherine Tuglus, Mark J. Van Der Laan
Targeted Maximum Likelihood Method For Repeated Measures Semiparametric Regression: Discovery For Transcription Factor Activity, Catherine Tuglus, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
In longitudinal and repeated measures data analysis, often the goal is to determine the effect of a treatment or aspect on a particular outcome (e.g. disease progression). We consider semiparametric repeated measures regression model, where the parametric component models effect of the variable of interest and any modification by other covariates. The expectation of this parametric component over the other covariates is a measure of variable importance. Here we present a targeted maximum likelihood estimator of the finite dimensional regression parameter, which is easily estimated using standard software for generalized estimating equations. The targeted maximum likelihood method provides double robust …
Graphical Procedures For Evaluating Overall And Subject-Specific Incremental Values From New Predictors With Censored Event Time Data, Hajime Uno, Tianxi Cai, Lu Tian, L. J. Wei
Graphical Procedures For Evaluating Overall And Subject-Specific Incremental Values From New Predictors With Censored Event Time Data, Hajime Uno, Tianxi Cai, Lu Tian, L. J. Wei
Harvard University Biostatistics Working Paper Series
No abstract provided.
Doubly Regularized Reml For Estimation And Selection Of Fixed And Random Effects In Linear Mixed-Effects Models, Sijian Wang, Peter Xuewin Song, Ji Zhu
Doubly Regularized Reml For Estimation And Selection Of Fixed And Random Effects In Linear Mixed-Effects Models, Sijian Wang, Peter Xuewin Song, Ji Zhu
The University of Michigan Department of Biostatistics Working Paper Series
The linear mixed effects model (LMM) is widely used in the analysis of clustered or longitudinal data. In the practice of LMM, the inference on the structure of the random effects component is of great importance, not only to yield proper interpretation of subject-specific effects but also to draw valid statistical conclusions. This task of inference becomes significantly challenging when a large number of fixed effects and random effects are involved in the analysis. The difficulty of variable selection arises from the need of simultaneously regularizing both mean model and covariance structures, with possible parameter constraints between the two. In …
Multilevel Sparse Functional Principal Component Analysis, Chong-Zhi Di, Ciprian M. Crainiceanu
Multilevel Sparse Functional Principal Component Analysis, Chong-Zhi Di, Ciprian M. Crainiceanu
Johns Hopkins University, Dept. of Biostatistics Working Papers
The basic observational unit in this paper is a function. Data are assumed to have a natural hierarchy of basic units. A simple example is when functions are recorded at multiple visits for the same subject. Di et al. (2009) proposed Multilevel Functional Principal Component Analysis (MFPCA) for this type of data structure when functions are densely sampled. Here we consider the case when functions are sparsely sampled and may contain as few as 2 or 3 observations per function. As with MFPCA, we exploit the multilevel structure of covariance operators and data reduction induced by the use of principal …
Targeting The Optimal Design In Randomized Clinical Trials With Binary Outcomes And No Covariate, Antoine Chambaz, Mark J. Van Der Laan
Targeting The Optimal Design In Randomized Clinical Trials With Binary Outcomes And No Covariate, Antoine Chambaz, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
This article is devoted to the asymptotic study of adaptive group sequential designs in the case of randomized clinical trials with binary treatment, binary outcome and no covariate. By adaptive design, we mean in this setting a clinical trial design that allows the investigator to dynamically modify its course through data-driven adjustment of the randomization probability based on data accrued so far, without negatively impacting on the statistical integrity of the trial. By adaptive group sequential design, we refer to the fact that group sequential testing methods can be equally well applied on top of adaptive designs. Prior to collection …
Targeted Maximum Likelihood Based Causal Inference, Mark J. Van Der Laan
Targeted Maximum Likelihood Based Causal Inference, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
Given causal graph assumptions, intervention-specific counterfactual distributions of the data can be defined by the so called G-computation formula, which is obtained by carrying out these interventions on the likelihood of the data factorized according to the causal graph. The obtained G-computation formula represents the counterfactual distribution the data would have had if this intervention would have been enforced on the system generating the data. A causal effect of interest can now be defined as some difference between these counterfactual distributions indexed by different interventions. For example, the interventions can represent static treatment regimens or individualized treatment rules that assign …
Bio-Creep In Non-Inferiority Clinical Trials, Siobhan P. Everson-Stewart, Scott S. Emerson
Bio-Creep In Non-Inferiority Clinical Trials, Siobhan P. Everson-Stewart, Scott S. Emerson
UW Biostatistics Working Paper Series
After a non-inferiority clinical trial, a new therapy may be accepted as effective, even if its treatment effect is slightly smaller than the current standard. It is therefore possible that, after a series of trials where the new therapy is slightly worse than the preceding drugs, an ineffective or harmful therapy might be incorrectly declared efficacious; this is known as “bio-creep.” Several factors may influence the rate at which bio-creep occurs, including the distribution of the effects of the new agents being tested and how that changes over time, the choice of active comparator, the method used to model the …
Estimates Of Information Growth In Longitudinal Clinical Trials, Abigail Shoben, Kyle Rudser, Scott S. Emerson
Estimates Of Information Growth In Longitudinal Clinical Trials, Abigail Shoben, Kyle Rudser, Scott S. Emerson
UW Biostatistics Working Paper Series
In group sequential clinical trials, it is necessary to estimate the amount of information present at interim analysis times relative to the amount of information that would be present at the final analysis. If only one measurement is made per individual, this is often the ratio of sample sizes available at the interim and final analyses. However, as discussed by Wu and Lan (1992), when the statistic of interest is a change over time, as with longitudinal data, such an approach overstates the information. In this paper, we discuss other problems that can result in overestimating the information, such as …
Simple, Efficient Estimators Of Treatment Effects In Randomized Trials Using Generalized Linear Models To Leverage Baseline Variables, Michael Rosenblum, Mark J. Van Der Laan
Simple, Efficient Estimators Of Treatment Effects In Randomized Trials Using Generalized Linear Models To Leverage Baseline Variables, Michael Rosenblum, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
Models, such as logistic regression and Poisson regression models, are often used to estimate treatment effects in randomized trials. These models leverage information in variables collected before randomization, in order to obtain more precise estimates of treatment effects. However, there is the danger that model misspecification will lead to bias. We show that certain easy to compute, model-based estimators are asymptotically unbiased even when the working model used is arbitrarily misspecified. Furthermore, these estimators are locally efficient. As a special case of our main result, we consider a simple Poisson working model containing only main terms; in this case, we …
Targeted Maximum Likelihood Estimation Of The Parameter Of A Marginal Structural Model, Michael Rosenblum, Mark J. Van Der Laan
Targeted Maximum Likelihood Estimation Of The Parameter Of A Marginal Structural Model, Michael Rosenblum, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
Targeted maximum likelihood estimation is a versatile tool for estimating parameters in semiparametric and nonparametric models. We work through an example applying targeted maximum likelihood methodology to estimate the parameter of a marginal structural model. In the case we consider, we show how this can be easily done by clever use of standard statistical software. We point out differences between targeted maximum likelihood estimation and other approaches (including estimating function based methods). The application we consider is to estimate the effect of adherence to antiretroviral medications on virologic failure in HIV positive individuals.
Is Survival The Only Or Even The Right Outcome For Evaluating Treatments For Out-Of-Hospital Cardiac Arrest? A Proposed Test Based On Both An Intermediate And Ultimate Outcome., Al Hallstrom
UW Biostatistics Working Paper Series
It is generally agreed that the goal of resuscitation is survival with neurological and physiological status similar to that preceding the cardiac arrest. Previously I have argued that the lack of improvement in outcome from resuscitation over the past 3 to 4 decades, as compared to the substantial progress made in treatment of ischemic heart disease, is a consequence of the absence of randomized clinical trials of new interventions and the use of intermediate endpoints such as return of spontaneous circulation or admittance to hospital. Proponents of these intermediate endpoints have argued that those involved in the resuscitation have no …
Two-Stage Decompositions For The Analysis Of Functional Connectivity For Fmri With Application To Alzheimer's Disease Risk, Brian S. Caffo, Ciprian M. Crainiceanu, Guillermo Verduzco, Stewart H. Mostofsky, Susan Spear-Bassett, James J. Pekar
Two-Stage Decompositions For The Analysis Of Functional Connectivity For Fmri With Application To Alzheimer's Disease Risk, Brian S. Caffo, Ciprian M. Crainiceanu, Guillermo Verduzco, Stewart H. Mostofsky, Susan Spear-Bassett, James J. Pekar
COBRA Preprint Series
Functional connectivity is the study of correlations in measured neurophysiological signals. Altered functional connectivity has been shown to be associated with numerous diseases including Alzheimer's disease and mild cognitive impairment. In this manuscript we use a two-stage application of the singular value decomposition to obtain data driven population-level measures of functional connectivity in functional magnetic resonance imaging (fMRI). The method is computationally simple and amenable to high dimensional fMRI data with large numbers of subjects. Simulation studies suggest the ability of the decomposition methods to recover population brain networks and their associated loadings. We further demonstrate the utility of these …
Bayesian Functional Data Analysis Using Winbugs, Ciprian M. Crainiceanu, A. Jeffrey Goldsmith
Bayesian Functional Data Analysis Using Winbugs, Ciprian M. Crainiceanu, A. Jeffrey Goldsmith
Johns Hopkins University, Dept. of Biostatistics Working Papers
We provide user friendly software for Bayesian analysis of Functional Data Models using WinBUGS 1.4. The excellent properties of Bayesian analysis in this context are due to: 1) dimensionality reduction, which leads to low dimensional projection bases; 2)the mixed model representation of functional models, which provides a modular approach to model extension; and 3) the orthogonality of the principal component bases, which contributes to excellent chain convergence and mixing properties. Our paper provides one more, essential, reason for using Bayesian analysis for Functional models: the existence of software.
Composite Likelihood Em Algorithm With Applications To Multivariate Hidden Markov Model , Xin Gao, Peter Xuekun Song
Composite Likelihood Em Algorithm With Applications To Multivariate Hidden Markov Model , Xin Gao, Peter Xuekun Song
COBRA Preprint Series
The method of composite likelihood is useful to deal with estimation and inference in parametric models with high-dimensional data, where the full likelihood approach renders to intractable computational complexity. We develop an extension of the EM algorithm in the framework of composite likelihood estimation in the presence of missing data or latent variables. We establish three key theoretical properties of the composite likelihood EM (CLEM) algorithm, including the ascent property, the algorithmic convergence and the convergence rate. The proposed method is applied to estimate the transition probabilities in multivariate hidden Markov model. Simulation studies are presented to demonstrate the empirical …
Readings In Targeted Maximum Likelihood Estimation, Mark J. Van Der Laan, Sherri Rose, Susan Gruber
Readings In Targeted Maximum Likelihood Estimation, Mark J. Van Der Laan, Sherri Rose, Susan Gruber
U.C. Berkeley Division of Biostatistics Working Paper Series
This is a compilation of current and past work on targeted maximum likelihood estimation. It features the original targeted maximum likelihood learning paper as well as chapters on super (machine) learning using cross validation, randomized controlled trials, realistic individualized treatment rules in observational studies, biomarker discovery, case-control studies, and time-to-event outcomes with censored data, among others. We hope this collection is helpful to the interested reader and stimulates additional research in this important area.
Robustness Of Semiparametric Efficiency In Nearly-Correct Models For Two-Phase Samples, Thomas Lumley
Robustness Of Semiparametric Efficiency In Nearly-Correct Models For Two-Phase Samples, Thomas Lumley
UW Biostatistics Working Paper Series
Augmented inverse-probability weighted (AIPW) estimators for incomplete-data models typically do not have full semiparametric efficiency, but do have model-robustness properties not shared by the efficient estimator. We examine the performance of efficient and AIPW estimators when the complete-data model is nearly correctly specified, in the sense that the misspecification is not reliably detectable from the data by any possible diagnostic or test. Asymptotic results for these nearly true models are obtained by representing them as sequences of misspecified models that are mutually contiguous with a correctly specified model. For some least favorable direction of model misspecification the bias in the …
Causal Inference For Nested Case-Control Studies Using Targeted Maximum Likelihood Estimation, Sherri Rose, Mark J. Van Der Laan
Causal Inference For Nested Case-Control Studies Using Targeted Maximum Likelihood Estimation, Sherri Rose, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
A nested case-control study is conducted within a well-defined cohort arising out of a population of interest. This design is often used in epidemiology to reduce the costs associated with collecting data on the full cohort; however, the case control sample within the cohort is a biased sample. Methods for analyzing case-control studies have largely focused on logistic regression models that provide conditional and not marginal causal estimates of the odds ratio. We previously developed a Case-Control Weighted Targeted Maximum Likelihood Estimation (TMLE) procedure for case-control study designs, which relies on the prevalence probability q0. We propose the use of …