Biostatistics最新文献_第5页

The winner's curse under dependence: repairing empirical Bayes using convoluted densities. 依赖下的赢家诅咒：用卷积密度修复经验贝叶斯。

IF 2 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxaf025

Stijn Hawinkel, Olivier Thas, Steven Maere

{"title":"The winner's curse under dependence: repairing empirical Bayes using convoluted densities.","authors":"Stijn Hawinkel, Olivier Thas, Steven Maere","doi":"10.1093/biostatistics/kxaf025","DOIUrl":"https://doi.org/10.1093/biostatistics/kxaf025","url":null,"abstract":"The winner's curse is a form of selection bias that arises when estimates are obtained for a large number of features, but only a subset of most extreme estimates is reported. It occurs in large scale significance testing as well as in rank-based selection, and imperils reproducibility of findings and follow-up study design. Several methods correcting for this selection bias have been proposed, but questions remain on their susceptibility to dependence between features since theoretical analyses and comparative studies are few. We prove that estimation through Tweedie's formula is biased in presence of strong dependence, and propose a convolution of its density estimator to restore its competitive performance, which also aids other empirical Bayes methods. Furthermore, we perform a comprehensive simulation study comparing different classes of winner's curse correction methods for point estimates as well as confidence intervals under dependence. We find a bootstrap method and empirical Bayes methods with density convolution to perform best at correcting the selection bias, although this correction generally does not improve the feature ranking. Finally, we apply the methods to a comparison of single-feature versus multi-feature prediction models in predicting Brassica napus phenotypes from gene expression data, demonstrating that the superiority of the best single-feature model may be illusory.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":"26 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144979577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A scalable two-stage Bayesian approach accounting for exposure measurement error in environmental epidemiology. 在环境流行病学中考虑暴露测量误差的可扩展两阶段贝叶斯方法。

IF 2 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxae038

Changwoo J Lee, Elaine Symanski, Amal Rammah, Dong Hun Kang, Philip K Hopke, Eun Sug Park

{"title":"A scalable two-stage Bayesian approach accounting for exposure measurement error in environmental epidemiology.","authors":"Changwoo J Lee, Elaine Symanski, Amal Rammah, Dong Hun Kang, Philip K Hopke, Eun Sug Park","doi":"10.1093/biostatistics/kxae038","DOIUrl":"10.1093/biostatistics/kxae038","url":null,"abstract":"Accounting for exposure measurement errors has been recognized as a crucial problem in environmental epidemiology for over two decades. Bayesian hierarchical models offer a coherent probabilistic framework for evaluating associations between environmental exposures and health effects, which take into account exposure measurement errors introduced by uncertainty in the estimated exposure as well as spatial misalignment between the exposure and health outcome data. While two-stage Bayesian analyses are often regarded as a good alternative to fully Bayesian analyses when joint estimation is not feasible, there has been minimal research on how to properly propagate uncertainty from the first-stage exposure model to the second-stage health model, especially in the case of a large number of participant locations along with spatially correlated exposures. We propose a scalable two-stage Bayesian approach, called a sparse multivariate normal (sparse MVN) prior approach, based on the Vecchia approximation for assessing associations between exposure and health outcomes in environmental epidemiology. We compare its performance with existing approaches through simulation. Our sparse MVN prior approach shows comparable performance with the fully Bayesian approach, which is a gold standard but is impossible to implement in some cases. We investigate the association between source-specific exposures and pollutant (nitrogen dioxide [NO2])-specific exposures and birth weight of full-term infants born in 2012 in Harris County, Texas, using several approaches, including the newly developed method.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11823266/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A modeling framework for detecting and leveraging node-level information in Bayesian network inference. 在贝叶斯网络推理中检测和利用节点级信息的建模框架。

IF 1.8 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxae021

Xiaoyue Xi, Hélène Ruffieux

{"title":"A modeling framework for detecting and leveraging node-level information in Bayesian network inference.","authors":"Xiaoyue Xi, Hélène Ruffieux","doi":"10.1093/biostatistics/kxae021","DOIUrl":"10.1093/biostatistics/kxae021","url":null,"abstract":"Bayesian graphical models are powerful tools to infer complex relationships in high dimension, yet are often fraught with computational and statistical challenges. If exploited in a principled way, the increasing information collected alongside the data of primary interest constitutes an opportunity to mitigate these difficulties by guiding the detection of dependence structures. For instance, gene network inference may be informed by the use of publicly available summary statistics on the regulation of genes by genetic variants. Here we present a novel Gaussian graphical modeling framework to identify and leverage information on the centrality of nodes in conditional independence graphs. Specifically, we consider a fully joint hierarchical model to simultaneously infer (i) sparse precision matrices and (ii) the relevance of node-level information for uncovering the sought-after network structure. We encode such information as candidate auxiliary variables using a spike-and-slab submodel on the propensity of nodes to be hubs, which allows hypothesis-free selection and interpretation of a sparse subset of relevant variables. As efficient exploration of large posterior spaces is needed for real-world applications, we develop a variational expectation conditional maximization algorithm that scales inference to hundreds of samples, nodes and auxiliary variables. We illustrate and exploit the advantages of our approach in simulations and in a gene network study which identifies hub genes involved in biological pathways relevant to immune-mediated diseases.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11823055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification and estimation of causal effects with confounders missing not at random. 非随机缺失混杂因素的因果效应识别和估计。

IF 1.8 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxaf015

Jian Sun, Bo Fu

引用次数: 0

Connectivity Regression. 连接回归。

IF 1.8 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxaf002

Neel Desai, Veera Baladandayuthapani, Russell T Shinohara, Jeffrey S Morris

{"title":"Connectivity Regression.","authors":"Neel Desai, Veera Baladandayuthapani, Russell T Shinohara, Jeffrey S Morris","doi":"10.1093/biostatistics/kxaf002","DOIUrl":"10.1093/biostatistics/kxaf002","url":null,"abstract":"Assessing how brain functional connectivity networks vary across individuals promises to uncover important scientific questions such as patterns of healthy brain aging through the lifespan or dysconnectivity associated with disease. In this article, we introduce a general regression framework, Connectivity Regression (ConnReg), for regressing subject-specific functional connectivity networks on covariates while accounting for within-network inter-edge dependence. ConnReg utilizes a multivariate generalization of Fisher's transformation to project network objects into an alternative space where Gaussian assumptions are justified and positive semidefinite constraints are automatically satisfied. Penalized multivariate regression is fit in the transformed space to simultaneously induce sparsity in regression coefficients and in covariance elements, which capture within network inter-edge dependence. We use permutation tests to perform multiplicity-adjusted inference to identify covariates associated with connectivity, and stability selection scores to identify network edges that vary with selected covariates. Simulation studies validate the inferential properties of our proposed method and demonstrate how estimating and accounting for within-network inter-edge dependence leads to more efficient estimation, more powerful inference, and more accurate selection of covariate-dependent network edges. We apply ConnReg to the Human Connectome Project Young Adult study, revealing insights into how connectivity varies with language processing covariates and structural brain features.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":"26 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12020475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143996159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Bayesian semi-parametric approach to causal mediation for longitudinal mediators and time-to-event outcomes with application to a cardiovascular disease cohort study. 贝叶斯半参数方法对纵向介质和事件发生时间结果的因果中介的应用于心血管疾病队列研究。

IF 2 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxaf027

Saurabh Bhandari, Michael J Daniels, Maria Josefsson, Donald M Lloyd-Jones, Juned Siddique

{"title":"A Bayesian semi-parametric approach to causal mediation for longitudinal mediators and time-to-event outcomes with application to a cardiovascular disease cohort study.","authors":"Saurabh Bhandari, Michael J Daniels, Maria Josefsson, Donald M Lloyd-Jones, Juned Siddique","doi":"10.1093/biostatistics/kxaf027","DOIUrl":"10.1093/biostatistics/kxaf027","url":null,"abstract":"Causal mediation analysis of observational data is an important tool for investigating the potential causal effects of medications on disease-related risk factors, and on time-to-death (or disease progression) through these risk factors. However, when analyzing data from a cohort study, such analyses are complicated by the longitudinal structure of the risk factors and the presence of time-varying confounders. Leveraging data from the Atherosclerosis Risk in Communities (ARIC) cohort study, we develop a causal mediation approach, using (semi-parametric) Bayesian Additive Regression Tree (BART) models for the longitudinal and survival data. Our framework is developed using static longitudinal exposure regimes and allows for time-varying confounders and mediators, both of which can be either continuous or binary. We also identify and estimate direct and indirect causal effects in the presence of a competing event. We apply our methods to assess how medication, prescribed to target cardiovascular disease (CVD) risk factors, affects the time-to-CVD death.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":"26 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12479244/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145193833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bayesian subtyping for multi-state brain functional connectome with application on preadolescent brain cognition. 多状态脑功能连接体贝叶斯分型及其在青春期前脑认知中的应用。

IF 2 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxae045

Tianqi Chen, Hongyu Zhao, Chichun Tan, Todd Constable, Sarah Yip, Yize Zhao

{"title":"Bayesian subtyping for multi-state brain functional connectome with application on preadolescent brain cognition.","authors":"Tianqi Chen, Hongyu Zhao, Chichun Tan, Todd Constable, Sarah Yip, Yize Zhao","doi":"10.1093/biostatistics/kxae045","DOIUrl":"10.1093/biostatistics/kxae045","url":null,"abstract":"Converging evidence indicates that the heterogeneity of cognitive profiles may arise through detectable alternations in brain functional connectivity. Despite an unprecedented opportunity to uncover neurobiological subtypes through clustering or subtyping analyses on multi-state functional connectivity, few existing approaches are applicable to accommodate the network topology and unique biological architecture. To address this issue, we propose an innovative Bayesian nonparametric network-variate clustering analysis to uncover subgroups of individuals with homogeneous brain functional network patterns under multiple cognitive states. In light of the existing neuroscience literature, we assume there are unknown state-specific modular structures within functional connectivity. Concurrently, we identify informative network features essential for defining subtypes. To further facilitate practical use, we develop a computationally efficient variational inference algorithm to approximate posterior inference with satisfactory estimation accuracy. Extensive simulations show the superiority of our method. We apply the method to the Adolescent Brain Cognitive Development (ABCD) study, and identify neurodevelopmental subtypes and brain sub-network phenotypes under each state to signal neurobiological heterogeneity, suggesting promising directions for further exploration and investigation in neuroscience.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11823269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A semiparametric Gaussian mixture model for chest CT-based 3D blood vessel reconstruction. 基于胸部 CT 的三维血管重建半参数高斯混合物模型

IF 1.8 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxae013

Qianhan Zeng, Jing Zhou, Ying Ji, Hansheng Wang

{"title":"A semiparametric Gaussian mixture model for chest CT-based 3D blood vessel reconstruction.","authors":"Qianhan Zeng, Jing Zhou, Ying Ji, Hansheng Wang","doi":"10.1093/biostatistics/kxae013","DOIUrl":"10.1093/biostatistics/kxae013","url":null,"abstract":"Computed tomography (CT) has been a powerful diagnostic tool since its emergence in the 1970s. Using CT data, 3D structures of human internal organs and tissues, such as blood vessels, can be reconstructed using professional software. This 3D reconstruction is crucial for surgical operations and can serve as a vivid medical teaching example. However, traditional 3D reconstruction heavily relies on manual operations, which are time-consuming, subjective, and require substantial experience. To address this problem, we develop a novel semiparametric Gaussian mixture model tailored for the 3D reconstruction of blood vessels. This model extends the classical Gaussian mixture model by enabling nonparametric variations in the component-wise parameters of interest according to voxel positions. We develop a kernel-based expectation-maximization algorithm for estimating the model parameters, accompanied by a supporting asymptotic theory. Furthermore, we propose a novel regression method for optimal bandwidth selection. Compared to the conventional cross-validation-based (CV) method, the regression method outperforms the CV method in terms of computational and statistical efficiency. In application, this methodology facilitates the fully automated reconstruction of 3D blood vessel structures with remarkable accuracy.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140869271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bayesian thresholded modeling for integrating brain node and network predictors. 脑节点和网络预测器集成的贝叶斯阈值建模。

IF 1.8 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxae048

Zhe Sun, Wanwan Xu, Tianxi Li, Jian Kang, Gregorio Alanis-Lobato, Yize Zhao

{"title":"Bayesian thresholded modeling for integrating brain node and network predictors.","authors":"Zhe Sun, Wanwan Xu, Tianxi Li, Jian Kang, Gregorio Alanis-Lobato, Yize Zhao","doi":"10.1093/biostatistics/kxae048","DOIUrl":"10.1093/biostatistics/kxae048","url":null,"abstract":"Progress in neuroscience has provided unprecedented opportunities to advance our understanding of brain alterations and their correspondence to phenotypic profiles. With data collected from various imaging techniques, studies have integrated different types of information ranging from brain structure, function, or metabolism. More recently, an emerging way to categorize imaging traits is through a metric hierarchy, including localized node-level measurements and interactive network-level metrics. However, limited research has been conducted to integrate these different hierarchies and achieve a better understanding of the neurobiological mechanisms and communications. In this work, we address this literature gap by proposing a Bayesian regression model under both vector-variate and matrix-variate predictors. To characterize the interplay between different predicting components, we propose a set of biologically plausible prior models centered on an innovative joint thresholded prior. This captures the coupling and grouping effect of signal patterns, as well as their spatial contiguity across brain anatomy. By developing a posterior inference, we can identify and quantify the uncertainty of signaling node- and network-level neuromarkers, as well as their predictive mechanism for phenotypic outcomes. Through extensive simulations, we demonstrate that our proposed method outperforms the alternative approaches substantially in both out-of-sample prediction and feature selection. By implementing the model to study children's general mental abilities, we establish a powerful predictive mechanism based on the identified task contrast traits and resting-state sub-networks.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":"26 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11823287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Estimating causal effects for binary outcomes using per-decision inverse probability weighting. 使用每次决定的反概率加权法估算二元结果的因果效应。

IF 1.8 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxae025

Yihan Bao, Lauren Bell, Elizabeth Williamson, Claire Garnett, Tianchen Qian

{"title":"Estimating causal effects for binary outcomes using per-decision inverse probability weighting.","authors":"Yihan Bao, Lauren Bell, Elizabeth Williamson, Claire Garnett, Tianchen Qian","doi":"10.1093/biostatistics/kxae025","DOIUrl":"10.1093/biostatistics/kxae025","url":null,"abstract":"Micro-randomized trials are commonly conducted for optimizing mobile health interventions such as push notifications for behavior change. In analyzing such trials, causal excursion effects are often of primary interest, and their estimation typically involves inverse probability weighting (IPW). However, in a micro-randomized trial, additional treatments can often occur during the time window over which an outcome is defined, and this can greatly inflate the variance of the causal effect estimator because IPW would involve a product of numerous weights. To reduce variance and improve estimation efficiency, we propose two new estimators using a modified version of IPW, which we call \"per-decision IPW.\" The second estimator further improves efficiency using the projection idea from the semiparametric efficiency theory. These estimators are applicable when the outcome is binary and can be expressed as the maximum of a series of sub-outcomes defined over sub-intervals of time. We establish the estimators' consistency and asymptotic normality. Through simulation studies and real data applications, we demonstrate substantial efficiency improvement of the proposed estimator over existing estimators. The new estimators can be used to improve the precision of primary and secondary analyses for micro-randomized trials with binary outcomes.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141794123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0