Biostatistics最新文献_第4页

Predicting distributions of physical activity profiles in the National Health and Nutrition Examination Survey database using a partially linear Fréchet single index model. 使用部分线性fr<s:1>单指数模型预测国家健康和营养检查调查数据库中身体活动概况的分布。

IF 1.8 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxaf013

Marcos Matabuena, Aritra Ghosal, Wendy Meiring, Alexander Petersen

{"title":"Predicting distributions of physical activity profiles in the National Health and Nutrition Examination Survey database using a partially linear Fréchet single index model.","authors":"Marcos Matabuena, Aritra Ghosal, Wendy Meiring, Alexander Petersen","doi":"10.1093/biostatistics/kxaf013","DOIUrl":"10.1093/biostatistics/kxaf013","url":null,"abstract":"Object-oriented data analysis is a fascinating and evolving field in modern statistical science, with the potential to make significant contributions to biomedical applications. This statistical framework facilitates the development of new methods to analyze complex data objects that capture more information than traditional clinical biomarkers. This paper applies the object-oriented framework to analyze physical activity levels, measured by accelerometers, as response objects in a regression model. Unlike traditional summary metrics, we utilize a recently proposed representation of physical activity data as a distributional object, providing a more nuanced and complete profile of individual energy expenditure across all ranges of monitoring intensity. A novel hybrid Fréchet regression model is proposed and applied to US population accelerometer data from National Health and Nutrition Examination Survey (NHANES) 2011 to 2014. The semi-parametric nature of the model allows for the inclusion of nonlinear effects for critical variables, such as age, which are biologically known to have subtle impacts on physical activity. Simultaneously, the inclusion of linear effects preserves interpretability for other variables, particularly categorical covariates such as ethnicity and sex. The results obtained are valuable from a public health perspective and could lead to new strategies for optimizing physical activity interventions in specific American subpopulations.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":"26 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129647","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 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

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 1.8 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":1.8,"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

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":"https://doi.org/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

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

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

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

Covariate-adjusted estimators of diagnostic accuracy in randomized trials. 随机试验中诊断准确性的协变量校正估计值。

IF 1.8 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxaf005

Jon A Steingrimsson

{"title":"Covariate-adjusted estimators of diagnostic accuracy in randomized trials.","authors":"Jon A Steingrimsson","doi":"10.1093/biostatistics/kxaf005","DOIUrl":"10.1093/biostatistics/kxaf005","url":null,"abstract":"Randomized controlled trials evaluating the diagnostic accuracy of a marker frequently collect information on baseline covariates in addition to information on the marker and the reference standard. However, standard estimators of sensitivity and specificity do not use data on baseline covariates and restrict the analysis to data from participants with a positive reference standard in the intervention arm being evaluated. Covariate-adjusted estimators for marginal treatment effects have been developed and been advocated for by regulatory agencies because they can improve power compared to unadjusted estimators. Despite this, similar covariate-adjusted estimators for marginal sensitivity and specificity have not yet been developed. In this manuscript, we address this gap by developing covariate-adjusted estimators for marginal sensitivity and specificity of a diagnostic test that leverage baseline covariate information. The estimators also use data from all participants, not just participants with a positive reference standard in the intervention arm being evaluated. We derive the asymptotic properties of the estimators and evaluate the finite sample properties of the estimators using simulations and by analyzing data on lung cancer screening.","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":"26 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626881","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

Exposure proximal immune correlates analysis. 接触近端免疫相关性分析。

IF 1.8 3区数学

Biostatistics Pub Date : 2024-12-31 DOI: 10.1093/biostatistics/kxae031

Ying Huang, Dean Follmann

{"title":"Exposure proximal immune correlates analysis.","authors":"Ying Huang, Dean Follmann","doi":"10.1093/biostatistics/kxae031","DOIUrl":"10.1093/biostatistics/kxae031","url":null,"abstract":"Immune response decays over time, and vaccine-induced protection often wanes. Understanding how vaccine efficacy changes over time is critical to guiding the development and application of vaccines in preventing infectious diseases. The objective of this article is to develop statistical methods that assess the effect of decaying immune responses on the risk of disease and on vaccine efficacy, within the context of Cox regression with sparse sampling of immune responses, in a baseline-naive population. We aim to further disentangle the various aspects of the time-varying vaccine effect, whether direct on disease or mediated through immune responses. Based on time-to-event data from a vaccine efficacy trial and sparse sampling of longitudinal immune responses, we propose a weighted estimated induced likelihood approach that models the longitudinal immune response trajectory and the time to event separately. This approach assesses the effects of the decaying immune response, the peak immune response, and/or the waning vaccine effect on the risk of disease. The proposed method is applicable not only to standard randomized trial designs but also to augmented vaccine trial designs that re-vaccinate uninfected placebo recipients at the end of the standard trial period. We conducted simulation studies to evaluate the performance of our method and applied the method to analyze immune correlates from a phase III SARS-CoV-2 vaccine trial.","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/PMC11823265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141984050","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