Annals of Applied Statistics最新文献_第3页

PAIRWISE NONLINEAR DEPENDENCE ANALYSIS OF GENOMIC DATA. 基因组数据的两两非线性相关性分析。

IF 1.8 4区数学

Annals of Applied Statistics Pub Date : 2023-12-01 Epub Date: 2023-10-30 DOI: 10.1214/23-aoas1745

Siqi Xiang, Wan Zhang, Siyao Liu, Katherine A Hoadley, Charles M Perou, Kai Zhang, J S Marron

引用次数: 0

TARGETING UNDERREPRESENTED POPULATIONS IN PRECISION MEDICINE: A FEDERATED TRANSFER LEARNING APPROACH. 针对精准医疗中代表性不足的人群：一种联合转移学习方法。

IF 1.3 4区数学

Annals of Applied Statistics Pub Date : 2023-12-01 Epub Date: 2023-10-30 DOI: 10.1214/23-AOAS1747

By Sai Li, Tianxi Cai, Rui Duan

{"title":"TARGETING UNDERREPRESENTED POPULATIONS IN PRECISION MEDICINE: A FEDERATED TRANSFER LEARNING APPROACH.","authors":"By Sai Li, Tianxi Cai, Rui Duan","doi":"10.1214/23-AOAS1747","DOIUrl":"10.1214/23-AOAS1747","url":null,"abstract":"The limited representation of minorities and disadvantaged populations in large-scale clinical and genomics research poses a significant barrier to translating precision medicine research into practice. Prediction models are likely to underperform in underrepresented populations due to heterogeneity across populations, thereby exacerbating known health disparities. To address this issue, we propose FETA, a two-way data integration method that leverages a federated transfer learning approach to integrate heterogeneous data from diverse populations and multiple healthcare institutions, with a focus on a target population of interest having limited sample sizes. We show that FETA achieves performance comparable to the pooled analysis, where individual-level data is shared across institutions, with only a small number of communications across participating sites. Our theoretical analysis and simulation study demonstrate how FETA's estimation accuracy is influenced by communication budgets, privacy restrictions, and heterogeneity across populations. We apply FETA to multisite data from the electronic Medical Records and Genomics (eMERGE) Network to construct genetic risk prediction models for extreme obesity. Compared to models trained using target data only, source data only, and all data without accounting for population-level differences, FETA shows superior predictive performance. FETA has the potential to improve estimation and prediction accuracy in underrepresented populations and reduce the gap in model performance across populations.","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"17 4","pages":"2970-2992"},"PeriodicalIF":1.3,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

ADDRESSING SELECTION BIAS AND MEASUREMENT ERROR IN COVID-19 CASE COUNT DATA USING AUXILIARY INFORMATION. 利用辅助信息解决 covid-19 病例计数数据中的选择偏差和测量误差。

IF 1.3 4区数学

Annals of Applied Statistics Pub Date : 2023-12-01 Epub Date: 2023-10-30 DOI: 10.1214/23-aoas1744

Walter Dempsey

{"title":"ADDRESSING SELECTION BIAS AND MEASUREMENT ERROR IN COVID-19 CASE COUNT DATA USING AUXILIARY INFORMATION.","authors":"Walter Dempsey","doi":"10.1214/23-aoas1744","DOIUrl":"https://doi.org/10.1214/23-aoas1744","url":null,"abstract":"Coronavirus case-count data has influenced government policies and drives most epidemiological forecasts. Limited testing is cited as the key driver behind minimal information on the COVID-19 pandemic. While expanded testing is laudable, measurement error and selection bias are the two greatest problems limiting our understanding of the COVID-19 pandemic; neither can be fully addressed by increased testing capacity. In this paper, we demonstrate their impact on estimation of point prevalence and the effective reproduction number. We show that estimates based on the millions of molecular tests in the US has the same mean square error as a small simple random sample. To address this, a procedure is presented that combines case-count data and random samples over time to estimate selection propensities based on key covariate information. We then combine these selection propensities with epidemiological forecast models to construct a doubly robust estimation method that accounts for both measurement-error and selection bias. This method is then applied to estimate Indiana's active infection prevalence using case-count, hospitalization, and death data with demographic information, a statewide random molecular sample collected from April 25-29th, and Delphi's COVID-19 Trends and Impact Survey. We end with a series of recommendations based on the proposed methodology.","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"17 4","pages":"2903-2923"},"PeriodicalIF":1.3,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

GENERALIZED MATRIX DECOMPOSITION REGRESSION: ESTIMATION AND INFERENCE FOR TWO-WAY STRUCTURED DATA. 广义矩阵分解回归：双向结构化数据的估计和推断。

IF 1.3 4区数学

Annals of Applied Statistics Pub Date : 2023-12-01 Epub Date: 2023-10-30 DOI: 10.1214/23-aoas1746

Yue Wang, Ali Shojaie, Timothy Randolph, Parker Knight, Jing Ma

{"title":"GENERALIZED MATRIX DECOMPOSITION REGRESSION: ESTIMATION AND INFERENCE FOR TWO-WAY STRUCTURED DATA.","authors":"Yue Wang, Ali Shojaie, Timothy Randolph, Parker Knight, Jing Ma","doi":"10.1214/23-aoas1746","DOIUrl":"10.1214/23-aoas1746","url":null,"abstract":"Motivated by emerging applications in ecology, microbiology, and neuroscience, this paper studies high-dimensional regression with two-way structured data. To estimate the high-dimensional coefficient vector, we propose the generalized matrix decomposition regression (GMDR) to efficiently leverage auxiliary information on row and column structures. GMDR extends the principal component regression (PCR) to two-way structured data, but unlike PCR, GMDR selects the components that are most predictive of the outcome, leading to more accurate prediction. For inference on regression coefficients of individual variables, we propose the generalized matrix decomposition inference (GMDI), a general high-dimensional inferential framework for a large family of estimators that include the proposed GMDR estimator. GMDI provides more flexibility for incorporating relevant auxiliary row and column structures. As a result, GMDI does not require the true regression coefficients to be sparse, but constrains the coordinate system representing the regression coefficients according to the column structure. GMDI also allows dependent and heteroscedastic observations. We study the theoretical properties of GMDI in terms of both the type-I error rate and power and demonstrate the effectiveness of GMDR and GMDI in simulation studies and an application to human microbiome data.","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"17 4","pages":"2944-2969"},"PeriodicalIF":1.3,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10751029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139040863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 DYNAMIC ADDITIVE AND MULTIPLICATIVE EFFECTS NETWORK MODEL WITH APPLICATION TO THE UNITED NATIONS VOTING BEHAVIORS. 将动态加乘效应网络模型应用于联合国投票行为。

IF 1.8 4区数学

Annals of Applied Statistics Pub Date : 2023-12-01 Epub Date: 2023-10-30 DOI: 10.1214/23-aoas1762

Bomin Kim, Xiaoyue Niu, David Hunter, Xun CaO

引用次数: 0

Debiased lasso for stratified Cox models with application to the national kidney transplant data. 分层 Cox 模型的去偏套索，并应用于全国肾移植数据。

IF 1.8 4区数学

Annals of Applied Statistics Pub Date : 2023-12-01 Epub Date: 2023-10-30 DOI: 10.1214/23-aoas1775

Lu Xia, Bin Nan, Yi Li

{"title":"Debiased lasso for stratified Cox models with application to the national kidney transplant data.","authors":"Lu Xia, Bin Nan, Yi Li","doi":"10.1214/23-aoas1775","DOIUrl":"https://doi.org/10.1214/23-aoas1775","url":null,"abstract":"The Scientific Registry of Transplant Recipients (SRTR) system has become a rich resource for understanding the complex mechanisms of graft failure after kidney transplant, a crucial step for allocating organs effectively and implementing appropriate care. As transplant centers that treated patients might strongly confound graft failures, Cox models stratified by centers can eliminate their confounding effects. Also, since recipient age is a proven non-modifiable risk factor, a common practice is to fit models separately by recipient age groups. The moderate sample sizes, relative to the number of covariates, in some age groups may lead to biased maximum stratified partial likelihood estimates and unreliable confidence intervals even when samples still outnumber covariates. To draw reliable inference on a comprehensive list of risk factors measured from both donors and recipients in SRTR, we propose a de-biased lasso approach via quadratic programming for fitting stratified Cox models. We establish asymptotic properties and verify via simulations that our method produces consistent estimates and confidence intervals with nominal coverage probabilities. Accounting for nearly 100 confounders in SRTR, the de-biased method detects that the graft failure hazard nonlinearly increases with donor's age among all recipient age groups, and that organs from older donors more adversely impact the younger recipients. Our method also delineates the associations between graft failure and many risk factors such as recipients' primary diagnoses (e.g. polycystic disease, glomerular disease, and diabetes) and donor-recipient mismatches for human leukocyte antigen loci across recipient age groups. These results may inform the refinement of donor-recipient matching criteria for stakeholders.","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"17 4","pages":"3550-3569"},"PeriodicalIF":1.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10720921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138813084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 HIERARCHICAL MODELING AND ANALYSIS FOR ACTIGRAPH DATA FROM WEARABLE DEVICES. 对来自可穿戴设备的动作图数据进行贝叶斯分层建模和分析。

IF 1.8 4区数学

Annals of Applied Statistics Pub Date : 2023-12-01 Epub Date: 2023-10-30 DOI: 10.1214/23-aoas1742

Pierfrancesco Alaimo Di Loro, Marco Mingione, Jonah Lipsitt, Christina M Batteate, Michael Jerrett, Sudipto Banerjee

{"title":"BAYESIAN HIERARCHICAL MODELING AND ANALYSIS FOR ACTIGRAPH DATA FROM WEARABLE DEVICES.","authors":"Pierfrancesco Alaimo Di Loro, Marco Mingione, Jonah Lipsitt, Christina M Batteate, Michael Jerrett, Sudipto Banerjee","doi":"10.1214/23-aoas1742","DOIUrl":"10.1214/23-aoas1742","url":null,"abstract":"The majority of Americans fail to achieve recommended levels of physical activity, which leads to numerous preventable health problems such as diabetes, hypertension, and heart diseases. This has generated substantial interest in monitoring human activity to gear interventions toward environmental features that may relate to higher physical activity. Wearable devices, such as wrist-worn sensors that monitor gross motor activity (actigraph units) continuously record the activity levels of a subject, producing massive amounts of high-resolution measurements. Analyzing actigraph data needs to account for spatial and temporal information on trajectories or paths traversed by subjects wearing such devices. Inferential objectives include estimating a subject's physical activity levels along a given trajectory; identifying trajectories that are more likely to produce higher levels of physical activity for a given subject; and predicting expected levels of physical activity in any proposed new trajectory for a given set of health attributes. Here, we devise a Bayesian hierarchical modeling framework for spatial-temporal actigraphy data to deliver fully model-based inference on trajectories while accounting for subject-level health attributes and spatial-temporal dependencies. We undertake a comprehensive analysis of an original dataset from the Physical Activity through Sustainable Transport Approaches in Los Angeles (PASTA-LA) study to ascertain spatial zones and trajectories exhibiting significantly higher levels of physical activity while accounting for various sources of heterogeneity.","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"17 4","pages":"2865-2886"},"PeriodicalIF":1.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139572045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 DYNAMIC SPATIAL FILTERING APPROACH TO MITIGATE UNDERESTIMATION BIAS IN FIELD CALIBRATED LOW-COST SENSOR AIR POLLUTION DATA. 一种动态空间过滤方法，用于减轻现场校准的低成本传感器空气污染数据的低估偏差。

IF 1.8 4区数学

Annals of Applied Statistics Pub Date : 2023-12-01 Epub Date: 2023-10-30 DOI: 10.1214/23-aoas1751

Claire Heffernan, Roger PenG, Drew R Gentner, Kirsten Koehler, Abhirup Datta

{"title":"A DYNAMIC SPATIAL FILTERING APPROACH TO MITIGATE UNDERESTIMATION BIAS IN FIELD CALIBRATED LOW-COST SENSOR AIR POLLUTION DATA.","authors":"Claire Heffernan, Roger PenG, Drew R Gentner, Kirsten Koehler, Abhirup Datta","doi":"10.1214/23-aoas1751","DOIUrl":"https://doi.org/10.1214/23-aoas1751","url":null,"abstract":"Low-cost air pollution sensors, offering hyper-local characterization of pollutant concentrations, are becoming increasingly prevalent in environmental and public health research. However, low-cost air pollution data can be noisy, biased by environmental conditions, and usually need to be field-calibrated by collocating low-cost sensors with reference-grade instruments. We show, theoretically and empirically, that the common procedure of regression-based calibration using collocated data systematically underestimates high air pollution concentrations, which are critical to diagnose from a health perspective. Current calibration practices also often fail to utilize the spatial correlation in pollutant concentrations. We propose a novel spatial filtering approach to collocation-based calibration of low-cost networks that mitigates the underestimation issue by using an inverse regression. The inverse-regression also allows for incorporating spatial correlations by a second-stage model for the true pollutant concentrations using a conditional Gaussian Process. Our approach works with one or more collocated sites in the network and is dynamic, leveraging spatial correlation with the latest available reference data. Through extensive simulations, we demonstrate how the spatial filtering substantially improves estimation of pollutant concentrations, and measures peak concentrations with greater accuracy. We apply the methodology for calibration of a low-cost PM2.5 network in Baltimore, Maryland, and diagnose air pollution peaks that are missed by the regression-calibration.","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"17 4","pages":"3056-3087"},"PeriodicalIF":1.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11031266/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 combinatorial MultiStudy factor analysis. 贝叶斯组合多因素分析。

IF 1.3 4区数学

Annals of Applied Statistics Pub Date : 2023-09-01 Epub Date: 2023-09-07 DOI: 10.1214/22-aoas1715

Isabella N Grabski, Roberta De Vito, Lorenzo Trippa, Giovanni Parmigiani

{"title":"Bayesian combinatorial MultiStudy factor analysis.","authors":"Isabella N Grabski, Roberta De Vito, Lorenzo Trippa, Giovanni Parmigiani","doi":"10.1214/22-aoas1715","DOIUrl":"10.1214/22-aoas1715","url":null,"abstract":"Mutations in the BRCA1 and BRCA2 genes are known to be highly associated with breast cancer. Identifying both shared and unique transcript expression patterns in blood samples from these groups can shed insight into if and how the disease mechanisms differ among individuals by mutation status, but this is challenging in the high-dimensional setting. A recent method, Bayesian Multi-Study Factor Analysis (BMSFA), identifies latent factors common to all studies (or equivalently, groups) and latent factors specific to individual studies. However, BMSFA does not allow for factors shared by more than one but less than all studies. This is critical in our context, as we may expect some but not all signals to be shared by BRCA1-and BRCA2-mutation carriers but not necessarily other high-risk groups. We extend BMSFA by introducing a new method, Tetris, for Bayesian combinatorial multi-study factor analysis, which identifies latent factors that any combination of studies or groups can share. We model the subsets of studies that share latent factors with an Indian Buffet Process, and offer a way to summarize uncertainty in the sharing patterns using credible balls. We test our method with an extensive range of simulations, and showcase its utility not only in dimension reduction but also in covariance estimation. When applied to transcript expression data from high-risk families grouped by mutation status, Tetris reveals the features and pathways characterizing each group and the sharing patterns among them. Finally, we further extend Tetris to discover groupings of samples when group labels are not provided, which can elucidate additional structure in these data.","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"17 3","pages":"2212-2235"},"PeriodicalIF":1.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10543692/pdf/nihms-1926927.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41156472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

THE SCALABLE BIRTH-DEATH MCMC ALGORITHM FOR MIXED GRAPHICAL MODEL LEARNING WITH APPLICATION TO GENOMIC DATA INTEGRATION. 用于混合图形模型学习的可扩展出生路径MCMC算法及其在基因组数据集成中的应用。

IF 1.8 4区数学

Annals of Applied Statistics Pub Date : 2023-09-01 Epub Date: 2023-10-07 DOI: 10.1214/22-aoas1701

Nanwei Wang, Hélène Massam, Xin Gao, Laurent Briollais

{"title":"THE SCALABLE BIRTH-DEATH MCMC ALGORITHM FOR MIXED GRAPHICAL MODEL LEARNING WITH APPLICATION TO GENOMIC DATA INTEGRATION.","authors":"Nanwei Wang, Hélène Massam, Xin Gao, Laurent Briollais","doi":"10.1214/22-aoas1701","DOIUrl":"10.1214/22-aoas1701","url":null,"abstract":"Recent advances in biological research have seen the emergence of high-throughput technologies with numerous applications that allow the study of biological mechanisms at an unprecedented depth and scale. A large amount of genomic data is now distributed through consortia like The Cancer Genome Atlas (TCGA), where specific types of biological information on specific type of tissue or cell are available. In cancer research, the challenge is now to perform integrative analyses of high-dimensional multi-omic data with the goal to better understand genomic processes that correlate with cancer outcomes, e.g. elucidate gene networks that discriminate a specific cancer subgroups (cancer sub-typing) or discovering gene networks that overlap across different cancer types (pan-cancer studies). In this paper, we propose a novel mixed graphical model approach to analyze multi-omic data of different types (continuous, discrete and count) and perform model selection by extending the Birth-Death MCMC (BDMCMC) algorithm initially proposed by Stephens (2000) and later developed by Mohammadi and Wit (2015). We compare the performance of our method to the LASSO method and the standard BDMCMC method using simulations and find that our method is superior in terms of both computational efficiency and the accuracy of the model selection results. Finally, an application to the TCGA breast cancer data shows that integrating genomic information at different levels (mutation and expression data) leads to better subtyping of breast cancers.","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"17 3","pages":"1958-1983"},"PeriodicalIF":1.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10569451/pdf/nihms-1886934.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41219379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1