Annals of Applied Statistics最新文献

{"title":"BAYESIAN FUNCTIONAL REGISTRATION OF FMRI ACTIVATION MAPS.","authors":"Guoqing Wang, Abhirup Datta, Martin A Lindquist","doi":"10.1214/21-aoas1562","DOIUrl":"10.1214/21-aoas1562","url":null,"abstract":"<p><p>Functional magnetic resonance imaging (fMRI) has provided invaluable insight into our understanding of human behavior. However, large inter-individual differences in both brain anatomy and functional localization <i>after</i> anatomical alignment remain a major limitation in conducting group analyses and performing population level inference. This paper addresses this problem by developing and validating a new computational technique for reducing misalignment across individuals in functional brain systems by spatially transforming each subjects functional data to a common reference map. Our proposed Bayesian functional registration approach allows us to assess differences in brain function across subjects and individual differences in activation topology. It combines intensity-based and feature-based information into an integrated framework, and allows inference to be performed on the transformation via the posterior samples. We evaluate the method in a simulation study and apply it to data from a study of thermal pain. We find that the proposed approach provides increased sensitivity for group-level inference.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 3","pages":"1676-1699"},"PeriodicalIF":1.3,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312483/pdf/nihms-1910200.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10138002","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}

{"title":"SENSITIVITY ANALYSIS FOR EVALUATING PRINCIPAL SURROGATE ENDPOINTS RELAXING THE EQUAL EARLY CLINICAL RISK ASSUMPTION.","authors":"Ying Huang, Yingying Zhuang, Peter Gilbert","doi":"10.1214/21-aoas1566","DOIUrl":"10.1214/21-aoas1566","url":null,"abstract":"<p><p>This article addresses the evaluation of post-randomization immune response biomarkers as principal surrogate endpoints of a vaccine's protective effect, based on data from randomized vaccine trials. An important metric for quantifying a biomarker's principal surrogacy in vaccine research is the vaccine efficacy curve, which shows a vaccine's efficacy as a function of potential biomarker values if receiving vaccine, among an 'early-always-at-risk' principal stratum of trial participants who remain disease-free at the time of biomarker measurement whether having received vaccine or placebo. Earlier work in principal surrogate evaluation relied on an 'equal-early-clinical-risk' assumption for identifiability of the vaccine curve, based on observed disease status at the time of biomarker measurement. This assumption is violated in the common setting that the vaccine has an early effect on the clinical endpoint before the biomarker is measured. In particular, a vaccine's early protective effect observed in two phase III dengue vaccine trials (CYD14/CYD15) has motivated our current research development. We relax the 'equal-early-clinical-risk' assumption and propose a new sensitivity analysis framework for principal surrogate evaluation allowing for early vaccine efficacy. Under this framework, we develop inference procedures for vaccine efficacy curve estimators based on the estimated maximum likelihood approach. We then use the proposed methodology to assess the surrogacy of post-randomization neutralization titer in the motivating dengue application.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 3","pages":"1774-1794"},"PeriodicalIF":1.8,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10065750/pdf/nihms-1836703.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10190558","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}

{"title":"MEASURING PERFORMANCE FOR END-OF-LIFE CARE.","authors":"Sebastien Haneuse,&nbsp;Deborah Schrag,&nbsp;Francesca Dominici,&nbsp;Sharon-Lise Normand,&nbsp;Kyu Ha Lee","doi":"10.1214/21-aoas1558","DOIUrl":"https://doi.org/10.1214/21-aoas1558","url":null,"abstract":"<p><p>Although not without controversy, readmission is entrenched as a hospital quality metric with statistical analyses generally based on fitting a logistic-Normal generalized linear mixed model. Such analyses, however, ignore death as a competing risk, although doing so for clinical conditions with high mortality can have profound effects; a hospital's seemingly good performance for readmission may be an artifact of it having poor performance for mortality. in this paper we propose novel multivariate hospital-level performance measures for readmission and mortality that derive from framing the analysis as one of cluster-correlated semi-competing risks data. We also consider a number of profiling-related goals, including the identification of extreme performers and a bivariate classification of whether the hospital has higher-/lower-than-expected readmission and mortality rates via a Bayesian decision-theoretic approach that characterizes hospitals on the basis of minimizing the posterior expected loss for an appropriate loss function. in some settings, particularly if the number of hospitals is large, the computational burden may be prohibitive. To resolve this, we propose a series of analysis strategies that will be useful in practice. Throughout, the methods are illustrated with data from CMS on <i>N</i> = 17,685 patients diagnosed with pancreatic cancer between 2000-2012 at one of <i>J</i> = 264 hospitals in California.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 3","pages":"1586-1607"},"PeriodicalIF":1.8,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9728673/pdf/nihms-1842846.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10333686","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}

{"title":"A FLEXIBLE SENSITIVITY ANALYSIS APPROACH FOR UNMEASURED CONFOUNDING WITH MULTIPLE TREATMENTS AND A BINARY OUTCOME WITH APPLICATION TO SEER-MEDICARE LUNG CANCER DATA.","authors":"Liangyuan Hu, Jungang Zou, Chenyang Gu, Jiayi Ji, Michael Lopez, Minal Kale","doi":"10.1214/21-aoas1530","DOIUrl":"10.1214/21-aoas1530","url":null,"abstract":"<p><p>In the absence of a randomized experiment, a key assumption for drawing causal inference about treatment effects is the ignorable treatment assignment. Violations of the ignorability assumption may lead to biased treatment effect estimates. Sensitivity analysis helps gauge how causal conclusions will be altered in response to the potential magnitude of departure from the ignorability assumption. However, sensitivity analysis approaches for unmeasured confounding in the context of multiple treatments and binary outcomes are scarce. We propose a flexible Monte Carlo sensitivity analysis approach for causal inference in such settings. We first derive the general form of the bias introduced by unmeasured confounding, with emphasis on theoretical properties uniquely relevant to multiple treatments. We then propose methods to encode the impact of unmeasured confounding on potential outcomes and adjust the estimates of causal effects in which the presumed unmeasured confounding is removed. Our proposed methods embed nested multiple imputation within the Bayesian framework, which allow for seamless integration of the uncertainty about the values of the sensitivity parameters and the sampling variability, as well as use of the Bayesian Additive Regression Trees for modeling flexibility. Expansive simulations validate our methods and gain insight into sensitivity analysis with multiple treatments. We use the SEER-Medicare data to demonstrate sensitivity analysis using three treatments for early stage non-small cell lung cancer. The methods developed in this work are readily available in the R package SAMTx.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 2","pages":"1014-1037"},"PeriodicalIF":1.8,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9835106/pdf/nihms-1859782.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10538891","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}

{"title":"A FLEXIBLE BAYESIAN FRAMEWORK TO ESTIMATE AGE- AND CAUSE-SPECIFIC CHILD MORTALITY OVER TIME FROM SAMPLE REGISTRATION DATA.","authors":"Austin E Schumacher,&nbsp;Tyler H McCormick,&nbsp;Jon Wakefield,&nbsp;Yue Chu,&nbsp;Jamie Perin,&nbsp;Francisco Villavicencio,&nbsp;Noah Simon,&nbsp;Li Liu","doi":"10.1214/21-aoas1489","DOIUrl":"https://doi.org/10.1214/21-aoas1489","url":null,"abstract":"<p><p>In order to implement disease-specific interventions in young age groups, policy makers in low- and middle-income countries require timely and accurate estimates of age- and cause-specific child mortality. High-quality data is not available in settings where these interventions are most needed, but there is a push to create sample registration systems that collect detailed mortality information. current methods that estimate mortality from this data employ multistage frameworks without rigorous statistical justification that separately estimate all-cause and cause-specific mortality and are not sufficiently adaptable to capture important features of the data. We propose a flexible Bayesian modeling framework to estimate age- and cause-specific child mortality from sample registration data. We provide a theoretical justification for the framework, explore its properties via simulation, and use it to estimate mortality trends using data from the Maternal and Child Health Surveillance System in China.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 1","pages":"124-143"},"PeriodicalIF":1.8,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10448806/pdf/nihms-1862449.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10103673","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}

{"title":"PREDICTION OF HEREDITARY CANCERS USING NEURAL NETWORKS.","authors":"By Zoe Guan,&nbsp;Giovanni Parmigiani,&nbsp;Danielle Braun,&nbsp;Lorenzo Trippa","doi":"10.1214/21-aoas1510","DOIUrl":"10.1214/21-aoas1510","url":null,"abstract":"<p><p>Family history is a major risk factor for many types of cancer. Mendelian risk prediction models translate family histories into cancer risk predictions, based on knowledge of cancer susceptibility genes. These models are widely used in clinical practice to help identify high-risk individuals. Mendelian models leverage the entire family history, but they rely on many assumptions about cancer susceptibility genes that are either unrealistic or challenging to validate, due to low mutation prevalence. Training more flexible models, such as neural networks, on large databases of pedigrees can potentially lead to accuracy gains. In this paper we develop a framework to apply neural networks to family history data and investigate their ability to learn inherited susceptibility to cancer. While there is an extensive literature on neural networks and their state-of-the-art performance in many tasks, there is little work applying them to family history data. We propose adaptations of fully-connected neural networks and convolutional neural networks to pedigrees. In data simulated under Mendelian inheritance, we demonstrate that our proposed neural network models are able to achieve nearly optimal prediction performance. Moreover, when the observed family history includes misreported cancer diagnoses, neural networks are able to outperform the Mendelian BRCAPRO model embedding the correct inheritance laws. Using a large dataset of over 200,000 family histories, the Risk Service cohort, we train prediction models for future risk of breast cancer. We validate the models using data from the Cancer Genetics Network.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 1","pages":"495-520"},"PeriodicalIF":1.8,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10593124/pdf/nihms-1937267.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49693607","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}

{"title":"PARTITIONING AROUND MEDOIDS CLUSTERING AND RANDOM FOREST CLASSIFICATION FOR GIS-INFORMED IMPUTATION OF FLUORIDE CONCENTRATION DATA.","authors":"Yu Gu,&nbsp;John S Preisser,&nbsp;Donglin Zeng,&nbsp;Poojan Shrestha,&nbsp;Molina Shah,&nbsp;Miguel A Simancas-Pallares,&nbsp;Jeannie Ginnis,&nbsp;Kimon Divaris","doi":"10.1214/21-aoas1516","DOIUrl":"https://doi.org/10.1214/21-aoas1516","url":null,"abstract":"<p><p>Community water fluoridation is an important component of oral health promotion, as fluoride exposure is a well-documented dental caries-preventive agent. Direct measurements of domestic water fluoride content provide valuable information regarding individuals' fluoride exposure and thus caries risk; however, they are logistically challenging to carry out at a large scale in oral health research. This article describes the development and evaluation of a novel method for the imputation of missing domestic water fluoride concentration data informed by spatial autocorrelation. The context is a state-wide epidemiologic study of pediatric oral health in North Carolina, where domestic water fluoride concentration information was missing for approximately 75% of study participants with clinical data on dental caries. A new machine-learning-based imputation method that combines partitioning around medoids clustering and random forest classification (PAMRF) is developed and implemented. Imputed values are filtered according to allowable error rates or target sample size, depending on the requirements of each application. In leave-one-out cross-validation and simulation studies, PAMRF outperforms four existing imputation approaches-two conventional spatial interpolation methods (i.e., inverse-distance weighting, IDW and universal kriging, UK) and two supervised learning methods (<i>k</i>-nearest neighbors, KNN and classification and regression trees, CART). The inclusion of multiply imputed values in the estimation of the association between fluoride concentration and dental caries prevalence resulted in essentially no change in PAMRF estimates but substantial gains in precision due to larger effective sample size. PAMRF is a powerful new method for the imputation of missing fluoride values where geographical information exists.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 1","pages":"551-572"},"PeriodicalIF":1.8,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8963777/pdf/nihms-1731052.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9615691","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}

{"title":"ORDINAL PROBIT FUNCTIONAL OUTCOME REGRESSION WITH APPLICATION TO COMPUTER-USE BEHAVIOR IN RHESUS MONKEYS.","authors":"Mark J Meyer,&nbsp;Jeffrey S Morris,&nbsp;Regina Paxton Gazes,&nbsp;Brent A Coull","doi":"10.1214/21-aoas1513","DOIUrl":"https://doi.org/10.1214/21-aoas1513","url":null,"abstract":"<p><p>Research in functional regression has made great strides in expanding to non-Gaussian functional outcomes, but exploration of ordinal functional outcomes remains limited. Motivated by a study of computer-use behavior in rhesus macaques (<i>Macaca mulatta</i>), we introduce the Ordinal Probit Functional Outcome Regression model (OPFOR). OPFOR models can be fit using one of several basis functions including penalized B-splines, wavelets, and O'Sullivan splines-the last of which typically performs best. Simulation using a variety of underlying covariance patterns shows that the model performs reasonably well in estimation under multiple basis functions with near nominal coverage for joint credible intervals. Finally, in application, we use Bayesian model selection criteria adapted to functional outcome regression to best characterize the relation between several demographic factors of interest and the monkeys' computer use over the course of a year. In comparison with a standard ordinal longitudinal analysis, OPFOR outperforms a cumulative-link mixed-effects model in simulation and provides additional and more nuanced information on the nature of the monkeys' computer-use behavior.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 1","pages":"537-550"},"PeriodicalIF":1.8,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9629817/pdf/nihms-1805320.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10428988","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}

{"title":"BAYESIAN MITIGATION OF SPATIAL COARSENING FOR A HAWKES MODEL APPLIED TO GUNFIRE, WILDFIRE AND VIRAL CONTAGION.","authors":"Andrew J Holbrook, Xiang Ji, Marc A Suchard","doi":"10.1214/21-aoas1517","DOIUrl":"10.1214/21-aoas1517","url":null,"abstract":"<p><p>Self-exciting spatiotemporal Hawkes processes have found increasing use in the study of large-scale public health threats, ranging from gun violence and earthquakes to wildfires and viral contagion. Whereas many such applications feature locational uncertainty, that is, the exact spatial positions of individual events are unknown, most Hawkes model analyses to date have ignored spatial coarsening present in the data. Three particular 21st century public health crises-urban gun violence, rural wildfires and global viral spread-present qualitatively and quantitatively varying uncertainty regimes that exhibit: (a) different collective magnitudes of spatial coarsening, (b) uniform and mixed magnitude coarsening, (c) differently shaped uncertainty regions and-less orthodox-(d) locational data distributed within the \"wrong\" effective space. We explicitly model such uncertainties in a Bayesian manner and jointly infer unknown locations together with all parameters of a reasonably flexible Hawkes model, obtaining results that are practically and statistically distinct from those obtained while ignoring spatial coarsening. This work also features two different secondary contributions: first, to facilitate Bayesian inference of locations and background rate parameters, we make a subtle yet crucial change to an established kernel-based rate model, and second, to facilitate the same Bayesian inference at scale, we develop a massively parallel implementation of the model's log-likelihood gradient with respect to locations and thus avoid its quadratic computational cost in the context of Hamiltonian Monte Carlo. Our examples involve thousands of observations and allow us to demonstrate practicality at moderate scales.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 1","pages":"573-595"},"PeriodicalIF":1.3,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9536472/pdf/nihms-1797628.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9194379","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}

{"title":"BIDIMENSIONAL LINKED MATRIX FACTORIZATION FOR PAN-OMICS PAN-CANCER ANALYSIS.","authors":"Eric F Lock, Jun Young Park, Katherine A Hoadley","doi":"10.1214/21-AOAS1495","DOIUrl":"https://doi.org/10.1214/21-AOAS1495","url":null,"abstract":"<p><p>Several modern applications require the integration of multiple large data matrices that have shared rows and/or columns. For example, cancer studies that integrate multiple omics platforms across multiple types of cancer, <i>pan-omics pan-cancer analysis</i>, have extended our knowledge of molecular heterogeneity beyond what was observed in single tumor and single platform studies. However, these studies have been limited by available statistical methodology. We propose a flexible approach to the simultaneous factorization and decomposition of variation across such <i>bidimensionally linked</i> matrices, BIDIFAC+. BIDIFAC+ decomposes variation into a series of low-rank components that may be shared across any number of row sets (e.g., omics platforms) or column sets (e.g., cancer types). This builds on a growing literature for the factorization and decomposition of linked matrices which has primarily focused on multiple matrices that are linked in one dimension (rows or columns) only. Our objective function extends nuclear norm penalization, is motivated by random matrix theory, gives a unique decomposition under relatively mild conditions, and can be shown to give the mode of a Bayesian posterior distribution. We apply BIDIFAC+ to pan-omics pan-cancer data from TCGA, identifying shared and specific modes of variability across <i>four</i> different omics platforms and 29 different cancer types.</p>","PeriodicalId":50772,"journal":{"name":"Annals of Applied Statistics","volume":"16 1","pages":"193-215"},"PeriodicalIF":1.8,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9060567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71523301","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}