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BAYESIAN FUNCTIONAL REGISTRATION OF FMRI ACTIVATION MAPS. FMRI 激活图的贝叶斯功能配准。
IF 1.3 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-09-01 Epub Date: 2022-07-19 DOI: 10.1214/21-aoas1562
Guoqing Wang, Abhirup Datta, Martin A Lindquist

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 after 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.

功能磁共振成像(fMRI)为我们了解人类行为提供了宝贵的洞察力。然而,解剖配准后大脑解剖和功能定位方面的巨大个体间差异仍然是进行群体分析和群体推断的主要限制因素。本文针对这一问题,开发并验证了一种新的计算技术,通过将每个受试者的功能数据空间转换到一个共同的参考图,减少大脑功能系统中的个体间错位。我们提出的贝叶斯功能配准方法允许我们评估不同受试者大脑功能的差异以及激活拓扑的个体差异。它将基于强度的信息和基于特征的信息整合到一个综合框架中,并允许通过后验样本对转换进行推断。我们在一项模拟研究中对该方法进行了评估,并将其应用于一项热痛研究的数据中。我们发现,所提出的方法提高了组级推断的灵敏度。
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引用次数: 0
SENSITIVITY ANALYSIS FOR EVALUATING PRINCIPAL SURROGATE ENDPOINTS RELAXING THE EQUAL EARLY CLINICAL RISK ASSUMPTION. 评估主要替代终点的灵敏度分析放松了早期临床风险相同的假设。
IF 1.8 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-09-01 Epub Date: 2022-07-19 DOI: 10.1214/21-aoas1566
Ying Huang, Yingying Zhuang, Peter Gilbert

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.

本文以随机疫苗试验的数据为基础,对作为疫苗保护效果主要替代终点的随机化后免疫反应生物标志物进行了评估。疫苗疗效曲线是疫苗研究中量化生物标志物主要代用性的一个重要指标,它显示了疫苗的疗效与接受疫苗时潜在生物标志物值的函数关系,而疫苗的疗效是由 "早期一直处于风险中 "的主要试验参与者组成的。早期的主要替代物评估工作依赖于 "早期临床风险相同 "的假设,根据生物标记物测量时观察到的疾病状态来确定疫苗曲线的可识别性。在生物标记物测量前疫苗对临床终点产生早期影响的常见情况下,这一假设就被打破了。特别是,在登革热疫苗 III 期试验(CYD14/CYD15)中观察到的疫苗早期保护效果激发了我们目前的研究发展。我们放宽了 "早期临床风险相等 "的假设,并提出了一个新的敏感性分析框架,用于主要替代物评估,允许早期疫苗疗效。在这一框架下,我们基于最大似然估计法开发了疫苗疗效曲线估计器的推断程序。然后,我们在登革热应用中使用所提出的方法来评估随机化后中和滴度的代用性。
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引用次数: 0
MEASURING PERFORMANCE FOR END-OF-LIFE CARE. 衡量临终关怀的表现。
IF 1.8 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-09-01 DOI: 10.1214/21-aoas1558
Sebastien Haneuse, Deborah Schrag, Francesca Dominici, Sharon-Lise Normand, Kyu Ha Lee

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 N = 17,685 patients diagnosed with pancreatic cancer between 2000-2012 at one of J = 264 hospitals in California.

虽然并非没有争议,但再入院率被确立为医院质量指标,其统计分析通常基于拟合logistic-Normal广义线性混合模型。然而,这种分析忽略了死亡作为一种竞争风险,尽管对高死亡率的临床条件这样做可能会产生深远的影响;一家医院在再入院率方面表现良好,可能是它在死亡率方面表现不佳的假象。在本文中,我们提出了新的多变量医院水平的再入院和死亡率的绩效指标,这些指标来源于将分析框架作为集群相关的半竞争风险数据之一。我们还考虑了一些与分析相关的目标,包括识别极端表现者,以及通过贝叶斯决策理论方法对医院是否有高于/低于预期的再入院率和死亡率进行双变量分类,该方法以最小化适当损失函数的后验预期损失为基础来表征医院。在某些情况下,特别是在医院数量众多的情况下,计算负担可能令人望而却步。为了解决这个问题,我们提出了一系列在实践中有用的分析策略。在整个过程中,这些方法用CMS对2000年至2012年间在加利福尼亚州J = 264家医院中的一家诊断为胰腺癌的N = 17,685例患者的数据进行了说明。
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引用次数: 1
A FLEXIBLE SENSITIVITY ANALYSIS APPROACH FOR UNMEASURED CONFOUNDING WITH MULTIPLE TREATMENTS AND A BINARY OUTCOME WITH APPLICATION TO SEER-MEDICARE LUNG CANCER DATA. 一种灵活的敏感性分析方法,用于对多种治疗方法和二元结果的未测量混杂因素进行分析,并应用于 SEER-medicare 肺癌数据。
IF 1.8 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-06-01 Epub Date: 2022-06-13 DOI: 10.1214/21-aoas1530
Liangyuan Hu, Jungang Zou, Chenyang Gu, Jiayi Ji, Michael Lopez, Minal Kale

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.

在没有随机实验的情况下,对治疗效果进行因果推断的一个关键假设是治疗分配不可忽略。违反可忽略性假设可能会导致治疗效果估计值出现偏差。敏感性分析有助于衡量因果推断会因偏离可忽略性假设的潜在程度而发生怎样的变化。然而,在多重治疗和二元结果的背景下,针对未测量混杂因素的敏感性分析方法还很缺乏。我们提出了一种灵活的蒙特卡罗敏感性分析方法,用于在这种情况下进行因果推断。我们首先推导出未测量混杂引入的偏差的一般形式,重点是与多重治疗独特相关的理论属性。然后,我们提出了对未测量混杂因素对潜在结果的影响进行编码的方法,并对去除假定未测量混杂因素的因果效应估计值进行调整。我们提出的方法在贝叶斯框架内嵌入了嵌套多重归因法,可以无缝整合敏感性参数值的不确定性和抽样变异性,并使用贝叶斯加性回归树来灵活建模。大量模拟验证了我们的方法,并深入了解了多种治疗方法的敏感性分析。我们使用 SEER-Medicare 数据演示了早期非小细胞肺癌三种治疗方法的敏感性分析。本研究中开发的方法可通过 R 软件包 SAMTx 轻松获得。
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引用次数: 0
A FLEXIBLE BAYESIAN FRAMEWORK TO ESTIMATE AGE- AND CAUSE-SPECIFIC CHILD MORTALITY OVER TIME FROM SAMPLE REGISTRATION DATA. 一个灵活的贝叶斯框架估计年龄和原因特定的儿童死亡率随时间的样本登记数据。
IF 1.8 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-03-01 DOI: 10.1214/21-aoas1489
Austin E Schumacher, Tyler H McCormick, Jon Wakefield, Yue Chu, Jamie Perin, Francisco Villavicencio, Noah Simon, Li Liu

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.

为了在年轻群体中实施针对特定疾病的干预措施,低收入和中等收入国家的决策者需要及时和准确地估计针对特定年龄和原因的儿童死亡率。在最需要这些干预措施的环境中没有高质量的数据,但正在推动建立收集详细死亡率信息的样本登记系统。目前根据这些数据估计死亡率的方法采用多阶段框架,没有严格的统计依据,分别估计全因死亡率和特定原因死亡率,适应性不足,无法捕捉数据的重要特征。我们提出了一个灵活的贝叶斯建模框架来估计年龄和特定原因的儿童死亡率从样本登记数据。我们为该框架提供了理论依据,通过模拟探索其特性,并利用中国妇幼健康监测系统的数据来估计死亡率趋势。
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引用次数: 3
PREDICTION OF HEREDITARY CANCERS USING NEURAL NETWORKS. 使用神经网络预测遗传性癌症。
IF 1.8 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-03-01 Epub Date: 2022-03-28 DOI: 10.1214/21-aoas1510
By Zoe Guan, Giovanni Parmigiani, Danielle Braun, Lorenzo Trippa

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.

家族史是多种癌症的主要危险因素。孟德尔风险预测模型基于癌症易感性基因的知识,将家族史转化为癌症风险预测。这些模型在临床实践中被广泛用于帮助识别高危个体。孟德尔模型利用了整个家族史,但它们依赖于许多关于癌症易感性基因的假设,由于突变率低,这些假设要么不切实际,要么难以验证。在大型谱系数据库上训练更灵活的模型,如神经网络,可能会提高准确性。在这篇论文中,我们开发了一个将神经网络应用于家族史数据的框架,并研究了他们学习癌症遗传易感性的能力。虽然有大量关于神经网络及其在许多任务中最先进性能的文献,但很少有工作将其应用于家族史数据。我们提出了全连接神经网络和卷积神经网络对谱系的适应。在孟德尔遗传下模拟的数据中,我们证明了我们提出的神经网络模型能够实现几乎最优的预测性能。此外,当观察到的家族史包括误报的癌症诊断时,神经网络能够优于嵌入正确遗传规律的孟德尔BRCAPRO模型。使用一个包含20多万家族史的大型数据集,即风险服务队列,我们训练了癌症未来风险的预测模型。我们使用癌症遗传学网络的数据来验证这些模型。
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引用次数: 0
PARTITIONING AROUND MEDOIDS CLUSTERING AND RANDOM FOREST CLASSIFICATION FOR GIS-INFORMED IMPUTATION OF FLUORIDE CONCENTRATION DATA. 基于地理信息系统的氟化物浓度数据的聚类和随机森林分类划分。
IF 1.8 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-03-01 DOI: 10.1214/21-aoas1516
Yu Gu, John S Preisser, Donglin Zeng, Poojan Shrestha, Molina Shah, Miguel A Simancas-Pallares, Jeannie Ginnis, Kimon Divaris

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 (k-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.

社区饮水加氟是促进口腔健康的一个重要组成部分,因为氟化物暴露是一种有充分证据的龋齿预防剂。对生活用水氟化物含量的直接测量提供了有关个人接触氟化物的宝贵信息,从而提供了龋齿风险;然而,在口腔健康研究中进行大规模的后勤挑战。本文介绍了一种基于空间自相关信息的生活用水氟化物浓度缺失数据补全新方法的开发与评价。本研究的背景是北卡罗来纳州一项全州范围的儿童口腔健康流行病学研究,其中约75%的研究参与者缺少有关龋齿临床数据的家庭用水氟化物浓度信息。提出并实现了一种基于机器学习的围绕介质聚类和随机森林分类相结合的插值方法。根据每个应用程序的要求,根据允许错误率或目标样本量对输入值进行过滤。在留一交叉验证和仿真研究中,PAMRF优于四种现有的插值方法,即两种传统的空间插值方法(即逆距离加权,IDW和通用克里格,UK)和两种监督学习方法(k-近邻,KNN和分类与回归树,CART)。在估计氟化物浓度与龋齿患病率之间的关系时纳入多个估算值,导致PAMRF估计值基本上没有变化,但由于有效样本量的增加,精度大大提高。PAMRF是一种强大的新方法,用于在存在地理信息的情况下计算缺失的氟化物值。
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引用次数: 2
ORDINAL PROBIT FUNCTIONAL OUTCOME REGRESSION WITH APPLICATION TO COMPUTER-USE BEHAVIOR IN RHESUS MONKEYS. 序概率函数结果回归及其在恒河猴计算机使用行为中的应用。
IF 1.8 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-03-01 DOI: 10.1214/21-aoas1513
Mark J Meyer, Jeffrey S Morris, Regina Paxton Gazes, Brent A Coull

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 (Macaca mulatta), 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.

泛函回归的研究在扩展到非高斯函数结果方面取得了很大进展,但对有序函数结果的探索仍然有限。基于对恒河猴计算机使用行为的研究,我们引入了有序概率函数结果回归模型(OPFOR)。OPFOR模型可以使用几种基函数中的一种进行拟合,包括惩罚b样条、小波和奥沙利文样条——最后一种通常表现最好。利用多种底层协方差模式进行的仿真表明,该模型在多个基函数下的估计效果相当好,联合可信区间的覆盖范围接近名义范围。最后,在应用中,我们使用贝叶斯模型选择标准来适应功能结果回归,以最好地表征一年中几个感兴趣的人口统计学因素与猴子计算机使用之间的关系。与标准的有序纵向分析相比,OPFOR在模拟中优于累积链接混合效应模型,并提供了关于猴子计算机使用行为本质的额外和更细致的信息。
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引用次数: 2
BAYESIAN MITIGATION OF SPATIAL COARSENING FOR A HAWKES MODEL APPLIED TO GUNFIRE, WILDFIRE AND VIRAL CONTAGION. 应用于枪火、野火和病毒传染的霍克斯模型的空间粗化的贝叶斯缓解。
IF 1.3 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-03-01 Epub Date: 2022-03-28 DOI: 10.1214/21-aoas1517
Andrew J Holbrook, Xiang Ji, Marc A Suchard

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.

自激时空霍克斯过程越来越多地应用于大规模公共健康威胁的研究,从枪支暴力和地震到野火和病毒传染。许多此类应用都具有位置不确定性,即单个事件的确切空间位置是未知的,而迄今为止的大多数霍克斯模型分析都忽略了数据中存在的空间粗化现象。21 世纪的三个特殊公共卫生危机--城市枪支暴力、农村野火和全球病毒传播--呈现出定性和定量不同的不确定性机制,表现出:(a)不同的集体空间粗化幅度,(b)均匀和混合幅度的粗化,(c)不同形状的不确定性区域,以及(d)分布在 "错误 "有效空间内的定位数据。我们以贝叶斯方式对这些不确定性进行了明确建模,并将未知位置与合理灵活的霍克斯模型的所有参数一起进行了联合推断,得到的结果与忽略空间粗化时得到的结果在实践和统计上都截然不同。这项工作还有两个不同的次要贡献:首先,为了便于对位置和背景速率参数进行贝叶斯推断,我们对一个已建立的基于核的速率模型做了一个微妙而关键的改动;其次,为了便于在规模上进行同样的贝叶斯推断,我们开发了一种大规模并行实施该模型关于位置的对数似然梯度的方法,从而避免了在汉密尔顿蒙特卡罗背景下的二次计算成本。我们的例子涉及成千上万的观测数据,使我们能够证明在中等规模下的实用性。
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引用次数: 0
BIDIMENSIONAL LINKED MATRIX FACTORIZATION FOR PAN-OMICS PAN-CANCER ANALYSIS. 用于泛组学泛癌分析的二维链接矩阵因子分解。
IF 1.8 4区 数学 Q2 STATISTICS & PROBABILITY Pub Date : 2022-03-01 Epub Date: 2022-03-28 DOI: 10.1214/21-AOAS1495
Eric F Lock, Jun Young Park, Katherine A Hoadley

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, pan-omics pan-cancer analysis, 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 bidimensionally linked 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 four different omics platforms and 29 different cancer types.

一些现代应用程序需要集成具有共享行和/或列的多个大型数据矩阵。例如,整合多种类型癌症的多组学平台的癌症研究,即全组学全癌分析,扩展了我们对分子异质性的认识,超出了单肿瘤和单平台研究的范围。然而,这些研究受到现有统计方法的限制。我们提出了一种灵活的方法来同时分解和分解这种二维链接矩阵的变化,BIDIFC+。BIDIFAC+将变化分解为一系列低阶分量,这些分量可以在任何数量的行集(例如组学平台)或列集(例如癌症类型)之间共享。这建立在越来越多的链接矩阵的因子分解和分解文献的基础上,这些文献主要关注仅在一维(行或列)中链接的多个矩阵。我们的目标函数扩展了核范数惩罚,受随机矩阵理论的激励,在相对温和的条件下给出了唯一的分解,并且可以证明给出了贝叶斯后验分布的模式。我们将BIDIFAC+应用于TCGA的全组学全癌数据,确定了四个不同组学平台和29种不同癌症类型的共享和特定变异模式。
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引用次数: 13
期刊
Annals of Applied Statistics
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