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High-Performance Statistical Computing in the Computing Environments of the 2020s. 2020 年代计算环境中的高性能统计计算。
IF 3.9 1区 数学
Statistical Science Pub Date : 2022-11-01 Epub Date: 2022-10-13 DOI: 10.1214/21-sts835
Seyoon Ko, Hua Zhou, Jin J Zhou, Joong-Ho Won
{"title":"High-Performance Statistical Computing in the Computing Environments of the 2020s.","authors":"Seyoon Ko, Hua Zhou, Jin J Zhou, Joong-Ho Won","doi":"10.1214/21-sts835","DOIUrl":"10.1214/21-sts835","url":null,"abstract":"<p><p>Technological advances in the past decade, hardware and software alike, have made access to high-performance computing (HPC) easier than ever. We review these advances from a statistical computing perspective. Cloud computing makes access to supercomputers affordable. Deep learning software libraries make programming statistical algorithms easy and enable users to write code once and run it anywhere-from a laptop to a workstation with multiple graphics processing units (GPUs) or a supercomputer in a cloud. Highlighting how these developments benefit statisticians, we review recent optimization algorithms that are useful for high-dimensional models and can harness the power of HPC. Code snippets are provided to demonstrate the ease of programming. We also provide an easy-to-use distributed matrix data structure suitable for HPC. Employing this data structure, we illustrate various statistical applications including large-scale positron emission tomography and <i>ℓ</i><sub>1</sub>-regularized Cox regression. Our examples easily scale up to an 8-GPU workstation and a 720-CPU-core cluster in a cloud. As a case in point, we analyze the onset of type-2 diabetes from the UK Biobank with 200,000 subjects and about 500,000 single nucleotide polymorphisms using the HPC <i>ℓ</i><sub>1</sub>-regularized Cox regression. Fitting this half-million-variate model takes less than 45 minutes and reconfirms known associations. To our knowledge, this is the first demonstration of the feasibility of penalized regression of survival outcomes at this scale.</p>","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":"37 4","pages":"494-518"},"PeriodicalIF":3.9,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10168006/pdf/nihms-1884249.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9502219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Comments on Confidence as Likelihood by Pawitan and Lee in Statistical Science, November 2021 Pawitan和Lee在《统计科学》杂志上对置信度作为可能性的评论,2021年11月
IF 5.7 1区 数学
Statistical Science Pub Date : 2022-11-01 DOI: 10.1214/22-sts862
M. Lavine, J. F. Bjørnstad
{"title":"Comments on Confidence as Likelihood by Pawitan and Lee in Statistical Science, November 2021","authors":"M. Lavine, J. F. Bjørnstad","doi":"10.1214/22-sts862","DOIUrl":"https://doi.org/10.1214/22-sts862","url":null,"abstract":". Pawitan and Lee (2021) attempt to show a correspondence between confidence and likelihood, specifically, that “confidence is in fact an extended likelihood” (Pawitan and Lee, 2021, abstract). The word “extended” means that the likelihood function can accommodate unobserved random variables such as random effects and future values; see Bjørnstad (1996) for details. Here we argue that the extended likelihood presented by Pawitan and Lee (2021) is not the correct extended likelihood and does not justify interpreting confidence as likelihood.","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42862716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 Regression Perspective on Generalized Distance Covariance and the Hilbert–Schmidt Independence Criterion 广义距离协方差与Hilbert–Schmidt独立性准则的回归分析
IF 5.7 1区 数学
Statistical Science Pub Date : 2022-11-01 DOI: 10.1214/21-sts841
Dominic Edelmann, J. Goeman
{"title":"A Regression Perspective on Generalized Distance Covariance and the Hilbert–Schmidt Independence Criterion","authors":"Dominic Edelmann, J. Goeman","doi":"10.1214/21-sts841","DOIUrl":"https://doi.org/10.1214/21-sts841","url":null,"abstract":"In a seminal paper, Sejdinovic, et al. [49] showed the equivalence of the Hilbert-Schmidt Independence Criterion (HSIC) [20] and a generalization of distance covariance [62]. In this paper the two notions of dependence are unified with a third prominent concept for independence testing, the “global test” introduced in [16]. The new viewpoint provides novel insights into all three test traditions, as well as a unified overall view of the way all three tests contrast with classical association tests. As our main result, a regression perspective on HSIC and generalized distance covariance is obtained, allowing such tests to be used with nuisance covariates or for survival data. Several more examples of cross-fertilization of the three traditions are provided, involving theoretical results and novel methodology. To illustrate the difference between classical statistical tests and the unified HSIC/distance covariance/global tests we investigate the case of association between two categorical variables in depth.","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46642491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 2
Approximate Confidence Intervals for a Binomial p—Once Again 二项p的近似置信区间
IF 5.7 1区 数学
Statistical Science Pub Date : 2022-11-01 DOI: 10.1214/21-sts837
Per Gösta Andersson
{"title":"Approximate Confidence Intervals for a Binomial p—Once Again","authors":"Per Gösta Andersson","doi":"10.1214/21-sts837","DOIUrl":"https://doi.org/10.1214/21-sts837","url":null,"abstract":"The problem of constructing a reasonably simple yet well behaved confidence interval for a binomial parameter p is old but still fascinating and surprisingly complex. During the last century many alternatives to the poorly behaved standard Wald interval have been suggested. It seems though that the Wald interval is still much in use in spite of many efforts over the years through publications to point out its deficiencies. This paper constitutes yet another attempt to provide an alternative and it builds on a special case of a general technique for adjusted intervals primarily based on Wald type statistics. The main idea is to construct an approximate pivot with uncorrelated, or nearly uncorrelated, components. The resulting (AN) Andersson-Nerman interval, as well as a modification thereof, is compared with the well renowned Wilson and AC (Agresti-Coull) intervals and the subsequent discussion will in itself hopefully shed some new light on this seemingly elementary interval estimation situation. Generally, an alternative to the Wald interval is to be judged not only by performance, its expression should also indicate why we will obtain a better behaved interval. It is argued that the well-behaved AN interval meets this requirement.","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41959851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 1
Interpreting p-Values and Confidence Intervals Using Well-Calibrated Null Preference Priors 使用校准良好的零偏好先验解释p值和置信区间
IF 5.7 1区 数学
Statistical Science Pub Date : 2022-11-01 DOI: 10.1214/21-sts833
M. Fay, M. Proschan, E. Brittain, R. Tiwari
{"title":"Interpreting p-Values and Confidence Intervals Using Well-Calibrated Null Preference Priors","authors":"M. Fay, M. Proschan, E. Brittain, R. Tiwari","doi":"10.1214/21-sts833","DOIUrl":"https://doi.org/10.1214/21-sts833","url":null,"abstract":"We propose well-calibrated null preference priors for use with one-sided hypothesis tests, such that resulting Bayesian and frequentist inferences agree. Null preference priors mean that they have nearly 100% of their prior belief in the null hypothesis, and well-calibrated priors mean that the resulting posterior beliefs in the alternative hypothesis are not overconfident. This formulation expands the class of problems giving Bayes-frequentist agreement to include problems involving discrete distributions such as binomial and negative binomial oneand two-sample exact (i.e., valid) tests. When applicable, these priors give posterior belief in the null hypothesis that is a valid p-value, and the null preference prior emphasizes that large p-values may simply represent insufficient data to overturn prior belief. This formulation gives a Bayesian interpretation of some common frequentist tests, as well as more intuitively explaining lesser known and less straightforward confidence intervals for two-sample tests.","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41886684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 2
A Probabilistic View on Predictive Constructions for Bayesian Learning 贝叶斯学习预测结构的概率观
IF 5.7 1区 数学
Statistical Science Pub Date : 2022-08-14 DOI: 10.1214/23-sts884
P. Berti, E. Dreassi, F. Leisen, P. Rigo, L. Pratelli
{"title":"A Probabilistic View on Predictive Constructions for Bayesian Learning","authors":"P. Berti, E. Dreassi, F. Leisen, P. Rigo, L. Pratelli","doi":"10.1214/23-sts884","DOIUrl":"https://doi.org/10.1214/23-sts884","url":null,"abstract":"Given a sequence $X=(X_1,X_2,ldots)$ of random observations, a Bayesian forecaster aims to predict $X_{n+1}$ based on $(X_1,ldots,X_n)$ for each $nge 0$. To this end, in principle, she only needs to select a collection $sigma=(sigma_0,sigma_1,ldots)$, called ``strategy\"in what follows, where $sigma_0(cdot)=P(X_1incdot)$ is the marginal distribution of $X_1$ and $sigma_n(cdot)=P(X_{n+1}incdotmid X_1,ldots,X_n)$ the $n$-th predictive distribution. Because of the Ionescu-Tulcea theorem, $sigma$ can be assigned directly, without passing through the usual prior/posterior scheme. One main advantage is that no prior probability is to be selected. In a nutshell, this is the predictive approach to Bayesian learning. A concise review of the latter is provided in this paper. We try to put such an approach in the right framework, to make clear a few misunderstandings, and to provide a unifying view. Some recent results are discussed as well. In addition, some new strategies are introduced and the corresponding distribution of the data sequence $X$ is determined. The strategies concern generalized P'olya urns, random change points, covariates and stationary sequences.","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2022-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48914546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 Conversation with Stephen Portnoy 对话斯蒂芬波特诺伊
IF 5.7 1区 数学
Statistical Science Pub Date : 2022-08-01 DOI: 10.1214/21-sts845
Xu He, Xi-bin Shao
{"title":"A Conversation with Stephen Portnoy","authors":"Xu He, Xi-bin Shao","doi":"10.1214/21-sts845","DOIUrl":"https://doi.org/10.1214/21-sts845","url":null,"abstract":"Steve Portnoy was born in Kankakee, Illinois in 1942. He did his undergraduate studies in mathematics at Massachusetts Institute of Technology, and then earned a master’s degree and a Ph.D. degree from the statistics department at Stanford University in 1966 and 1969, respectively. Steve Portnoy has had a distinguished career and is widely recognized as a preeminent mathematical statistician. He has made pioneering and influential contributions in several areas in statistics, including asymptotic theory, robust statistics, quantile regression, and statistics in biology. He has published more than 100 research articles. He is a former co-editor of Journal of the American Statistical Association, Theory and Methods, an elected fellow of American Statistical Association (ASA), Institute of Mathematical Statistics (IMS) and American Association for the Advancement of Science (AAAS). Steve’s professional positions have included being on the faculty of the Department of Statistics at Harvard University and the University of Illinois at Urbana-Champaign for more than 30 years. He was a founding member of the Department of Statistics at the University of Illinois in 1985 and served as the division chair (1983-1985) for Statistics Program in the Mathematics department before the Statistics department was established.","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44370837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Intention-to-Treat Comparisons in Randomized Trials 随机试验中的意向治疗比较
IF 5.7 1区 数学
Statistical Science Pub Date : 2022-08-01 DOI: 10.1214/21-sts830
R. Prentice, A. Aragaki
{"title":"Intention-to-Treat Comparisons in Randomized Trials","authors":"R. Prentice, A. Aragaki","doi":"10.1214/21-sts830","DOIUrl":"https://doi.org/10.1214/21-sts830","url":null,"abstract":"Intention-to-treat (ITT) comparisons have a central place in reporting on randomized controlled trials, though there are typically additional analyses of interest such as those making adjustments for nonadherence. In our ITT reporting of results from the Women’s Health Initiative (WHI) randomized trials we have relied primarily on highly flexible hazard ratio (Cox) regression methods. However, these methods, especially the proportional hazards special case, have been criticized for being difficult to interpret and frequently oversimplified, and for not being consistent with modern causality theories using potential outcomes. Here we address these topics and extend our use of hazard rate methods for ITT comparisons in the WHI trials.","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48775066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 4
Computing Bayes: From Then ‘Til Now 计算贝叶斯:从那时到现在
IF 5.7 1区 数学
Statistical Science Pub Date : 2022-08-01 DOI: 10.1214/22-STS876
G. Martin, David T. Frazier, C. Robert
{"title":"Computing Bayes: From Then ‘Til Now","authors":"G. Martin, David T. Frazier, C. Robert","doi":"10.1214/22-STS876","DOIUrl":"https://doi.org/10.1214/22-STS876","url":null,"abstract":"This paper takes the reader on a journey through the history of Bayesian computation, from the 18th century to the present day. Beginning with the one-dimensional integral first confronted by Bayes in 1763, we highlight the key contributions of: Laplace, Metropolis (and, importantly, his co-authors!), Hammersley and Handscomb, and Hastings, all of which set the foundations for the computational revolution in the late 20th century -- led, primarily, by Markov chain Monte Carlo (MCMC) algorithms. A very short outline of 21st century computational methods -- including pseudo-marginal MCMC, Hamiltonian Monte Carlo, sequential Monte Carlo, and the various `approximate' methods -- completes the paper.","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42305986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 7
Learning and Predicting from Dynamic Models for COVID-19 Patient Monitoring. 从动态模型中学习和预测 COVID-19 患者监测。
IF 3.9 1区 数学
Statistical Science Pub Date : 2022-05-01 Epub Date: 2022-05-16 DOI: 10.1214/22-sts861
Zitong Wang, Mary Grace Bowring, Antony Rosen, Brian Garibaldi, Scott Zeger, Akihiko Nishimura
{"title":"Learning and Predicting from Dynamic Models for COVID-19 Patient Monitoring.","authors":"Zitong Wang, Mary Grace Bowring, Antony Rosen, Brian Garibaldi, Scott Zeger, Akihiko Nishimura","doi":"10.1214/22-sts861","DOIUrl":"10.1214/22-sts861","url":null,"abstract":"<p><p>COVID-19 has challenged health systems to learn how to learn. This paper describes the context, methods and challenges for learning to improve COVID-19 care at one academic health center. Challenges to learning include: (1) choosing a right clinical target; (2) designing methods for accurate predictions by borrowing strength from prior patients' experiences; (3) communicating the methodology to clinicians so they understand and trust it; (4) communicating the predictions to the patient at the moment of clinical decision; and (5) continuously evaluating and revising the methods so they adapt to changing patients and clinical demands. To illustrate these challenges, this paper contrasts two statistical modeling approaches - prospective longitudinal models in common use and retrospective analogues complementary in the COVID-19 context - for predicting future biomarker trajectories and major clinical events. The methods are applied to and validated on a cohort of 1,678 patients who were hospitalized with COVID-19 during the early months of the pandemic. We emphasize graphical tools to promote physician learning and inform clinical decision making.</p>","PeriodicalId":51172,"journal":{"name":"Statistical Science","volume":"37 2","pages":"251-265"},"PeriodicalIF":3.9,"publicationDate":"2022-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10198065/pdf/nihms-1844199.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9864796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
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