{"title":"Empirical Bayes Covariance Decomposition, and a Solution to the Multiple Tuning Problem in Sparse PCA.","authors":"Joonsuk Kang, Matthew Stephens","doi":"10.1080/10618600.2026.2653766","DOIUrl":"10.1080/10618600.2026.2653766","url":null,"abstract":"<p><p>Sparse Principal Components Analysis (PCA) has been proposed as a way to improve both interpretability and reliability of PCA. However, use of sparse PCA in practice is hindered by the difficulty of tuning the multiple hyperparameters that control the sparsity of different PCs (the \"multiple tuning problem\", MTP). Here we present a solution to the MTP using Empirical Bayes methods. We first introduce a general formulation for penalized PCA of a data matrix <math><mi>X</mi></math> , which includes some existing sparse PCA methods as special cases. We show that this formulation also leads to a penalized decomposition of the covariance (or Gram) matrix, <math> <msup><mrow><mi>X</mi></mrow> <mrow><mi>T</mi></mrow> </msup> <mi>X</mi></math> . We introduce empirical Bayes versions of these penalized problems, in which the penalties are determined by prior distributions that are estimated from the data by maximum likelihood rather than cross-validation. The resulting \"Empirical Bayes Covariance Decomposition\" provides a principled and efficient solution to the MTP in sparse PCA, and one that can be immediately extended to incorporate other structural assumptions (e.g., non-negative PCA). We illustrate the effectiveness of this approach on both simulated and real data examples.</p>","PeriodicalId":15422,"journal":{"name":"Journal of Computational and Graphical Statistics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13249372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148217733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Joint Registration and Conformal Prediction for Partially Observed Functional Data.","authors":"Fangyi Wang, Sebastian Kurtek, Yuan Zhang","doi":"10.1080/10618600.2026.2634823","DOIUrl":"10.1080/10618600.2026.2634823","url":null,"abstract":"<p><p>Predicting missing segments in partially observed functions is challenging due to infinite-dimensionality, complex dependence within and across observations, and irregular noise. These challenges are further exacerbated by the existence of two distinct sources of variation in functional data, termed amplitude (variation along the <math><mi>y</mi></math> -axis) and phase (variation along the <math><mi>x</mi></math> -axis). While registration can disentangle them from complete functional data, the process is more difficult for partial observations. Thus, existing methods for functional data prediction often treat phase variation as negligible. Furthermore, they typically require precise model specifications and/or rely on computationally intensive tools, such as bootstrapping, to construct prediction intervals. We propose a unified registration and prediction approach for partially observed functions using conformal prediction. Our method integrates registration and prediction in one algorithm while ensuring exchangeability through carefully constructed predictor-response pairs. Using a neighborhood smoothing algorithm, the framework produces pointwise prediction bands with finite-sample marginal coverage guarantees under weak assumptions. The method is easy to implement, computationally efficient, and permits simple parallelization. Numerical studies and real-world data examples demonstrate the effectiveness and practical utility of our method. Supplementary materials for this article are available online.</p>","PeriodicalId":15422,"journal":{"name":"Journal of Computational and Graphical Statistics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13160368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147929691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Statistical Functional Approach to Estimating Common Treatment Effects in Causal Inference","authors":"Kuan-Hsun Wu, Li-Pang Chen","doi":"10.1080/10618600.2026.2648597","DOIUrl":"https://doi.org/10.1080/10618600.2026.2648597","url":null,"abstract":"","PeriodicalId":15422,"journal":{"name":"Journal of Computational and Graphical Statistics","volume":"14 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147492796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Edoardo Fibbi, Domenico Perrotta, Francesca Torti, Stefan Van Aelst, Tim Verdonck
{"title":"Cell-TRICC: a Model-Based Approach to Cellwise-Trimmed Co-Clustering","authors":"Edoardo Fibbi, Domenico Perrotta, Francesca Torti, Stefan Van Aelst, Tim Verdonck","doi":"10.1080/10618600.2026.2634828","DOIUrl":"https://doi.org/10.1080/10618600.2026.2634828","url":null,"abstract":"","PeriodicalId":15422,"journal":{"name":"Journal of Computational and Graphical Statistics","volume":"31 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147454413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Reluctant Interaction Modeling in Generalized Linear Models","authors":"Hai Lu, Guo Yu","doi":"10.1080/10618600.2026.2638491","DOIUrl":"https://doi.org/10.1080/10618600.2026.2638491","url":null,"abstract":"","PeriodicalId":15422,"journal":{"name":"Journal of Computational and Graphical Statistics","volume":"10 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147454415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Raphiel J. Murden, Ganzhong Tian, Deqiang Qiu, Benjamin B. Risk
{"title":"Probabilistic Joint and Individual Variation Explained (ProJIVE) for Data Integration","authors":"Raphiel J. Murden, Ganzhong Tian, Deqiang Qiu, Benjamin B. Risk","doi":"10.1080/10618600.2026.2639081","DOIUrl":"https://doi.org/10.1080/10618600.2026.2639081","url":null,"abstract":"","PeriodicalId":15422,"journal":{"name":"Journal of Computational and Graphical Statistics","volume":"106 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147454414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"FDR control in feature screening for ultrahigh-dimensional right-censored data via data-driven threshold selection","authors":"Jing Zhang, Hengjian Cui","doi":"10.1080/10618600.2026.2632808","DOIUrl":"https://doi.org/10.1080/10618600.2026.2632808","url":null,"abstract":"","PeriodicalId":15422,"journal":{"name":"Journal of Computational and Graphical Statistics","volume":"11 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146260757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Scalable skewed Bayesian inference for latent Gaussian models using INLA and variational Bayes","authors":"Shourya Dutta, Janet van Niekerk, Håvard Rue","doi":"10.1080/10618600.2026.2628274","DOIUrl":"https://doi.org/10.1080/10618600.2026.2628274","url":null,"abstract":"","PeriodicalId":15422,"journal":{"name":"Journal of Computational and Graphical Statistics","volume":"83 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146260758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}