BiometricsPub Date : 2025-04-02DOI: 10.1093/biomtc/ujaf072
Mihai Giurcanu, Theodore Karrison
{"title":"Non-parametric estimators of hazard ratios for comparing two survival curves.","authors":"Mihai Giurcanu, Theodore Karrison","doi":"10.1093/biomtc/ujaf072","DOIUrl":"10.1093/biomtc/ujaf072","url":null,"abstract":"<p><p>We propose non-parametric estimators of the hazard ratio for comparing two survival curves using estimating equations defined in terms of group-specific cumulative hazard functions. We first describe the methods and their asymptotic properties in the case of a constant hazard ratio. We then extend the methods and the asymptotic results when the hazard ratio is time dependent and well approximated by a locally constant function. We propose a method to select the change points in the local hazard ratios. We extend the methods to stratified estimators and propose tests for heterogeneity of constant and time-dependent hazard ratios across strata. In a simulation study, we describe the finite sample properties of the proposed estimators and compare their performance with the Cox partial maximum likelihood estimator (MLE) in terms of efficiency and accuracy of coverage rates. An example is provided to illustrate an application of the proposed methods in practice.</p>","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Semiparametric joint modeling for biomarker trajectory before disease onset.","authors":"Yifei Sun, Xiwen Zhao, Kwun Chuen Gary Chan, Wanwan Xu, Heather Allore, Yize Zhao","doi":"10.1093/biomtc/ujaf064","DOIUrl":"10.1093/biomtc/ujaf064","url":null,"abstract":"<p><p>Understanding how biomarkers change in relation to disease pathogenesis is a key area in biomedical research. We propose a semiparametric joint model to analyze the temporal evolution of biomarkers prior to the onset of disease. The model allows for a flexible biomarker trajectory that depends on two time scales: a natural time scale such as age and time to disease onset. In practice, the natural time scale often differs from time-on-study, leading to analytical challenges such as left-truncation bias. We introduce a profile kernel estimating equation approach to estimate regression coefficients and unspecified baseline mean trajectory functions. We establish the large-sample properties of the proposed estimators and conduct simulation studies to evaluate their finite-sample performance. Our method is applied to investigate brain biomarker trajectories before the onset of preclinical Alzheimer's disease. We observed a decline in cortical thickness prior to disease onset across brain regions, with APOE4 carriers showing lower levels compared to non-carriers.</p>","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156246","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}
BiometricsPub Date : 2025-04-02DOI: 10.1093/biomtc/ujaf045
Brian D Richardson, Bryan S Blette, Peter B Gilbert, Michael G Hudgens
{"title":"Addressing confounding and continuous exposure measurement error using corrected score functions.","authors":"Brian D Richardson, Bryan S Blette, Peter B Gilbert, Michael G Hudgens","doi":"10.1093/biomtc/ujaf045","DOIUrl":"10.1093/biomtc/ujaf045","url":null,"abstract":"<p><p>Confounding and exposure measurement error can introduce bias when drawing inference about the marginal effect of an exposure on an outcome of interest. While there are broad methodologies for addressing each source of bias individually, confounding and exposure measurement error frequently co-occur, and there is a need for methods that address them simultaneously. In this paper, corrected score methods are derived under classical additive measurement error to draw inference about marginal exposure effects using only measured variables. Three estimators are proposed based on g-formula, inverse probability weighting, and doubly-robust estimation techniques. The estimators are shown to be consistent and asymptotically normal, and the doubly-robust estimator is shown to exhibit its namesake property. The methods, which are implemented in the R package mismex, perform well in finite samples under both confounding and measurement error as demonstrated by simulation studies. The proposed doubly-robust estimator is applied to study the effects of two biomarkers on HIV-1 infection using data from the HVTN 505 preventative vaccine trial.</p>","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143962773","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}
BiometricsPub Date : 2025-04-02DOI: 10.1093/biomtc/ujaf002
E Huch, I Nahum-Shani, L Potter, C Lam, D W Wetter, W Dempsey
{"title":"Data integration methods for micro-randomized trials.","authors":"E Huch, I Nahum-Shani, L Potter, C Lam, D W Wetter, W Dempsey","doi":"10.1093/biomtc/ujaf002","DOIUrl":"10.1093/biomtc/ujaf002","url":null,"abstract":"<p><p>Existing statistical methods for the analysis of micro-randomized trials (MRTs) are designed to estimate causal excursion effects using data from a single MRT. In practice, however, researchers can often find previous MRTs that employ similar interventions. In this paper, we develop data integration methods that capitalize on this additional information, leading to statistical efficiency gains. To further increase efficiency, we demonstrate how to combine these approaches according to a generalization of multivariate precision weighting that allows for correlation between estimates, and we show that the resulting meta-estimator possesses an asymptotic optimality property. We illustrate our methods in simulation and in a case study involving 2 MRTs in the area of smoking cessation, finding that the proposed methods can reduce standard errors by over 30% without sacrificing asymptotic unbiasedness or calibrated statistical inference.</p>","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12444755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143973579","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}
BiometricsPub Date : 2025-04-02DOI: 10.1093/biomtc/ujaf080
Eun Jeong Oh, Seungjun Ahn, Tristan Tham, Min Qian
{"title":"Leveraging two-phase data for improved prediction of survival outcomes with application to nasopharyngeal cancer.","authors":"Eun Jeong Oh, Seungjun Ahn, Tristan Tham, Min Qian","doi":"10.1093/biomtc/ujaf080","DOIUrl":"https://doi.org/10.1093/biomtc/ujaf080","url":null,"abstract":"<p><p>Accurate survival predicting models are essential for improving targeted cancer therapies and clinical care among cancer patients. In this article, we investigate and develop a method to improve predictions of survival in cancer by leveraging two-phase data with expert knowledge and prognostic index. Our work is motivated by two-phase data in nasopharyngeal cancer (NPC), where traditional covariates are readily available for all subjects, but the primary viral factor, human papillomavirus (HPV), is substantially missing. To address this challenge, we propose an expert-guided method that incorporates prognostic index based on the observed covariates and clinical importance of key factors. The proposed method makes efficient use of available data, not simply discarding patients with unknown HPV status. We apply the proposed method and evaluate it against other existing approaches through a series of simulation studies and real data example of NPC patients. Under various settings, the proposed method consistently outperforms competing methods in terms of c-index, calibration slope, and integrated Brier score. By efficiently leveraging two-phase data, the model provides a more accurate and reliable predictive ability of survival models.</p>","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiometricsPub Date : 2025-04-02DOI: 10.1093/biomtc/ujaf069
Nina Deliu, Sofia S Villar
{"title":"On the finite-sample and asymptotic error control of a randomization-probability test for response-adaptive clinical trials.","authors":"Nina Deliu, Sofia S Villar","doi":"10.1093/biomtc/ujaf069","DOIUrl":"https://doi.org/10.1093/biomtc/ujaf069","url":null,"abstract":"<p><p>It is now commonly known that using response-adaptive designs for data collection offers great potential in terms of optimizing expected outcomes, but poses multiple challenges for inferential goals. In many settings, such as phase-II or confirmatory clinical trials, a main barrier to their practical use is the lack of type-I error guarantees and/or power efficiency, especially in finite samples. This work addresses this gap. Specifically, focusing on a novel test statistic defined on the randomization probabilities of the (randomized) adaptive design, we derive its finite-sample and asymptotic guarantees. Further theoretical properties are evaluated for Thompson sampling, a Bayesian response-adaptive design that is commonly used both in clinical applications and beyond (eg, recommendation systems or mobile health). The frequentist error control advantages of the proposed approach-also able to preserve expected outcome optimalities-are illustrated in a real-world phase-II oncology trial and in simulation experiments.</p>","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144282250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiometricsPub Date : 2025-04-02DOI: 10.1093/biomtc/ujaf058
Wilson J Wright, Mevin B Hooten
{"title":"Rejoinder to the discussion on \"Continuous-space occupancy models\".","authors":"Wilson J Wright, Mevin B Hooten","doi":"10.1093/biomtc/ujaf058","DOIUrl":"https://doi.org/10.1093/biomtc/ujaf058","url":null,"abstract":"<p><p>The discussions of our paper consider some assumptions of continuous-space occupancy models, alternative approaches, and directions for future research. In this short rejoinder, we expand on some of these ideas and provide additional comments.</p>","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Discussion on \"Continuous-space occupancy models\" by Wilson J. Wright and Mevin B. Hooten.","authors":"Léa Pautrel, Marie-Pierre Etienne, Olivier Gimenez","doi":"10.1093/biomtc/ujaf057","DOIUrl":"https://doi.org/10.1093/biomtc/ujaf057","url":null,"abstract":"","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143964284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiometricsPub Date : 2025-04-02DOI: 10.1093/biomtc/ujaf056
Jeffrey W Doser, Krishna Pacifici
{"title":"Discussion on \"Continuous-space occupancy models\" by Wilson J. Wright and Mevin B. Hooten.","authors":"Jeffrey W Doser, Krishna Pacifici","doi":"10.1093/biomtc/ujaf056","DOIUrl":"https://doi.org/10.1093/biomtc/ujaf056","url":null,"abstract":"","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143953086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiometricsPub Date : 2025-04-02DOI: 10.1093/biomtc/ujaf034
Danning Li, Lingzhou Xue, Haoyi Yang, Xiufan Yu
{"title":"Power-enhanced two-sample mean tests for high-dimensional microbiome compositional data.","authors":"Danning Li, Lingzhou Xue, Haoyi Yang, Xiufan Yu","doi":"10.1093/biomtc/ujaf034","DOIUrl":"10.1093/biomtc/ujaf034","url":null,"abstract":"<p><p>Testing differences in mean vectors is a fundamental task in the analysis of high-dimensional microbiome compositional data. Existing methods may suffer from low power if the underlying signal pattern is in a situation that does not favor the deployed test. In this work, we develop 2-sample power-enhanced mean tests for high-dimensional compositional data based on the combination of $P$-values, which integrates strengths from 2 popular types of tests: the maximum-type test and the quadratic-type test. We provide rigorous theoretical guarantees on the proposed tests, showing accurate Type-I error rate control and enhanced testing power. Our method boosts the testing power toward a broader alternative space, which yields robust performance across a wide range of signal pattern settings. Our methodology and theory also contribute to the literature on power enhancement and Gaussian approximation for high-dimensional hypothesis testing. We demonstrate the performance of our method on both simulated data and real-world microbiome data, showing that our proposed approach improves the testing power substantially compared to existing methods.</p>","PeriodicalId":8930,"journal":{"name":"Biometrics","volume":"81 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11962435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762714","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}