Biometrical Journal最新文献

{"title":"Interpretability of bi-level variable selection methods","authors":"Gregor Buch,&nbsp;Andreas Schulz,&nbsp;Irene Schmidtmann,&nbsp;Konstantin Strauch,&nbsp;Philipp S. Wild","doi":"10.1002/bimj.202300063","DOIUrl":"https://doi.org/10.1002/bimj.202300063","url":null,"abstract":"<p>Variable selection is usually performed to increase interpretability, as sparser models are easier to understand than full models. However, a focus on sparsity is not always suitable, for example, when features are related due to contextual similarities or high correlations. Here, it may be more appropriate to identify groups and their predictive members, a task that can be accomplished with bi-level selection procedures. To investigate whether such techniques lead to increased interpretability, group exponential LASSO (GEL), sparse group LASSO (SGL), composite minimax concave penalty (cMCP), and least absolute shrinkage, and selection operator (LASSO) as reference methods were used to select predictors in time-to-event, regression, and classification tasks in bootstrap samples from a cohort of 1001 patients. Different groupings based on prior knowledge, correlation structure, and random assignment were compared in terms of selection relevance, group consistency, and collinearity tolerance. The results show that bi-level selection methods are superior to LASSO in all criteria. The cMCP demonstrated superiority in selection relevance, while SGL was convincing in group consistency. An all-round capacity was achieved by GEL: the approach jointly selected correlated and content-related predictors while maintaining high selection relevance. This method seems recommendable when variables are grouped, and interpretation is of primary interest.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202300063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140192168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pairwise fitting of piecewise mixed models for the joint modeling of multivariate longitudinal outcomes, in a randomized crossover trial","authors":"Moses Mwangi,&nbsp;Geert Molenberghs,&nbsp;Edmund Njeru Njagi,&nbsp;Samuel Mwalili,&nbsp;Roel Braekers,&nbsp;Alvaro Jose Florez,&nbsp;Susan Gachau,&nbsp;Zipporah N. Bukania,&nbsp;Geert Verbeke","doi":"10.1002/bimj.202200333","DOIUrl":"10.1002/bimj.202200333","url":null,"abstract":"&lt;p&gt;Many statistical models have been proposed in the literature for the analysis of longitudinal data. One may propose to model two or more correlated longitudinal processes simultaneously, with a goal of understanding their association over time. Joint modeling is then required to carefully study the association structure among the outcomes as well as drawing joint inferences about the different outcomes. In this study, we sought to model the associations among six nutrition outcomes while circumventing the computational challenge posed by their clustered and high-dimensional nature. We analyzed data from a 2 &lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mo&gt;×&lt;/mo&gt;\u0000 &lt;annotation&gt;$times$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; 2 randomized crossover trial conducted in Kenya, to compare the effect of high-dose and low-dose iodine in household salt on systolic blood pressure (SBP) and diastolic blood pressure (DBP) in women of reproductive age and their household matching pair of school-aged children. Two additional outcomes, namely, urinary iodine concentration (UIC) in women and children were measured repeatedly to monitor the amount of iodine excreted through urine. We extended the model proposed by Mwangi et al. (2021, &lt;i&gt;Communications in Statistics: Case Studies, Data Analysis and Applications&lt;/i&gt;, &lt;i&gt;7&lt;/i&gt;(3), 413–431) allowing flexible piecewise joint models for six outcomes to depend on separate random effects, which are themselves correlated. This entailed fitting 15 bivariate general linear mixed models and deriving inference for the joint model using pseudo-likelihood theory. We analyzed the outcomes separately and jointly using piecewise linear mixed-effects (PLME) model and further validated the results using current state-of-the-art Jones and Kenward methodology (JKME model) used for analyzing randomized crossover trials. The results indicate that high-dose iodine in salt significantly reduced blood pressure (BP) compared to low-dose iodine in salt. Estimates for the random effects and residual error components showed that SBP and DBP had strong positive correlation, with effect of the random slope indicating that significantly related outcomes are strongly associated in their evolution. There was a moderately strong inverse relationship between evolutions of UIC and BP both in women and children. These findings confirmed the original hypothesis that high-dose iodine salt has significant lowering effect on BP. We further sought to evaluate the performance of our proposed PLME model against the widely used JKME model, within the multivariate joint modeling framework through a simulation study mimicking a &lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;mo&gt;×&lt;/mo&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$2times 2$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; crossover design. From our findings, the multivariate joint PLME model p","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140159619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Explained variation and degrees of necessity and of sufficiency for competing risks survival data","authors":"Andreas Gleiss,&nbsp;Michael Gnant,&nbsp;Michael Schemper","doi":"10.1002/bimj.202300140","DOIUrl":"10.1002/bimj.202300140","url":null,"abstract":"<p>In this contribution, the Schemper–Henderson measure of explained variation for survival outcomes is extended to accommodate competing events (CEs) in addition to events of interest. The extension is achieved by moving from the unconditional and conditional survival functions of the original measure to unconditional and conditional cumulative incidence functions, the latter obtained, for example, from Fine and Gray models. In the absence of CEs, the original measure is obtained as a special case. We define explained variation on the population level and provide two different types of estimates. Recently, the authors have achieved a multiplicative decomposition of explained variation into degrees of necessity and degrees of sufficiency. These measures are also extended to the case of competing risks survival data. A SAS macro and an R function are provided to facilitate application. Interesting empirical properties of the measures are explored on the population level and by an extensive simulation study. Advantages of the approach are exemplified by an Austrian study of breast cancer with a high proportion of CEs.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202300140","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139974736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nonparametric analysis of delayed treatment effects using single-crossing constraints","authors":"Nicholas C. Henderson,&nbsp;Kijoeng Nam,&nbsp;Dai Feng","doi":"10.1002/bimj.202200165","DOIUrl":"10.1002/bimj.202200165","url":null,"abstract":"<p>Clinical trials involving novel immuno-oncology therapies frequently exhibit survival profiles which violate the proportional hazards assumption due to a delay in treatment effect, and, in such settings, the survival curves in the two treatment arms may have a crossing before the two curves eventually separate. To flexibly model such scenarios, we describe a nonparametric approach for estimating the treatment arm-specific survival functions which constrains these two survival functions to cross at most once without making any additional assumptions about how the survival curves are related. A main advantage of our approach is that it provides an estimate of a crossing time if such a crossing exists, and, moreover, our method generates interpretable measures of treatment benefit including crossing-conditional survival probabilities and crossing-conditional estimates of restricted residual mean life. Our estimates of these measures may be used together with efficacy measures from a primary analysis to provide further insight into differences in survival across treatment arms. We demonstrate the use and effectiveness of our approach with a large simulation study and an analysis of reconstructed outcomes from a recent combination therapy trial.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202200165","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139967911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial for the special collection “Towards neutral comparison studies in methodological research”","authors":"Anne-Laure Boulesteix,&nbsp;Mark Baillie,&nbsp;Dominic Edelmann,&nbsp;Leonhard Held,&nbsp;Tim P. Morris,&nbsp;Willi Sauerbrei","doi":"10.1002/bimj.202400031","DOIUrl":"10.1002/bimj.202400031","url":null,"abstract":"&lt;p&gt;Biomedical researchers are frequently faced with an array of methods they might potentially use for the analysis and/or design of studies. It can be difficult to understand the absolute and relative merits of candidate methods beyond one's own particular interests and expertise. Choosing a method can be difficult even in simple settings but an increase in the volume of data collected, computational power, and methods proposed in the literature makes the choice all the more difficult. In this context, it is crucial to provide researchers with evidence-supported guidance derived from appropriately designed studies comparing statistical methods in a neutral way, in particular through well-designed simulation studies.&lt;/p&gt;&lt;p&gt;While neutral comparison studies are an essential cornerstone toward the improvement of this situation, a number of challenges remain with regard to their methodology and acceptance. Numerous difficulties arise when designing, conducting, and reporting neutral comparison studies. Practical experience is still scarce and literature on these issues almost inexistent. Furthermore, authors of neutral comparison studies are often faced with incomprehension from a large part of the scientific community, which is more interested in the development of “new” approaches and evaluates the importance of research primarily based on the novelty of the presented methods. Consequently, meaningful comparisons of competing approaches (especially reproducible studies including publicly available code and data) are rarely available and evidence-supported state of the art guidance is largely missing, often resulting in the use of suboptimal methods in practice.&lt;/p&gt;&lt;p&gt;The final special collection includes 11 contributions of the first type and 12 of the second, covering a wide range of methods and issues. Our expectations were fully met and even exceeded! We thank the authors for these outstanding contributions and the many reviewers for their very helpful comments.&lt;/p&gt;&lt;p&gt;The papers from the first category explore a wide range of highly relevant biostatistical methods. They present interesting implementations of various neutrality concepts and methodologies aiming at more reliability and transparency, for example, study protocols.&lt;/p&gt;&lt;p&gt;The topics include methodology to analyze data from randomized trials, such as the use of baseline covariates to analyze small cluster-randomized trials with a rare binary outcome (Zhu et al.) and the characterization of treatment effect heterogeneity (Sun et al.). The special collection also presents comparison studies that explore a variety of modeling approaches in other contexts. These include the analysis of survival data with nonproportional hazards with propensity score–weighted methods (Handorf et al.), the impact of the matching algorithm on the treatment effect estimate in causal analyses based on the propensity score (Heinz et al.), statistical methods for analyzing longitudinally measured ordinal outcomes","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202400031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139898346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A generalized calibrated Bayesian hierarchical modeling approach to basket trials with multiple endpoints","authors":"Xiaohan Chi,&nbsp;Ying Yuan,&nbsp;Zhangsheng Yu,&nbsp;Ruitao Lin","doi":"10.1002/bimj.202300122","DOIUrl":"10.1002/bimj.202300122","url":null,"abstract":"<p>A basket trial simultaneously evaluates a treatment in multiple cancer subtypes, offering an effective way to accelerate drug development in multiple indications. Many basket trials are designed and monitored based on a single efficacy endpoint, primarily the tumor response. For molecular targeted or immunotherapy agents, however, a single efficacy endpoint cannot adequately characterize the treatment effect. It is increasingly important to use more complex endpoints to comprehensively assess the risk–benefit profile of such targeted therapies. We extend the calibrated Bayesian hierarchical modeling approach to monitor phase II basket trials with multiple endpoints. We propose two generalizations, one based on the latent variable approach and the other based on the multinomial–normal hierarchical model, to accommodate different types of endpoints and dependence assumptions regarding information sharing. We introduce shrinkage parameters as functions of statistics measuring homogeneity among subgroups and propose a general calibration approach to determine the functional forms. Theoretical properties of the generalized hierarchical models are investigated. Simulation studies demonstrate that the monitoring procedure based on the generalized approach yields desirable operating characteristics.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139898345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sparse multiway canonical correlation analysis for multimodal stroke recovery data","authors":"Subham Das,&nbsp;Franklin D. West,&nbsp;Cheolwoo Park","doi":"10.1002/bimj.202300037","DOIUrl":"10.1002/bimj.202300037","url":null,"abstract":"<p>Conventional canonical correlation analysis (CCA) measures the association between two datasets and identifies relevant contributors. However, it encounters issues with execution and interpretation when the sample size is smaller than the number of variables or there are more than two datasets. Our motivating example is a stroke-related clinical study on pigs. The data are multimodal and consist of measurements taken at multiple time points and have many more variables than observations. This study aims to uncover important biomarkers and stroke recovery patterns based on physiological changes. To address the issues in the data, we develop two sparse CCA methods for multiple datasets. Various simulated examples are used to illustrate and contrast the performance of the proposed methods with that of the existing methods. In analyzing the pig stroke data, we apply the proposed sparse CCA methods along with dimension reduction techniques, interpret the recovery patterns, and identify influential variables in recovery.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139898347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimating the proportion of true null hypotheses and adaptive false discovery rate control in discrete paradigm","authors":"Aniket Biswas,&nbsp;Gaurangadeb Chattopadhyay","doi":"10.1002/bimj.202200204","DOIUrl":"10.1002/bimj.202200204","url":null,"abstract":"<p>Storey's estimator for the proportion of true null hypotheses, originally proposed under the continuous framework, has been modified in this work under the discrete framework. The modification results in improved estimation of the parameter of interest. The proposed estimator is used to formulate an adaptive version of the Benjamini–Hochberg procedure. Control over the false discovery rate by the proposed adaptive procedure has been proved analytically. The proposed estimate is also used to formulate an adaptive version of the Benjamini–Hochberg–Heyse procedure. Simulation experiments establish the conservative nature of this new adaptive procedure. Substantial amount of gain in power is observed for the new adaptive procedures over the standard procedures. For demonstration of the proposed method, two important real life gene expression data sets, one related to the study of HIV and the other related to methylation study, are used.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139736834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A review on statistical and machine learning competing risks methods","authors":"Karla Monterrubio-Gómez,&nbsp;Nathan Constantine-Cooke,&nbsp;Catalina A. Vallejos","doi":"10.1002/bimj.202300060","DOIUrl":"10.1002/bimj.202300060","url":null,"abstract":"<p>When modeling competing risks (CR) survival data, several techniques have been proposed in both the statistical and machine learning literature. State-of-the-art methods have extended classical approaches with more flexible assumptions that can improve predictive performance, allow high-dimensional data and missing values, among others. Despite this, modern approaches have not been widely employed in applied settings. This article aims to aid the uptake of such methods by providing a condensed compendium of CR survival methods with a unified notation and interpretation across approaches. We highlight available software and, when possible, demonstrate their usage via reproducible R vignettes. Moreover, we discuss two major concerns that can affect benchmark studies in this context: the choice of performance metrics and reproducibility.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202300060","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139731093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial Board: Biometrical Journal 2'24","authors":"","doi":"10.1002/bimj.202470002","DOIUrl":"https://doi.org/10.1002/bimj.202470002","url":null,"abstract":"","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":"66 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202470002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139676560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}