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Non-Markov Nonparametric Estimation of Complex Multistate Outcomes After Hematopoietic Stem Cell Transplantation 造血干细胞移植后复杂多状态结果的非马尔可夫非参数估计。
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-10-29 DOI: 10.1002/bimj.70082
Judith Vilsmeier, Sandra Schmeller, Daniel Fürst, Jan Beyersmann

Often probabilities of nonstandard time-to-event endpoints are of interest, which are more complex than overall survival. One such probability is chronic graft-versus-host disease (GvHD-) and relapse-free survival, the probability of being alive, in remission, and not suffering from chronic GvHD after stem cell transplantation, with chronic GvHD being a recurrent event. Because the probabilities for endpoints with recurrent events may not fall monotonically, one should not use the Kaplan–Meier estimator for estimation, but the Aalen–Johansen estimator. The Aalen–Johansen is a consistent estimator even in non-Markov scenarios if state occupation probabilities are being estimated and censoring is random. In some multistate models, it is also possible to use linear combinations of Kaplan–Meier estimators, which do not depend on the Markov assumption but can estimate probabilities to be out of bounds. For these linear combinations, we propose a wild bootstrap procedure for inference and compare it with the wild bootstrap for the Aalen–Johansen estimator in non-Markov scenarios. In the proposed procedure, the limiting distribution of the Nelson–Aalen estimator is approximated using the wild bootstrap and transformed via the functional delta method. This approach is adaptable to different multistate models. Using real data, confidence bands are generated using the wild bootstrap for chronic GvHD- and relapse-free survival. Additionally, coverage probabilities of confidence intervals and confidence bands generated by Efron's bootstrap and the wild bootstrap are examined with simulations.

通常,非标准时间到事件端点的概率是令人感兴趣的,这比总体生存要复杂得多。其中一种可能性是慢性移植物抗宿主病(GvHD-)和无复发生存,即干细胞移植后存活、缓解和不患慢性移植物抗宿主病的概率,慢性移植物抗宿主病是复发事件。由于具有循环事件的端点的概率可能不会单调下降,因此不应该使用Kaplan-Meier估计量进行估计,而应该使用aallen - johansen估计量。即使在非马尔可夫情况下,如果估计国家占领概率并且审查是随机的,aallen - johansen也是一致估计器。在一些多状态模型中,也可以使用Kaplan-Meier估计器的线性组合,它不依赖于马尔可夫假设,但可以估计出超出边界的概率。对于这些线性组合,我们提出了一个野生自举推理过程,并将其与非马尔可夫场景下aallen - johansen估计的野生自举进行了比较。在所提出的程序中,Nelson-Aalen估计量的极限分布使用野自举近似,并通过泛函增量方法进行变换。这种方法适用于不同的多状态模型。使用真实数据,使用野生bootstrap生成慢性GvHD和无复发生存的置信带。此外,通过仿真检验了Efron自举法和野生自举法生成的置信区间和置信带的覆盖概率。
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引用次数: 0
Variable Selection via Fused Sparse-Group Lasso Penalized Multi-state Models Incorporating Molecular Data 结合分子数据的融合稀疏群套索惩罚多态模型的变量选择
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-10-27 DOI: 10.1002/bimj.70087
Kaya Miah, Jelle J. Goeman, Hein Putter, Annette Kopp-Schneider, Axel Benner

In multi-state models based on high-dimensional data, effective modeling strategies are required to determine an optimal, ideally parsimonious model. In particular, linking covariate effects across transitions is needed to conduct joint variable selection. A useful technique to reduce model complexity is to address homogeneous covariate effects for distinct transitions. We integrate this approach to data-driven variable selection by extended regularization methods within multi-state model building. We propose the fused sparse-group lasso (FSGL) penalized Cox-type regression in the framework of multi-state models combining the penalization concepts of pairwise differences of covariate effects along with transition-wise grouping. For optimization, we adapt the alternating direction method of multipliers (ADMM) algorithm to transition-specific hazards regression in the multi-state setting. In a simulation study and application to acute myeloid leukemia (AML) data, we evaluate the algorithm's ability to select a sparse model incorporating relevant transition-specific effects and similar cross-transition effects. We investigate settings in which the combined penalty is beneficial compared to global lasso regularization.

Clinical Trial Registration: The AMLSG 09-09 trial is registered with ClinicalTrials.gov (NCT00893399) and has been completed.

在基于高维数据的多状态模型中,需要有效的建模策略来确定最优的、理想的简约模型。特别是,需要将跨过渡的协变量效应联系起来进行联合变量选择。降低模型复杂性的一个有用技术是处理不同过渡的同质协变量效应。我们通过扩展正则化方法将这种方法集成到多状态模型构建中的数据驱动变量选择中。在多状态模型框架下,结合协变量效应两两差异的惩罚概念和过渡明智分组,提出了融合稀疏群套索惩罚cox型回归。为了优化,我们将乘法器的交替方向法(ADMM)算法应用于多状态下的过渡风险回归。在对急性髓性白血病(AML)数据的模拟研究和应用中,我们评估了该算法选择包含相关过渡特异性效应和类似交叉过渡效应的稀疏模型的能力。我们研究了与全局套索正则化相比,组合惩罚是有益的设置。临床试验注册:AMLSG 09-09试验已在ClinicalTrials.gov (NCT00893399)注册并已完成。
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引用次数: 0
Efficient Testing Using Surrogate Information 使用代理信息进行有效测试
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-10-27 DOI: 10.1002/bimj.70086
Rebecca Knowlton, Layla Parast

In modern clinical trials, there is immense pressure to use surrogate markers in place of an expensive or long-term primary outcome to make more timely decisions about treatment effectiveness. However, using a surrogate marker to test for a treatment effect can be difficult and controversial. Existing methods tend to either rely on fully parametric methods where strict assumptions are made about the relationship between the surrogate and the outcome, or assume the surrogate marker is valid for the entire study population. In this paper, we develop a fully nonparametric method for efficient testing using surrogate information (ETSI). Our approach is specifically designed for settings where there is heterogeneity in the utility of the surrogate marker, that is, the surrogate is valid for certain patient subgroups and not others. ETSI enables treatment effect estimation and hypothesis testing via kernel-based estimation for a setting where the surrogate is used in place of the primary outcome for individuals for whom the surrogate is valid, and the primary outcome is purposefully only measured in the remaining patients. In addition, we provide a framework for future study design with power and sample size estimates based on our proposed testing procedure. Throughout, we assume a continuous surrogate and a primary outcome that may be discrete or continuous. We demonstrate the performance of our methods via a simulation study and application to two distinct HIV clinical trials.

在现代临床试验中,为了对治疗效果做出更及时的决定,使用替代标记物代替昂贵的或长期的主要结果存在巨大的压力。然而,使用替代标记物来测试治疗效果可能是困难和有争议的。现有的方法要么依赖于全参数方法,对替代指标与结果之间的关系做出严格的假设,要么假设替代指标对整个研究人群有效。在本文中,我们开发了一种利用替代信息(ETSI)进行有效测试的完全非参数方法。我们的方法是专门为替代标记物的应用存在异质性的情况而设计的,也就是说,替代标记物对某些患者亚组有效,而对其他患者无效。ETSI能够通过基于核的估计进行治疗效果估计和假设检验,在这种情况下,替代物被用于替代替代物有效的个体的主要结果,并且主要结果有目的地仅在剩余患者中进行测量。此外,我们为未来的研究设计提供了一个框架,根据我们提出的测试程序估计功率和样本量。在整个过程中,我们假设一个连续的替代结果和一个可能是离散或连续的主要结果。我们通过模拟研究和应用于两个不同的HIV临床试验来证明我们的方法的性能。
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引用次数: 0
Generalized Bayesian Inference for Causal Effects Using the Covariate Balancing Procedure 利用协变量平衡程序对因果效应进行广义贝叶斯推断
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-10-27 DOI: 10.1002/bimj.70085
Shunichiro Orihara, Tomotaka Momozaki, Tomoyuki Nakagawa

In observational studies, the propensity score plays a central role in estimating causal effects of interest. The inverse probability weighting (IPW) estimator is commonly used for this purpose. However, if the propensity score model is misspecified, the IPW estimator may produce biased estimates of causal effects. Previous studies have proposed some robust propensity score estimation procedures. However, these methods require considering parameters that dominate the uncertainty of sampling and treatment allocation. This study proposes a novel Bayesian estimating procedure that necessitates probabilistically deciding the parameter, rather than deterministically. Since the IPW estimator and propensity score estimator can be derived as solutions to certain loss functions, the general Bayesian paradigm, which does not require considering the full likelihood, can be applied. Therefore, our proposed method only requires the same level of assumptions as ordinary causal inference contexts. The proposed Bayesian method demonstrates equal or superior results compared to some previous methods in simulation experiments and is also applied to real data, namely the Whitehall dataset.

在观察性研究中,倾向得分在估计兴趣的因果效应方面起着核心作用。逆概率加权(IPW)估计器通常用于此目的。然而,如果倾向评分模型指定不当,IPW估计器可能会对因果效应产生偏差估计。以前的研究已经提出了一些稳健的倾向得分估计程序。然而,这些方法需要考虑控制采样和处理分配不确定性的参数。本研究提出了一种新的贝叶斯估计方法,它需要概率性地决定参数,而不是确定性地决定参数。由于IPW估计量和倾向分数估计量可以作为某些损失函数的解导出,因此可以应用不需要考虑完全似然的一般贝叶斯范式。因此,我们提出的方法只需要与普通因果推理上下文相同水平的假设。本文提出的贝叶斯方法在模拟实验中与之前的一些方法相比,取得了相同或更好的结果,并将其应用于真实数据,即Whitehall数据集。
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引用次数: 0
Issue Information: Biometrical Journal 6'25 期刊信息:biometic Journal 6'25
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-10-27 DOI: 10.1002/bimj.70095
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引用次数: 0
Sharp Bounds for Continuous-Valued Treatment Effects with Unobserved Confounders 具有未观察混杂因素的连续值治疗效果的锐界。
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-10-14 DOI: 10.1002/bimj.70084
Jean-Baptiste Baitairian, Bernard Sebastien, Rana Jreich, Sandrine Katsahian, Agathe Guilloux

In causal inference, treatment effects are typically estimated under the ignorability, or unconfoundedness, assumption, which is often unrealistic in observational data. By relaxing this assumption and conducting a sensitivity analysis, we introduce novel bounds and derive confidence intervals for the Average Potential Outcome (APO)—a standard metric for evaluating continuous-valued treatment or exposure effects. We demonstrate that these bounds are sharp under a continuous sensitivity model, in the sense that they give the smallest possible interval under this model, and propose a doubly robust version of our estimators. In a comparative analysis with another method from the literature, using both simulated and real data sets, we show that our approach not only yields sharper bounds but also achieves good coverage of the true APO, with significantly reduced computation times.

在因果推理中,治疗效果通常是在可忽略性或非混淆性假设下估计的,这在观察数据中往往是不现实的。通过放宽这一假设并进行敏感性分析,我们引入了新的界限并推导了平均潜在结果(APO)的置信区间——APO是评估连续值治疗或暴露效应的标准度量。我们证明了这些边界在连续灵敏度模型下是尖锐的,在某种意义上,它们给出了该模型下最小的可能区间,并提出了我们估计的双鲁棒版本。在与文献中的另一种方法(使用模拟和真实数据集)的比较分析中,我们表明,我们的方法不仅产生更清晰的边界,而且还实现了对真实APO的良好覆盖,大大减少了计算时间。
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引用次数: 0
Multivariate Bayesian Dynamic Borrowing for Repeated Measures Data With Application to External Control Arms in Open-Label Extension Studies 重复测量数据的多元贝叶斯动态借用及其在开放标签扩展研究中的应用。
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-10-07 DOI: 10.1002/bimj.70079
Benjamin F. Hartley, Matthew A. Psioda, Adrian P. Mander

Borrowing analyses are increasingly important in clinical trials. We develop a method for using robust mixture priors in multivariate dynamic borrowing. The method was motivated by a desire to produce causally valid, long-term treatment effect estimates of a continuous endpoint from a single active-arm open-label extension study following a randomized clinical trial by dynamically incorporating prior beliefs from a long-term external control arm. The proposed method is a generally applicable Bayesian dynamic borrowing analysis for estimates of multivariate summary metrics based on a multivariate normal likelihood function for various parameter models, some of which we describe. There are important connections to estimation incorporating a prior belief for a hypothetical estimand strategy, that is, had the event not occurred, for intercurrent events which lead to missing data.

借用分析在临床试验中越来越重要。提出了一种在多元动态借贷中使用鲁棒混合先验的方法。该方法的动机是希望在随机临床试验之后,通过动态地结合长期外部对照组的先验信念,对单个主动臂开放标签扩展研究的连续终点进行因果有效的长期治疗效果估计。本文提出的方法是一种基于多元正态似然函数的多元汇总指标估计的贝叶斯动态借用分析方法,适用于各种参数模型,我们描述了其中的一些。对于一个假设的估计策略,也就是说,如果事件没有发生,对于导致丢失数据的交互事件,与纳入先验信念的估计有重要的联系。
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引用次数: 0
Weibull Regression With Both Measurement Error and Misclassification in Covariates 协变量存在测量误差和误分类的威布尔回归。
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-10-07 DOI: 10.1002/bimj.70083
Zhiqiang Cao, Man Yu Wong

The problem of measurement error and misclassification in covariates is ubiquitous in nutritional epidemiology and some other research areas, which often leads to biased estimate and loss of power. However, addressing both measurement error and misclassification simultaneously in a single analysis is challenged and less actively studied, especially in regression model for survival data with censoring. The approximate maximum likelihood estimation (AMLE) has been proved to be an effective method to correct both measurement error and misclassification simultaneously in a logistic regression model. However, its impact on survival analysis models has not been studied. In this paper, we study biases caused by both measurement error and misclassification in covariates from a Weibull accelerated failure time model, and explore the use of AMLE and its asymptotic properties to correct these biases. Extensive simulation studies are conducted to evaluate the finite-sample performance of the resulting estimator. The proposed method is then applied to deal with measurement error and misclassification in some nutrients of interest from the EPIC-InterAct Study.

在营养流行病学和其他一些研究领域中,协变量的测量误差和误分类问题普遍存在,这往往导致估计的偏倚和功率损失。然而,在单一分析中同时解决测量误差和错误分类是一个挑战,而且研究较少,特别是在带有审查的生存数据的回归模型中。近似最大似然估计(AMLE)已被证明是一种同时校正逻辑回归模型测量误差和误分类的有效方法。然而,它对生存分析模型的影响尚未得到研究。在本文中,我们研究了威布尔加速失效时间模型中由测量误差和误分类引起的偏差,并探索了利用AMLE及其渐近性质来纠正这些偏差。进行了广泛的仿真研究,以评估所得估计器的有限样本性能。提出的方法随后被应用于处理EPIC-InterAct研究中一些感兴趣的营养物质的测量误差和错误分类。
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引用次数: 0
Improving Genomic Prediction Using High-Dimensional Secondary Phenotypes: The Genetic Latent Factor Approach 利用高维次级表型改进基因组预测:遗传潜在因子方法。
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-10-07 DOI: 10.1002/bimj.70081
Killian A. C. Melsen, Jonathan F. Kunst, José Crossa, Margaret R. Krause, Fred A. van Eeuwijk, Willem Kruijer, Carel F. W. Peeters

Decreasing costs and new technologies have led to an increase in the amount of data available to plant breeding programs. High-throughput phenotyping (HTP) platforms routinely generate high-dimensional datasets of secondary features that may be used to improve genomic prediction accuracy. However, integration of these data comes with challenges such as multicollinearity, parameter estimation in p>n$p > n$ settings, and the computational complexity of many standard approaches. Several methods have emerged to analyze such data, but interpretation of model parameters often remains challenging. We propose genetic latent factor best linear unbiased prediction (glfBLUP), a prediction pipeline that reduces the dimensionality of the original secondary HTP data using generative factor analysis. In short, glfBLUP uses redundancy filtered and regularized genetic and residual correlation matrices to fit a maximum likelihood factor model and estimate genetic latent factor scores. These latent factors are subsequently used in multitrait genomic prediction. Our approach performs better than alternatives in extensive simulations and a real-world application, while producing easily interpretable and biologically relevant parameters. We discuss several possible extensions and highlight glfBLUP as the basis for a flexible and modular multitrait genomic prediction framework.

成本的降低和新技术的发展使得植物育种项目的数据量有所增加。高通量表型(HTP)平台通常生成次要特征的高维数据集,可用于提高基因组预测的准确性。然而,这些数据的集成带来了多重共线性、p > n$设置中的参数估计以及许多标准方法的计算复杂性等挑战。已经出现了几种方法来分析这些数据,但模型参数的解释往往仍然具有挑战性。我们提出了遗传潜在因子最佳线性无偏预测(glfBLUP),这是一种利用生成因子分析降低原始次要HTP数据维数的预测管道。简而言之,glfBLUP使用冗余过滤和正则化的遗传和残差相关矩阵来拟合最大似然因子模型并估计遗传潜在因子得分。这些潜在因素随后被用于多性状基因组预测。我们的方法在广泛的模拟和实际应用中比其他方法表现得更好,同时产生易于解释和生物相关的参数。我们讨论了几种可能的扩展,并强调glfBLUP作为灵活和模块化多性状基因组预测框架的基础。
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引用次数: 0
Federated Mixed Effects Logistic Regression Based on One-Time Shared Summary Statistics 基于一次性共享汇总统计的联邦混合效应逻辑回归。
IF 1.8 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-09-29 DOI: 10.1002/bimj.70080
Marie Analiz April Limpoco, Christel Faes, Niel Hens

Upholding data privacy, especially in medical research, has become tantamount to facing difficulties in accessing individual-level patient data. Estimating mixed effects binary logistic regression models involving data from multiple data providers, like hospitals, thus becomes more challenging. Federated learning has emerged as an option to preserve the privacy of individual observations while still estimating a global model that can be interpreted on the individual level, but it usually involves iterative communication between the data providers and the data analyst. In this paper, we present a strategy to estimate a mixed effects binary logistic regression model that requires data providers to share summary statistics only once. It involves generating pseudo-data whose summary statistics match those of the actual data and using these in the model estimation process instead of the actual unavailable data. Our strategy is able to include multiple predictors, which can be a combination of continuous and categorical variables. Through simulation, we show that our approach estimates the true model at least as good as the one that requires the pooled individual observations. An illustrative example using real data is provided. Unlike typical federated learning algorithms, our approach eliminates infrastructure requirements and security issues while being communication efficient and while accounting for heterogeneity.

维护数据隐私,特别是在医学研究方面,已经等同于在获取个人层面的患者数据方面面临困难。因此,估计涉及多个数据提供者(如医院)数据的混合效应二元逻辑回归模型变得更具挑战性。联邦学习作为一种保护个人观察的隐私的选择而出现,同时仍然估计可以在个人级别上解释的全局模型,但它通常涉及数据提供者和数据分析师之间的迭代通信。在本文中,我们提出了一种估计混合效应二元逻辑回归模型的策略,该模型要求数据提供者只共享一次汇总统计数据。它涉及生成与实际数据的汇总统计相匹配的伪数据,并在模型估计过程中使用这些伪数据,而不是实际的不可用数据。我们的策略能够包含多个预测因子,这些预测因子可以是连续变量和分类变量的组合。通过模拟,我们表明我们的方法估计真实模型至少与需要汇集个人观测的模型一样好。给出了一个使用实际数据的示例。与典型的联邦学习算法不同,我们的方法消除了基础设施需求和安全问题,同时保证了通信效率和异构性。
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引用次数: 0
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Biometrical Journal
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