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Outcomes Truncated by Death in RCTs: A Simulation Study on the Survivor Average Causal Effect 随机对照试验中被死亡截断的结果:幸存者平均因果效应的模拟研究
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-06-11 DOI: 10.1002/bimj.70061
Stefanie von Felten, Chiara Vanetta, Christoph M. Rüegger, Sven Wellmann, Leonhard Held

Continuous outcome measurements truncated by death present a challenge for the estimation of unbiased treatment effects in randomized controlled trials (RCTs). One way to deal with such situations is to estimate the survivor average causal effect (SACE), but this requires making nontestable assumptions. Motivated by an ongoing RCT in very preterm infants with intraventricular hemorrhage, we performed a simulation study to compare an SACE estimator with complete case analysis (CCA) and analysis after multiple imputation of missing outcomes. We set up nine scenarios combining positive, negative, and no treatment effect on the outcome (cognitive development) and on survival at 2 years of age. Treatment effect estimates from all methods were compared in terms of bias, mean squared error, and coverage with regard to two true treatment effects: the treatment effect on the outcome used in the simulation and the SACE, which was derived by simulation of both potential outcomes per patient. Despite targeting different estimands (principal stratum estimand, hypothetical estimand), the SACE-estimator and multiple imputation gave similar estimates of the treatment effect and efficiently reduced the bias compared to CCA. Also, both methods were relatively robust to omission of one covariate in the analysis, and thus violation of relevant assumptions. Although the SACE is not without controversy, we find it useful if mortality is inherent to the study population. Some degree of violation of the required assumptions is almost certain, but may be acceptable in practice.

被死亡截断的连续结局测量对随机对照试验(rct)中无偏治疗效果的估计提出了挑战。处理这种情况的一种方法是估计幸存者平均因果效应(SACE),但这需要做出不可检验的假设。在一项正在进行的针对极早产儿脑室内出血的随机对照试验的激励下,我们进行了一项模拟研究,将SACE估计值与完整病例分析(CCA)和多次缺失结果归因后的分析进行比较。我们设置了9个场景,包括对结果(认知发展)和2岁生存率的积极、消极和无治疗效果。对所有方法的治疗效果估计进行偏倚、均方误差和两种真实治疗效果的覆盖范围的比较:模拟中使用的治疗效果和SACE, SACE是通过模拟每个患者的两种潜在结果得出的。尽管针对不同的估计(主地层估计,假设估计),sace估计器和多重imputation给出了类似的处理效果估计,并有效地减少了与CCA相比的偏差。此外,这两种方法对于分析中遗漏一个协变量,从而违反相关假设都相对稳健。尽管SACE并非没有争议,但我们发现,如果死亡率是研究人群固有的,它是有用的。在一定程度上违反所要求的假设几乎是肯定的,但在实践中可能是可以接受的。
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引用次数: 0
Statistical Modeling to Adjust for Time Trends in Adaptive Platform Trials Utilizing Non-Concurrent Controls 利用非并发控制的自适应平台试验中调整时间趋势的统计建模
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-06-10 DOI: 10.1002/bimj.70059
Pavla Krotka, Martin Posch, Mohamed Gewily, Günter Höglinger, Marta Bofill Roig

Utilizing non-concurrent control (NCC) data in the analysis of late-entering arms in platform trials has recently received considerable attention. While incorporating NCC can lead to increased power and lower sample sizes, it might introduce bias to the effect estimators if temporal drifts are present. Aiming to mitigate this potential bias, we propose various frequentist model-based approaches that leverage the NCC, while adjusting for time. One of the currently available models incorporates time as a categorical fixed effect, separating the trial duration into periods, defined as time intervals bounded by any arm entering or leaving the platform. In this work, we propose two extensions of this model. First, we consider an alternative definition of time by dividing the trial into fixed-length calendar time intervals. Second, we propose alternative model-based time adjustments. Specifically, we investigate adjusting for random effects and employing splines to model time with a polynomial function. We evaluate the performance of the proposed approaches in a simulation study and illustrate their use through a case study. We show that adjusting for time via a spline function controls the type I error in trials with a sufficiently smooth time trend pattern and may lead to power gains compared to the standard fixed effect model. However, the fixed effect model with period adjustment is the most robust model for arbitrary time trends, provided that the trend is equal across all arms. Especially, in trials with sudden changes in the time trend, the period-adjustment model is preferred if NCCs are included.

利用非并发控制(NCC)数据分析平台试验中进入后期的分支最近受到了相当大的关注。虽然合并NCC可能导致功率增加和样本量减少,但如果存在时间漂移,它可能会给效果估计器引入偏差。为了减轻这种潜在的偏见,我们提出了各种基于频率模型的方法,利用NCC,同时根据时间进行调整。目前可用的一种模型将时间作为分类固定效应,将试验持续时间划分为几个时间段,定义为以任何进入或离开平台的手臂为界的时间间隔。在这项工作中,我们提出了该模型的两个扩展。首先,我们通过将试验划分为固定长度的日历时间间隔来考虑时间的另一种定义。其次,我们提出了基于模型的时间调整方案。具体来说,我们研究了调整随机效应和使用样条曲线用多项式函数来模拟时间。我们在模拟研究中评估了所提出方法的性能,并通过案例研究说明了它们的使用。我们表明,通过样条函数对时间进行调整可以控制具有足够平滑的时间趋势模式的试验中的I型误差,并且可能导致与标准固定效应模型相比的功率增益。然而,具有周期调整的固定效应模型对于任意时间趋势是最稳健的模型,前提是所有臂的趋势是相等的。特别是在时间趋势突变的试验中,如果包含ncc,则首选周期调整模型。
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引用次数: 0
A Bivariate Finite Mixture Random Effects Model for Identifying and Accommodating Outliers in Diagnostic Test Accuracy Meta-Analyses 诊断测试准确性荟萃分析中识别和容纳异常值的二元有限混合随机效应模型
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-06-09 DOI: 10.1002/bimj.70062
Zelalem F. Negeri

Outlying studies are prevalent in meta-analyses of diagnostic test accuracy studies and may lead to misleading inferences and decision-making unless their negative effect is appropriately dealt with. Statistical methods for detecting and down-weighting the impact of such studies have recently gained the attention of many researchers. However, these methods dichotomize each study in the meta-analysis as outlying or non-outlying and focus on examining the effect of outlying studies on the summary sensitivity and specificity only. We developed and evaluated a robust and flexible random-effects bivariate finite mixture model for meta-analyzing diagnostic test accuracy studies. The proposed model accounts for both the within- and across-study heterogeneity in diagnostic test results, generates the probability that each study in a meta-analysis is outlying instead of dichotomizing the status of the studies, and allows assessing the impact of outlying studies on the pooled sensitivity, pooled specificity, and between-study heterogeneity. Our simulation study and real-life data examples demonstrated that the proposed model was robust to the existence of outlying studies, produced precise point and interval estimates of the pooled sensitivity and specificity, and yielded similar results to the standard models when there were no outliers. Extensive simulations demonstrated relatively better bias and confidence interval width, but comparable root mean squared error and lesser coverage probability of the proposed model. Practitioners can use our proposed model as a stand-alone model to conduct a meta-analysis of diagnostic test accuracy studies or as an alternative sensitivity analysis model when outlying studies are present in a meta-analysis.

离群研究在诊断测试准确性研究的荟萃分析中普遍存在,除非其负面影响得到适当处理,否则可能导致误导性推论和决策。用于检测和降低此类研究影响的统计方法最近引起了许多研究人员的注意。然而,这些方法将meta分析中的每项研究分为离群研究和非离群研究,并且只关注离群研究对总体敏感性和特异性的影响。我们开发并评估了一个稳健和灵活的随机效应双变量有限混合模型,用于荟萃分析诊断测试准确性研究。所提出的模型考虑了诊断测试结果中的研究内部和研究间异质性,产生了meta分析中每个研究是孤立的概率,而不是对研究的状态进行二分类,并允许评估孤立研究对合并敏感性、合并特异性和研究间异质性的影响。我们的模拟研究和实际数据示例表明,所提出的模型对离群研究的存在具有鲁棒性,对合并敏感性和特异性产生了精确的点和区间估计,并且在没有离群值的情况下产生了与标准模型相似的结果。广泛的模拟表明,该模型的偏差和置信区间宽度相对较好,但均方根误差相当,覆盖概率较小。从业者可以使用我们提出的模型作为独立模型来进行诊断测试准确性研究的荟萃分析,或者在荟萃分析中存在离群研究时作为替代敏感性分析模型。
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引用次数: 0
Hazards Constitute Key Quantities for Analyzing, Interpreting and Understanding Time-to-Event Data 危害构成了分析、解释和理解事件发生时间数据的关键量
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-06-06 DOI: 10.1002/bimj.70057
Jan Beyersmann, Claudia Schmoor, Martin Schumacher

Censoring makes time-to-event data special and requires customized statistical techniques. Survival and event history analysis therefore builds on hazards as the identifiable quantities in the presence of rather general censoring schemes. The reason is that hazards are conditional quantities, given previous survival, which enables estimation based on the current risk set—those still alive and under observation. But it is precisely their conditional nature that has made hazards subject of critique from a causal perspective: A beneficial treatment will help patients survive longer than had they remained untreated. Hence, in a randomized trial, randomization is broken in later risk sets, which, however, are the basis for statistical inference. We survey this dilemma—after all, mapping analyses of hazards onto probabilities in randomized trials is viewed as still having a causal interpretation—and argue that a causal interpretation is possible taking a functional point of view. We illustrate matters with examples from benefit–risk assessment: Prolonged survival may lead to more adverse events, but this need not imply a worse safety profile of the novel treatment. These examples illustrate that the situation at hand is conveniently parameterized using hazards, that the need to use survival techniques is not always fully appreciated and that censoring not necessarily leads to the question of “what, if no censoring?” The discussion should concentrate on how to correctly interpret causal hazard contrasts and analyses of hazards should routinely be translated onto probabilities.

审查使时间到事件的数据变得特别,需要定制的统计技术。因此,生存和事件历史分析建立在危险作为可识别数量的基础上,存在相当普遍的审查方案。原因是,危险是有条件的数量,根据以前的生存情况,这使得可以根据当前的风险集进行估计——那些仍然活着并在观察中的风险集。但恰恰是它们的条件性质,使它们成为了从因果关系的角度进行批判的对象:有益的治疗将帮助患者比不治疗的情况下活得更长。因此,在随机试验中,随机化在后来的风险集中被打破,然而,这是统计推断的基础。我们调查了这一困境——毕竟,在随机试验中,将风险分析映射到概率上仍然被认为是有因果解释的——并认为从功能的角度来看,因果解释是可能的。我们用获益-风险评估的例子来说明问题:延长生存期可能导致更多的不良事件,但这并不意味着新疗法的安全性更差。这些例子说明,手头的情况是通过危险来方便地参数化的,使用生存技术的必要性并不总是被充分认识到,审查并不一定会导致“如果不审查会怎么样?”讨论应集中于如何正确地解释因果风险对比,对风险的分析应常规地转化为概率。
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引用次数: 0
Estimating the Optimal Time to Perform a Positron Emission Tomography With Prostate-Specific Membrane Antigen in Prostatectomized Patients, Based on Data From Clinical Practice 基于临床实践的数据估计前列腺切除术患者进行前列腺特异性膜抗原正电子发射断层扫描的最佳时间
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-05-22 DOI: 10.1002/bimj.70058
Martina Amongero, Gianluca Mastrantonio, Stefano De Luca, Mauro Gasparini

Prostatectomized patients are at risk of resurgence, and for this reason, during a follow-up period, they are monitored for prostate-specific antigen (PSA) growth, an indicator of tumor progression. The presence of tumors can be evaluated with an expensive exam, called positron emission tomography with prostate-specific membrane antigen (PET-PSMA). To justify the high cost of the PET-PSMA and, at the same time, to contain the risk for the patient, this exam should be recommended only when the evidence of tumor progression is strong. With the aim of estimating the optimal time to recommend the exam based on the patient's history and collected data, we build a hierarchical Bayesian model that describes, jointly, the PSA growth curve and the probability of a positive PET-PSMA. With our proposal, we process all past and present information about the patients PSA measurement and PET-PSMA results, in order to give an informed estimate of the optimal time, improving current practice.

前列腺切除术患者有复发的风险,因此,在随访期间,他们被监测前列腺特异性抗原(PSA)的生长,这是肿瘤进展的一个指标。肿瘤的存在可以通过昂贵的检查来评估,称为前列腺特异性膜抗原正电子发射断层扫描(PET-PSMA)。为了证明PET-PSMA的高成本是合理的,同时,为了控制患者的风险,只有当肿瘤进展的证据很明显时,才应该推荐这项检查。为了根据患者的病史和收集的数据估计推荐检查的最佳时间,我们建立了一个分层贝叶斯模型,该模型共同描述了PSA生长曲线和PET-PSMA阳性的概率。根据我们的建议,我们处理所有关于患者PSA测量和PET-PSMA结果的过去和现在的信息,以便给出最佳时间的知情估计,改进当前的实践。
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引用次数: 0
Issue Information: Biometrical Journal 3'25 期刊信息:bioometic Journal 3'25
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-05-12 DOI: 10.1002/bimj.70060
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引用次数: 0
Semi-Markov Multistate Modeling Approaches for Multicohort Event History Data 多队列事件历史数据的半马尔可夫多状态建模方法
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-05-08 DOI: 10.1002/bimj.70051
Xavier Piulachs, Klaus Langohr, Mireia Besalú, Natàlia Pallarès, Jordi Carratalà, Cristian Tebé, Guadalupe Gómez Melis

Two Cox-based multistate modeling approaches are compared for modeling a complex multicohort event history process. The first approach incorporates cohort information as a fixed covariate, thereby providing a direct estimation of the cohort-specific effects. The second approach includes the cohort as a stratum variable, which offers an extra flexibility in estimating the transition probabilities. Additionally, both approaches may include possible interaction terms between the cohort and a given prognostic predictor. Furthermore, the Markov property conditional on observed prognostic covariates is assessed using a global score test. Whenever departures from the Markovian assumption are revealed for a given transition, the time of entry into the current state is incorporated as a fixed covariate, yielding a semi-Markov process. The two proposed methods are applied to a three-wave dataset of COVID-19-hospitalized adults in the southern Barcelona metropolitan area (Spain), and the corresponding performance is discussed. While both semi-Markovian approaches are shown to be useful, the preferred one will depend on the focus of the inference. To summarize, the cohort–covariate approach enables an insightful discussion on the behavior of the cohort effects, whereas the stratum–cohort approach provides flexibility to estimate transition-specific underlying risks according to the different cohorts.

比较了两种基于cox的多状态建模方法对复杂多队列事件历史过程的建模。第一种方法将队列信息作为固定协变量,从而提供对队列特定效应的直接估计。第二种方法将队列作为地层变量,这在估计过渡概率方面提供了额外的灵活性。此外,这两种方法可能包括队列和给定预后预测因子之间可能的相互作用项。此外,马尔可夫性质条件观察到的预后协变量是评估使用全局得分测试。每当偏离马尔可夫假设时,对于给定的过渡,进入当前状态的时间被合并为固定的协变量,产生半马尔可夫过程。将这两种方法应用于西班牙巴塞罗那南部城区新冠肺炎住院成年人的三波数据集,并讨论了相应的性能。虽然两种半马尔可夫方法都被证明是有用的,但首选的方法将取决于推理的焦点。总之,队列协变量方法能够对队列效应的行为进行有见地的讨论,而分层队列方法提供了根据不同队列估计过渡特定潜在风险的灵活性。
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引用次数: 0
How Should Parallel Cluster Randomized Trials With a Baseline Period be Analyzed?—A Survey of Estimands and Common Estimators 有基线期的平行群随机试验应该如何分析?-估价及一般估价员概览
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-04-29 DOI: 10.1002/bimj.70052
Kenneth Menglin Lee, Fan Li

The parallel cluster randomized trial with baseline (PB-CRT) is a common variant of the standard parallel cluster randomized trial (P-CRT). We define two natural estimands in the context of PB-CRTs with informative cluster sizes, the individual-average treatment effect (iATE) and cluster-average treatment effect (cATE), to address individual and cluster-level hypotheses. In this work, we theoretically derive the convergence of the unweighted and inverse cluster-period size weighted (i) independence estimating equation (IEE), (ii) fixed-effects (FE) model, (iii) exchangeable mixed-effects (EME) model, and (iv) nested-exchangeable mixed-effects (NEME) model treatment effect estimators in a PB-CRT with informative cluster sizes and continuous outcomes. Overall, we theoretically show that the unweighted and weighted IEE and FE models yield consistent estimators for the iATE and cATE estimands. Although mixed-effects models yield inconsistent estimators to these two natural estimands under informative cluster sizes, we empirically demonstrate that the EME model is surprisingly robust to bias. This is in sharp contrast to the corresponding analyses in P-CRTs and the NEME model in PB-CRTs when informative cluster sizes are present, carrying implications for practice. We report a simulation study and conclude with a re-analysis of a PB-CRT examining the effects of community youth teams on improving mental health among adolescent girls in rural eastern India.

基线平行群随机试验(PB-CRT)是标准平行群随机试验(P-CRT)的一种常见变体。我们在具有信息簇大小的pb - crt的背景下定义了两个自然估计,即个体平均治疗效果(iATE)和集群平均治疗效果(cATE),以解决个人和集群水平的假设。在这项工作中,我们从理论上推导了PB-CRT中具有信息簇大小和连续结果的未加权和逆簇周期大小加权(i)独立性估计方程(IEE), (ii)固定效应(FE)模型,(iii)可交换混合效应(EME)模型和(iv)嵌套可交换混合效应(NEME)模型治疗效果估计器的收敛性。总体而言,我们从理论上表明,未加权和加权的IEE和FE模型对ate和cATE估计产生一致的估计。尽管混合效应模型在信息簇大小下对这两种自然估计产生不一致的估计,但我们通过经验证明,EME模型对偏差具有惊人的鲁棒性。这与p - crt中的相应分析和pb - crt中的NEME模型形成鲜明对比,当信息簇大小存在时,具有实践意义。我们报告了一项模拟研究,并以重新分析PB-CRT来结束,该研究检查了社区青年团队对改善印度东部农村少女心理健康的影响。
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引用次数: 0
Bayesian Inference of Phenotypic Plasticity of Cancer Cells Based on Dynamic Model for Temporal Cell Proportion Data 基于时间细胞比例数据动态模型的癌细胞表型可塑性贝叶斯推断
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-04-29 DOI: 10.1002/bimj.70055
Shuli Chen, Yuman Wang,  Da Zhou, Jie Hu

Mounting evidence underscores the prevalent hierarchical organization of cancer tissues. At the foundation of this hierarchy reside cancer stem cells, a subset of cells endowed with the pivotal role of engendering the entire cancer tissue through cell differentiation. In recent times, substantial attention has been directed toward the phenomenon of cancer cell plasticity, where the dynamic interconversion between cancer stem cells and nonstem cancer cells has garnered significant interest. Since the task of detecting cancer cell plasticity from empirical data remains a formidable challenge, we propose a Bayesian statistical framework designed to infer phenotypic plasticity within cancer cells, utilizing temporal data on cancer stem cell proportions. Our approach is grounded in a stochastic model, adept at capturing the dynamic behaviors of cells. Leveraging Bayesian analysis, we scrutinize the moment equation governing cancer stem cell proportions, derived from the Kolmogorov forward equation of our stochastic model. Our methodology introduces an improved Euler method for parameter estimation within nonlinear ordinary differential equation models, also extending insights to compositional data. Extensive simulations robustly validate the efficacy of our proposed method. To further corroborate our findings, we apply our approach to analyze published data from SW620 colon cancer cell lines. Our results harmonize with in situ experiments, thereby reinforcing the utility of our method in discerning and quantifying phenotypic plasticity within cancer cells.

越来越多的证据强调了癌症组织普遍存在的等级组织。在这一层次结构的基础上是癌症干细胞,这是一类细胞,通过细胞分化,具有形成整个癌症组织的关键作用。近年来,癌细胞可塑性现象引起了人们的广泛关注,癌症干细胞和非干细胞之间的动态相互转化引起了人们的极大兴趣。由于从经验数据中检测癌细胞可塑性的任务仍然是一个艰巨的挑战,我们提出了一个贝叶斯统计框架,旨在利用癌症干细胞比例的时间数据推断癌细胞内的表型可塑性。我们的方法基于随机模型,擅长捕捉细胞的动态行为。利用贝叶斯分析,我们仔细研究了控制癌症干细胞比例的矩方程,该方程来自我们随机模型的Kolmogorov正演方程。我们的方法引入了一种改进的欧拉方法,用于非线性常微分方程模型中的参数估计,也扩展了对成分数据的见解。大量的仿真实验有力地验证了该方法的有效性。为了进一步证实我们的发现,我们应用我们的方法分析了来自SW620结肠癌细胞系的已发表数据。我们的结果与原位实验相一致,从而加强了我们的方法在识别和量化癌细胞内表型可塑性方面的实用性。
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引用次数: 0
A Regularized MANOVA Test for Semicontinuous High-Dimensional Data 半连续高维数据的正则化方差检验
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-04-29 DOI: 10.1002/bimj.70054
Elena Sabbioni, Claudio Agostinelli, Alessio Farcomeni

We propose a MANOVA test for semicontinuous data that is applicable also when the dimension exceeds the sample size. The test statistic is obtained as a likelihood ratio, where the numerator and denominator are computed at the maxima of penalized likelihood functions under each hypothesis. Closed form solutions for the regularized estimators allow us to avoid computational overheads. We derive the null distribution using a permutation scheme. The power and level of the resulting test are evaluated in a simulation study. We illustrate the new methodology with two original data analyses, one regarding microRNA expression in human blastocyst cultures, and another regarding alien plant species invasion in the island of Socotra (Yemen).

我们建议对半连续数据进行方差分析,当维度超过样本量时也适用。检验统计量以似然比的形式得到,其中分子和分母是在每个假设下惩罚似然函数的最大值处计算的。正则估计的闭形式解允许我们避免计算开销。利用置换格式导出了零分布。在模拟研究中评估了结果测试的功率和水平。我们用两个原始数据分析来说明新方法,一个是关于人类囊胚培养物中的microRNA表达,另一个是关于索科特拉岛(也门)的外来植物物种入侵。
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引用次数: 0
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Biometrical Journal
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