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Meta-analyzing correlation matrices in the presence of hierarchical effect size multiplicity. 对存在层次效应大小多重性的相关矩阵进行meta分析。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-08-07 DOI: 10.1017/rsm.2025.10027
Ronny Scherer, Diego G Campos

To synthesize evidence on the relations among multiple constructs, measures, or concepts, meta-analyzing correlation matrices across primary studies has become a crucial analytic approach. Common meta-analytic approaches employ univariate or multivariate models to estimate a pooled correlation matrix, which is subjected to further analyses, such as structural equation modeling. In practice, meta-analysts often extract multiple correlation matrices per study from various samples, study sites, labs, or countries, thus introducing hierarchical effect size multiplicity into the meta-analytic data. However, this feature has largely been ignored when pooling correlation matrices for meta-analysis. To contribute to the methodological development in this area, we describe a multilevel, multivariate, and random-effects modeling approach, which pools correlation matrices meta-analytically and, at the same time, addresses hierarchical effect size multiplicity. Specifically, it allows meta-analysts to test various assumptions on the dependencies among random effects, aiding the selection of a meta-analytic baseline model. We describe this approach, present four working models within it, and illustrate them with an example and the corresponding R code.

为了综合多个构念、测量或概念之间关系的证据,跨主要研究的meta分析相关矩阵已成为一种重要的分析方法。常见的元分析方法采用单变量或多变量模型来估计汇总的相关矩阵,这是进一步分析的结果,如结构方程模型。在实践中,元分析通常从不同的样本、研究地点、实验室或国家中提取多个相关矩阵,从而在元分析数据中引入层次效应大小的多重性。然而,当汇集相关矩阵进行meta分析时,这一特征在很大程度上被忽略了。为了促进这一领域的方法学发展,我们描述了一种多层次、多变量和随机效应的建模方法,该方法对相关矩阵进行荟萃分析,同时解决了分层效应大小的多样性。具体来说,它允许元分析人员测试随机效应之间的依赖关系的各种假设,帮助选择元分析基线模型。我们描述了这种方法,给出了其中的四个工作模型,并用一个示例和相应的R代码来说明它们。
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引用次数: 0
Regression augmented weighting adjustment for indirect comparisons in health decision modelling. 健康决策模型中间接比较的回归增强加权调整。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-07-10 DOI: 10.1017/rsm.2025.10021
Chengyang Gao, Anna Heath, Gianluca Baio

Background: Understanding the relative costs and effectiveness of all competing interventions is crucial to informing health resource allocations. However, to receive regulatory approval for efficacy, novel pharmaceuticals are typically only compared against placebo or standard of care. The relative efficacy against the best alternative intervention relies on indirect comparisons of different interventions. When treatment effect modifiers are distributed differently across trials, population adjustment is necessary to ensure a fair comparison. Matching-Adjusted Indirect Comparisons (MAIC) is the most widely adopted weighting-based method for this purpose. Nevertheless, MAIC can exhibit instability under poor population overlap. Regression-based approaches to overcome this issue are heavily dependent on parametric assumptions.

Methods: We introduce a novel method, 'G-MAIC,' which combines outcome regression and weighting-adjustment to address these limitations. Inspired by Bayesian survey inference, G-MAIC employs Bayesian bootstrap to propagate the uncertainty of population-adjusted estimates. We evaluate the performance of G-MAIC against standard non-adjusted methods, MAIC and Parametric G-computation, in a simulation study encompassing 18 scenarios with varying trial sample sizes, population overlaps, and covariate structures.

Results: Under poor overlap and small sample sizes, MAIC can produce non-sensible variance estimations or increased bias compared to non-adjusted methods, depending on covariate structures in the two trials compared. G-MAIC mitigates this issue, achieving comparable performance to parametric G-computation with reduced reliance on parametric assumptions.

Conclusion: G-MAIC presents a robust alternative to the widely adopted MAIC for population-adjusted indirect comparisons. The underlying framework is flexible such that it can accommodate advanced nonparametric outcome models and alternative weighting schemes.

背景:了解所有相互竞争的干预措施的相对成本和有效性对卫生资源分配至关重要。然而,为了获得监管机构对疗效的批准,新药通常只与安慰剂或标准护理进行比较。对最佳替代干预措施的相对有效性依赖于对不同干预措施的间接比较。当治疗效果调节剂在不同试验中分布不同时,需要进行人群调整以确保公平比较。匹配调整间接比较(MAIC)是最广泛采用的基于权重的方法。然而,在低种群重叠情况下,MAIC可能表现出不稳定性。克服这一问题的基于回归的方法严重依赖于参数假设。方法:我们引入了一种新的方法,“G-MAIC”,它结合了结果回归和加权调整来解决这些局限性。受贝叶斯调查推断的启发,G-MAIC采用贝叶斯自举法传播人口调整估计的不确定性。我们在一项模拟研究中评估了G-MAIC与标准非调整方法、MAIC和参数g计算的性能,该研究包括18种不同试验样本量、总体重叠和协变量结构的情景。结果:在低重叠和小样本量的情况下,与未调整的方法相比,MAIC可能产生不合理的方差估计或偏差增加,这取决于所比较的两个试验的协变量结构。G-MAIC减轻了这个问题,实现了与参数g计算相当的性能,减少了对参数假设的依赖。结论:G-MAIC提供了一个强大的替代广泛采用的人口调整间接比较的MAIC。底层框架是灵活的,因此它可以容纳先进的非参数结果模型和可选的加权方案。
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引用次数: 0
Assessing risk of bias of cohort studies with large language models. 评估大型语言模型队列研究的偏倚风险。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-08-07 DOI: 10.1017/rsm.2025.10028
Danni Xia, Honghao Lai, Weilong Zhao, Jiajie Huang, Jiayi Liu, Ziying Ye, Jianing Liu, Mingyao Sun, Liangying Hou, Bei Pan, Long Ge

This study aims to explore the feasibility and accuracy of utilizing large language models (LLMs) to assess the risk of bias (ROB) in cohort studies. We conducted a pilot and feasibility study in 30 cohort studies randomly selected from reference lists of published Cochrane reviews. We developed a structured prompt to guide the ChatGPT-4o, Moonshot-v1-128k, and DeepSeek-V3 to assess the ROB of each cohort twice. We used the ROB results assessed by three evidence-based medicine experts as the gold standard, and then we evaluated the accuracy of LLMs by calculating the correct assessment rate, sensitivity, specificity, and F1 scores for overall and item-specific levels. The consistency of the overall and item-specific assessment results was evaluated using Cohen's kappa (κ) and prevalence-adjusted bias-adjusted kappa. Efficiency was estimated by the mean assessment time required. This study assessed three LLMs (ChatGPT-4o, Moonshot-v1-128k, and DeepSeek-V3) and revealed distinct performance across eight assessment items. Overall accuracy was comparable (80.8%-83.3%). Moonshot-v1-128k showed superior sensitivity in population selection (0.92 versus ChatGPT-4o's 0.55, P < 0.001). In terms of F1 scores, Moonshot-v1-128k led in population selection (F = 0.80 versus ChatGPT-4o's 0.67, P = 0.004). ChatGPT-4o demonstrated the highest consistency (mean κ = 96.5%), with perfect agreement (100%) in outcome confidence. ChatGPT-4o was 97.3% faster per article (32.8 seconds versus 20 minutes manually) and outperformed Moonshot-v1-128k and DeepSeek-V3 by 47-50% in processing speed. The efficient and accurate assessment of ROB in cohort studies by ChatGPT-4o, Moonshot-v1-128k, and DeepSeek-V3 highlights the potential of LLMs to enhance the systematic review process.

本研究旨在探讨在队列研究中利用大语言模型(LLMs)评估偏倚风险(ROB)的可行性和准确性。我们从Cochrane已发表综述的参考文献列表中随机选择30项队列研究进行了试点和可行性研究。我们开发了一个结构化提示来指导chatgpt - 40、Moonshot-v1-128k和DeepSeek-V3对每个队列的ROB进行两次评估。我们采用三位循证医学专家评估的ROB结果作为金标准,然后通过计算总体和单项水平的正确评估率、敏感性、特异性和F1评分来评估llm的准确性。采用Cohen's kappa (κ)和流行校正偏倚校正kappa来评估整体和特定项目评估结果的一致性。效率是通过平均评估时间来估计的。该研究评估了三种llm (chatgpt - 40、Moonshot-v1-128k和DeepSeek-V3),并在八个评估项目中显示了不同的性能。总体准确度相当(80.8% ~ 83.3%)。Moonshot-v1-128k在种群选择上表现出更强的敏感性(P = 0.92,高于chatgpt - 40的0.55,P = 0.004)。Moonshot-v1-128k在种群选择上领先(F = 0.80,高于chatgpt - 40的0.67,P = 0.004)。chatgpt - 40表现出最高的一致性(平均κ = 96.5%),结果置信度完全一致(100%)。chatgpt - 40每篇文章的处理速度快97.3%(32.8秒,手动20分钟),处理速度比Moonshot-v1-128k和DeepSeek-V3快47-50%。chatgpt - 40、Moonshot-v1-128k和DeepSeek-V3在队列研究中高效准确地评估了ROB,这凸显了llm在加强系统评价过程中的潜力。
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引用次数: 0
Novel approaches for random-effects meta-analysis of a small number of studies under normality. 在正态性下对少量研究进行随机效应荟萃分析的新方法。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-07-10 DOI: 10.1017/rsm.2025.10022
Yajie Duan, Thomas Mathew, Demissie Alemayehu, Ge Cheng

Random-effects meta-analyses with only a few studies often face challenges in accurately estimating between-study heterogeneity, leading to biased effect estimates and confidence intervals with poor coverage. This issue is especially the case when dealing with rare diseases. To address this problem for normally distributed outcomes, two new approaches have been proposed to provide confidence limits of the global mean: one based on fiducial inference, and the other involving two modifications of the signed log-likelihood ratio test statistic in order to have improved performance with small numbers of studies. The performance of the proposed methods was evaluated numerically and compared with the Hartung-Knapp-Sidik-Jonkman approach and its modification to handle small numbers of studies. The simulation results indicated that the proposed methods achieved coverage probabilities closer to the nominal level and produced shorter confidence intervals compared to those based on existing methods. Two real examples are used to illustrate the proposed methods.

只有少数研究的随机效应荟萃分析经常面临准确估计研究间异质性的挑战,导致效果估计偏倚和置信区间覆盖率低。在处理罕见疾病时,这个问题尤其如此。为了解决正态分布结果的这个问题,已经提出了两种新的方法来提供全局均值的置信限:一种基于基准推断,另一种涉及对有符号对数似然比检验统计量的两次修改,以便在少量研究中提高性能。对所提出方法的性能进行了数值评估,并与Hartung-Knapp-Sidik-Jonkman方法及其修正进行了比较,以处理少量研究。仿真结果表明,与现有方法相比,所提方法获得的覆盖概率更接近标称水平,产生的置信区间更短。用两个实例来说明所提出的方法。
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引用次数: 0
Ten practices for successful study coding in research syntheses: Developing coding manuals and coding forms. 在综合研究中成功学习编码的十个实践:开发编码手册和编码形式。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-06-23 DOI: 10.1017/rsm.2025.10019
Gena Nelson, Sarah Quinn, Sean Grant, Shaina D Trevino, Elizabeth Day, Maria Schweer-Collins, Hannah Carter, Peter Boedeker, Emily Tanner-Smith

Study coding is an essential component of the research synthesis process. Data extracted during study coding serve as a direct link between the included studies and the synthesis results, allowing reviewers to justify claims about the findings from a set of related studies. The purpose of this tutorial is to provide authors, particularly those new to research synthesis, with recommendations to develop study coding manuals and forms that result in efficient, high-quality data extraction. Each of the 10 easy-to-follow practices is supported with additional resources, examples, or non-examples to help authors develop high-quality study coding materials. With the increase in publication of meta-analyses in recent years across many disciplines, a primary goal of this article is to enhance the quality of study coding materials that authors develop.

研究编码是研究综合过程的重要组成部分。在研究编码过程中提取的数据作为纳入研究和综合结果之间的直接联系,使审稿人能够证明对一组相关研究结果的主张。本教程的目的是为作者,特别是那些刚开始研究合成的作者,提供开发研究编码手册和表单的建议,从而实现高效、高质量的数据提取。这10个易于遵循的实践中的每一个都有额外的资源、示例或非示例支持,以帮助作者开发高质量的学习编码材料。近年来,随着多学科荟萃分析发表的增加,本文的主要目标是提高作者开发的研究编码材料的质量。
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引用次数: 0
Authors' reply: Continuity corrections with Mantel-Haenszel estimators in Cochrane reviews. 作者回复:在Cochrane综述中使用Mantel-Haenszel估计量进行连续性修正。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-07-10 DOI: 10.1017/rsm.2025.10013
Yasushi Tsujimoto, Yusuke Tsutsumi, Yuki Kataoka, Akihiro Shiroshita, Orestis Efthimiou, Toshi A Furukawa
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引用次数: 0
Subgroup identification using individual participant data from multiple trials: An application in low back pain. 使用来自多个试验的个体参与者数据进行亚组识别:腰痛的应用。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-06-18 DOI: 10.1017/rsm.2025.10010
Cynthia Huber, Tim Friede

Model-based recursive partitioning (MOB) and its extension, metaMOB, are tools for identifying subgroups with differential treatment effects. When pooling data from various trials the metaMOB approach uses random effects to model the heterogeneity of treatment effects. In situations where interventions offer only small overall benefits and require extensive, costly trials with a large participant enrollment, leveraging individual-participant data (IPD) from multiple trials can help identify individuals who are most likely to benefit from the intervention. We explore the application of MOB and metaMOB in the context of non-specific low back pain treatment, using synthetic data based on a subset of the individual participant data meta-analysis by Patel et al. 1 Our study underscores the need to explore heterogeneity in intercepts and treatment effects to identify subgroups with differential treatment effects in IPD meta-analyses.

基于模型的递归划分(MOB)及其扩展metaMOB是用于识别具有不同处理效果的子组的工具。当汇集来自不同试验的数据时,metaMOB方法使用随机效应来模拟治疗效果的异质性。在干预措施只能提供很小的整体效益,并且需要大量参与者参与的广泛、昂贵的试验的情况下,利用来自多个试验的个体参与者数据(IPD)可以帮助确定最有可能从干预中受益的个体。我们探索了MOB和metaMOB在非特异性腰痛治疗背景下的应用,使用基于Patel等人的个体参与者数据荟萃分析的合成数据1。我们的研究强调需要探索阻断和治疗效果的异质性,以确定IPD荟萃分析中治疗效果差异的亚组。
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引用次数: 0
Hierarchical imputation of categorical variables in the presence of systematically and sporadically missing data. 在存在系统和零星缺失数据的情况下,分类变量的分层代入。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-06-10 DOI: 10.1017/rsm.2025.10017
Shahab Jolani

Modern quantitative evidence synthesis methods often combine patient-level data from different sources, known as individual participants data (IPD) sets. A specific challenge in meta-analysis of IPD sets is the presence of systematically missing data, when certain variables are not measured in some studies, and sporadically missing data, when measurements of certain variables are incomplete across different studies. Multiple imputation (MI) is among the better approaches to deal with missing data. However, MI of hierarchical data, such as IPD meta-analysis, requires advanced imputation routines that preserve the hierarchical data structure and accommodate the presence of both systematically and sporadically missing data. We have recently developed a new class of hierarchical imputation methods within the MICE framework tailored for continuous variables. This article discusses the extensions of this methodology to categorical variables, accommodating the simultaneous presence of systematically and sporadically missing data in nested designs with arbitrary missing data patterns. To address the challenge of the categorical nature of the data, we propose an accept-reject algorithm during the imputation process. Following theoretical discussions, we evaluate the performance of the new methodology through simulation studies and demonstrate its application using an IPD set from patients with kidney disease.

现代定量证据合成方法通常结合来自不同来源的患者水平数据,称为个体参与者数据(IPD)集。IPD集合荟萃分析的一个具体挑战是,当某些研究没有测量某些变量时,存在系统缺失的数据;当不同研究中对某些变量的测量不完整时,存在零星缺失的数据。多重插值(MI)是处理缺失数据的较好方法之一。然而,分层数据的MI,如IPD荟萃分析,需要高级的imputation例程来保留分层数据结构,并适应系统和零星缺失数据的存在。我们最近在MICE框架内开发了一种新的针对连续变量的分层imputation方法。本文讨论了将该方法扩展到分类变量,以适应在具有任意丢失数据模式的嵌套设计中系统地和零星地丢失数据的同时存在。为了解决数据的分类性质的挑战,我们提出了一种接受-拒绝算法在imputation过程中。在理论讨论之后,我们通过模拟研究评估了新方法的性能,并使用肾脏疾病患者的IPD集演示了其应用。
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引用次数: 0
Methodology for mapping reviews, evidence maps, and gap maps. 评价制图、证据图和差距图的方法学。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-06-16 DOI: 10.1017/rsm.2025.25
Hanan Khalil, Vivian Welch, Matthew Grainger, Fiona Campbell

Mapping reviews are valuable tools for synthesizing and visualizing research evidence, providing a comprehensive overview of studies within a specific field. Their visual approach enhances accessibility, enabling researchers, policymakers, and practitioners to efficiently identify key findings, trends, and knowledge gaps. These reviews are particularly significant in guiding future research, informing funding decisions, and shaping evidence-based policymaking. In environmental science-similar to health and social sciences-mapping reviews play a crucial role in identifying effective conservation strategies, tracking interventions, and supporting targeted programs.Unlike systematic reviews, which assess intervention effectiveness, mapping reviews focus on broad research questions, aiming to chart the existing evidence on a given topic. They use structured methodologies to identify patterns, gaps, and trends, often employing visual tools to enhance data accessibility. A well-defined scope, guided by inclusion and exclusion criteria, ensures a transparent study selection process. Comprehensive search strategies, often spanning multiple databases, maximize evidence capture. Effective screening, combining automated and manual processes, ensures relevance, while data extraction emphasizes high-level categories such as study design and population demographics. Advanced software tools, including EPPI-Reviewer and MindMeister, support data extraction and visualization, with evidence gap maps highlighting robust areas and research voids.Despite their advantages, mapping reviews present challenges. The categorization and coding of studies can introduce subjective biases, and the process demands substantial resources. Automation and artificial intelligence offer promising solutions, improving efficiency while addressing integration and multilingual limitations. As methodological advancements continue, interdisciplinary collaboration will be essential to fully realize the potential of mapping reviews across scientific disciplines.

地图评论是合成和可视化研究证据的宝贵工具,为特定领域的研究提供了全面的概述。他们的可视化方法增强了可访问性,使研究人员、政策制定者和从业者能够有效地识别关键发现、趋势和知识差距。这些审查在指导未来的研究、为资助决策提供信息和形成基于证据的政策制定方面尤其重要。在环境科学中——类似于健康和社会科学——制图审查在确定有效的保护策略、跟踪干预措施和支持有针对性的项目方面起着至关重要的作用。与评估干预有效性的系统评价不同,地图评价侧重于广泛的研究问题,旨在将给定主题的现有证据绘制成图表。他们使用结构化的方法来识别模式、差距和趋势,通常使用可视化工具来增强数据的可访问性。明确定义的范围,以纳入和排除标准为指导,确保透明的研究选择过程。综合搜索策略,通常跨越多个数据库,最大限度地获取证据。结合自动化和人工流程的有效筛选确保了相关性,而数据提取则强调研究设计和人口统计等高级类别。先进的软件工具,包括EPPI-Reviewer和MindMeister,支持数据提取和可视化,证据差距图突出了强大的领域和研究空白。尽管有其优势,但地图审查也带来了挑战。研究的分类和编码可能会引入主观偏见,这一过程需要大量的资源。自动化和人工智能提供了有前途的解决方案,在解决集成和多语言限制的同时提高了效率。随着方法学的不断进步,跨学科合作对于充分实现跨科学学科绘制评论的潜力至关重要。
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引用次数: 0
Continuity corrections with Mantel-Haenszel estimators in Cochrane reviews. Cochrane综述中使用Mantel-Haenszel估计量进行连续性校正。
IF 6.1 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-06-06 DOI: 10.1017/rsm.2025.10012
A E Ades, Deborah M Caldwell, Sumayya Anwer, Sofia Dias
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引用次数: 0
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