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Impact of Methodological Assumptions and Covariates on the Cutoff Estimation in ROC Analysis 方法假设和协变量对ROC分析中截止估计的影响
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-04-27 DOI: 10.1002/bimj.70053
Soutik Ghosal

The receiver operating characteristic (ROC) curve stands as a cornerstone in assessing the efficacy of biomarkers for disease diagnosis. Beyond merely evaluating performance, it provides with an optimal cutoff for biomarker values, crucial for disease categorization. While diverse methodologies exist for cutoff estimation, less attention has been paid to integrating covariate impact into this process. Covariates can strongly impact diagnostic summaries, leading to variations across different covariate levels. Therefore, a tailored covariate-based framework is imperative for outlining covariate-specific optimal cutoffs. Moreover, recent investigations into cutoff estimators have overlooked the influence of ROC curve estimation methodologies. This study endeavors to bridge this gap by addressing the research void. Extensive simulation studies are conducted to scrutinize the performance of ROC curve estimation models in estimating different cutoffs in varying scenarios, encompassing diverse data-generating mechanisms and covariate effects. In addition, leveraging the Alzheimer's Disease Neuroimaging Initiative (ADNI) data set, the research assesses the performance of different biomarkers in diagnosing Alzheimer's disease and determines the suitable optimal cutoffs.

受试者工作特征(ROC)曲线是评估生物标志物在疾病诊断中的有效性的基础。除了仅仅评估性能之外,它还提供了对疾病分类至关重要的生物标志物值的最佳截止值。虽然存在各种各样的截止估计方法,但很少有人关注将协变量影响整合到这一过程中。协变量可以强烈地影响诊断摘要,导致不同协变量水平的变化。因此,一个定制的基于协变量的框架是必要的,以概述协变量特定的最佳截止点。此外,最近对截止估计量的研究忽略了ROC曲线估计方法的影响。本研究试图通过解决研究空白来弥合这一差距。我们进行了大量的模拟研究,以仔细检查ROC曲线估计模型在不同情景下估计不同截止点的性能,包括不同的数据产生机制和协变量效应。此外,利用阿尔茨海默病神经成像倡议(ADNI)数据集,该研究评估了不同生物标志物在诊断阿尔茨海默病中的表现,并确定了合适的最佳截止值。
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引用次数: 0
On Sample Size Determination for Augmented Tests Based on Restricted Mean Survival Time in Randomized Clinical Trials 随机临床试验中基于限制平均生存时间的增强试验的样本量确定
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-03-24 DOI: 10.1002/bimj.70046
Satoshi Hattori, Hajime Uno

Restricted mean survival time (RMST) is gaining attention as a measure to quantify the treatment effect on survival outcomes in randomized clinical trials. Several methods to determine sample size based on the RMST-based tests have been proposed. However, to the best of our knowledge, there is no discussion about the power and sample size regarding the augmented version of RMST-based tests, which utilize baseline covariates for a gain in estimation efficiency and in power for testing no treatment effect. The conventional event-driven study design based on the logrank test allows us to calculate the power for a given hazard ratio without specifying the survival functions. In contrast, the existing sample size determination methods for the RMST-based tests relies on the adequacy of the assumptions of the entire survival curves of two groups. Furthermore, to handle the augmented test, the correlation between the baseline covariates and the martingale residuals must be handled. To address these issues, we propose an approximated sample size formula for the augmented version of the RMST-based test, which does not require specifying the entire survival curve in the treatment group, and also a sample size recalculation approach to update the correlations between the baseline covariates and the martingale residuals with the blinded data. The proposed procedure will enable the studies to have the target power for a given RMST difference even when correct survival functions cannot be specified at the design stage.

在随机临床试验中,限制平均生存时间(RMST)作为一种量化治疗对生存结果影响的指标,正受到越来越多的关注。提出了几种基于rmst的测试确定样本量的方法。然而,据我们所知,对于基于rmst的增强版本的测试,没有关于功率和样本量的讨论,它利用基线协变量来获得估计效率和测试无治疗效果的功率。基于logrank检验的传统事件驱动研究设计允许我们在不指定生存函数的情况下计算给定风险比的功率。相比之下,现有的基于rmst测试的样本量确定方法依赖于两组的整个生存曲线假设的充分性。此外,为了处理增广检验,必须处理基线协变量与鞅残差之间的相关性。为了解决这些问题,我们提出了一个基于rmst的增强版检验的近似样本量公式,该公式不需要指定治疗组的整个生存曲线,并且还提出了一个样本量重新计算方法,以更新基线协变量与盲法数据的鞅残差之间的相关性。所建议的程序将使研究具有给定RMST差异的目标功率,即使在设计阶段无法指定正确的生存函数。
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引用次数: 0
Editorial for the Special Collection “MCP 2022” 《MCP 2022》特辑社论
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-03-24 DOI: 10.1002/bimj.70047
Werner Brannath, Thorsten Dickhaus, Ruth Heller, Jesse Hemerik

This special collection on Multiple Comparisons arose from the 12th International Conference on Multiple Comparison Procedures (MCP 2022) that took place from August 30 to September 2, 2022, at the University of Bremen, Germany. The conference was hosted locally by Professors Werner Brannath and Thorsten Dickhaus. MCP 2022 continued the tradition of this conference series. The contributions to the conference covered the latest methodological and applied developments in the areas of simultaneous and selective inference, including testing, confidence intervals, estimation, adaptive designs, statistical modelling, and machine learning approaches, under a variety of error rates to be controlled.

This article collection contains theoretical papers on multiple comparisons by Budig et al. (2024), Chen et al. (2024), Pöhlmann et al. (2024), and by Ochieng et al. (2024). Several sessions of MCP 2022 included contributions dealing with online control of the family-wise error rate or the false discovery rate, respectively. The papers by Fischer et al. (2024) and by Fisher (2024) in this special collection reflect this current research direction. Bounding the number or the proportion, respectively, of false discoveries is considered in the papers by Xu et al. (2024) and by Zheng et al. (2024). Statistical methods for planning and evaluating studies with adaptive or group-sequential designs are developed in the papers by Danzer et al. (2024) and by Zhao et al. (2025), and platform trials are studied by Greenstreet et al. (2025).

After the long time without face-to-face meetings because of the COVID-19 pandemic, the conference delegates (Figure 1) enjoyed the social program of MCP 2022, which included an evening reception in Bremen's historic Town Hall as well as a boat trip to Bremerhaven.

第 12 届多重比较程序国际会议(MCP 2022)于 2022 年 8 月 30 日至 9 月 2 日在德国不来梅大学举行,本多重比较专集就是在这次会议上出版的。会议由 Werner Brannath 教授和 Thorsten Dickhaus 教授在当地主办。MCP 2022 延续了该系列会议的传统。本次会议的投稿涵盖了同时推断和选择性推断领域的最新方法学和应用发展,包括测试、置信区间、估计、自适应设计、统计建模和机器学习方法,以及各种需要控制的误差率。MCP 2022 的几场会议分别讨论了族内误差率或错误发现率的在线控制问题。本专集中 Fischer 等人(2024 年)和 Fisher(2024 年)的论文反映了当前的研究方向。Xu 等人(2024 年)和 Zheng 等人(2024 年)的论文分别对错误发现的数量或比例进行了限制。Danzer等人(2024年)和Zhao等人(2025年)的论文提出了规划和评估适应性或分组序列设计研究的统计方法,Greenstreet等人(2025年)则对平台试验进行了研究。
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引用次数: 0
The Shared Weighted Lindley Frailty Model for Clustered Failure Time Data 聚类故障时间数据的共享加权Lindley脆弱性模型
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-03-19 DOI: 10.1002/bimj.70044
Diego I. Gallardo, Marcelo Bourguignon, John L. Santibáñez

The primary goal of this paper is to introduce a novel frailty model based on the weighted Lindley (WL) distribution for modeling clustered survival data. We study the statistical properties of the proposed model. In particular, the amount of unobserved heterogeneity is directly parameterized by the variance of the frailty distribution such as gamma and inverse Gaussian frailty models. Parametric and semiparametric versions of the WL frailty model are studied. A simple expectation–maximization (EM) algorithm is proposed for parameter estimation. Simulation studies are conducted to evaluate its finite sample performance. Finally, we apply the proposed model to a real data set to analyze times after surgery in patients diagnosed with infiltrating ductal carcinoma and compare our results with classical frailty models carried out in this application, which shows the superiority of the proposed model. We implement an R package that includes estimation for fitting the proposed model based on the EM algorithm.

本文的主要目标是引入一种新的基于加权林德利(WL)分布的脆弱性模型来建模聚类生存数据。我们研究了所提出模型的统计性质。特别是,未观察到的异质性的数量是由脆弱性分布的方差直接参数化的,如伽马和逆高斯脆弱性模型。研究了WL脆弱性模型的参数化和半参数化版本。提出了一种简单的参数估计期望最大化算法。对其有限样本性能进行了仿真研究。最后,我们将所提出的模型应用于实际数据集,分析浸润性导管癌患者的术后次数,并将结果与该应用中经典的脆性模型进行比较,显示了所提出模型的优越性。我们实现了一个R包,其中包括基于EM算法拟合所提出模型的估计。
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引用次数: 0
A New Frequentist Implementation of the Daniels and Hughes Bivariate Meta-Analysis Model for Surrogate Endpoint Evaluation 丹尼尔斯和休斯双变量元分析模型的新频率实现替代终点评估
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-03-19 DOI: 10.1002/bimj.70048
Dan Jackson, Michael Sweeting, Robbie C. M. van Aert, Sylwia Bujkiewicz, Keith R. Abrams, Wolfgang Viechtbauer

Surrogate endpoints are used when the primary outcome is difficult to measure accurately. Determining if a measure is suitable to use as a surrogate endpoint is a challenging task and a variety of meta-analysis models have been proposed for this purpose. The Daniels and Hughes bivariate model for trial-level surrogate endpoint evaluation is gaining traction but presents difficulties for frequentist estimation and hitherto only Bayesian solutions have been available. This is because the marginal model is not a conventional linear model and the number of unknown parameters increases at the same rate as the number of studies. This second property raises immediate concerns that the maximum likelihood estimator of the model's unknown variance component may be downwardly biased. We derive maximum likelihood estimating equations to motivate a bias adjusted estimator of this parameter. The bias correction terms in our proposed estimating equation are easily computed and have an intuitively appealing algebraic form. A simulation study is performed to illustrate how this estimator overcomes the difficulties associated with maximum likelihood estimation. We illustrate our methods using two contrasting examples from oncology.

当主要结果难以准确测量时,使用替代终点。确定一项测量是否适合用作替代终点是一项具有挑战性的任务,为此提出了各种元分析模型。用于试验水平替代终点评估的Daniels和Hughes双变量模型正在获得关注,但在频率估计方面存在困难,迄今为止只有贝叶斯解决方案可用。这是因为边际模型不是传统的线性模型,未知参数的数量随着研究数量的增加而增加。这第二个性质引起了人们的直接关注,即模型的未知方差成分的最大似然估计量可能向下偏置。我们推导了极大似然估计方程来激励该参数的偏差调整估计量。我们提出的估计方程中的偏差校正项易于计算,并且具有直观吸引人的代数形式。仿真研究说明了该估计器如何克服与最大似然估计相关的困难。我们用肿瘤学的两个对比例子来说明我们的方法。
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引用次数: 0
Spatially Informed Nonnegative Matrix Trifactorization for Coclustering Mass Spectrometry Data 聚类质谱数据的空间通知非负矩阵三因子分解
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-03-19 DOI: 10.1002/bimj.70031
Andrea Sottosanti, Francesco Denti, Stefania Galimberti, Davide Risso, Giulia Capitoli

Mass spectrometry imaging techniques measure molecular abundance in a tissue sample at a cellular resolution, all while preserving the spatial structure of the tissue. This kind of technology offers a detailed understanding of the role of several molecular factors in biological systems. For this reason, the development of fast and efficient computational methods that can extract relevant signals from massive experiments has become necessary. A key goal in mass spectrometry data analysis is the identification of molecules with similar functions in the analyzed biological system. This result can be achieved by studying the spatial distribution of the molecules' abundance patterns. To do so, one can perform coclustering, that is, dividing the molecules into groups according to their expression patterns over the tissue and segmenting the tissue according to the molecules' abundance levels. We present TRIFASE, a semi-nonnegative matrix trifactorization technique that performs coclustering while accounting for the spatial correlation of the data. We propose an estimation algorithm that solves the proposed matrix trifactorization problem. Moreover, to improve scalability, we also propose two heuristic approximations of the most expensive steps, which help the algorithm converge while significantly streamlining the computational cost. We validated our method on a series of simulation experiments, comparing the different estimating strategies discussed in the article. Last, we analyzed a mouse brain tissue sample processed with MALDI-MSI technology, showing how TRIFASE extracts specific expression patterns of molecule abundance in localized tissue areas and discovers blocks of proteins whose activation is directly linked to specific biological mechanisms.

质谱成像技术以细胞分辨率测量组织样品中的分子丰度,同时保留组织的空间结构。这种技术提供了对生物系统中几个分子因子的作用的详细了解。因此,开发能够从大量实验中提取相关信号的快速高效的计算方法变得十分必要。质谱数据分析的一个关键目标是识别被分析生物系统中具有相似功能的分子。这一结果可以通过研究分子丰度模式的空间分布来实现。为此,可以执行共聚,即根据分子在组织中的表达模式将分子分成组,并根据分子的丰度水平对组织进行分割。我们提出了TRIFASE,一种半非负矩阵三因子分解技术,在考虑数据的空间相关性的同时执行共聚类。我们提出了一种估计算法来解决所提出的矩阵三分解问题。此外,为了提高可扩展性,我们还提出了两个最昂贵步骤的启发式近似,这有助于算法收敛,同时显着简化计算成本。我们在一系列模拟实验中验证了我们的方法,比较了文中讨论的不同估计策略。最后,我们分析了用MALDI-MSI技术处理的小鼠脑组织样本,展示了TRIFASE如何提取局部组织区域分子丰度的特定表达模式,并发现其激活与特定生物机制直接相关的蛋白质块。
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引用次数: 0
Toward Power Analysis for Partial Least Squares-Based Methods 基于偏最小二乘方法的功率分析研究
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-03-13 DOI: 10.1002/bimj.70050
Angela Andreella, Livio Finos, Bruno Scarpa, Matteo Stocchero

In recent years, power analysis has become widely used in applied sciences, with the increasing importance of the replicability issue. When distribution-free methods, such as partial least squares (PLS)-based approaches, are considered, formulating power analysis is challenging. In this study, we introduce the methodological framework of a new procedure for performing power analysis when PLS-based methods are used. Data are simulated by the Monte Carlo method, assuming the null hypothesis of no effect is false and exploiting the latent structure estimated by PLS in the pilot data. In this way, the complex correlation data structure is explicitly considered in power analysis and sample size estimation. The paper offers insights into selecting test statistics for the power analysis procedure, comparing accuracy-based tests and those based on continuous parameters estimated by PLS. Simulated and real data sets are investigated to show how the method works in practice.

近年来,功率分析在应用科学中得到了广泛的应用,其可重复性问题也越来越受到重视。当考虑无分布方法时,例如基于偏最小二乘(PLS)的方法,制定功率分析是具有挑战性的。在本研究中,我们介绍了在使用基于pls的方法时执行功率分析的新程序的方法学框架。采用蒙特卡罗方法模拟数据,假设无效应的零假设为假,并利用PLS在试点数据中估计的潜在结构。这样,在功率分析和样本量估计中明确地考虑了复杂的相关数据结构。本文为功率分析程序选择测试统计量提供了见解,比较了基于精度的测试和基于PLS估计的连续参数的测试。模拟数据集和真实数据集进行了调查,以显示该方法在实践中如何工作。
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引用次数: 0
Two-Arm Crossover Randomized Controlled Trial Versus Meta-Analysis of N-of-1 Studies: Comparison of Statistical Efficiency in Determining an Intervention Effect 两组交叉随机对照试验与N-of-1研究的荟萃分析:确定干预效果的统计效率比较
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-03-12 DOI: 10.1002/bimj.70045
Anna Eleonora Carrozzo, Georg Zimmermann, Arne C. Bathke, Daniel Neunhaeuserer, Josef Niebauer, Stefan T. Kulnik

N-of-1 trials are currently receiving broader attention in healthcare research when assessing the effectiveness of interventions. In contrast to the most commonly applied two-arm randomized controlled trial (RCT), in an N-of-1 design, the individual acts as their own control condition in the sense of a multiple crossover trial. N-of-1 trials can lead to a higher quality of patient by examining the effectiveness of an intervention at an individual level. Moreover, when a series of N-of-1 trials are properly aggregated, it becomes possible to detect an intervention effect at a population level. This work investigates whether a meta-analysis of summary data of a series of N-of-1 trials allows us to detect a statistically significant intervention effect with fewer participants than in a traditional, prospectively powered two-arm RCT and crossover design when evaluating a digital health intervention in cardiovascular care. After introducing these different analysis approaches, we compared the empirical properties in a simulation study both under the null hypothesis and with respect to power with different between-subject heterogeneity settings and in the presence of a carry-over effect. We further investigate the performance of a sequential aggregation procedure. In terms of simulated power, the threshold of 80% was achieved earlier for the aggregating procedure, requiring fewer participants.

在评估干预措施的有效性时,N-of-1试验目前在医疗保健研究中受到广泛关注。与最常用的双臂随机对照试验(RCT)相比,在N-of-1设计中,个体在多重交叉试验的意义上作为自己的对照条件。N-of-1试验可以通过在个体水平上检查干预措施的有效性来提高患者的质量。此外,当一系列N-of-1试验被适当地汇总时,就有可能在总体水平上检测到干预效应。本研究调查了在评估心血管护理的数字健康干预时,对一系列N-of-1试验的汇总数据进行荟萃分析是否允许我们在参与者较少的情况下发现具有统计学意义的干预效果,而不是传统的前瞻性双臂随机对照试验和交叉设计。在介绍了这些不同的分析方法之后,我们在模拟研究中比较了零假设下的经验特性,以及在不同受试者异质性设置和存在结转效应的情况下的功率。我们进一步研究了顺序聚合过程的性能。在模拟功率方面,聚合过程较早达到80%的阈值,需要较少的参与者。
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引用次数: 0
Nonparametric Estimation of a Biometric Function Using Ranked Set Sampling With Ties Information 带联系信息的排序集抽样生物特征函数的非参数估计
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-03-12 DOI: 10.1002/bimj.70007
Leila Jabari Koopaei, Ehsan Zamanzade, Afshin Parvardeh, Xinlei Wang

The mean residual life (MRL) function plays an important role in the summary and analysis of survival data. The main advantage of this function is that it summarizes the information in units of time instead of a probability scale, which requires careful interpretation. Ranked set sampling (RSS) is a sampling technique designed for situations, where obtaining precise measurements of sample units is expensive or difficult, but ranking them without referring to their accurate values is cost-effective or easy. However, the practical application of RSS is hindered because each sample unit is required to assign a unique rank. To alleviate this difficulty, Frey developed a novel variation of RSS, called RSS-t, that records and utilizes the tie structure in the ranking process. In this paper, we propose several different nonparametric estimators for the MRL function based on RSS-t. Then, we compare the proposed estimators with their counterparts in simple random sampling (SRS) and RSS, where tie information is not utilized. We also implemented our proposed estimators on a real data set related to patient waiting times for liver transplantation, to show their applicability and efficiency in practice. Our results show that using ties information leads to an improved statistical inference for the MRL function, and therefore a smaller sample size is needed to reach a predetermined precision.

平均剩余寿命(MRL)函数在总结和分析生存数据中起着重要的作用。这个函数的主要优点是它以时间为单位来总结信息,而不是需要仔细解释的概率尺度。排序集抽样(RSS)是一种抽样技术,设计用于这样的情况:获得样本单位的精确测量是昂贵或困难的,但不参考其准确值对它们进行排序是经济有效的或容易的。然而,RSS的实际应用受到阻碍,因为每个样本单元都需要分配一个唯一的秩。为了减轻这一困难,Frey开发了一种新的RSS变体,称为RSS-t,它记录并利用了排名过程中的领带结构。本文提出了基于RSS-t的MRL函数的几种不同的非参数估计。然后,我们将所提出的估计量与不使用信息的简单随机抽样(SRS)和RSS中的估计量进行比较。我们还在一个与肝移植患者等待时间相关的真实数据集上实现了我们提出的估计器,以显示其在实践中的适用性和效率。我们的研究结果表明,使用关系信息可以改善MRL函数的统计推断,因此需要更小的样本量来达到预定的精度。
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引用次数: 0
Stacking Model-Based Classifiers for Dealing With Multiple Sets of Noisy Labels 基于堆叠模型的多组噪声标签分类器
IF 1.3 3区 生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2025-03-12 DOI: 10.1002/bimj.70042
Giulia Montani, Andrea Cappozzo

Supervised learning in presence of multiple sets of noisy labels is a challenging task that is receiving increasing interest in the ever-evolving landscape of healthcare analytics. Such an issue arises when multiple annotators are tasked to manually label the same training samples, potentially giving rise to discrepancies in class assignments among the supplied labels with respect to the ground truth. Commonly, the labeling process is entrusted to a small group of domain experts, and different level of experience and subjectivity may result in noisy training labels. To solve the classification task leveraging on the availability of multiple data annotators, we introduce a novel ensemble methodology constructed combining model-based classifiers separately trained on single sets of noisy labels. Eigenvalue Decomposition Discriminant Analysis is employed for the definition of the base learners, and six distinct averaging strategies are proposed to combine them. Two solutions necessitate a priori information, such as the partial knowledge of the ground truth labels or the annotators' level of expertise. Differently, the remaining four approaches are entirely data-driven. A simulation study and an application on real data showcase the improved predictive performance of our proposal, while also demonstrating the ability of automatically inferring annotators' expertise level as a by-product of the learning process.

存在多组噪声标签的监督学习是一项具有挑战性的任务,在不断发展的医疗保健分析领域受到越来越多的关注。当多个注释者被要求手动标记相同的训练样本时,就会出现这样的问题,这可能会导致所提供标签之间的类分配与基本事实存在差异。通常,标记过程委托给一小群领域专家,不同的经验水平和主观性可能导致嘈杂的训练标签。为了利用多个数据注释器的可用性来解决分类任务,我们引入了一种新的集成方法,该方法将基于模型的分类器组合在单个噪声标签集上单独训练。采用特征值分解判别分析对基学习器进行定义,并提出6种不同的平均策略将基学习器组合在一起。两种解决方案需要先验信息,例如对基础真值标签的部分知识或注释者的专业水平。不同的是,其余四种方法完全是数据驱动的。仿真研究和在实际数据上的应用表明,我们的建议提高了预测性能,同时也证明了自动推断注释者的专业水平作为学习过程的副产品的能力。
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引用次数: 0
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