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A New Algorithm for Convex Biclustering and Its Extension to the Compositional Data 一种新的凸双聚类算法及其在合成数据中的推广
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-11-24 DOI: 10.1007/s12561-022-09356-4
Binhuan Wang, Lanqiu Yao, Jiyuan Hu, Huilin Li
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引用次数: 0
An Application of the Cure Model to a Cardiovascular Clinical Trial 治愈模型在心血管疾病临床试验中的应用
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-11-12 DOI: 10.1007/s12561-020-09297-w
V. Sevilimedu, Shuangge Ma, P. Hartigan, T. Kyriakides
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引用次数: 1
An Approach to Analyze Longitudinal Zero-Inflated Microbiome Count Data Using Two-Stage Mixed Effects Models 用两阶段混合效应模型分析纵向零膨胀微生物组计数数据的方法
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-10-01 DOI: 10.1007/s12561-020-09295-y
Jian Wang, C. Reyes-Gibby, S. Shete
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引用次数: 3
Can the Concept Be Proven? 这个概念可以被证明吗?
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-09-07 DOI: 10.1007/s12561-020-09290-3
Ying-Ying Zhang, Naitee Ting
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引用次数: 0
Survival Modeling of Suicide Risk with Rare and Uncertain Diagnoses 罕见和不确定诊断的自杀风险生存模型
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-09-05 DOI: 10.1007/s12561-023-09374-w
Wenjie Wang, Chongliang Luo, R. Aseltine, Fei Wang, Jun Yan, Kun Chen
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引用次数: 0
Correction to: A Simulation Study of Statistical Approaches to Data Analysis in the Stepped Wedge Design 修正:阶梯式楔形设计中数据分析统计方法的模拟研究
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-08-17 DOI: 10.1007/s12561-020-09289-w
Yuqi Ren, James P. Hughes, P. Heagerty
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引用次数: 1
Competing Risks Model with Short-Term and Long-Term Covariate Effects for Cancer Studies 癌症研究中具有短期和长期协变量效应的竞争风险模型
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-07-21 DOI: 10.1007/s12561-020-09288-x
G. Diao, A. Vidyashankar, S. Zohar, S. Katsahian
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引用次数: 0
A curve free Bayesian decision-theoretic design for phase Ia/Ib trials considering both safety and efficacy outcomes. 考虑安全性和有效性结果的Ia/Ib期试验无曲线贝叶斯决策理论设计。
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-07-01 Epub Date: 2020-03-26 DOI: 10.1007/s12561-020-09272-5
Shenghua Fan, Bee Leng Lee, Ying Lu

A curve-free, Bayesian decision-theoretic two-stage design is proposed to select biological efficacious doses (BEDs) for phase Ia/Ib trials in which both toxicity and efficacy signals are observed. No parametric models are assumed to govern the dose-toxicity, dose-efficacy, and toxicity-efficacy relationships. We assume that the dose-toxicity curve is monotonic non-decreasing and the dose-efficacy curve is unimodal. In the phase Ia stage, a Bayesian model on the toxicity rates is used to locate the maximum tolerated dose. In the phase Ib stage, we model the dose-efficacy curve using a step function while continuing to monitor the toxicity rates. Furthermore, a measure of the goodness of fit of a candidate step function is proposed, and the interval of BEDs associated with the best fitting step function is recommended. At the end of phase Ib, if some doses are recommended as BEDs, a cohort of confirmation is recruited and assigned at these doses to improve the precision of estimates at these doses. Extensive simulation studies show that the proposed design has desirable operating characteristics across different shapes of the underlying true toxicity and efficacy curves.

提出了一种无曲线的贝叶斯决策理论两阶段设计,以选择Ia/Ib期试验的生物有效剂量(bed),其中毒性和有效性信号都被观察到。没有假设参数模型来控制剂量-毒性、剂量-功效和毒性-功效关系。我们假设剂量-毒性曲线是单调不递减的,剂量-功效曲线是单峰的。在Ia期,使用贝叶斯毒性率模型确定最大耐受剂量。在Ib期,我们使用阶跃函数对剂量-功效曲线建模,同时继续监测毒性率。在此基础上,提出了候选阶跃函数拟合优度的度量方法,并推荐了与最佳拟合阶跃函数相关联的bed区间。在Ib期结束时,如果推荐某些剂量作为bed,则招募确认队列并按这些剂量分配,以提高这些剂量估计的准确性。广泛的模拟研究表明,所提出的设计在不同形状的潜在真实毒性和功效曲线上具有理想的操作特性。
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引用次数: 3
Flexible Phase I-II design for partially ordered regimens with application to therapeutic cancer vaccines. 灵活的I-II期设计,部分有序方案应用于治疗性癌症疫苗。
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-07-01 Epub Date: 2019-06-04 DOI: 10.1007/s12561-019-09245-3
Nolan A Wages, Craig L Slingluff

Existing methodology for the design of Phase I-II studies has been intended to search for the optimal regimen, based on a trade-off between toxicity and efficacy, from a set of regimens comprised of doses of a new agent. The underlying assumptions guiding allocation are that the dose-toxicity curve is monotonically increasing, and that the dose-efficacy curve either plateaus or decreases beyond an intermediate dose. This article considers the problem of designing Phase I-II studies that violate these assumptions for both outcomes. The motivating application studies regimens that are not defined by doses of a new agent, but rather a peptide vaccine plus novel adjuvants for the treatment of melanoma. All doses of each adjuvant are fixed, and the regimens vary by the number and selection of adjuvants. This structure produces regimen-toxicity curves that are partially ordered, and regimen-efficacy curves that may deviate from a plateau or unimodal shape. Application of a Bayesian model-based design is described in determining the optimal biologic regimen, based on bivariate binary measures of toxicity and biologic activity. A simulation study of the design's operating characteristics is conducted, and its versatility in handling other Phase I-II problems is discussed.

设计I-II期研究的现有方法旨在从一组由新药物剂量组成的方案中,基于毒性和有效性之间的权衡,寻找最佳方案。指导分配的基本假设是,剂量-毒性曲线单调增加,剂量-功效曲线在超过中间剂量后趋于平稳或下降。本文考虑的问题是设计I-II期研究违反这些假设的两个结果。激励应用研究方案不是由一种新药物的剂量来定义的,而是一种肽疫苗加新型佐剂来治疗黑色素瘤。每种佐剂的剂量都是固定的,治疗方案因佐剂的数量和选择而异。这种结构产生部分有序的方案-毒性曲线,以及可能偏离平台或单峰形状的方案-功效曲线。应用贝叶斯模型为基础的设计描述了在确定最佳的生物方案,基于二元二元措施的毒性和生物活性。对该设计的工作特性进行了仿真研究,并讨论了其在处理其他I-II期问题中的通用性。
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引用次数: 3
Quantile-Based Subgroup Identification for Randomized Clinical Trials 随机临床试验中基于分位数的亚组识别
IF 1 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2020-06-26 DOI: 10.1007/s12561-020-09286-z
Youngjoo Cho, Debashis Ghosh
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引用次数: 2
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