Holger R Roth, Ziyue Xu, Chester Chen, Daguang Xu, Prerna Dogra, Mona Flores, Yan Cheng, Andrew Feng
{"title":"Overview of real-world applications of federated learning with NVIDIA FLARE.","authors":"Holger R Roth, Ziyue Xu, Chester Chen, Daguang Xu, Prerna Dogra, Mona Flores, Yan Cheng, Andrew Feng","doi":"10.1080/10543406.2025.2456174","DOIUrl":"https://doi.org/10.1080/10543406.2025.2456174","url":null,"abstract":"<p><p>Today's challenges around global healthcare emphasize the need for large-scale collaborations between the clinical and sciesntific communities. However, regulatory constraints around data sharing and patient privacy might hinder access to data genuinely representing clinically relevant patient populations. We have developed an open-source federated learning framework, NVIDIA FLARE, to work around such restrictions while maintaining patient privacy using modern cryptographic and information-theoretic methods such as homomorphic encryption and differential privacy. In this work, we show how NVIDIA FLARE addresses clinical questions, such as predicting clinical outcomes in patients with COVID-19 and other real-world applications, including federated statistics and parameter-efficient adaptation of large language models under a collaborative setting, while allowing participants to retain governance over their data.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"1-11"},"PeriodicalIF":1.2,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bayesian design of clinical trials with multiple time-to-event outcomes subject to functional cure.","authors":"Seoyoon Cho, Matthew A Psioda, Joseph G Ibrahim","doi":"10.1080/10543406.2025.2451152","DOIUrl":"https://doi.org/10.1080/10543406.2025.2451152","url":null,"abstract":"<p><p>With the continuous advancement of medical treatments, there is an increasing demand for clinical trial designs and analyses using cure rate models to accommodate a plateau in the survival curve. This is especially pertinent in oncology, where high proportions of patients, such as those with melanoma, lung cancer, and endometrial cancer, exhibit usual life spans post-cancer detection. A Bayesian clinical trial design methodology for multivariate time-to-event outcomes with cured fractions is developed. This approach employs a copula to jointly model the multivariate time-to-event outcomes. We propose a model that uses a Gaussian copula on the population survival function, irrespective of cure status. The minimum sample size required to achieve high statistical power while maintaining reasonable control over the type I error rate from a Bayesian perspective is identified using point-mass sampling priors. The methodology is demonstrated in simulation studies inspired by an endometrial cancer trial.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"1-12"},"PeriodicalIF":1.2,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jun Tamura, Yusuke Saigusa, Junichi Fujita, Kouji Yamamoto
{"title":"Bayesian method for comparing F1 scores in the absence of a gold standard.","authors":"Jun Tamura, Yusuke Saigusa, Junichi Fujita, Kouji Yamamoto","doi":"10.1080/10543406.2025.2450319","DOIUrl":"10.1080/10543406.2025.2450319","url":null,"abstract":"<p><p>In the field of medicine, evaluating the diagnostic performance of new diagnostic methods can be challenging, especially in the absence of a gold standard. This study proposes a methodology for assessing the performance of diagnostic tests by estimating the posterior distribution of the <math><mrow><msub><mi>F</mi><mn>1</mn></msub></mrow></math> score using latent class analysis, without relying on a gold standard. The proposed method utilizes Markov Chain Monte Carlo sampling to estimate the posterior distribution of the <math><mrow><msub><mi>F</mi><mn>1</mn></msub></mrow></math> score, enabling a comprehensive evaluation of diagnostic test methods. By applying this method to internet addiction, we demonstrate how latent class analysis can be effectively used to assess diagnostic performance, offering a practical solution for situations where no gold standard is available. The effectiveness of the proposed approach was evaluated through simulation studies by examining the coverage probability of the 95% highest density interval of the estimated posterior distributions.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"1-11"},"PeriodicalIF":1.2,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Liangcai Zhang, Ming Chen, Vladimir Dragalin, Bin Eddy Jia, Cunyi Wang, Leixin Xia, Chaohui Yuan, Fei Chen
{"title":"Bayesian efficient safety monitoring: a simple and well-performing framework to continuous safety monitoring of adverse events in randomized clinical trials.","authors":"Liangcai Zhang, Ming Chen, Vladimir Dragalin, Bin Eddy Jia, Cunyi Wang, Leixin Xia, Chaohui Yuan, Fei Chen","doi":"10.1080/10543406.2025.2456176","DOIUrl":"https://doi.org/10.1080/10543406.2025.2456176","url":null,"abstract":"<p><p>During randomized controlled trials, it is critical to remain vigilant in safety monitoring. A common approach is to present information over time, such as frequency tables and graphs, when analyzing adverse events. Nevertheless, there is still a need for developing statistical methods for analyzing safety data of a dynamic nature. The process is typically challenging due to small sample sizes, a lack of observational data sources, difficulties in false-positive control, and the necessity for early detection of serious adverse events. In this article, we propose a simple and effective framework called Bayesian Efficient sAfety Monitoring (BEAM) to analyze evidence aggregation of potentially serious adverse events that may arise during the trial, as well as a timeline for when concrete evidence for safety concerns of unlikely outcomes becomes available. BEAM can be easily tabulated and visualized before the trial starts, making evaluations transparent and easy to use in practice, while maintaining flexibility when the underlying adverse event rate varies. Simulation studies have shown that BEAM supports continuous monitoring, can incorporate external information, and demonstrates good operating characteristics across various scenarios. In most practical situations, it has a reasonable likelihood of detecting elevated risks and identifying safety signals early on when safety concerns arise regarding the investigational drug.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"1-12"},"PeriodicalIF":1.2,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Bayesian joint bent-cable model for longitudinal measurements and survival time with heterogeneous random-effects distributions.","authors":"Oludare Ariyo, Kehinde Olobatuyi, Taban Baghfalaki","doi":"10.1080/10543406.2025.2450321","DOIUrl":"https://doi.org/10.1080/10543406.2025.2450321","url":null,"abstract":"<p><p>Biomarkers are measured repeatedly in clinical studies until a pre-defined endpoint, such as death from certain causes, is reached. Such repeated measurements may present a dynamic process for understanding when to expect the study's endpoint. Joint modelling is often employed to handle such a model. Typically, shared random effects are assumed to be common to both the longitudinal component and the study's endpoint. These shared random effects usually assume homogeneous and follow a normal distribution. However, identifying homogeneous subgroups is important when the underlying population is heterogeneous. This issue has received little attention in the literature, particularly for multi-phase longitudinal responses. In this paper, we propose a joint modelling approach for longitudinal and survival models using a bent-cable mixed model for longitudinal measurements and a Weibull distribution for the survival component. We also incorporate a finite mixture of normal distribution assumptions to account for the unobserved heterogeneity in the shared random effects model. A Bayesian MCMC is developed for parameter estimation and inferences. The proposed method is evaluated using simulation studies and the Tehran Lipid and Glucose Study dataset.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"1-14"},"PeriodicalIF":1.2,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Missing data in the eligibility criteria of synthetic controls from real-world data.","authors":"Liang Li, Thomas Jemielita, Cong Chen","doi":"10.1080/10543406.2025.2450330","DOIUrl":"https://doi.org/10.1080/10543406.2025.2450330","url":null,"abstract":"<p><p>Randomized clinical trials (RCTs) can benefit from using Real-World Data (RWD) as a supplementary data source to enhance their analysis. An Augmented RCT combines randomized treatment and control groups with synthetic controls derived from RWD. This way, the trial can achieve less prospective enrollment, higher statistical power, and lower costs. However, to ensure scientific validity, the synthetic controls must satisfy the same eligibility criteria as the trial participants. A major challenge is that RWD often have missing data that hinder the eligibility assessment. This problem has been overlooked in the literature and this paper offers statistical solutions to address it. We use multiple imputations to handle missing data in the variables involved in the eligibility criteria. We also propose a generalized propensity score weighting procedure to adjust for the life expectancy requirement, a common eligibility criterion in oncology clinical trials but usually unavailable in RWD. Since the life expectancy is an unmeasured confounder, we discuss the statistical assumptions required to correct its bias. We validate the proposed solutions through simulation studies and the analysis of an Augmented RCT in oncology.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"1-16"},"PeriodicalIF":1.2,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A composite semiparametric homogeneity test for the distributions of multigroup interval-bounded longitudinal data.","authors":"Zhanfeng Wang, Wenmei Li, Hao Ding, Dongsheng Tu","doi":"10.1080/10543406.2023.2275769","DOIUrl":"10.1080/10543406.2023.2275769","url":null,"abstract":"<p><p>Motivated by comparing the distribution of longitudinal quality of life (QoL) data among different treatment groups from a cancer clinical trial, we propose a semiparametric test statistic for the homogeneity of the distributions of multigroup longitudinal measurements, which are bounded in a closed interval with excess observations taking the boundary values. Our procedure is based on a three-component mixed density ratio model and a composite empirical likelihood for the longitudinal data taking values inside the interval. A nonparametric bootstrap method is applied to calculate the p-value of the proposed test. Simulation studies are conducted to evaluate the proposed procedure, which show that the proposed test is effective in controlling type I errors and more powerful than the procedure which ignores the values on the boundaries. It is also robust to the model mispecification than the parametric test. The proposed procedure is also applied to compare the distributions of the scores of Physical Function subscale and Global Heath Status between the patients randomized to two treatment groups in a cancer clinical trial.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"58-69"},"PeriodicalIF":1.2,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134650477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Duolao Wang, Sirui Zheng, Ying Cui, Nengjie He, Tao Chen, Bo Huang
{"title":"Adjusted win ratio using the inverse probability of treatment weighting.","authors":"Duolao Wang, Sirui Zheng, Ying Cui, Nengjie He, Tao Chen, Bo Huang","doi":"10.1080/10543406.2023.2275759","DOIUrl":"10.1080/10543406.2023.2275759","url":null,"abstract":"<p><p>The win ratio method has been increasingly applied in the design and analysis of clinical trials. However, the win ratio method is a univariate approach that does not allow for adjusting for baseline imbalances in covariates, although a stratified win ratio can be calculated when the number of strata is small. This paper proposes an adjusted win ratio to control for such imbalances by inverse probability of treatment weighting (IPTW) method. We derive the adjusted win ratio with its variance and suggest three IPTW adjustments: IPTW-average treatment effect (IPTW-ATE), stabilized IPTW-ATE (SIPTW-ATE) and IPTW-average treatment effect in the treated (IPTW-ATT). The proposed adjusted methods are applied to analyse a composite outcome in the CHARM trial. The statistical properties of the methods are assessed through simulations. Results show that adjusted win ratio methods can correct the win ratio for covariate imbalances at baseline. Simulation results show that the three proposed adjusted win ratios have similar power to detect the treatment difference and have slightly lower power than the corresponding adjusted Cox models when the assumption of proportional hazards holds true but have consistently higher power than adjusted Cox models when the proportional hazard assumption is violated.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"21-36"},"PeriodicalIF":1.2,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72016204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Data-driven monitoring for phase II clinical trial designs based on percentile event time test.","authors":"Yeonhee Park, Zhanpeng Xu","doi":"10.1080/10543406.2023.2292209","DOIUrl":"10.1080/10543406.2023.2292209","url":null,"abstract":"<p><p>The goal of phase II clinical trials is to evaluate the therapeutic efficacy of a new drug. Some investigators want to use the time-to-event endpoint as the primary endpoint of the phase II study to see the improvement of the therapeutic efficacy of a new drug in median survival time. Recently, median event time test (METT) has been proposed to provide a simple and straightforward rule which compares the observed median survival time with the prespecified threshold. However, median survival time would not be observed during the trial if the drug performs well and indeed cures most patients or if the accrual rate is so fast. To address the issues in clinical practice, we first propose a percentile event time test (PETT), which generalizes METT to any percentile of the survival time, and develop data-driven monitoring for phase II clinical trial designs based on PETT. We evaluate the performance of the method through simulations and illustrate the proposed method with a trial example.</p>","PeriodicalId":54870,"journal":{"name":"Journal of Biopharmaceutical Statistics","volume":" ","pages":"125-144"},"PeriodicalIF":1.2,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138833055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}