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Ruitao Lin

Publications and source records attributed to Ruitao Lin.

9 recordsLinked to original sources
arXiv2024

Online robust estimation and bootstrap inference for function-on-scalar regression

We propose a novel and robust online function-on-scalar regression technique via geometric median to learn associations between functional responses and scalar covariates based on massive or streaming datasets. The online estimation procedure, developed using the average stochastic gradient descent algorithm, offers an efficient and cost-effective method for analyzing sequentially augmented datasets, eliminating the need to store large volumes of data in memory. We establish the almost sure consistency, $L_p$ convergence, and asymptotic normality of the online estimator. To enable efficient and fast inference of the parameters of interest, including the derivation of confidence intervals, we also develop an innovative two-step online bootstrap procedure to approximate the limiting error distribution of the robust online estimator. Numerical studies under a variety of scenarios demonstrate the effectiveness and efficiency of the proposed online learning method. A real application analyzing PM$_{2.5}$ air-quality data is also included to exemplify the proposed online approach.

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arXiv2024

DEMO: Dose Exploration, Monitoring, and Optimization Using a Biological Mediator for Clinical Outcomes

Phase 1-2 designs provide a methodological advance over phase 1 designs for dose finding by using both clinical response and toxicity. A phase 1-2 trial still may fail to select a truly optimal dose. because early response is not a perfect surrogate for long term therapeutic success. To address this problem, a generalized phase 1-2 design first uses a phase 1-2 design's components to identify a set of candidate doses, adaptively randomizes patients among the candidates, and after longer follow up selects a dose to maximize long-term success rate. In this paper, we extend this paradigm by proposing a design that exploits an early treatment-related, real-valued biological outcome, such as pharmacodynamic activity or an immunological effect, that may act as a mediator between dose and clinical outcomes, including tumor response, toxicity, and survival time. We assume multivariate dose-outcome models that include effects appearing in causal pathways from dose to the clinical outcomes. Bayesian model selection is used to identify and eliminate biologically inactive doses. At the end of the trial, a therapeutically optimal dose is chosen from the set of doses that are acceptably safe, clinically effective, and biologically active to maximize restricted mean survival time. Results of a simulation study show that the proposed design may provide substantial improvements over designs that ignore the biological variable.

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arXiv2023

Design and Sample Size Determination for Multiple-dose Randomized Phase II Trials for Dose Optimization

The conventional more-is-better dose selection paradigm, which targets the maximum tolerated dose (MTD), is not suitable for the development of targeted therapies and immunotherapies as the efficacy of these novel therapies may not increase with the dose. The U.S. Food and Drug Administration (FDA) has launched Project Optimus "to reform the dose optimization and dose selection paradigm in oncology drug development", and recently published a draft guidance on dose optimization, which outlines various approaches to achieve this goal. One highlighted approach involves conducting a randomized phase II trial following the completion of a phase I trial, where multiple doses (typically including the MTD and one or two doses lower than the MTD) are compared to identify the optimal dose that maximizes the benefit-risk tradeoff. This paper focuses on the design of such a multiple-dose randomized trial, specifically the determination of the sample size. We propose a MERIT (Multiple-dosE RandomIzed Trial design for dose optimization based on toxicity and efficacy) design that can be easily implemented with pre-calculated decision boundaries included in the protocol. We generalized the standard definitions of type I error and power to accommodate the unique characteristics of dose optimization and derived a decision rule along with an algorithm to determine the optimal sample size. Simulation studies demonstrate that the resulting MERIT design has desirable operating characteristics. To facilitate the implementation of the MERIT design, we provide software, available at www.trialdesign.org.

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arXiv2022

On singular values of large dimensional lag-tau sample autocorrelation matrices

We study the limiting behavior of singular values of a lag-$\tau$ sample auto-correlation matrix $\bf{R}_{\tau}^{\epsilon}$ of error term $\epsilon$ in the high-dimensional factor model. We establish the limiting spectral distribution (LSD) which characterizes the global spectrum of $\bf{R}_{\tau}^{\epsilon}$, and derive the limit of its largest singular value. All the asymptotic results are derived under the high-dimensional asymptotic regime where the data dimension and sample size go to infinity proportionally. Under mild assumptions, we show that the LSD of $\bf{R}_{\tau}^{\epsilon}$ is the same as that of the lag-$\tau$ sample auto-covariance matrix. Based on this asymptotic equivalence, we additionally show that the largest singular value of $\bf{R}_{\tau}^{\epsilon}$ converges almost surely to the right end point of the support of its LSD. Our results take the first step to identify the number of factors in factor analysis using lag-$\tau$ sample auto-correlation matrices. Our theoretical results are fully supported by numerical experiments as well.

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arXiv2020

Mixture of Finite Mixtures Model for Basket Trial

With the recent paradigm shift from cytotoxic drugs to new generation of target therapy and immuno-oncology therapy during oncology drug developments, patients with various cancer (sub)types may be eligible to participate in a basket trial if they have the same molecular target. Bayesian hierarchical modeling (BHM) are widely used in basket trial data analysis, where they adaptively borrow information among different cohorts (subtypes) rather than fully pool the data together or doing stratified analysis based on each cohort. Those approaches, however, may have the risk of over shrinkage estimation because of the invalidated exchangeable assumption. We propose a two-step procedure to find the balance between pooled and stratified analysis. In the first step, we treat it as a clustering problem by grouping cohorts into clusters that share the similar treatment effect. In the second step, we use shrinkage estimator from BHM to estimate treatment effects for cohorts within each cluster under exchangeable assumption. For clustering part, we adapt the mixture of finite mixtures (MFM) approach to have consistent estimate of the number of clusters. We investigate the performance of our proposed method in simulation studies and apply this method to Vemurafenib basket trial data analysis.

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arXiv2018

TOP: Time-to-Event Bayesian Optimal Phase II Trial Design for Cancer Immunotherapy

Immunotherapies have revolutionized cancer treatment. Unlike chemotherapies, immune agents often take longer time to show benefit, and the complex and unique mechanism of action of these agents renders the use of multiple endpoints more appropriate in some trials. These new features of immunotherapy make conventional phase II trial designs, which assume a single binary endpoint that is quickly ascertainable, inefficient and dysfunctional. We propose a flexible and efficient time-to-event Bayesian optimal phase II (TOP) design. The TOP design is efficient in that it allows real-time "go/no-go" interim decision making in the presence of late-onset responses by using all available data, and maximizes the statistical power for detecting effective treatments. TOP is flexible in the number of interim looks and capable of handling simple and complicated endpoints under a unified framework. We conduct simulation studies to evaluate the operating characteristics of the TOP design.Compared to some existing designs, the TOP design shortens the trial duration and has higher power to detect effective treatment with well controlled type I errors. The TOP design allows for making real-time "go/no-go" interim decisions in the presence of late-onset responses, and is capable of handling various types of endpoints under a unified framework. It is transparent and easy to implement as its decision rules can be tabulated and included in the protocol prior to the conduct of the trial. The TOP design provides a flexible, efficient and easy-to-implement method to accelerate and improve the development of immunotherapies.

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arXiv2018

Time-to-Event Model-Assisted Designs to Accelerate Phase I Clinical Trials

Two useful strategies to speed up drug development are to increase the patient accrual rate and use novel adaptive designs. Unfortunately, these two strategies often conflict when the evaluation of the outcome cannot keep pace with the patient accrual rate and thus the interim data cannot be observed in time to make adaptive decisions. A similar logistic difficulty arises when the outcome is of late onset. Based on a novel formulation and approximation of the likelihood of the observed data, we propose a general methodology for model-assisted designs to handle toxicity data that are pending due to fast accrual or late-onset toxicity, and facilitate seamless decision making in phase I dose-finding trials. The dose escalation/de-escalation rules of the proposed time-to-event model-assisted designs can be tabulated before the trial begins, which greatly simplifies trial conduct in practice compared to that under existing methods. We show that the proposed designs have desirable finite and large-sample properties and yield performance that is superior to that of more complicated model-based designs. We provide user-friendly software for implementing the designs.

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arXiv2017

Statistical Properties of the Keyboard Design with Extension to Drug-Combination Trials

The keyboard design is a novel phase I dose-finding method that is simple and has good operating characteristics. This paper studies theoretical properties of the keyboard design, including the optimality of its decision rules, coherence in dose transition, and convergence to the target dose. Establishing these theoretical properties explains the mechanism of the design and provides assurance to practitioners regarding the behavior of the keyboard design. We further extend the keyboard design to dual-agent dose-finding trials, which inherit the same statistical properties and simplicity as the single-agent keyboard design. Extensive simulations are conducted to evaluate the performance of the proposed keyboard drug-combination design using a novel, random two-dimensional dose--toxicity scenario generating algorithm. The simulation results confirm the desirable and competitive operating characteristics of the keyboard design as established by the theoretical study. An R Shiny application is developed to facilitate implementing the keyboard combination design in practice.

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