A key and challenging step toward personalized/precision medicine is the ability to redesign dose-finding clinical trials. This work studies a problem of fully response-adaptive Bayesian design of phase II dose-finding clinical trials with patient information, where the decision maker seeks to identify the right dose for each patient type (often defined as an effective target dose for each group of patients) by minimizing the expected (over patient types) variance of the right dose. We formulate this problem by a stochastic dynamic program and exploit a few properties of this class of learning problems. Because the optimal solution is intractable, we propose an approximate policy by an adaptation of a one-step look-ahead framework. We show the optimality of the proposed policy for a setting with homogeneous patients and two doses and find its asymptotic rate of sampling. We adapt a number of commonly applied allocation policies in dose-finding clinical trials, such as posterior adaptive sampling, and test their performance against our proposed policy via extensive simulations with synthetic and real data. Our numerical analyses provide insights regarding the connection between the structure of the dose-response curve for each patient type and the performance of allocation policies. This paper provides a practical framework for the Food and Drug Administration and pharmaceutical companies to transition from the current phase II procedures to the era of personalized dose-finding clinical trials. Funding: This research is supported by the National Science Foundation [Grant 1651912]. Supplemental Material: The online appendices are available at https://doi.org/10.1287/serv.2022.0306 .
more »
« less
Min-Max Optimal Design of Two-Armed Trials with Side Information
In this work, we study the optimal design of two-armed clinical trials to maximize the accuracy of parameter estimation in a statistical model, where the interaction between patient covariates and treatment are explicitly incorporated to enable precision medication decisions. Such a modeling extension leads to significant complexities for the produced optimization problems because they include optimization over design and covariates concurrently. We take a min-max optimization model and minimize (over design) the maximum (over population) variance of the estimated interaction effect between treatment and patient covariates. This results in a min-max bilevel mixed integer nonlinear programming problem, which is notably challenging to solve. To address this challenge, we introduce a surrogate optimization model by approximating the objective function, for which we propose two solution approaches. The first approach provides an exact solution based on reformulation and decomposition techniques. In the second approach, we provide a lower bound for the inner optimization problem and solve the outer optimization problem over the lower bound. We test our proposed algorithms with synthetic and real-world data sets and compare them with standard (re)randomization methods. Our numerical analysis suggests that the proposed approaches provide higher-quality solutions in terms of the variance of estimators and probability of correct selection. We also show the value of covariate information in precision medicine clinical trials by comparing our proposed approaches to an alternative optimal design approach that does not consider the interaction terms between covariates and treatment. Summary of Contribution: Precision medicine is the future of healthcare where treatment is prescribed based on each patient information. Designing precision medicine clinical trials, which are the cornerstone of precision medicine, is extremely challenging because sample size is limited and patient information may be multidimensional. This work proposes a novel approach to optimally estimate the treatment effect for each patient type in a two-armed clinical trial by reducing the largest variance of personalized treatment effect. We use several statistical and optimization techniques to produce efficient solution methodologies. Results have the potential to save countless lives by transforming the design and implementation of future clinical trials to ensure the right treatments for the right patients. Doing so will reduce patient risks and reduce costs in the healthcare system.
more »
« less
- Award ID(s):
- 1651912
- NSF-PAR ID:
- 10397879
- Date Published:
- Journal Name:
- INFORMS Journal on Computing
- Volume:
- 34
- Issue:
- 1
- ISSN:
- 1091-9856
- Page Range / eLocation ID:
- 165 to 182
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Controlled experiments are widely applied in many areas such as clinical trials or user behavior studies in IT companies. Recently, it is popular to study experimental design problems to facilitate personalized decision making. In this paper, we investigate the problem of optimal design of multiple treatment allocation for personalized decision making in the presence of observational covariates associated with experimental units (often, patients or users). We assume that the response of a subject assigned to a treatment follows a linear model which includes the interaction between covariates and treatments to facilitate precision decision making. We define the optimal objective as the maximum variance of estimated personalized treatment effects over different treatments and different covariates values. The optimal design is obtained by minimizing this objective. Under a semi-definite program reformulation of the original optimization problem, we use a YALMIP and MOSEK based optimization solver to provide the optimal design. Numerical studies are provided to assess the quality of the optimal design.more » « less
-
more » « less
In precision medicine, the ultimate goal is to recommend the most effective treatment to an individual patient based on patient‐specific molecular and clinical profiles, possibly high‐dimensional. To advance cancer treatment, large‐scale screenings of cancer cell lines against chemical compounds have been performed to help better understand the relationship between genomic features and drug response; existing machine learning approaches use exclusively supervised learning, including penalized regression and recommender systems. However, it would be more efficient to apply reinforcement learning to sequentially learn as data accrue, including selecting the most promising therapy for a patient given individual molecular and clinical features and then collecting and learning from the corresponding data. In this article, we propose a novel personalized ranking system called Proximal Policy Optimization Ranking (PPORank), which ranks the drugs based on their predicted effects per cell line (or patient) in the framework of deep reinforcement learning (DRL). Modeled as a Markov decision process, the proposed method learns to recommend the most suitable drugs sequentially and continuously over time. As a proof‐of‐concept, we conduct experiments on two large‐scale cancer cell line data sets in addition to simulated data. The results demonstrate that the proposed DRL‐based PPORank outperforms the state‐of‐the‐art competitors based on supervised learning. Taken together, we conclude that novel methods in the framework of DRL have great potential for precision medicine and should be further studied.
-
It has been recently shown that an additional therapeutic gain may be achieved if a radiotherapy plan is altered over the treatment course using a new treatment paradigm referred to in the literature as spatiotemporal fractionation. Because of the nonconvex and large-scale nature of the corresponding treatment plan optimization problem, the extent of the potential therapeutic gain that may be achieved from spatiotemporal fractionation has been investigated using stylized cancer cases to circumvent the arising computational challenges. This research aims at developing scalable optimization methods to obtain high-quality spatiotemporally fractionated plans with optimality bounds for clinical cancer cases. In particular, the treatment-planning problem is formulated as a quadratically constrained quadratic program and is solved to local optimality using a constraint-generation approach, in which each subproblem is solved using sequential linear/quadratic programming methods. To obtain optimality bounds, cutting-plane and column-generation methods are combined to solve the Lagrangian relaxation of the formulation. The performance of the developed methods are tested on deidentified clinical liver and prostate cancer cases. Results show that the proposed method is capable of achieving local-optimal spatiotemporally fractionated plans with an optimality gap of around 10%–12% for cancer cases tested in this study. Summary of Contribution: The design of spatiotemporally fractionated radiotherapy plans for clinical cancer cases gives rise to a class of nonconvex and large-scale quadratically constrained quadratic programming (QCQP) problems, the solution of which requires the development of efficient models and solution methods. To address the computational challenges posed by the large-scale and nonconvex nature of the problem, we employ large-scale optimization techniques to develop scalable solution methods that find local-optimal solutions along with optimality bounds. We test the performance of the proposed methods on deidentified clinical cancer cases. The proposed methods in this study can, in principle, be applied to solve other QCQP formulations, which commonly arise in several application domains, including graph theory, power systems, and signal processing.more » « less
-
Learning optimal individualized treatment rules (ITRs) has become increasingly important in the modern era of precision medicine. Many statistical and machine learning methods for learning optimal ITRs have been developed in the literature. However, most existing methods are based on data collected from traditional randomized controlled trials and thus cannot take advantage of the accumulative evidence when patients enter the trials sequentially. It is also ethically important that future patients should have a high probability to be treated optimally based on the updated knowledge so far. In this work, we propose a new design called sequentially rule-adaptive trials to learn optimal ITRs based on the contextual bandit framework, in contrast to the response-adaptive design in traditional adaptive trials. In our design, each entering patient will be allocated with a high probability to the current best treatment for this patient, which is estimated using the past data based on some machine learning algorithm (for example, outcome weighted learning in our implementation). We explore the tradeoff between training and test values of the estimated ITR in single-stage problems by proving theoretically that for a higher probability of following the estimated ITR, the training value converges to the optimal value at a faster rate, while the test value converges at a slower rate. This problem is different from traditional decision problems in the sense that the training data are generated sequentially and are dependent. We also develop a tool that combines martingale with empirical process to tackle the problem that cannot be solved by previous techniques for i.i.d. data. We show by numerical examples that without much loss of the test value, our proposed algorithm can improve the training value significantly as compared to existing methods. Finally, we use a real data study to illustrate the performance of the proposed method.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1287/ijoc.2021.1068
