1
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Yang B, Guo X, Loh JM, Wang Q, Wang Y. Learning optimal biomarker-guided treatment policy for chronic disorders. Stat Med 2024; 43:2765-2782. [PMID: 38700103 PMCID: PMC11178467 DOI: 10.1002/sim.10099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/17/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024]
Abstract
Electroencephalogram (EEG) provides noninvasive measures of brain activity and is found to be valuable for the diagnosis of some chronic disorders. Specifically, pre-treatment EEG signals in the alpha and theta frequency bands have demonstrated some association with antidepressant response, which is well-known to have a low response rate. We aim to design an integrated pipeline that improves the response rate of patients with major depressive disorder by developing a treatment policy guided by the resting state pre-treatment EEG recordings and other treatment effects modifiers. First, we design an innovative automatic site-specific EEG preprocessing pipeline to extract features with stronger signals than raw data. We then estimate the conditional average treatment effect (CATE) using causal forests and use a doubly robust technique to improve efficiency in the estimation of the average treatment effect. We present evidence of heterogeneity in the treatment effect and the modifying power of the EEG features, as well as a significant average treatment effect, a result that cannot be obtained with conventional methods. Finally, we employ an efficient policy learning algorithm to learn an optimal depth-2 treatment assignment decision tree and compare its performance with Q-Learning and outcome-weighted learning via simulation studies and an application to a large multi-site, double-blind, randomized controlled clinical trial, EMBARC.
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Affiliation(s)
- Bin Yang
- Department of Biostatistics, Columbia University, New York, New York, USA
| | - Xingche Guo
- Department of Biostatistics, Columbia University, New York, New York, USA
| | - Ji Meng Loh
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Qinxia Wang
- Novartis Pharmaceuticals Corporation, East Hanover, New Jersey, USA
| | - Yuanjia Wang
- Department of Biostatistics, Columbia University, New York, New York, USA
- Department of Psychiatry, Columbia University, New York, New York, USA
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2
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Bian Z, Moodie EEM, Shortreed SM, Lambert SD, Bhatnagar S. Variable selection for individualised treatment rules with discrete outcomes. J R Stat Soc Ser C Appl Stat 2024; 73:298-313. [PMID: 38487498 PMCID: PMC10930223 DOI: 10.1093/jrsssc/qlad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/31/2023] [Accepted: 09/29/2023] [Indexed: 03/17/2024]
Abstract
An individualised treatment rule (ITR) is a decision rule that aims to improve individuals' health outcomes by recommending treatments according to subject-specific information. In observational studies, collected data may contain many variables that are irrelevant to treatment decisions. Including all variables in an ITR could yield low efficiency and a complicated treatment rule that is difficult to implement. Thus, selecting variables to improve the treatment rule is crucial. We propose a doubly robust variable selection method for ITRs, and show that it compares favourably with competing approaches. We illustrate the proposed method on data from an adaptive, web-based stress management tool.
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Affiliation(s)
- Zeyu Bian
- Department of Epidemiology and Biostatistics, McGill University, Montreal, Quebec H3A 0G4, Canada
- Miami Herbert Business School, University of Miami, Miami, FL 33146, USA
| | - Erica E M Moodie
- Department of Epidemiology and Biostatistics, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Susan M Shortreed
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Sylvie D Lambert
- Ingram School of Nursing, McGill University, Montreal, Quebec, Canada
- St.Mary’s Research Centre, Montreal, Quebec, Canada
| | - Sahir Bhatnagar
- Department of Epidemiology and Biostatistics, McGill University, Montreal, Quebec H3A 0G4, Canada
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3
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Li X, Logan BR, Hossain SMF, Moodie EEM. Dynamic Treatment Regimes Using Bayesian Additive Regression Trees for Censored Outcomes. LIFETIME DATA ANALYSIS 2024; 30:181-212. [PMID: 37659991 PMCID: PMC10764602 DOI: 10.1007/s10985-023-09605-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 07/16/2023] [Indexed: 09/04/2023]
Abstract
To achieve the goal of providing the best possible care to each individual under their care, physicians need to customize treatments for individuals with the same health state, especially when treating diseases that can progress further and require additional treatments, such as cancer. Making decisions at multiple stages as a disease progresses can be formalized as a dynamic treatment regime (DTR). Most of the existing optimization approaches for estimating dynamic treatment regimes including the popular method of Q-learning were developed in a frequentist context. Recently, a general Bayesian machine learning framework that facilitates using Bayesian regression modeling to optimize DTRs has been proposed. In this article, we adapt this approach to censored outcomes using Bayesian additive regression trees (BART) for each stage under the accelerated failure time modeling framework, along with simulation studies and a real data example that compare the proposed approach with Q-learning. We also develop an R wrapper function that utilizes a standard BART survival model to optimize DTRs for censored outcomes. The wrapper function can easily be extended to accommodate any type of Bayesian machine learning model.
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Affiliation(s)
- Xiao Li
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brent R Logan
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
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4
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Hu L. A new method for clustered survival data: Estimation of treatment effect heterogeneity and variable selection. Biom J 2024; 66:e2200178. [PMID: 38072661 PMCID: PMC10953775 DOI: 10.1002/bimj.202200178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/31/2023] [Accepted: 08/11/2023] [Indexed: 01/30/2024]
Abstract
We recently developed a new method random-intercept accelerated failure time model with Bayesian additive regression trees (riAFT-BART) to draw causal inferences about population treatment effect on patient survival from clustered and censored survival data while accounting for the multilevel data structure. The practical utility of this method goes beyond the estimation of population average treatment effect. In this work, we exposit how riAFT-BART can be used to solve two important statistical questions with clustered survival data: estimating the treatment effect heterogeneity and variable selection. Leveraging the likelihood-based machine learning, we describe a way in which we can draw posterior samples of the individual survival treatment effect from riAFT-BART model runs, and use the drawn posterior samples to perform an exploratory treatment effect heterogeneity analysis to identify subpopulations who may experience differential treatment effects than population average effects. There is sparse literature on methods for variable selection among clustered and censored survival data, particularly ones using flexible modeling techniques. We propose a permutation-based approach using the predictor's variable inclusion proportion supplied by the riAFT-BART model for variable selection. To address the missing data issue frequently encountered in health databases, we propose a strategy to combine bootstrap imputation and riAFT-BART for variable selection among incomplete clustered survival data. We conduct an expansive simulation study to examine the practical operating characteristics of our proposed methods, and provide empirical evidence that our proposed methods perform better than several existing methods across a wide range of data scenarios. Finally, we demonstrate the methods via a case study of predictors for in-hospital mortality among severe COVID-19 patients and estimating the heterogeneous treatment effects of three COVID-specific medications. The methods developed in this work are readily available in the R ${\textsf {R}}$ package riAFTBART $\textsf {riAFTBART}$ .
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Affiliation(s)
- Liangyuan Hu
- Department of Biostatistics and Epidemiology, Rutgers University, Piscataway, New Jersey 08854
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5
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Suk Y, Park C. Designing Optimal, Data-Driven Policies from Multisite Randomized Trials. PSYCHOMETRIKA 2023; 88:1171-1196. [PMID: 37874510 DOI: 10.1007/s11336-023-09937-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Indexed: 10/25/2023]
Abstract
Optimal treatment regimes (OTRs) have been widely employed in computer science and personalized medicine to provide data-driven, optimal recommendations to individuals. However, previous research on OTRs has primarily focused on settings that are independent and identically distributed, with little attention given to the unique characteristics of educational settings, where students are nested within schools and there are hierarchical dependencies. The goal of this study is to propose a framework for designing OTRs from multisite randomized trials, a commonly used experimental design in education and psychology to evaluate educational programs. We investigate modifications to popular OTR methods, specifically Q-learning and weighting methods, in order to improve their performance in multisite randomized trials. A total of 12 modifications, 6 for Q-learning and 6 for weighting, are proposed by utilizing different multilevel models, moderators, and augmentations. Simulation studies reveal that all Q-learning modifications improve performance in multisite randomized trials and the modifications that incorporate random treatment effects show the most promise in handling cluster-level moderators. Among weighting methods, the modification that incorporates cluster dummies into moderator variables and augmentation terms performs best across simulation conditions. The proposed modifications are demonstrated through an application to estimate an OTR of conditional cash transfer programs using a multisite randomized trial in Colombia to maximize educational attainment.
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Affiliation(s)
- Youmi Suk
- Department of Human Development, Teachers College, Columbia University, 525 West 120th Street, New York, NY, 10027, USA.
| | - Chan Park
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, 265 South 37th Street, Philadelphia, USA
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6
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Moodie EEM, Talbot D. On "Reflections on the concept of optimality of single decision point treatment regimes". Biom J 2023; 65:e2300027. [PMID: 37797173 DOI: 10.1002/bimj.202300027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/26/2023] [Accepted: 06/22/2023] [Indexed: 10/07/2023]
Abstract
This is a discussion of "Reflections on the concept of optimality of single decision point treatment regimes" by Trung Dung Tran, Ariel Alonso Abad, Geert Verbeke, Geert Molenberghs, and Iven Van Mechelen. The authors propose a thoughtful consideration of optimization targets and the implications of such targets for the resulting optimal treatment rule. However, we contest the assertation that targets of optimization have been overlooked and suggest additional considerations that researchers must contemplate as part of a complete framework for learning about optimal treatment regimes.
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Affiliation(s)
- Erica E M Moodie
- Department of Epidemiology & Biostatistics, McGill University, Montreal, Quebec, Canada
| | - Denis Talbot
- Department of Social and Preventive Medicine, Université Laval, Quebec, Canada
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7
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Park HG, Wu D, Petkova E, Tarpey T, Ogden RT. Bayesian Index Models for Heterogeneous Treatment Effects on a Binary Outcome. STATISTICS IN BIOSCIENCES 2023; 15:397-418. [PMID: 37313546 PMCID: PMC10197073 DOI: 10.1007/s12561-023-09370-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/02/2023] [Accepted: 03/21/2023] [Indexed: 06/15/2023]
Abstract
This paper develops a Bayesian model with a flexible link function connecting a binary treatment response to a linear combination of covariates and a treatment indicator and the interaction between the two. Generalized linear models allowing data-driven link functions are often called "single-index models" and are among popular semi-parametric modeling methods. In this paper, we focus on modeling heterogeneous treatment effects, with the goal of developing a treatment benefit index (TBI) incorporating prior information from historical data. The model makes inference on a composite moderator of treatment effects, summarizing the effect of the predictors within a single variable through a linear projection of the predictors. This treatment benefit index can be useful for stratifying patients according to their predicted treatment benefit levels and can be especially useful for precision health applications. The proposed method is applied to a COVID-19 treatment study.
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Affiliation(s)
- Hyung G. Park
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
| | - Danni Wu
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
| | - Eva Petkova
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
| | - Thaddeus Tarpey
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
| | - R. Todd Ogden
- Department of Biostatistics, Columbia University, New York, NY 10032 USA
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8
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Blette BS, Granholm A, Li F, Shankar-Hari M, Lange T, Munch MW, Møller MH, Perner A, Harhay MO. Causal Bayesian machine learning to assess treatment effect heterogeneity by dexamethasone dose for patients with COVID-19 and severe hypoxemia. Sci Rep 2023; 13:6570. [PMID: 37085591 PMCID: PMC10120498 DOI: 10.1038/s41598-023-33425-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023] Open
Abstract
The currently recommended dose of dexamethasone for patients with severe or critical COVID-19 is 6 mg per day (mg/d) regardless of patient features and variation. However, patients with severe or critical COVID-19 are heterogenous in many ways (e.g., age, weight, comorbidities, disease severity, and immune features). Thus, it is conceivable that a standardized dosing protocol may not be optimal. We assessed treatment effect heterogeneity in the COVID STEROID 2 trial, which compared 6 mg/d to 12 mg/d, using a causal inference framework with Bayesian Additive Regression Trees, a flexible modeling method that detects interactive effects and nonlinear relationships among multiple patient characteristics simultaneously. We found that 12 mg/d of dexamethasone, relative to 6 mg/d, was probably associated with better long-term outcomes (days alive without life support and mortality after 90 days) among the entire trial population (i.e., no signals of harm), and probably more beneficial among those without diabetes mellitus, that were older, were not using IL-6 inhibitors at baseline, weighed less, or had higher level respiratory support at baseline. This adds more evidence supporting the use of 12 mg/d in practice for most patients not receiving other immunosuppressants and that additional study of dosing could potentially optimize clinical outcomes.
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Affiliation(s)
- Bryan S Blette
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Clinical Trials Methods and Outcomes Lab, Palliative and Advanced Illness Research (PAIR) Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anders Granholm
- Department of Intensive Care, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
- Collaboration for Research in Intensive Care, Copenhagen, Denmark
| | - Fan Li
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
- Center for Methods in Implementation and Prevention Science, Yale University School of Public Health, New Haven, CT, USA
| | - Manu Shankar-Hari
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Theis Lange
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Marie Warrer Munch
- Department of Intensive Care, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
- Collaboration for Research in Intensive Care, Copenhagen, Denmark
| | - Morten Hylander Møller
- Department of Intensive Care, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
- Collaboration for Research in Intensive Care, Copenhagen, Denmark
| | - Anders Perner
- Department of Intensive Care, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
- Collaboration for Research in Intensive Care, Copenhagen, Denmark
| | - Michael O Harhay
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Clinical Trials Methods and Outcomes Lab, Palliative and Advanced Illness Research (PAIR) Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 304 Blockley Hall, 423 Guardian Drive, Philadelphia, PA, 19104-6021, USA.
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9
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Hu L, Ji J, Liu H, Ennis R. A Flexible Approach for Assessing Heterogeneity of Causal Treatment Effects on Patient Survival Using Large Datasets with Clustered Observations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14903. [PMID: 36429621 PMCID: PMC9690785 DOI: 10.3390/ijerph192214903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Personalized medicine requires an understanding of treatment effect heterogeneity. Evolving toward causal evidence for scenarios not studied in randomized trials necessitates a methodology using real-world evidence. Herein, we demonstrate a methodology that generates causal effects, assesses the heterogeneity of the effects and adjusts for the clustered nature of the data. This study uses a state-of-the-art machine learning survival model, riAFT-BART, to draw causal inferences about individual survival treatment effects, while accounting for the variability in institutional effects; further, it proposes a data-driven approach to agnostically (as opposed to a priori hypotheses) ascertain which subgroups exhibit an enhanced treatment effect from which intervention, relative to global evidence-average treatment effects measured at the population level. Comprehensive simulations show the advantages of the proposed method in terms of bias, efficiency and precision in estimating heterogeneous causal effects. The empirically validated method was then used to analyze the National Cancer Database.
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Affiliation(s)
- Liangyuan Hu
- Department of Biostatistics and Epidemiology, Rutgers University, New Brunswick, NJ 07102, USA
| | - Jiayi Ji
- Department of Biostatistics and Epidemiology, Rutgers University, New Brunswick, NJ 07102, USA
| | - Hao Liu
- Department of Biostatistics and Epidemiology, Rutgers University, New Brunswick, NJ 07102, USA
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 07102, USA
| | - Ronald Ennis
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 07102, USA
- Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 07102, USA
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10
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Bargagli-Stoffi FJ, De Witte K, Gnecco G. Heterogeneous causal effects with imperfect compliance: A Bayesian machine learning approach. Ann Appl Stat 2022. [DOI: 10.1214/21-aoas1579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Li P, Taylor JMG, Boonstra PS, Lawrence TS, Schipper MJ. Utility based approach in individualized optimal dose selection using machine learning methods. Stat Med 2022; 41:2957-2977. [PMID: 35343595 PMCID: PMC9233043 DOI: 10.1002/sim.9396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/07/2022] [Accepted: 03/11/2022] [Indexed: 11/23/2022]
Abstract
The goal in personalized medicine is to individualize treatment using patient characteristics and improve health outcomes. Selection of optimal dose must balance the effect of dose on both treatment efficacy and toxicity outcomes. We consider a setting with one binary efficacy and one binary toxicity outcome. The goal is to find the optimal dose for each patient using clinical features and biomarkers from available dataset. We propose to use flexible machine learning methods such as random forest and Gaussian process models to build models for efficacy and toxicity depending on dose and biomarkers. A copula is used to model the joint distribution of the two outcomes and the estimates are constrained to have non‐decreasing dose‐efficacy and dose‐toxicity relationships. Numerical utilities are elicited from clinicians for each potential bivariate outcome. For each patient, the optimal dose is chosen to maximize the posterior mean of the utility function. We also propose alternative approaches to optimal dose selection by adding additional toxicity based constraints and an approach taking into account the uncertainty in the estimation of the utility function. The proposed methods are evaluated in a simulation study to compare expected utility outcomes under various estimated optimal dose rules. Gaussian process models tended to have better performance than random forest. Enforcing monotonicity during modeling provided small benefits. Whether and how, correlation between efficacy and toxicity, was modeled, had little effect on performance. The proposed methods are illustrated with a study of patients with liver cancer treated with stereotactic body radiation therapy.
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Affiliation(s)
- Pin Li
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeremy M G Taylor
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Philip S Boonstra
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew J Schipper
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
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12
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Hu L, Lin JY, Sigel K, Kale M. Estimating heterogeneous survival treatment effects of lung cancer screening approaches: A causal machine learning analysis. Ann Epidemiol 2021; 62:36-42. [PMID: 34157399 PMCID: PMC8463451 DOI: 10.1016/j.annepidem.2021.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/18/2021] [Accepted: 06/14/2021] [Indexed: 12/20/2022]
Abstract
The National Lung Screening Trial (NLST) found that low-dose computed tomography (LDCT) screening provided lung cancer (LC) mortality benefit compared to chest radiography (CXR). Considerable research concerns identifying the differential treatment effects that may exist in certain subpopulations. We shed light on several important issues in existing research and highlight the need for further investigation of the heterogeneous comparative effect of LDCT versus CXR, using more flexible and rigorous statistical approaches. We used a high-performance Bayesian machine learning approach designed for censored survival data, accelerated failure time Bayesian additive regression trees model (AFT-BART), to flexibly capture the relationships between the failure time and predictors. We then used the counterfactual framework to draw Markov chain Monte Carlo samples of the individual treatment effect for each participant. Using these posterior samples, we explored the possible treatment effect heterogeneity via a stepwise binary tree approach. When re-analyzed with AFT-BART, LDCT did not have a statistically significant LC or overall mortality benefit compared to CXR. The Asian and Black (particularly those with pack-year ≥ 37 years and without emphysema) NLST population were shown to have enhanced overall mortality benefit from LDCT than the population average. Although inconclusive for LC mortality benefit, Asians, Blacks and Whites with history of chronic obstructive pulmonary disease showed a small trend towards benefit from LDCT. Causal inference with flexible machine learning modeling can provide valuable knowledge for informing treatment decision and planning targeted clinical trials emphasizing personalized medicine approaches.
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Affiliation(s)
- Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Biostatistics and Epidemiology, Rutgers University, Piscataway, NJ.
| | - Jung-Yi Lin
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; Icahn School of Medicine at Mount Sinai, Institute for Health Care Delivery Science, New York, NY
| | - Keith Sigel
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Minal Kale
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
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13
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Hu L, Ji J, Li F. Estimating heterogeneous survival treatment effect in observational data using machine learning. Stat Med 2021; 40:4691-4713. [PMID: 34114252 PMCID: PMC9827499 DOI: 10.1002/sim.9090] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 01/12/2023]
Abstract
Methods for estimating heterogeneous treatment effect in observational data have largely focused on continuous or binary outcomes, and have been relatively less vetted with survival outcomes. Using flexible machine learning methods in the counterfactual framework is a promising approach to address challenges due to complex individual characteristics, to which treatments need to be tailored. To evaluate the operating characteristics of recent survival machine learning methods for the estimation of treatment effect heterogeneity and inform better practice, we carry out a comprehensive simulation study presenting a wide range of settings describing confounded heterogeneous survival treatment effects and varying degrees of covariate overlap. Our results suggest that the nonparametric Bayesian Additive Regression Trees within the framework of accelerated failure time model (AFT-BART-NP) consistently yields the best performance, in terms of bias, precision, and expected regret. Moreover, the credible interval estimators from AFT-BART-NP provide close to nominal frequentist coverage for the individual survival treatment effect when the covariate overlap is at least moderate. Including a nonparametrically estimated propensity score as an additional fixed covariate in the AFT-BART-NP model formulation can further improve its efficiency and frequentist coverage. Finally, we demonstrate the application of flexible causal machine learning estimators through a comprehensive case study examining the heterogeneous survival effects of two radiotherapy approaches for localized high-risk prostate cancer.
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Affiliation(s)
- Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Fan Li
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
- Center for Methods in Implementation and Prevention Science, Yale University School of Public Health, New Haven, Connecticut
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14
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Affiliation(s)
- Anne Hecksteden
- Saarland University, Institute of Sports and Preventive Medicine, Saarbruecken, Germany
| | - Ralf Kellner
- Saarland University, Chair for Quantitative Methods and Statistics, Saarbruecken, Germany
| | - Lars Donath
- Department of Intervention Research in Exercise Training, German Sport University, Cologne, Germany
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15
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Cao M, Li X. Effectiveness of modified constraint-induced movement therapy for upper limb function intervention following stroke: A brief review. SPORTS MEDICINE AND HEALTH SCIENCE 2021; 3:134-137. [PMID: 35784520 PMCID: PMC9219327 DOI: 10.1016/j.smhs.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 11/19/2022] Open
Abstract
Neglecting the use of the affected limb in stroke patients can result in learned non-use. Modified constraint-induced movement therapy (mCIMT) is a form of rehabilitation therapy that limits the less paretic side, and through repeated and concentrated training improve the upper limb function of the paretic side. The aim of this paper is to develop a critical systematic review on the research evidence evaluating the effectiveness of applying mCIMT in the recovery of upper limb function in stroke patients. The outcome of this evaluation support that mCIMT significantly improves the upper limb function of stroke patients. Moreover, group mCIMT modality and TR (trunk restraint)+mCIMT modality provide greater benefits than mCIMT alone.
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Affiliation(s)
- Manting Cao
- Corresponding author. Rehabilitation department, Zhejiang Chinese Medical University, Hangzhou 310053, China.
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16
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Logan BR, Maiers MJ, Sparapani RA, Laud PW, Spellman SR, McCulloch RE, Shaw BE. Optimal Donor Selection for Hematopoietic Cell Transplantation Using Bayesian Machine Learning. JCO Clin Cancer Inform 2021; 5:494-507. [PMID: 33950708 DOI: 10.1200/cci.20.00185] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Donor selection practices for matched unrelated donor (MUD) hematopoietic cell transplantation (HCT) vary, and the impact of optimizing donor selection in a patient-specific way using modern machine learning (ML) models has not been studied. METHODS We trained a Bayesian ML model in 10,318 patients who underwent MUD HCT from 1999 to 2014 to provide patient- and donor-specific predictions of clinically severe (grade 3 or 4) acute graft-versus-host disease or death by day 180. The model was validated in 3,501 patients from 2015 to 2016 with archived records of potential donors at search. Donor selection optimizing predicted outcomes was implemented over either an unlimited donor pool or the donors in the search archives. Posterior mean differences in outcomes from optimal donor selection versus actual practice were summarized per patient and across the population with 95% intervals. RESULTS Event rates were 33% (training) and 37% (validation). Among donor features, only age affected outcomes, with the effect consistent regardless of patient features. The median (interquartile range) difference in age between the youngest donor at search and the selected donor was 6 (1-10) years, whereas the number of donors per patient younger than the selected donor was 6 (1-36). Fourteen percent of the validation data set had an approximate 5% absolute reduction in event rates from selecting the youngest donor at search versus the actual donor used, leading to an absolute population reduction of 1% (95% interval, 0 to 3). CONCLUSION We confirmed the singular importance of selecting the youngest available MUD, irrespective of patient features, identified potential for improved HCT outcomes by selecting a younger MUD, and demonstrated use of novel ML models transferable to optimize other complex treatment decisions in a patient-specific way.
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Affiliation(s)
- Brent R Logan
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin (MCW), Milwaukee, WI.,Center for International Blood and Marrow Transplant Research (CIBMTR), Medical College of Wisconsin, Milwaukee, WI
| | - Martin J Maiers
- National Marrow Donor Program and Center for International Blood and Marrow Transplant Research, Minneapolis, MN
| | - Rodney A Sparapani
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin (MCW), Milwaukee, WI
| | - Purushottam W Laud
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin (MCW), Milwaukee, WI
| | - Stephen R Spellman
- National Marrow Donor Program and Center for International Blood and Marrow Transplant Research, Minneapolis, MN
| | - Robert E McCulloch
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ
| | - Bronwen E Shaw
- Center for International Blood and Marrow Transplant Research (CIBMTR), Medical College of Wisconsin, Milwaukee, WI
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17
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Tewari P, Kashdan E, Walsh C, Martin CM, Parnell AC, O'Leary JJ. Estimating the conditional probability of developing human papilloma virus related oropharyngeal cancer by combining machine learning and inverse Bayesian modelling. PLoS Comput Biol 2021; 17:e1009289. [PMID: 34415913 PMCID: PMC8409636 DOI: 10.1371/journal.pcbi.1009289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 09/01/2021] [Accepted: 07/20/2021] [Indexed: 12/24/2022] Open
Abstract
The epidemic increase in the incidence of Human Papilloma Virus (HPV) related Oropharyngeal Squamous Cell Carcinomas (OPSCCs) in several countries worldwide represents a significant public health concern. Although gender neutral HPV vaccination programmes are expected to cause a reduction in the incidence rates of OPSCCs, these effects will not be evident in the foreseeable future. Secondary prevention strategies are currently not feasible due to an incomplete understanding of the natural history of oral HPV infections in OPSCCs. The key parameters that govern natural history models remain largely ill-defined for HPV related OPSCCs and cannot be easily inferred from experimental data. Mathematical models have been used to estimate some of these ill-defined parameters in cervical cancer, another HPV related cancer leading to successful implementation of cancer prevention strategies. We outline a "double-Bayesian" mathematical modelling approach, whereby, a Bayesian machine learning model first estimates the probability of an individual having an oral HPV infection, given OPSCC and other covariate information. The model is then inverted using Bayes' theorem to reverse the probability relationship. We use data from the Surveillance, Epidemiology, and End Results (SEER) cancer registry, SEER Head and Neck with HPV Database and the National Health and Nutrition Examination Surveys (NHANES), representing the adult population in the United States to derive our model. The model contains 8,106 OPSCC patients of which 73.0% had an oral HPV infection. When stratified by age, sex, marital status and race/ethnicity, the model estimated a higher conditional probability for developing OPSCCs given an oral HPV infection in non-Hispanic White males and females compared to other races/ethnicities. The proposed Bayesian model represents a proof-of-concept of a natural history model of HPV driven OPSCCs and outlines a strategy for estimating the conditional probability of an individual's risk of developing OPSCC following an oral HPV infection.
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Affiliation(s)
- Prerna Tewari
- Department Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland.,Molecular Pathology Research, Coombe Women & Infants University Hospital, Dublin, Ireland
| | - Eugene Kashdan
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Cathal Walsh
- Department Mathematics and Statistics, University of Limerick, Limerick, Ireland
| | - Cara M Martin
- Department Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland.,Molecular Pathology Research, Coombe Women & Infants University Hospital, Dublin, Ireland
| | - Andrew C Parnell
- Hamilton Institute, Insight Centre for Data Analytics, Maynooth University, Kildare, Ireland
| | - John J O'Leary
- Department Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland.,Molecular Pathology Research, Coombe Women & Infants University Hospital, Dublin, Ireland
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18
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Spanbauer C, Sparapani R. Nonparametric machine learning for precision medicine with longitudinal clinical trials and Bayesian additive regression trees with mixed models. Stat Med 2021; 40:2665-2691. [PMID: 33751659 DOI: 10.1002/sim.8924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 12/14/2020] [Accepted: 02/07/2021] [Indexed: 11/11/2022]
Abstract
Precision medicine is an active area of research that could offer an analytic paradigm shift for clinical trials and the subsequent treatment decisions based on them. Clinical trials are typically analyzed with the intent of discovering beneficial treatments if the same treatment is applied to the entire population under study. But, such a treatment strategy could be suboptimal if subsets of the population exhibit varying treatment effects. Identifying subsets of the population experiencing differential treatment effect and forming individualized treatment rules is a task well-suited to modern machine learning methods such as tree-based ensemble predictive models. Specifically, Bayesian additive regression trees (BART) has shown promise in this regard because of its exceptional performance in out-of-sample prediction. Due to the unique inferential needs of precision medicine for clinical trials, we have proposed the BART extensions explicated here. We incorporate random effects for longitudinal repeated measures and subject clustering within medical centers. The addition of a novel interaction detection prior to identify treatment heterogeneity among clinical trial patients and its association with patient characteristics. These extensions are unified under a framework that we call mixedBART. Simulation studies and applications of precision medicine based on real randomized clinical trials data examples are presented.
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Affiliation(s)
- Charles Spanbauer
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rodney Sparapani
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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19
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Meid AD, Ruff C, Wirbka L, Stoll F, Seidling HM, Groll A, Haefeli WE. Using the Causal Inference Framework to Support Individualized Drug Treatment Decisions Based on Observational Healthcare Data. Clin Epidemiol 2020; 12:1223-1234. [PMID: 33173350 PMCID: PMC7646479 DOI: 10.2147/clep.s274466] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/08/2020] [Indexed: 01/02/2023] Open
Abstract
When healthcare professionals have the choice between several drug treatments for their patients, they often experience considerable decision uncertainty because many decisions simply have no single “best” choice. The challenges are manifold and include that guideline recommendations focus on randomized controlled trials whose populations do not necessarily correspond to specific patients in everyday treatment. Further reasons may be insufficient evidence on outcomes, lack of direct comparison of distinct options, and the need to individually balance benefits and risks. All these situations will occur in routine care, its outcomes will be mirrored in routine data, and could thus be used to guide decisions. We propose a concept to facilitate decision-making by exploiting this wealth of information. Our working example for illustration assumes that the response to a particular (drug) treatment can substantially differ between individual patients depending on their characteristics (heterogeneous treatment effects, HTE), and that decisions will be more precise if they are based on real-world evidence of HTE considering this information. However, such methods must account for confounding by indication and effect measure modification, eg, by adequately using machine learning methods or parametric regressions to estimate individual responses to pharmacological treatments. The better a model assesses the underlying HTE, the more accurate are predicted probabilities of treatment response. After probabilities for treatment-related benefit and harm have been calculated, decision rules can be applied and patient preferences can be considered to provide individual recommendations. Emulated trials in observational data are a straightforward technique to predict the effects of such decision rules when applied in routine care. Prediction-based decision rules from routine data have the potential to efficiently supplement clinical guidelines and support healthcare professionals in creating personalized treatment plans using decision support tools.
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Affiliation(s)
- Andreas D Meid
- Department of Clinical Pharmacology and Pharmacoepidemiology, University of Heidelberg, Heidelberg 69120, Germany
| | - Carmen Ruff
- Department of Clinical Pharmacology and Pharmacoepidemiology, University of Heidelberg, Heidelberg 69120, Germany
| | - Lucas Wirbka
- Department of Clinical Pharmacology and Pharmacoepidemiology, University of Heidelberg, Heidelberg 69120, Germany
| | - Felicitas Stoll
- Department of Clinical Pharmacology and Pharmacoepidemiology, University of Heidelberg, Heidelberg 69120, Germany
| | - Hanna M Seidling
- Department of Clinical Pharmacology and Pharmacoepidemiology, University of Heidelberg, Heidelberg 69120, Germany.,Cooperation Unit Clinical Pharmacy, University of Heidelberg, Heidelberg 69120, Germany
| | - Andreas Groll
- Department of Statistics, TU Dortmund University, Dortmund 44227, Germany
| | - Walter E Haefeli
- Department of Clinical Pharmacology and Pharmacoepidemiology, University of Heidelberg, Heidelberg 69120, Germany.,Cooperation Unit Clinical Pharmacy, University of Heidelberg, Heidelberg 69120, Germany
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20
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Xu Y, Wood AM, Sweeting MJ, Roberts DJ, Tom BD. Optimal individualized decision rules from a multi-arm trial: A comparison of methods and an application to tailoring inter-donation intervals among blood donors in the UK. Stat Methods Med Res 2020; 29:3113-3134. [PMID: 32380893 PMCID: PMC7682530 DOI: 10.1177/0962280220920669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There is a growing interest in precision medicine where individual heterogeneity is incorporated into decision-making and treatments are tailored to individuals to provide better healthcare. One important aspect of precision medicine is the estimation of the optimal individualized treatment rule (ITR) that optimizes the expected outcome. Most methods developed for this purpose are restricted to the setting with two treatments, while clinical studies with more than two treatments are common in practice. In this work, we summarize methods to estimate the optimal ITR in the multi-arm setting and compare their performance in large-scale clinical trials via simulation studies. We then illustrate their utilities with a case study using the data from the INTERVAL trial, which randomly assigned over 20,000 male blood donors from England to one of the three inter-donation intervals (12-week, 10-week, and eight-week) over two years. We estimate the optimal individualized donation strategies under three different objectives. Our findings are fairly consistent across five different approaches that are applied: when we target the maximization of the total units of blood collected, almost all donors are assigned to the eight-week inter-donation interval, whereas if we aim at minimizing the low hemoglobin deferral rates, almost all donors are assigned to donate every 12 weeks. However, when the goal is to maximize the utility score that "discounts" the total units of blood collected by the incidences of low hemoglobin deferrals, we observe some heterogeneity in the optimal inter-donation interval across donors and the optimal donor assignment strategy is highly dependent on the trade-off parameter in the utility function.
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Affiliation(s)
- Yuejia Xu
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Angela M Wood
- Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Cambridge, UK
| | - Michael J Sweeting
- Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, UK.,Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Roberts
- BRC Haematology Theme and Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,National Health Service Blood and Transplant, Oxford, UK
| | - Brian Dm Tom
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
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21
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Moodie EEM, Krakow EF. Precision medicine: Statistical methods for estimating adaptive treatment strategies. Bone Marrow Transplant 2020; 55:1890-1896. [PMID: 32286507 DOI: 10.1038/s41409-020-0871-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 11/09/2022]
Abstract
SERIES EDITORS' NOTE The beauty of science is that all the important things are unpredictable. Freeman Dyson In the typescript which follows, Moodie and Krakow tackle the topical issue of precision medicine and statistical methods for estimating adaptive treatment strategies. This may be the most difficult typescript in our series so far for non-statisticians to understand. It even has equations! But please bear with the authors and give it a chance. One needs not to understand the equations to get the thrust of the strategy.Precision medicine as we discuss elsewhere, is misnamed. In statistics and mathematics precision refers to getting the same answer again and again. It does not mean getting the correct answer, the term for which is accuracy, not precision. However, precision is the current buzz word so there's no point trying to get this straight. When we think about precision we need to consider two elements, reproducibility and replicability. Reproducibility means you give me your data and computer code and I come to the same conclusion you did. Replicability is another matter. I try to replicate your experiment and hopefully reach the same conclusion. In medicine, replicability is obviously more important than reproducibility but things which cannot be reproduced are unlikely to be replicated.As the authors discuss, one can think about precision medicine as one does a family vacation. A best vacation depends on several co-variates: where you live, your prior travel experiences, advice from family and friends, online reviews, Wikitravel, cost, your travel budget, if you have kids and many other co-variates. Consequently, there is unlikely to be a best vacation for everyone. Yours might be a week at the Ritz Carlton Cancun with dinner at Careyes and ours, a week at the Pfister Hotel in Milwaukee with dinner at Mader's German Restaurant (bring simvastatin). Similarly, it is unlikely there is a best therapy of acute myeloid leukemia, a best donor, a best conditioning regimen, a best posttransplant immune suppressive regimen etc. and certainly no best combination of these co-variates for your patient.The question Moodie and Krakow tackle is how we can determine the best therapy or combination of therapies for someone receiving a haematopoietic cell transplant. Although the default answer is typically: randomized clinical trials are the gold standard, these inform us of the outcome of a cohort of subjects, not individuals. In many instances, although a new therapy may be shown to be better than an old one in a controlled randomized trial the benefit is not uniformly distributed. Some subjects in the experimental cohort may do worse with the new therapy compared with controls, others better. The question is who are the winners and losers? We cannot do a controlled randomized trial of one person. Moodie and Krakow discuss statistical tools to help us sort this out.Again, please do not be put off by the equations; forgetaboutit. The overriding message is not so complex, and important. We are always standing by on twitter @BMTStats to help. But don't confuse us with Match.com. And, by the way, Freeman Dyson was a professor at the Institute for Advanced Studies at Princeton but never got his PhD.Robert Peter Gale, Imperial College London, and Mei-Jie Zhang, Medical College of Wisconsin, Center for International Blood and Marrow Research (CIBMTR).
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Affiliation(s)
- Erica E M Moodie
- Department of Epidemiology and Biostatistics, McGill University, 1020 Pine Ave W, Montreal, QC, H3A 1A2, Canada
| | - Elizabeth F Krakow
- Fred Hutchinson Cancer Research Center and University of Washington, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
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22
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Ghosh P, Nahum-Shani I, Spring B, Chakraborty B. Noninferiority and equivalence tests in sequential, multiple assignment, randomized trials (SMARTs). Psychol Methods 2020; 25:182-205. [PMID: 31497981 PMCID: PMC7061067 DOI: 10.1037/met0000232] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Adaptive interventions (AIs) are increasingly popular in the behavioral sciences. An AI is a sequence of decision rules that specify for whom and under what conditions different intervention options should be offered, in order to address the changing needs of individuals as they progress over time. The sequential, multiple assignment, randomized trial (SMART) is a novel trial design that was developed to aid in empirically constructing effective AIs. The sequential randomizations in a SMART often yield multiple AIs that are embedded in the trial by design. Many SMARTs are motivated by scientific questions pertaining to the comparison of such embedded AIs. Existing data analytic methods and sample size planning resources for SMARTs are suitable only for superiority testing, namely for testing whether one embedded AI yields better primary outcomes on average than another. This calls for noninferiority/equivalence testing methods, because AIs are often motivated by the need to deliver support/care in a less costly or less burdensome manner, while still yielding benefits that are equivalent or noninferior to those produced by a more costly/burdensome standard of care. Here, we develop data-analytic methods and sample-size formulas for SMARTs testing the noninferiority or equivalence of one AI over another. Sample size and power considerations are discussed with supporting simulations, and online resources for sample size planning are provided. A simulated data analysis shows how to test noninferiority and equivalence hypotheses with SMART data. For illustration, we use an example from a SMART in the area of health psychology aiming to develop an AI for promoting weight loss among overweight/obese adults. (PsycINFO Database Record (c) 2020 APA, all rights reserved).
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Affiliation(s)
- Palash Ghosh
- Centre for Quantitative Medicine, Duke-NUS Medical School,
National University of Singapore, Singapore
| | | | - Bonnie Spring
- Center for Behavior and Health, Northwestern University
Feinberg School of Medicine
| | - Bibhas Chakraborty
- Centre for Quantitative Medicine, Duke-NUS Medical School,
National University of Singapore, Singapore
- Department of Statistics and Applied Probability, National
University of Singapore
- Department of Biostatistics and Bioinformatics, Duke
University
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23
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Starling JE, Murray JS, Carvalho CM, Bukowski RK, Scott JG. BART with targeted smoothing: An analysis of patient-specific stillbirth risk. Ann Appl Stat 2020. [DOI: 10.1214/19-aoas1268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Wen L, Shao H. Analysis of influencing factors of the CO 2 emissions in China: Nonparametric additive regression approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133724. [PMID: 31400680 DOI: 10.1016/j.scitotenv.2019.133724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/27/2019] [Accepted: 08/01/2019] [Indexed: 05/05/2023]
Abstract
As the maximal carbon dioxide (CO2) contributor in world, China is embracing severe stress from emission reduction. It is increasingly important to study the factors affecting China's CO2 emissions. Many researches had extensively researched the driving forces of CO2 emissions of China. However, majority of the researches adopt a conventional linear method based on time-series or cross-section data for researching the CO2 emissions as well as nearly neglect nonlinear relationships. To surmount the limitations of extant investigations, this research adopts a data-driven nonparametric additive regression approach to examine primary influencing factors of China's CO2 emissions. The results manifest that the nonlinear influence of economy on CO2 emissions is same as the Environmental Kuznets Curve hypothesis. The household consumption level embodies the inverted "U-type" pattern. The industrialization also embodies the overturned "U-type" relationship. Aggregate retail sales of consumer goods present a positive "U-type" effect upon CO2 emissions. Similarly, the urbanization signifies a positive "U-type" nexus upon CO2 emissions. Energy intensity indicates a positive "U-type" nexus. The paper ought to exert more attention to the dynamic effects of the driving forces above in order to abate the CO2 emissions of China. This study will also propose corresponding policies and recommendations according to the dynamic effects.
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Affiliation(s)
- Lei Wen
- Department of Economics and Management, North China Electric Power University, Baoding, Hebei, China.
| | - Hengyang Shao
- Department of Economics and Management, North China Electric Power University, Baoding, Hebei, China
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25
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Tan YV, Roy J. Bayesian additive regression trees and the General BART model. Stat Med 2019; 38:5048-5069. [PMID: 31460678 PMCID: PMC6800811 DOI: 10.1002/sim.8347] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/05/2019] [Accepted: 07/23/2019] [Indexed: 11/06/2022]
Abstract
Bayesian additive regression trees (BART) is a flexible prediction model/machine learning approach that has gained widespread popularity in recent years. As BART becomes more mainstream, there is an increased need for a paper that walks readers through the details of BART, from what it is to why it works. This tutorial is aimed at providing such a resource. In addition to explaining the different components of BART using simple examples, we also discuss a framework, the General BART model that unifies some of the recent BART extensions, including semiparametric models, correlated outcomes, and statistical matching problems in surveys, and models with weaker distributional assumptions. By showing how these models fit into a single framework, we hope to demonstrate a simple way of applying BART to research problems that go beyond the original independent continuous or binary outcomes framework.
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Affiliation(s)
- Yaoyuan Vincent Tan
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, 683 Hoes Lane West, Piscataway, New Jersey 08854, USA
| | - Jason Roy
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, 683 Hoes Lane West, Piscataway, New Jersey 08854, USA
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26
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Kaptein M. Personalization in biomedical-informatics: Methodological considerations and recommendations. J Biomed Inform 2019; 90:103088. [DOI: 10.1016/j.jbi.2018.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/19/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
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