Model-Based Recursive Partitioning for Subgroup Analyses

Abstract The identification of patient subgroups with differential treatment effects is the first step towards individualised treatments. A current draft guideline by the EMA discusses potentials and problems in subgroup analyses and formulated challenges to the development of appropriate statistical procedures for the data-driven identification of patient subgroups. We introduce model-based recursive partitioning as a procedure for the automated detection of patient subgroups that are identifiable by predictive factors. The method starts with a model for the overall treatment effect as defined for the primary analysis in the study protocol and uses measures for detecting parameter instabilities in this treatment effect. The procedure produces a segmented model with differential treatment parameters corresponding to each patient subgroup. The subgroups are linked to predictive factors by means of a decision tree. The method is applied to the search for subgroups of patients suffering from amyotrophic lateral sclerosis that differ with respect to their Riluzole treatment effect, the only currently approved drug for this disease.

[1]  M. Cudkowicz,et al.  The PRO-ACT database , 2014, Neurology.

[2]  K. Hornik,et al.  Generalized M‐fluctuation tests for parameter instability , 2007 .

[3]  J. M. Taylor,et al.  Subgroup identification from randomized clinical trial data , 2011, Statistics in medicine.

[4]  Antonio Ciampi,et al.  Tree-structured subgroup analysis for censored survival data: Validation of computationally inexpensive model selection criteria , 2005, Stat. Comput..

[5]  R Henderson,et al.  Joint modelling of longitudinal measurements and event time data. , 2000, Biostatistics.

[6]  Edward I. George,et al.  Bayesian Treed Models , 2002, Machine Learning.

[7]  Alberto Maria Segre,et al.  Programs for Machine Learning , 1994 .

[8]  João Gama,et al.  Functional Trees , 2001, Machine Learning.

[9]  W. Loh,et al.  REGRESSION TREES WITH UNBIASED VARIABLE SELECTION AND INTERACTION DETECTION , 2002 .

[10]  Achim Zeileis,et al.  A toolbox of permutation tests for structural change , 2013 .

[11]  A. Italiano,et al.  Prognostic or predictive? It's time to get back to definitions! , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[12]  S. Lagakos The challenge of subgroup analyses--reporting without distorting. , 2006, The New England journal of medicine.

[13]  Hans H. Jung,et al.  RandomForest4Life: A Random Forest for predicting ALS disease progression , 2014, Amyotrophic lateral sclerosis & frontotemporal degeneration.

[14]  P. Perron,et al.  Computation and Analysis of Multiple Structural-Change Models , 1998 .

[15]  Kurt Hornik,et al.  Implementing a Class of Permutation Tests: The coin Package , 2008 .

[16]  Hyunjoong Kim,et al.  Classification Trees With Unbiased Multiway Splits , 2001 .

[17]  Xiaogang Su,et al.  Joint Statistical Meetings- Statistical Computing Section Maximum Likelihood Regression Trees , 2022 .

[18]  B. M. Pötscher,et al.  MODEL SELECTION AND INFERENCE: FACTS AND FICTION , 2005, Econometric Theory.

[19]  K. Hornik,et al.  Unbiased Recursive Partitioning: A Conditional Inference Framework , 2006 .

[20]  H. Iyer,et al.  Unit–Treatment Interaction and Its Practical Consequences , 2000, Biometrics.

[21]  H. Chipman,et al.  Bayesian Treed Generalized Linear Models , 2003 .

[22]  Z Lou,et al.  Tree-structured prediction for censored survival data and the Cox model. , 1995, Journal of clinical epidemiology.

[23]  J. Morgan,et al.  Problems in the Analysis of Survey Data, and a Proposal , 1963 .

[24]  Nazem Atassi,et al.  Urate levels predict survival in amyotrophic lateral sclerosis: Analysis of the expanded Pooled Resource Open‐Access ALS clinical trials database , 2018, Muscle & nerve.

[25]  G. Tutz,et al.  An introduction to recursive partitioning: rationale, application, and characteristics of classification and regression trees, bagging, and random forests. , 2009, Psychological methods.

[26]  Kurt Ulm,et al.  Responder identification in clinical trials with censored data , 2006, Comput. Stat. Data Anal..

[27]  W. Loh,et al.  Improving the precision of classification trees , 2010, 1011.0608.

[28]  Torsten Hothorn TH's Data Archive , 2016 .

[29]  Johann S. Hawe,et al.  Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression , 2014, Nature Biotechnology.

[30]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[31]  E. Beghi,et al.  Prognostic factors in ALS: A critical review , 2009, Amyotrophic lateral sclerosis : official publication of the World Federation of Neurology Research Group on Motor Neuron Diseases.

[32]  W. Loh,et al.  LOTUS: An Algorithm for Building Accurate and Comprehensible Logistic Regression Trees , 2004 .

[33]  I. van Mechelen,et al.  Qualitative interaction trees: a tool to identify qualitative treatment–subgroup interactions , 2014, Statistics in medicine.

[34]  Iven Van Mechelen,et al.  A comparison of five recursive partitioning methods to find person subgroups involved in meaningful treatment–subgroup interactions , 2013, Advances in Data Analysis and Classification.

[35]  A. Chiò,et al.  Evidence of multidimensionality in the ALSFRS-R Scale: a critical appraisal on its measurement properties using Rasch analysis , 2013, Journal of Neurology, Neurosurgery & Psychiatry.

[36]  P. Holland Statistics and Causal Inference , 1985 .

[37]  Achim Zeileis,et al.  Partykit: a modular toolkit for recursive partytioning in R , 2015, J. Mach. Learn. Res..

[38]  Stanley R. Johnson,et al.  Varying Coefficient Models , 1984 .

[39]  I. Lipkovich,et al.  Subgroup identification based on differential effect search—A recursive partitioning method for establishing response to treatment in patient subpopulations , 2011, Statistics in medicine.

[40]  W. Loh,et al.  A regression tree approach to identifying subgroups with differential treatment effects , 2014, Statistics in medicine.

[41]  J. Ross Quinlan,et al.  C4.5: Programs for Machine Learning , 1992 .

[42]  K. Hornik,et al.  Model-Based Recursive Partitioning , 2008 .

[43]  Ilya Lipkovich,et al.  Strategies for Identifying Predictive Biomarkers and Subgroups with Enhanced Treatment Effect in Clinical Trials Using SIDES , 2014, Journal of biopharmaceutical statistics.

[44]  K. Hornik,et al.  A Lego System for Conditional Inference , 2006 .