arXiv subjects

Mark van der Laan

Publications and source records attributed to Mark van der Laan.

At least 55 records · Page 3Linked to original sources

arXiv2024

The Causal Roadmap and Simulations to Improve the Rigor and Reproducibility of Real-Data Applications

The Causal Roadmap outlines a systematic approach to asking and answering questions of cause-and-effect: define the quantity of interest, evaluate needed assumptions, conduct statistical estimation, and carefully interpret results. To protect research integrity, it is essential that the algorithm for statistical estimation and inference be pre-specified prior to conducting any effectiveness analyses. However, it is often unclear which algorithm will perform optimally for the real-data application. Instead, there is a temptation to simply implement one's favorite algorithm -- recycling prior code or relying on the default settings of a computing package. Here, we call for the use of simulations that realistically reflect the application, including key characteristics such as strong confounding and dependent or missing outcomes, to objectively compare candidate estimators and facilitate full specification of the Statistical Analysis Plan. Such simulations are informed by the Causal Roadmap and conducted after data collection but prior to effect estimation. We illustrate with two worked examples. First, in an observational longitudinal study, outcome-blind simulations are used to inform nuisance parameter estimation and variance estimation for longitudinal targeted minimum loss-based estimation (TMLE). Second, in a cluster randomized trial with missing outcomes, treatment-blind simulations are used to examine Type-I error control in Two-Stage TMLE. In both examples, realistic simulations empower us to pre-specify an estimation approach that is expected to have strong finite sample performance and also yield quality-controlled computing code for the actual analysis. Together, this process helps to improve the rigor and reproducibility of our research.

stat.ME↗

arXiv2024

A nonparametric framework for treatment effect modifier discovery in high dimensions

Heterogeneous treatment effects are driven by treatment effect modifiers, pre-treatment covariates that modify the effect of a treatment on an outcome. Current approaches for uncovering these variables are limited to low-dimensional data, data with weakly correlated covariates, or data generated according to parametric processes. We resolve these issues by developing a framework for defining model-agnostic treatment effect modifier variable importance parameters applicable to high-dimensional data with arbitrary correlation structure, deriving one-step, estimating equation and targeted maximum likelihood estimators of these parameters, and establishing these estimators' asymptotic properties. This framework is showcased by defining variable importance parameters for data-generating processes with continuous, binary, and time-to-event outcomes with binary treatments, and deriving accompanying multiply-robust and asymptotically linear estimators. Simulation experiments demonstrate that these estimators' asymptotic guarantees are approximately achieved in realistic sample sizes for observational and randomized studies alike. This framework is applied to gene expression data collected for a clinical trial assessing the effect of a monoclonal antibody therapy on disease-free survival in breast cancer patients. Genes predicted to have the greatest potential for treatment effect modification have previously been linked to breast cancer. An open-source R package implementing this methodology, unihtee, is made available on GitHub at https://github.com/insightsengineering/unihtee.

stat.ME↗

arXiv2023

Lassoed Tree Boosting

Gradient boosting performs exceptionally in most prediction problems and scales well to large datasets. In this paper we prove that a ``lassoed'' gradient boosted tree algorithm with early stopping achieves faster than $n^{-1/4}$ L2 convergence in the large nonparametric space of cadlag functions of bounded sectional variation. This rate is remarkable because it does not depend on the dimension, sparsity, or smoothness. We use simulation and real data to confirm our theory and demonstrate empirical performance and scalability on par with standard boosting. Our convergence proofs are based on a novel, general theorem on early stopping with empirical loss minimizers of nested Donsker classes.

stat.ML↗

arXiv2023

Applying the causal roadmap to longitudinal national Danish registry data: a case study of second-line diabetes medication and dementia

The causal roadmap is a formal framework for causal and statistical inference that supports clear specification of the causal question, interpretable and transparent statement of required causal assumptions, robust inference, and optimal precision. The roadmap is thus particularly well-suited to evaluating longitudinal causal effects using large scale registries; however, application of the roadmap to registry data also introduces particular challenges. In this paper we provide a detailed case study of the longitudinal causal roadmap applied to the Danish National Registry to evaluate the comparative effectiveness of second-line diabetes drugs on dementia risk. Specifically, we evaluate the difference in counterfactual five-year cumulative risk of dementia if a target population of adults with type 2 diabetes had initiated and remained on GLP-1 receptor agonists (a second-line diabetes drug) compared to a range of active comparator protocols. Time-dependent confounding is accounted for through use of the iterated conditional expectation representation of the longitudinal g-formula as a statistical estimand. Statistical estimation uses longitudinal targeted maximum likelihood, incorporating machine learning. We provide practical guidance on the implementation of the roadmap using registry data, and highlight how rare exposures and outcomes over long-term follow up can raise challenges for flexible and robust estimators, even in the context of the large sample sizes provided by the registry. We demonstrate how simulations can be used to help address these challenges by supporting careful estimator pre-specification. We find a protective effect of GLP-1RAs compared to some but not all other second-line treatments.

stat.AP↗

arXiv2023

Conformal Meta-learners for Predictive Inference of Individual Treatment Effects

We investigate the problem of machine learning-based (ML) predictive inference on individual treatment effects (ITEs). Previous work has focused primarily on developing ML-based meta-learners that can provide point estimates of the conditional average treatment effect (CATE); these are model-agnostic approaches for combining intermediate nuisance estimates to produce estimates of CATE. In this paper, we develop conformal meta-learners, a general framework for issuing predictive intervals for ITEs by applying the standard conformal prediction (CP) procedure on top of CATE meta-learners. We focus on a broad class of meta-learners based on two-stage pseudo-outcome regression and develop a stochastic ordering framework to study their validity. We show that inference with conformal meta-learners is marginally valid if their (pseudo outcome) conformity scores stochastically dominate oracle conformity scores evaluated on the unobserved ITEs. Additionally, we prove that commonly used CATE meta-learners, such as the doubly-robust learner, satisfy a model- and distribution-free stochastic (or convex) dominance condition, making their conformal inferences valid for practically-relevant levels of target coverage. Whereas existing procedures conduct inference on nuisance parameters (i.e., potential outcomes) via weighted CP, conformal meta-learners enable direct inference on the target parameter (ITE). Numerical experiments show that conformal meta-learners provide valid intervals with competitive efficiency while retaining the favorable point estimation properties of CATE meta-learners.

cs.LG↗

arXiv2023

Unveiling Causal Mediation Pathways in High-Dimensional Mixed Exposures: A Data-Adaptive Target Parameter Strategy

Mediation analysis in causal inference typically concentrates on one binary exposure, using deterministic interventions to split the average treatment effect into direct and indirect effects through a single mediator. Yet, real-world exposure scenarios often involve multiple continuous exposures impacting health outcomes through varied mediation pathways, which remain unknown a priori. Addressing this complexity, we introduce NOVAPathways, a methodological framework that identifies exposure-mediation pathways and yields unbiased estimates of direct and indirect effects when intervening on these pathways. By pairing data-adaptive target parameters with stochastic interventions, we offer a semi-parametric approach for estimating causal effects in the context of high-dimensional, continuous, binary, and categorical exposures and mediators. In our proposed cross-validation procedure, we apply sequential semi-parametric regressions to a parameter-generating fold of the data, discovering exposure-mediation pathways. We then use stochastic interventions on these pathways in an estimation fold of the data to construct efficient estimators of natural direct and indirect effects using flexible machine learning techniques. Our estimator proves to be asymptotically linear under conditions necessitating n to the negative quarter consistency of nuisance function estimation. Simulation studies demonstrate the square root n consistency of our estimator when the exposure is quantized, whereas for truly continuous data, approximations in numerical integration prevent square root n consistency. Our NOVAPathways framework, part of the open-source SuperNOVA package in R, makes our proposed methodology for high-dimensional mediation analysis available to researchers, paving the way for the application of modified exposure policies which can delivery more informative statistical results for public policy.

stat.ME↗

arXiv2023

A Causal Roadmap for Hybrid Randomized and Real-World Data Designs: Case Study of Semaglutide and Cardiovascular Outcomes

Introduction: Increasing interest in real-world evidence has fueled the development of study designs incorporating real-world data (RWD). Using the Causal Roadmap, we specify three designs to evaluate the difference in risk of major adverse cardiovascular events (MACE) with oral semaglutide versus standard-of-care: 1) the actual sequence of non-inferiority and superiority randomized controlled trials (RCTs), 2) a single RCT, and 3) a hybrid randomized-external data study. Methods: The hybrid design considers integration of the PIONEER 6 RCT with RWD controls using the experiment-selector cross-validated targeted maximum likelihood estimator. We evaluate 95% confidence interval coverage, power, and average patient-time during which participants would be precluded from receiving a glucagon-like peptide-1 receptor agonist (GLP1-RA) for each design using simulations. Finally, we estimate the effect of oral semaglutide on MACE for the hybrid PIONEER 6-RWD analysis. Results: In simulations, Designs 1 and 2 performed similarly. The tradeoff between decreased coverage and patient-time without the possibility of a GLP1-RA for Designs 1 and 3 depended on the simulated bias. In real data analysis using Design 3, external controls were integrated in 84% of cross-validation folds, resulting in an estimated risk difference of -1.53%-points (95% CI -2.75%-points to -0.30%-points). Conclusions: The Causal Roadmap helps investigators to minimize potential bias in studies using RWD and to quantify tradeoffs between study designs. The simulation results help to interpret the level of evidence provided by the real data analysis in support of the superiority of oral semaglutide versus standard-of-care for cardiovascular risk reduction.

stat.AP↗

arXiv2023

A Causal Roadmap for Generating High-Quality Real-World Evidence

Increasing emphasis on the use of real-world evidence (RWE) to support clinical policy and regulatory decision-making has led to a proliferation of guidance, advice, and frameworks from regulatory agencies, academia, professional societies, and industry. A broad spectrum of studies use real-world data (RWD) to produce RWE, ranging from randomized controlled trials with outcomes assessed using RWD to fully observational studies. Yet many RWE study proposals lack sufficient detail to evaluate adequacy, and many analyses of RWD suffer from implausible assumptions, other methodological flaws, or inappropriate interpretations. The Causal Roadmap is an explicit, itemized, iterative process that guides investigators to pre-specify analytic study designs; it addresses a wide range of guidance within a single framework. By requiring transparent evaluation of causal assumptions and facilitating objective comparisons of design and analysis choices based on pre-specified criteria, the Roadmap can help investigators to evaluate the quality of evidence that a given study is likely to produce, specify a study to generate high-quality RWE, and communicate effectively with regulatory agencies and other stakeholders. This paper aims to disseminate and extend the Causal Roadmap framework for use by clinical and translational researchers, with companion papers demonstrating application of the Causal Roadmap for specific use cases.

stat.ME↗

arXiv2023

Targeted Maximum Likelihood Based Estimation for Longitudinal Mediation Analysis

Causal mediation analysis with random interventions has become an area of significant interest for understanding time-varying effects with longitudinal and survival outcomes. To tackle causal and statistical challenges due to the complex longitudinal data structure with time-varying confounders, competing risks, and informative censoring, there exists a general desire to combine machine learning techniques and semiparametric theory. In this manuscript, we focus on targeted maximum likelihood estimation (TMLE) of longitudinal natural direct and indirect effects defined with random interventions. The proposed estimators are multiply robust, locally efficient, and directly estimate and update the conditional densities that factorize data likelihoods. We utilize the highly adaptive lasso (HAL) and projection representations to derive new estimators (HAL-EIC) of the efficient influence curves of longitudinal mediation problems and propose a fast one-step TMLE algorithm using HAL-EIC while preserving the asymptotic properties. The proposed method can be generalized for other longitudinal causal parameters that are smooth functions of data likelihoods, and thereby provides a novel and flexible statistical toolbox.

stat.ME↗

arXiv2023

Higher Order Spline Highly Adaptive Lasso Estimators of Functional Parameters: Pointwise Asymptotic Normality and Uniform Convergence Rates

We consider estimation of a functional of the data distribution based on i.i.d. observations. We assume the target function can be defined as the minimizer of the expectation of a loss function over a class of $d$-variate real valued cadlag functions that have finite sectional variation norm. For all $k=0,1,\ldots$, we define a $k$-th order smoothness class of functions as $d$-variate functions on the unit cube for which each of a sequentially defined $k$-th order Radon-Nikodym derivative w.r.t. Lebesgue measure is cadlag and of bounded variation. For a target function in this $k$-th order smoothness class we provide a representation of the target function as an infinite linear combination of tensor products of $\leq k$-th order spline basis functions indexed by a knot-point, where the lower (than $k$) order spline basis functions are used to represent the function at the $0$-edges. The $L_1$-norm of the coefficients represents the sum of the variation norms across all the $k$-th order derivatives, which is called the $k$-th order sectional variation norm of the target function. This generalizes the zero order spline representation of cadlag functions with bounded sectional variation norm to higher order smoothness classes. We use this $k$-th order spline representation of a function to define the $k$-th order spline sieve minimum loss estimator (MLE), Highly Adaptive Lasso (HAL) MLE, and Relax HAL-MLE. For first and higher order smoothness classes, in this article we analyze these three classes of estimators and establish pointwise asymptotic normality and uniform convergence at dimension free rate $n^{-k^*/(2k^*+1)}$ up till a power of $\log n$ depending on the dimension, where $k^*=k+1$, assuming appropriate undersmoothing is used in selecting the $L_1$-norm. We also establish asymptotic linearity of plug-in estimators of pathwise differentiable features of the target function.

math.ST↗

arXiv2022

Evaluating and improving real-world evidence with Targeted Learning

Purpose: The Targeted Learning roadmap provides a systematic guide for generating and evaluating real-world evidence (RWE). From a regulatory perspective, RWE arises from diverse sources such as randomized controlled trials that make use of real-world data, observational studies, and other study designs. This paper illustrates a principled approach to assessing the validity and interpretability of RWE. Methods: We applied the roadmap to a published observational study of the dose-response association between ritodrine hydrochloride and pulmonary edema among women pregnant with twins in Japan. The goal was to identify barriers to causal effect estimation beyond unmeasured confounding reported by the study's authors, and to explore potential options for overcoming the barriers that robustify results. Results: Following the roadmap raised issues that led us to formulate alternative causal questions that produced more reliable, interpretable RWE. The process revealed a lack of information in the available data to identify a causal dose-response curve. However, under explicit assumptions the effect of treatment with any amount of ritodrine versus none, albeit a less ambitious parameter, can be estimated from data. Conclusion: Before RWE can be used in support of clinical and regulatory decision-making, its quality and reliability must be systematically evaluated. The TL roadmap prescribes how to carry out a thorough, transparent, and realistic assessment of RWE. We recommend this approach be a routine part of any decision-making process.

stat.AP↗

arXiv2021

The Optimal Dynamic Treatment Rule SuperLearner: Considerations, Performance, and Application

The optimal dynamic treatment rule (ODTR) framework offers an approach for understanding which kinds of patients respond best to specific treatments -- in other words, treatment effect heterogeneity. Recently, there has been a proliferation of methods for estimating the ODTR. One such method is an extension of the SuperLearner algorithm -- an ensemble method to optimally combine candidate algorithms extensively used in prediction problems -- to ODTRs. Following the "causal roadmap," we causally and statistically define the ODTR and provide an introduction to estimating it using the ODTR SuperLearner. Additionally, we highlight practical choices when implementing the algorithm, including choice of candidate algorithms, metalearners to combine the candidates, and risk functions to select the best combination of algorithms. Using simulations, we illustrate how estimating the ODTR using this SuperLearner approach can uncover treatment effect heterogeneity more effectively than traditional approaches based on fitting a parametric regression of the outcome on the treatment, covariates and treatment-covariate interactions. We investigate the implications of choices in implementing an ODTR SuperLearner at various sample sizes. Our results show the advantages of: (1) including a combination of both flexible machine learning algorithms and simple parametric estimators in the library of candidate algorithms; (2) using an ensemble metalearner to combine candidates rather than selecting only the best-performing candidate; (3) using the mean outcome under the rule as a risk function. Finally, we apply the ODTR SuperLearner to the "Interventions" study, an ongoing randomized controlled trial, to identify which justice-involved adults with mental illness benefit most from cognitive behavioral therapy (CBT) to reduce criminal re-offending.

stat.AP↗

arXiv2021

Performance and Application of Estimators for the Value of an Optimal Dynamic Treatment Rule

Given an (optimal) dynamic treatment rule, it may be of interest to evaluate that rule -- that is, to ask the causal question: what is the expected outcome had every subject received treatment according to that rule? In this paper, we study the performance of estimators that approximate the true value of: 1) an $a$ $priori$ known dynamic treatment rule 2) the true, unknown optimal dynamic treatment rule (ODTR); 3) an estimated ODTR, a so-called "data-adaptive parameter," whose true value depends on the sample. Using simulations of point-treatment data, we specifically investigate: 1) the impact of increasingly data-adaptive estimation of nuisance parameters and/or of the ODTR on performance; 2) the potential for improved efficiency and bias reduction through the use of semiparametric efficient estimators; and, 3) the importance of sample splitting based on CV-TMLE for accurate inference. In the simulations considered, there was very little cost and many benefits to using the cross-validated targeted maximum likelihood estimator (CV-TMLE) to estimate the value of the true and estimated ODTR; importantly, and in contrast to non cross-validated estimators, the performance of CV-TMLE was maintained even when highly data-adaptive algorithms were used to estimate both nuisance parameters and the ODTR. In addition, we apply these estimators for the value of the rule to the "Interventions" Study, an ongoing randomized controlled trial, to identify whether assigning cognitive behavioral therapy (CBT) to criminal justice-involved adults with mental illness using an ODTR significantly reduces the probability of recidivism, compared to assigning CBT in a non-individualized way.

stat.ME↗

arXiv2021

Two-Stage TMLE to Reduce Bias and Improve Efficiency in Cluster Randomized Trials

Cluster randomized trials (CRTs) randomly assign an intervention to groups of individuals (e.g., clinics or communities) and measure outcomes on individuals in those groups. While offering many advantages, this experimental design introduces challenges that are only partially addressed by existing analytic approaches. First, outcomes are often missing for some individuals within clusters. Failing to appropriately adjust for differential outcome measurement can result in biased estimates and inference. Second, CRTs often randomize limited numbers of clusters, resulting in chance imbalances on baseline outcome predictors between arms. Failing to adaptively adjust for these imbalances and other predictive covariates can result in efficiency losses. To address these methodological gaps, we propose and evaluate a novel two-stage targeted minimum loss-based estimator (TMLE) to adjust for baseline covariates in a manner that optimizes precision, after controlling for baseline and post-baseline causes of missing outcomes. Finite sample simulations illustrate that our approach can nearly eliminate bias due to differential outcome measurement, while existing CRT estimators yield misleading results and inferences. Application to real data from the SEARCH community randomized trial demonstrates the gains in efficiency afforded through adaptive adjustment for baseline covariates, after controlling for missingness on individual-level outcomes.

stat.ME↗

arXiv2021

Higher Order Targeted Maximum Likelihood Estimation

Asymptotic efficiency of targeted maximum likelihood estimators (TMLE) of target features of the data distribution relies on a a second order remainder being asymptotically negligible. In previous work we proposed a nonparametric MLE termed Highly Adaptive Lasso (HAL) which parametrizes the relevant functional of the data distribution in terms of a multivariate real valued cadlag function that is assumed to have finite variation norm. We showed that the HAL-MLE converges in Kullback-Leibler dissimilarity at a rate n-1/3 up till logn factors. Therefore, by using HAL as initial density estimator in the TMLE, the resulting HAL-TMLE is an asymptotically efficient estimator only assuming that the relevant nuisance functions of the data density are cadlag and have finite variation norm. However, in finite samples, the second order remainder can dominate the sampling distribution so that inference based on asymptotic normality would be anti-conservative. In this article we propose a new higher order TMLE, generalizing the regular first order TMLE. We prove that it satisfies an exact linear expansion, in terms of efficient influence functions of sequentially defined higher order fluctuations of the target parameter, with a remainder that is a k+1th order remainder. As a consequence, this k-th order TMLE allows statistical inference only relying on the k+1th order remainder being negligible. We also provide a rationale for the higher order TMLE that it will be superior to the first order TMLE by (iteratively) locally minimizing the exact finite sample remainder of the first order TMLE. The second order TMLE is demonstrated for nonparametric estimation of the integrated squared density and for the treatment specific mean outcome. We also provide an initial simulation study for the second order TMLE of the treatment specific mean confirming the theoretical analysis.

math.ST↗

arXiv2021

Estimation of time-specific intervention effects on continuously distributed time-to-event outcomes by targeted maximum likelihood estimation

Targeted maximum likelihood estimation is a general methodology combining flexible ensemble learning and semiparametric efficiency theory in a two-step procedure for estimation of causal parameters. Proposed targeted maximum likelihood procedures for survival and competing risks analysis have so far focused on events taken values in discrete time. We here present a targeted maximum likelihood estimation procedure for event times that take values in R+. We focuson the estimation of intervention-specific mean outcomes with stochastic interventions on a time-fixed treatment. For data-adaptive estimation of nuisance parameters, we propose a new flexible highly adaptive lasso estimation method for continuous-time intensities that can be implemented with L1-penalized Poisson regression. In a simulation study the targeted maximum likelihood estimator based on the highly adaptive lasso estimator proves to be unbiased and achieve proper coverage in agreement with the asymptotic theory and further displays efficiency improvements relative to a Kaplan-Meier approach.

stat.ME↗

arXiv2021

Risk Minimization from Adaptively Collected Data: Guarantees for Supervised and Policy Learning

Empirical risk minimization (ERM) is the workhorse of machine learning, whether for classification and regression or for off-policy policy learning, but its model-agnostic guarantees can fail when we use adaptively collected data, such as the result of running a contextual bandit algorithm. We study a generic importance sampling weighted ERM algorithm for using adaptively collected data to minimize the average of a loss function over a hypothesis class and provide first-of-their-kind generalization guarantees and fast convergence rates. Our results are based on a new maximal inequality that carefully leverages the importance sampling structure to obtain rates with the right dependence on the exploration rate in the data. For regression, we provide fast rates that leverage the strong convexity of squared-error loss. For policy learning, we provide rate-optimal regret guarantees that close an open gap in the existing literature whenever exploration decays to zero, as is the case for bandit-collected data. An empirical investigation validates our theory.

stat.ML↗

arXiv2021

Post-Contextual-Bandit Inference

Contextual bandit algorithms are increasingly replacing non-adaptive A/B tests in e-commerce, healthcare, and policymaking because they can both improve outcomes for study participants and increase the chance of identifying good or even best policies. To support credible inference on novel interventions at the end of the study, nonetheless, we still want to construct valid confidence intervals on average treatment effects, subgroup effects, or value of new policies. The adaptive nature of the data collected by contextual bandit algorithms, however, makes this difficult: standard estimators are no longer asymptotically normally distributed and classic confidence intervals fail to provide correct coverage. While this has been addressed in non-contextual settings by using stabilized estimators, the contextual setting poses unique challenges that we tackle for the first time in this paper. We propose the Contextual Adaptive Doubly Robust (CADR) estimator, the first estimator for policy value that is asymptotically normal under contextual adaptive data collection. The main technical challenge in constructing CADR is designing adaptive and consistent conditional standard deviation estimators for stabilization. Extensive numerical experiments using 57 OpenML datasets demonstrate that confidence intervals based on CADR uniquely provide correct coverage.

stat.ML↗