arXiv subjects

Jon A. Steingrimsson

Publications and source records attributed to Jon A. Steingrimsson.

At least 19 recordsLinked to original sources

arXiv2025

Estimating and evaluating counterfactual prediction models

Counterfactual prediction methods are required when a model will be deployed in a setting where treatment policies differ from the setting where the model was developed, or when a model provides predictions under hypothetical interventions to support decision-making. However, estimating and evaluating counterfactual prediction models is challenging because, unlike traditional (factual) prediction, one does not observe the potential outcomes for all individuals under all treatment strategies of interest. Here, we discuss how to estimate a counterfactual prediction model, how to assess the model's performance, and how to perform model and tuning parameter selection. We provide identification and estimation results for counterfactual prediction models and for multiple measures of counterfactual model performance, including loss-based measures, the area under the receiver operating characteristic curve, and the calibration curve. Importantly, our results allow valid estimates of model performance under counterfactual intervention even if the candidate prediction model is misspecified, permitting a wider array of use cases. We illustrate these methods using simulation and apply them to the task of developing a statin-naive risk prediction model for cardiovascular disease.

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arXiv2024

A Bayesian Framework for Causal Analysis of Recurrent Events with Timing Misalignment

Observational studies of recurrent event rates are common in biomedical statistics. Broadly, the goal is to estimate differences in event rates under two treatments within a defined target population over a specified followup window. Estimation with observational data is challenging because, while membership in the target population is defined in terms of eligibility criteria, treatment is rarely observed exactly at the time of eligibility. Ad-hoc solutions to this timing misalignment can induce bias by incorrectly attributing prior event counts and person-time to treatment. Even if eligibility and treatment are aligned, a terminal event process (e.g. death) often stops the recurrent event process of interest. In practice, both processes can be censored so that events are not observed over the entire followup window. Our approach addresses misalignment by casting it as a time-varying treatment problem: some patients are on treatment at eligibility while others are off treatment but may switch to treatment at a specified time - if they survive long enough. We define and identify an average causal effect estimand under right-censoring. Estimation is done using a g-computation procedure with a joint semiparametric Bayesian model for the death and recurrent event processes. We apply the method to contrast hospitalization rates among patients with different opioid treatments using Medicare insurance claims data.

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arXiv2024

Interpretable meta-analysis of model or marker performance

Conventional meta analysis of model performance conducted using datasources from different underlying populations often result in estimates that cannot be interpreted in the context of a well defined target population. In this manuscript we develop methods for meta-analysis of several measures of model performance that are interpretable in the context of a well defined target population when the populations underlying the datasources used in the meta analysis are heterogeneous. This includes developing identifiablity conditions, inverse-weighting, outcome model, and doubly robust estimator. We illustrate the methods using simulations and data from two large lung cancer screening trials.

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arXiv2024

Cluster randomized trials designed to support generalizable inferences

Background: When planning a cluster randomized trial, evaluators often have access to an enumerated cohort representing the target population of clusters. Practicalities of conducting the trial, such as the need to oversample clusters with certain characteristics to improve trial economy or to support inference about subgroups of clusters, may preclude simple random sampling from the cohort into the trial, and thus interfere with the goal of producing generalizable inferences about the target population. Methods: We describe a nested trial design where the randomized clusters are embedded within a cohort of trial-eligible clusters from the target population and where clusters are selected for inclusion in the trial with known sampling probabilities that may depend on cluster characteristics (e.g., allowing clusters to be chosen to facilitate trial conduct or to examine hypotheses related to their characteristics). We develop and evaluate methods for analyzing data from this design to generalize causal inferences to the target population underlying the cohort. Results: We present identification and estimation results for the expectation of the average potential outcome and for the average treatment effect, in the entire target population of clusters and in its non-randomized subset. In simulation studies we show that all the estimators have low bias but markedly different precision. Conclusions: Cluster randomized trials where clusters are selected for inclusion with known sampling probabilities that depend on cluster characteristics, combined with efficient estimation methods, can precisely quantify treatment effects in the target population, while addressing objectives of trial conduct that require oversampling clusters on the basis of their characteristics.

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arXiv2023

Sensitivity analysis for studies transporting prediction models

We consider the estimation of measures of model performance in a target population when covariate and outcome data are available on a sample from some source population and covariate data, but not outcome data, are available on a simple random sample from the target population. When outcome data are not available from the target population, identification of measures of model performance is possible under an untestable assumption that the outcome and population (source or target population) are independent conditional on covariates. In practice, this assumption is uncertain and, in some cases, controversial. Therefore, sensitivity analysis may be useful for examining the impact of assumption violations on inferences about model performance. Here, we propose an exponential tilt sensitivity analysis model and develop statistical methods to determine how sensitive measures of model performance are to violations of the assumption of conditional independence between outcome and population. We provide identification results and estimators for the risk in the target population, examine the large-sample properties of the estimators, and apply the estimators to data on individuals with stable ischemic heart disease.

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arXiv2023

Generalizability analyses with a partially nested trial design: the Necrotizing Enterocolitis Surgery Trial

We discuss generalizability analyses under a partially nested trial design, where part of the trial is nested within a cohort of trial-eligible individuals, while the rest of the trial is not nested. This design arises, for example, when only some centers participating in a trial are able to collect data on non-randomized individuals, or when data on non-randomized individuals cannot be collected for the full duration of the trial. Our work is motivated by the Necrotizing Enterocolitis Surgery Trial (NEST) that compared initial laparotomy versus peritoneal drain for infants with necrotizing enterocolitis or spontaneous intestinal perforation. During the first phase of the study, data were collected from randomized individuals as well as consenting non-randomized individuals; during the second phase of the study, however, data were only collected from randomized individuals, resulting in a partially nested trial design. We propose methods for generalizability analyses with partially nested trial designs. We describe identification conditions and propose estimators for causal estimands in the target population of all trial-eligible individuals, both randomized and non-randomized, in the part of the data where the trial is nested, while using trial information spanning both parts. We evaluate the estimators in a simulation study.

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arXiv2022

Robust Estimation of Loss-Based Measures of Model Performance under Covariate Shift

We present methods for estimating loss-based measures of the performance of a prediction model in a target population that differs from the source population in which the model was developed, in settings where outcome and covariate data are available from the source population but only covariate data are available on a simple random sample from the target population. Prior work adjusting for differences between the two populations has used various weighting estimators with inverse odds or density ratio weights. Here, we develop more robust estimators for the target population risk (expected loss) that can be used with data-adaptive (e.g., machine learning-based) estimation of nuisance parameters. We examine the large-sample properties of the estimators and evaluate finite sample performance in simulations. Last, we apply the methods to data from lung cancer screening using nationally representative data from the National Health and Nutrition Examination Survey (NHANES) and extend our methods to account for the complex survey design of the NHANES.

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arXiv2022

Tree-based Subgroup Discovery In Electronic Health Records: Heterogeneity of Treatment Effects for DTG-containing Therapies

The rich longitudinal individual level data available from electronic health records (EHRs) can be used to examine treatment effect heterogeneity. However, estimating treatment effects using EHR data poses several challenges, including time-varying confounding, repeated and temporally non-aligned measurements of covariates, treatment assignments and outcomes, and loss-to-follow-up due to dropout. Here, we develop the Subgroup Discovery for Longitudinal Data (SDLD) algorithm, a tree-based algorithm for discovering subgroups with heterogeneous treatment effects using longitudinal data by combining the generalized interaction tree algorithm, a general data-driven method for subgroup discovery, with longitudinal targeted maximum likelihood estimation. We apply the algorithm to EHR data to discover subgroups of people living with human immunodeficiency virus (HIV) who are at higher risk of weight gain when receiving dolutegravir-containing antiretroviral therapies (ARTs) versus when receiving non dolutegravir-containing ARTs.

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arXiv2022

Global sensitivity analysis for studies extending inferences from a randomized trial to a target population

When individuals participating in a randomized trial differ with respect to the distribution of effect modifiers compared compared with the target population where the trial results will be used, treatment effect estimates from the trial may not directly apply to target population. Methods for extending -- generalizing or transporting -- causal inferences from the trial to the target population rely on conditional exchangeability assumptions between randomized and non-randomized individuals. The validity of these assumptions is often uncertain or controversial and investigators need to examine how violation of the assumptions would impact study conclusions. We describe methods for global sensitivity analysis that directly parameterize violations of the assumptions in terms of potential (counterfactual) outcome distributions. Our approach does not require detailed knowledge about the distribution of specific unmeasured effect modifiers or their relationship with the observed variables. We illustrate the methods using data from a trial nested within a cohort of trial-eligible individuals to compare coronary artery surgery plus medical therapy versus medical therapy alone for stable ischemic heart disease.

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arXiv2022

Systematically Missing Data in Causally Interpretable Meta-Analysis

Causally interpretable meta-analysis combines information from a collection of randomized controlled trials to estimate treatment effects in a target population in which experimentation may not be possible but covariate information can be collected from a simple random sample. In such analyses, a key practical challenge is systematically missing data when some baseline covariates are not collected in all trials. Here, we provide identification results for potential (counterfactual) outcome means and average treatment effects in the target population when covariate data are systematically missing from some of the trials in the meta-analysis. We propose three estimators for the average treatment effect in the target population, examine their asymptotic properties, and show that they have good finite-sample performance in simulation studies. We use the estimators to analyze data from two large lung cancer screening trials and target population data from the National Health and Nutrition Examination Survey (NHANES). To accommodate the complex survey design of the NHANES, we modify the methods to incorporate survey sampling weights and allow for clustering.

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arXiv2022

Extending inferences from a cluster randomized trial to a target population

We describe methods that extend (generalize or transport) causal inferences from cluster randomized trials to a target population of clusters, under a general nonparametric model that allows for arbitrary within-cluster dependence. We propose doubly robust estimators of potential outcome means in the target population that exploit individual-level data on covariates and outcomes to improve efficiency and are appropriate for use with machine learning methods. We illustrate the methods using a cluster randomized trial of influenza vaccination strategies conducted in 818 nursing homes nested in a cohort of 4,475 trial-eligible Medicare-certified nursing homes.

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arXiv2022

Randomized trials and their observational emulations: a framework for benchmarking and joint analysis

A randomized trial and an analysis of observational data designed to emulate the trial sample observations separately, but have the same eligibility criteria, collect information on some shared baseline covariates, and compare the effects of the same treatments on the same outcomes. Treatment effect estimates from the trial and its emulation can be compared to benchmark observational analysis methods. In a simplified setting with complete adherence to the assigned treatment strategy and no loss-to-follow-up, we show that benchmarking relies on an exchangeability condition between the populations underlying the trial and its emulation, to account for differences in the distribution of covariates between them. When this exchangeability condition holds, and the usual conditions needed for the estimates from the trial and its emulation to have a causal interpretation also hold, we derive restrictions on the law of the observed data. When the data are compatible with the restrictions, joint analysis of the trial and its emulation is possible. When the data are incompatible with the restrictions, a discrepancy between (1) estimates based on extending inferences from the trial to the population underlying the emulation and (2) the emulation itself may reflect either inability to benchmark (e.g., due to selective participation into the trial) or a failure of the emulation (e.g., due to unmeasured confounding), but we cannot use the data to determine which is the case. Our analysis reveals how benchmarking attempts combine causal assumptions, data analysis methods, and substantive knowledge to examine the validity of observational analysis methods.

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arXiv2022

Learning about treatment effects in a new target population under transportability assumptions for relative effect measures

Epidemiologists and applied statisticians often believe that relative effect measures conditional on covariates, such as risk ratios and mean ratios, are ``transportable'' across populations. Here, we examine the identification of causal effects in a target population using an assumption that conditional relative effect measures (e.g., conditional risk ratios or mean ratios) are transportable from a trial to the target population. We show that transportability for relative effect measures is largely incompatible with transportability for difference effect measures, unless the treatment has no effect on average or one is willing to make even stronger transportability assumptions, which imply the transportability of both relative and difference effect measures. We then describe how marginal causal estimands in a target population can be identified under the assumption of transportability of relative effect measures, when we are interested in the effectiveness of a new experimental treatment in a target population where the only treatment in use is the control treatment evaluated in the trial. We extend these results to consider cases where the control treatment evaluated in the trial is only one of the treatments in use in the target population, under an additional partial exchangeability assumption in the target population (i.e., a partial assumption of no unmeasured confounding in the target population). We also develop identification results that allow for the covariates needed for transportability of relative effect measures to be only a small subset of the covariates needed to control confounding in the target population. Last, we propose estimators that can be easily implemented in standard statistical software.

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arXiv2022

Efficient and robust methods for causally interpretable meta-analysis: transporting inferences from multiple randomized trials to a target population

We present methods for causally interpretable meta-analyses that combine information from multiple randomized trials to estimate potential (counterfactual) outcome means and average treatment effects in a target population. We consider identifiability conditions, derive implications of the conditions for the law of the observed data, and obtain identification results for transporting causal inferences from a collection of independent randomized trials to a new target population in which experimental data may not be available. We propose an estimator for the potential (counterfactual) outcome mean in the target population under each treatment studied in the trials. The estimator uses covariate, treatment, and outcome data from the collection of trials, but only covariate data from the target population sample. We show that it is doubly robust, in the sense that it is consistent and asymptotically normal when at least one of the models it relies on is correctly specified. We study the finite sample properties of the estimator in simulation studies and demonstrate its implementation using data from a multi-center randomized trial.

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arXiv2021

Sample size calculations for n-of-1 trials

N-of-1 trials, single participant trials in which multiple treatments are sequentially randomized over the study period, can give direct estimates of individual-specific treatment effects. Combining n-of-1 trials gives extra information for estimating the population average treatment effect compared with randomized controlled trials and increases precision for individual-specific treatment effect estimates. In this paper, we present a procedure for designing n-of-1 trials. We formally define the design components for determining the sample size of a series of n-of-1 trials, present models for analyzing these trials and use them to derive the sample size formula for estimating the population average treatment effect and the standard error of the individual-specific treatment effect estimates. We recommend first finding the possible designs that will satisfy the power requirement for estimating the population average treatment effect and then, if of interest, finalizing the design to also satisfy the standard error requirements for the individual-specific treatment effect estimates. The procedure is implemented and illustrated in the paper and through a Shiny app.

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arXiv2021

Estimating subgroup effects in generalizability and transportability analyses

Methods for extending -- generalizing or transporting -- inferences from a randomized trial to a target population involve conditioning on a large set of covariates that is sufficient for rendering the randomized and non-randomized groups exchangeable. Yet, decision-makers are often interested in examining treatment effects in subgroups of the target population defined in terms of only a few discrete covariates. Here, we propose methods for estimating subgroup-specific potential outcome means and average treatment effects in generalizability and transportability analyses, using outcome model-based (g-formula), weighting, and augmented weighting estimators. We consider estimating subgroup-specific average treatment effects in the target population and its non-randomized subset, and provide methods that are appropriate both for nested and non-nested trial designs. As an illustration, we apply the methods to data from the Coronary Artery Surgery Study to compare the effect of surgery plus medical therapy versus medical therapy alone for chronic coronary artery disease in subgroups defined by history of myocardial infarction.

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arXiv2021

Center-specific causal inference with multicenter trials: reinterpreting trial evidence in the context of each participating center

In multicenter randomized trials, when effect modifiers have a different distribution across centers, comparisons between treatment groups that average over centers may not apply to any of the populations underlying the individual centers. Here, we describe methods for reinterpreting the evidence produced by a multicenter trial in the context of the population underlying each center. We describe how to identify center-specific effects under identifiability conditions that are largely supported by the study design and when associations between center membership and the outcome may be present, given baseline covariates and treatment ("center-outcome associations"). We then consider an additional condition of no center-outcome associations given baseline covariates and treatment. We show that this condition can be assessed using the trial data; when it holds, center-specific treatment effects can be estimated using analyses that completely pool information across centers. We propose methods for estimating center-specific average treatment effects, when center-outcome associations may be present and when they are absent, and describe approaches for assessing whether center-specific treatment effects are homogeneous. We evaluate the performance of the methods in a simulation study and illustrate their implementation using data from the Hepatitis C Antiviral Long-Term Treatment Against Cirrhosis trial.

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arXiv2021

Transporting a prediction model for use in a new target population

We consider methods for transporting a prediction model and assessing its performance for use in a new target population, when outcome and covariate information for model development is available from a simple random sample from the source population, but only covariate information is available on a simple random sample from the target population. We discuss how to tailor the prediction model for use in the target population, how to assess model performance in the target population (e.g., by estimating the target population mean squared error), and how to perform model and tuning parameter selection in the context of the target population. We provide identifiability results for the target population mean squared error of a potentially misspecified prediction model under a sampling design where the source study and the target population samples are obtained separately. We also introduce the concept of prediction error modifiers that can be used to reason about the need for tailoring measures of model performance to the target population and provide an illustration of the methods using simulated data.

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