arXiv subjects

Arman Oganisian

Publications and source records attributed to Arman Oganisian.

16 recordsLinked to original sources

arXiv2026

Untangling Sample and Population Level Estimands in Bayesian Causal Computation

Model-based Bayesian inference for sample and population-level causal estimands has been growing in popularity. This literature routinely emphasizes clear specification of the target estimand, however blind implementation of standard computational procedures may implicitly target estimands that differ from the one specified at the outset. This sometimes leads to unwitting conflation of sample and population-level inference. In this paper, we elucidate the differences between sample and population-level inference with respect to identification, modeling, computation, and interpretation. For example, common sample-level estimands require cross-world Bayesian modeling, whereas many (but not all) population-level estimands do not. Similarly, the former requires explicit MCMC sampling of counterfactuals from their joint posterior, whereas the latter typically only requires a posterior distribution over parameters and, perhaps, post-hoc Monte Carlo approximations. We explore these issues across four examples, including with Bayesian nonparametric models, in which ostensibly similar Bayesian computational procedures yield posterior draws of fundamentally different estimands, leading to incorrect inferences. We end with a discussion of common mistakes and factors to consider when choosing an estimand.

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arXiv2026

Stress-Testing Assumptions: A Guide to Bayesian Sensitivity Analyses in Causal Inference

While observational data are routinely used to estimate causal effects of biomedical treatments, doing so requires special methods to adjust for observed confounding. These methods invariably rely on untestable statistical and causal identification assumptions. When these assumptions do not hold, sensitivity analysis methods can be used to characterize how different violations may change our inferences. The Bayesian approach to sensitivity analyses in causal inference has unique advantages as it allows users to encode subjective beliefs about the direction and magnitude of assumption violations via prior distributions and make inferences using the updated posterior. However, uptake of these methods remains low since implementation requires substantial methodological knowledge. Moreover, while implementation with publicly available software is possible, it is not straight-forward. At the same time, there are few papers that provide practical guidance on these fronts. In this paper, we walk through four examples of Bayesian sensitivity analyses: 1) exposure misclassification, 2) unmeasured confounding, and missing not-at-random outcomes with 3) parametric and 4) nonparametric Bayesian models. We show how all of these can be done using a unified Bayesian "missing data" approach. We also cover implementation using Stan, a publicly available open-source software for fitting Bayesian models. To the best of our knowledge, this is the first paper that presents a unified approach with code, examples, and methodology in a three-pronged illustration of sensitivity analyses in Bayesian causal inference. Our goal is for the reader to walk away with implementation-level knowledge.

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arXiv2026

Bayesian Nonparametric Causal Inference for High-Dimensional Nutritional Data via Factor-Based Exposure Mapping

Diet plays a crucial role in health, and understanding the causal effects of dietary patterns is essential for informing public health policy and personalized nutrition strategies. However, causal inference in nutritional epidemiology faces several challenges: (i) high-dimensional and correlated food/nutrient intake data induce massive treatment levels; (ii) nutritional studies are interested in latent dietary patterns rather than single food items; and (iii) the goal is to estimate heterogeneous causal effects of these dietary patterns on health outcomes. We address these challenges by introducing a sophisticated exposure mapping framework that reduces the high-dimensional treatment space via factor analysis and enables the identification of dietary patterns. We also extend the Bayesian Causal Forest to accommodate three ordered levels of dietary exposure, better capturing the complex structure of nutritional data and enabling estimation of heterogeneous causal effects. We evaluate the proposed method through extensive simulations and apply it to a multi-center epidemiological study of Hispanic/Latino adults residing in the US. Using high-dimensional dietary data, we identify six dietary patterns and estimate their causal link with two key health risk factors: body mass index and fasting insulin levels. Our findings suggest that higher consumption of plant lipid-antioxidant, plant-based, animal protein, and dairy product patterns is associated with reduced risk.

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arXiv2026

A Bayesian framework for cost-effectiveness analysis with time-varying treatment decisions

Cost-effectiveness analyses (CEAs) compare the costs and health outcomes of treatment regimes to inform medical decisions. With observational claims data, CEAs must address nonrandom treatment assignment, administrative censoring, and irregularly spaced medical visits that reflect the continuous timing of care and treatment initiation. In high-risk, early-stage endometrial cancer (HR-EC), adjuvant radiation is initiated at patient-specific times following hysterectomy, causing confounding between treatment and outcomes that can evolve with post-surgical recovery and clinical course. Most existing CEA methods use point-treatment or discrete-time models. However, point-treatment approaches break down with time-varying confounding, while discrete-time models bin continuous time, expand the data into a person-period format, and can induce zero-inflation by creating many intervals with no cost-accruing events. We propose a Bayesian framework for CEAs with sequential decision-making that jointly models costs and event times in continuous time, accounts for administrative censoring, and supports dynamic treatment regimes with minimal parametric assumptions. We use Bayesian g-computation to estimate causally interpretable cost-effectiveness measures, including net monetary benefit, and to compare regimes through posterior contrasts. We evaluate the finite-sample performance of the proposed method in simulations across censoring levels and compare it against discrete-time and fully parametric alternatives. We then use SEER-Medicare data to assess the cost-effectiveness of initiating adjuvant radiation therapy within six months following hysterectomy among HR-EC patients.

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arXiv2025

Bayesian shrinkage priors for penalized synthetic control estimators in the presence of spillovers

Synthetic control (SC) methods are widely used to estimate the effects of policy interventions, especially those targeting specific geographic regions, referred to as units. These methods construct a weighted combination of untreated units, forming a "synthetic" control that approximates the counterfactual outcomes of the treated unit had the intervention not occurred. Although neighboring areas are often selected as controls due to their similarity in observed and unobserved characteristics, their proximity can lead to spillover effects, where the intervention indirectly impacts control units, potentially biasing causal estimates. To address this challenge, we introduce a Bayesian SC framework with utility-based shrinkage priors. Our approach extends traditional penalization techniques (i.e., horseshoe, spike-and-slab) by incorporating a utility function that combines covariate similarity and spatial distance. This provides a metric that guides the data-driven selection of control units based on their relevance and spillover risk, which is assumed to increase with spatial proximity. Rather than outright excluding neighboring units, the method balances bias and variance by reducing the importance of potentially contaminated controls by spillovers. We evaluate the proposed method through simulation studies at varying spillover levels and apply it to assess the impact of Philadelphia's 2017 beverage tax on the sales of sugar-sweetened and artificially sweetened beverages in mass merchandise stores.

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arXiv2025

Considerations for Estimating Causal Effects of Informatively Timed Treatments

Epidemiological studies are often concerned with estimating causal effects of a sequence of treatment decisions on survival outcomes. In many settings, treatment decisions do not occur at fixed, pre-specified followup times. Rather, timing varies across subjects in ways that may be informative of subsequent treatment decisions and potential outcomes. Awareness of the issue and its potential solutions is lacking in the literature, which motivate this work. Here, we formalize the issue of informative timing, problems associated with ignoring it, and show how g-methods can be used to analyze sequential treatments that are informatively timed. As we describe, in such settings, the waiting times between successive treatment decisions may be properly viewed as a time-varying confounders. Using synthetic examples, we illustrate how g-methods that do not adjust for these waiting times may be biased and how adjustment can be done in scenarios where patients may die or be censored in between treatments. We draw connections between adjustment and identification with discrete-time versus continuous-time models. Finally, we provide implementation guidance and examples using publicly available software. Our concluding message is that 1) considering timing is important for valid inference and 2) correcting for informative timing can be done with g-methods that adjust for waiting times between treatments as time-varying confounders.

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arXiv2025

Bayesian Sensitivity Analyses for Policy Evaluation with Difference-in-Differences under Violations of Parallel Trends

Violations of the parallel trends assumption pose significant challenges for causal inference in difference-in-differences (DiD) studies, especially in policy evaluations where pre-treatment dynamics and external shocks may bias estimates. In this work, we propose a Bayesian DiD framework to allow us to estimate the effect of policies when parallel trends is violated. To address potential deviations from the parallel trends assumption, we introduce a formal sensitivity parameter representing the extent of the violation, specify an autoregressive AR(1) prior on this term to robustly model temporal correlation, and explore a range of prior specifications - including fixed, fully Bayesian, and empirical Bayes (EB) approaches calibrated from pre-treatment data. By systematically comparing posterior treatment effect estimates across prior configurations when evaluating Philadelphia's sweetened beverage tax using Baltimore as a control, we show how Bayesian sensitivity analyses support robust and interpretable policy conclusions under violations of parallel trends.

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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

Bayesian Counterfactual Prediction Models for HIV Care Retention with Incomplete Outcome and Covariate Information

Like many chronic diseases, human immunodeficiency virus (HIV) is managed over time at regular clinic visits. At each visit, patient features are assessed, treatments are prescribed, and a subsequent visit is scheduled. There is a need for data-driven methods for both predicting retention and recommending scheduling decisions that optimize retention. Prediction models can be useful for estimating retention rates across a range of scheduling options. However, training such models with electronic health records (EHR) involves several complexities. First, formal causal inference methods are needed to adjust for observed confounding when estimating retention rates under counterfactual scheduling decisions. Second, competing events such as death preclude retention, while censoring events render retention missing. Third, inconsistent monitoring of features such as viral load and CD4 count lead to covariate missingness. This paper presents an all-in-one approach for both predicting HIV retention and optimizing scheduling while accounting for these complexities. We formulate and identify causal retention estimands in terms of potential return-time under a hypothetical scheduling decision. Flexible Bayesian approaches are used to model the observed return-time distribution while accounting for competing and censoring events and form posterior point and uncertainty estimates for these estimands. We address the urgent need for data-driven decision support in HIV care by applying our method to EHR from the Academic Model Providing Access to Healthcare (AMPATH) - a consortium of clinics that treat HIV in Western Kenya.

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arXiv2023

causalBETA: An R Package for Bayesian Semiparametric Causal Inference with Event-Time Outcomes

Observational studies are often conducted to estimate causal effects of treatments or exposures on event-time outcomes. Since treatments are not randomized in observational studies, techniques from causal inference are required to adjust for confounding. Bayesian approaches to causal estimates are desirable because they provide 1) prior smoothing provides useful regularization of causal effect estimates, 2) flexible models that are robust to misspecification, 3) full inference (i.e. both point and uncertainty estimates) for causal estimands. However, Bayesian causal inference is difficult to implement manually and there is a lack of user-friendly software, presenting a significant barrier to wide-spread use. We address this gap by developing causalBETA (Bayesian Event Time Analysis) - an open-source R package for estimating causal effects on event-time outcomes using Bayesian semiparametric models. The package provides a familiar front-end to users, with syntax identical to existing survival analysis R packages such as survival. At the same time, it back-ends to Stan - a popular platform for Bayesian modeling and high performance statistical computing - for efficient posterior computation. To improve user experience, the package is built using customized S3 class objects and methods to facilitate visualizations and summaries of results using familiar generic functions like plot() and summary(). In this paper, we provide the methodological details of the package, a demonstration using publicly-available data, and computational guidance.

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arXiv2023

Hierarchical Bayesian Bootstrap for Heterogeneous Treatment Effect Estimation

A major focus of causal inference is the estimation of heterogeneous average treatment effects (HTE) - average treatment effects within strata of another variable of interest such as levels of a biomarker, education, or age strata. Inference involves estimating a stratum-specific regression and integrating it over the distribution of confounders in that stratum - which itself must be estimated. Standard practice involves estimating these stratum-specific confounder distributions independently (e.g. via the empirical distribution or Rubin's Bayesian bootstrap), which becomes problematic for sparsely populated strata with few observed confounder vectors. In this paper, we develop a nonparametric hierarchical Bayesian bootstrap (HBB) prior over the stratum-specific confounder distributions for HTE estimation. The HBB partially pools the stratum-specific distributions, thereby allowing principled borrowing of confounder information across strata when sparsity is a concern. We show that posterior inference under the HBB can yield efficiency gains over standard marginalization approaches while avoiding strong parametric assumptions about the confounder distribution. We use our approach to estimate the adverse event risk of proton versus photon chemoradiotherapy across various cancer types.

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arXiv2022

Bayesian Semiparametric Model for Sequential Treatment Decisions with Informative Timing

We develop a Bayesian semi-parametric model for the estimating the impact of dynamic treatment rules on survival among patients diagnosed with pediatric acute myeloid leukemia (AML). The data consist of a subset of patients enrolled in the phase III AAML1031 clinical trial in which patients move through a sequence of four treatment courses. At each course, they undergo treatment that may or may not include anthracyclines (ACT). While ACT is known to be effective at treating AML, it is also cardiotoxic and can lead to early death for some patients. Our task is to estimate the potential survival probability under hypothetical dynamic ACT treatment strategies, but there are several impediments. First, since ACT was not randomized in the trial, its effect on survival is confounded over time. Second, subjects initiate the next course depending on when they recover from the previous course, making timing potentially informative of subsequent treatment and survival. Third, patients may die or drop out before ever completing the full treatment sequence. We develop a generative Bayesian semi-parametric model based on Gamma Process priors to address these complexities. At each treatment course, the model captures subjects' transition to subsequent treatment or death in continuous time under a given rule. A g-computation procedure is used to compute a posterior over potential survival probability that is adjusted for time-varying confounding. Using this approach, we conduct posterior inference for the efficacy of hypothetical treatment rules that dynamically modify ACT based on evolving cardiac function.

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arXiv2020

Bayesian Nonparametric Cost-Effectiveness Analyses: Causal Estimation and Adaptive Subgroup Discovery

Cost-effectiveness analyses (CEAs) are at the center of health economic decision making. While these analyses help policy analysts and economists determine coverage, inform policy, and guide resource allocation, they are statistically challenging for several reasons. Cost and effectiveness are correlated and follow complex joint distributions which are difficult to capture parametrically. Effectiveness (often measured as increased survival time) and accumulated cost tends to be right-censored in many applications. Moreover, CEAs are often conducted using observational data with non-random treatment assignment. Policy-relevant causal estimation therefore requires robust confounding control. Finally, current CEA methods do not address cost-effectiveness heterogeneity in a principled way - often presenting population-averaged estimates even though significant effect heterogeneity may exist. Motivated by these challenges, we develop a nonparametric Bayesian model for joint cost-survival distributions in the presence of censoring. Our approach utilizes a joint Enriched Dirichlet Process prior on the covariate effects of cost and survival time, while using a Gamma Process prior on the baseline survival time hazard. Causal CEA estimands, with policy-relevant interpretations, are identified and estimated via a Bayesian nonparametric g-computation procedure. Finally, we outline how the induced clustering of the Enriched Dirichlet Process can be used to adaptively detect presence of subgroups with different cost-effectiveness profiles. We outline an MCMC procedure for full posterior inference and evaluate frequentist properties via simulations. We use our model to assess the cost-efficacy of chemotherapy versus radiation adjuvant therapy for treating endometrial cancer in the SEER-Medicare database.

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arXiv2020

A Practical Introduction to Bayesian Estimation of Causal Effects: Parametric and Nonparametric Approaches

Substantial advances in Bayesian methods for causal inference have been developed in recent years. We provide an introduction to Bayesian inference for causal effects for practicing statisticians who have some familiarity with Bayesian models and would like an overview of what it can add to causal estimation in practical settings. In the paper, we demonstrate how priors can induce shrinkage and sparsity on parametric models and be used to perform probabilistic sensitivity analyses around causal assumptions. We provide an overview of nonparametric Bayesian estimation and survey their applications in the causal inference literature. Inference in the point-treatment and time-varying treatment settings are considered. For the latter, we explore both static and dynamic treatment regimes. Throughout, we illustrate implementation using off-the-shelf open source software. We hope the reader will walk away with implementation-level knowledge of Bayesian causal inference using both parametric and nonparametric models. All synthetic examples and code used in the paper are publicly available on a companion GitHub repository.

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arXiv2019

A Bayesian Nonparametric Model for Zero-Inflated Outcomes: Prediction, Clustering, and Causal Estimation

Researchers are often interested in predicting outcomes, conducting clustering analysis to detect distinct subgroups of their data, or computing causal treatment effects. Pathological data distributions that exhibit skewness and zero-inflation complicate these tasks - requiring highly flexible, data-adaptive modeling. In this paper, we present a fully nonparametric Bayesian generative model for continuous, zero-inflated outcomes that simultaneously predicts structural zeros, captures skewness, and clusters patients with similar joint data distributions. The flexibility of our approach yields predictions that capture the joint data distribution better than commonly used zero-inflated methods. Moreover, we demonstrate that our model can be coherently incorporated into a standardization procedure for computing causal effect estimates that are robust to such data pathologies. Uncertainty at all levels of this model flow through to the causal effect estimates of interest - allowing easy point estimation, interval estimation, and posterior predictive checks verifying positivity, a required causal identification assumption. Our simulation results show point estimates to have low bias and interval estimates to have close to nominal coverage under complicated data settings. Under simpler settings, these results hold while incurring lower efficiency loss than comparator methods. Lastly, we use our proposed method to analyze zero-inflated inpatient medical costs among endometrial cancer patients receiving either chemotherapy and radiation therapy in the SEER medicare database.

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arXiv2017

A causal approach to analysis of censored medical costs in the presence of time-varying treatment

There has recently been a growing interest in the development of statistical methods to compare medical costs between treatment groups. When cumulative cost is the outcome of interest, right-censoring poses the challenge of informative missingness due to heterogeneity in the rates of cost accumulation across subjects. Existing approaches seeking to address the challenge of informative cost trajectories typically rely on inverse probability weighting and target a net "intent-to-treat" effect. However, no approaches capable of handling time-dependent treatment and confounding in this setting have been developed to date. A method to estimate the joint causal effect of a treatment regime on cost would be of value to inform public policy when comparing interventions. In this paper, we develop a nested g-computation approach to cost analysis in order to accommodate time-dependent treatment and repeated outcome measures. We demonstrate that our procedure is reasonably robust to departures from its distributional assumptions and can provide unique insights into fundamental differences in average cost across time-dependent treatment regimes.

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