Optimally Balanced Gaussian Process Propensity Scores for Estimating Treatment Effects.
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ABSTRACT:
SUBMITTER: Vegetabile BG
PROVIDER: S-EPMC8360444 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:We derive regression estimators that can compare longitudinal treatments using only the longitudinal propensity scores as regressors. These estimators, which assume knowledge of the variables used in the treatment assignment, are important for reducing the large dimension of covariates for two reasons. First, if the regression models on the longitudinal propensity scores are correct, then our estimators share advantages of correctly specified model-based estimators, a benefit not shared by estimators based on weights alone. Second, if the models are incorrect, the misspecification can be more easily limited through model checking than with models based on the full covariates. Thus, our estimators can also be better when used in place of the regression on the full covariates. We use our methods to compare longitudinal treatments for type II diabetes mellitus.
| S-EPMC4593705 | biostudies-literature
Project description:We consider estimating average treatment effects (ATE) of a binary treatment in observational data when data-driven variable selection is needed to select relevant covariates from a moderately large number of available covariates X . To leverage covariates among X predictive of the outcome for efficiency gain while using regularization to fit a parametric propensity score (PS) model, we consider a dimension reduction of X based on fitting both working PS and outcome models using adaptive LASSO. A novel PS estimator, the Double-index Propensity Score (DiPS), is proposed, in which the treatment status is smoothed over the linear predictors for X from both the initial working models. The ATE is estimated by using the DiPS in a normalized inverse probability weighting estimator, which is found to maintain double robustness and also local semiparametric efficiency with a fixed number of covariates p. Under misspecification of working models, the smoothing step leads to gains in efficiency and robustness over traditional doubly robust estimators. These results are extended to the case where p diverges with sample size and working models are sparse. Simulations show the benefits of the approach in finite samples. We illustrate the method by estimating the ATE of statins on colorectal cancer risk in an electronic medical record study and the effect of smoking on C-reactive protein in the Framingham Offspring Study.
| S-EPMC7370895 | biostudies-literature
Project description:Propensity score methods, such as subclassification, are a common approach to control for confounding when estimating causal effects in non-randomized studies. Propensity score subclassification groups individuals into subclasses based on their propensity score values. Effect estimates are obtained within each subclass and then combined by weighting by the proportion of observations in each subclass. Combining subclass-specific estimates by weighting by the inverse variance is a promising alternative approach; a similar strategy is used in meta-analysis for its efficiency. We use simulation to compare performance of each of the two methods while varying (i) the number of subclasses, (ii) extent of propensity score overlap between the treatment and control groups (i.e., positivity), (iii) incorporation of survey weighting, and (iv) presence of heterogeneous treatment effects across subclasses. Both methods perform well in the absence of positivity violations and with a constant treatment effect with weighting by the inverse variance performing slightly better. Weighting by the proportion in subclass performs better in the presence of heterogeneous treatment effects across subclasses. We apply these methods to an illustrative example estimating the effect of living in a disadvantaged neighborhood on risk of past-year anxiety and depressive disorders among U.S. urban adolescents. This example entails practical positivity violations but no evidence of treatment effect heterogeneity. In this case, weighting by the inverse variance when combining across propensity score subclasses results in more efficient estimates that ultimately change inference. Copyright © 2016 John Wiley & Sons, Ltd.
| S-EPMC5096953 | biostudies-literature
Project description:This article develops semiparametric approaches for estimation of propensity scores and causal survival functions from prevalent survival data. The analytical problem arises when the prevalent sampling is adopted for collecting failure times and, as a result, the covariates are incompletely observed due to their association with failure time. The proposed procedure for estimating propensity scores shares interesting features similar to the likelihood formulation in case-control study, but in our case it requires additional consideration in the intercept term. The result shows that the corrected propensity scores in logistic regression setting can be obtained through standard estimation procedure with specific adjustments on the intercept term. For causal estimation, two different types of missing sources are encountered in our model: one can be explained by potential outcome framework; the other is caused by the prevalent sampling scheme. Statistical analysis without adjusting bias from both sources of missingness will lead to biased results in causal inference. The proposed methods were partly motivated by and applied to the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked data for women diagnosed with breast cancer.
| S-EPMC3508756 | biostudies-literature
Project description:The propensity score (PS) method is widely used to estimate the average treatment effect (TE) in observational studies. However, it is generally confined to the binary treatment assignment. In an extension to the settings of a multi-level treatment, Imbens proposed a generalized propensity score which is the conditional probability of receiving a particular level of the treatment given pre-treatment variables. The average TE can then be estimated by conditioning solely on the generalized PS under the assumption of weak unconfounded-ness. In the present work, we adopted this approach and conducted extensive simulations to evaluate the performance of several methods using the generalized PS, including subclassification, matching, inverse probability of treatment weighting (IPTW), and covariate adjustment. Compared with other methods, IPTW had the preferred overall performance. We then applied these methods to a retrospective cohort study of 228,876 pregnant women. The impact of the exposure to different types of the antidepressant medications (no exposure, selective serotonin reuptake inhibitor (SSRI) only, non-SSRI only, and both) during pregnancy on several important infant outcomes (birth weight, gestation age, preterm labor, and respiratory distress) were assessed.
| S-EPMC6609155 | biostudies-literature
Project description:BackgroundIn randomised controlled trials with only few randomisation units, treatment allocation may be challenging if balanced distributions of many covariates or baseline outcome measures are desired across all treatment groups. Both traditional approaches, stratified randomisation and allocation by minimisation, have their own limitations. A third method for achieving balance consists of randomly choosing from a preselected list of sufficiently balanced allocations. As with minimisation, this method requires that heterogeneity between treatment groups is measured by specified imbalance metrics. Although certain imbalance measures are more commonly used than others, to the author's knowledge there is no generally accepted "gold standard", neither for categorical and even less so for continuous variables.MethodsAn intuitive and easily accessible web-based software tool was developed which allows for balancing multiple variables of different types and using various imbalance metrics. Different metrics were compared in a simulation study.ResultsUsing simulated data, it could be shown that for categorical variables, ?2-based imbalance measures seem to be viable alternatives to the established "quadratic imbalance" metric. For continuous variables, using the area between the empirical cumulative distribution functions or the largest difference in the three pairs of quartiles is recommended to measure imbalance. Another imbalance metric suggested in the literature for continuous variables, the (symmetrised) Kullback-Leibler divergence, should be used with caution.ConclusionThe Shiny Balancer offers the possibility to visually explore the balancing properties of several well established or newly suggested imbalance metrics, and its use is particularly advocated in clinical studies with few randomisation units, as it is typically the case in cluster randomised trials.
| S-EPMC6192202 | biostudies-literature
Project description:Consumption surveys often record zero purchases of a good because of a short observation window. Measures of distribution are then precluded and only mean consumption rates can be inferred. We show that Propensity Score Matching can be applied to recover the distribution of consumption rates. We demonstrate the method using the UK National Travel Survey, in which c.40% of motorist households purchase no fuel. Estimated consumption rates are plausible judging by households' annual mileages, and highly skewed. We apply the same approach to estimate CO2 emissions and outcomes of a carbon cap or tax. Reliance on means apparently distorts analysis of such policies because of skewness of the underlying distributions. The regressiveness of a simple tax or cap is overstated, and redistributive features of a revenue-neutral policy are understated.
| S-EPMC5636092 | biostudies-literature
Project description:Propensity score methods are widely used in comparative effectiveness research using claims data. In this context, the inaccuracy of procedural or billing codes in claims data frequently misclassifies patients into treatment groups, that is, the treatment assignment ($T$) is often measured with error. In the context of a validation data where treatment assignment is accurate, we show that misclassification of treatment assignment can impact three distinct stages of a propensity score analysis: (i) propensity score estimation; (ii) propensity score implementation; and (iii) outcome analysis conducted conditional on the estimated propensity score and its implementation. We examine how the error in $T$ impacts each stage in the context of three common propensity score implementations: subclassification, matching, and inverse probability of treatment weighting (IPTW). Using validation data, we propose a two-step likelihood-based approach which fully adjusts for treatment misclassification bias under subclassification. This approach relies on two common measurement error-assumptions; non-differential measurement error and transportability of the measurement error model. We use simulation studies to assess the performance of the adjustment under subclassification, and also investigate the method's performance under matching or IPTW. We apply the methods to Medicare Part A hospital claims data to estimate the effect of resection versus biopsy on 1-year mortality among $10\,284$ Medicare beneficiaries diagnosed with brain tumors. The ICD9 billing codes from Medicare Part A inaccurately reflect surgical treatment, but SEER-Medicare validation data are available with more accurate information.
| S-EPMC5862346 | biostudies-literature
Project description:PurposeA growing area of research in epidemiology is the identification of health-related sibling spillover effects, or the effect of one individual's exposure on their sibling's outcome. The health within families may be confounded by unobserved factors, rendering identification of sibling spillovers challenging.MethodsWe demonstrate a gain-score (fixed effects) regression method for identifying exposure-to-outcome spillover effects within sibling pairs in linear models. The method identifies the exposure-to-outcome spillover effect if only one sibling's exposure affects the other's outcome, and it identifies the difference between the spillover effects if both siblings' exposures affect the others' outcomes. The method fails with outcome-to-exposure spillover or with outcome-to-outcome spillover. Analytic results, Monte Carlo simulations, and a brief application demonstrate the method and its limitations.ResultsWe estimate the spillover effect of a child's preterm birth on an older sibling's literacy skills, measured by the Phonological Awareness Literacy Screening-Kindergarten test. We analyze 20,010 sibling pairs from a population-wide, Wisconsin-based (United States) birth cohort. Without covariate adjustment, we estimate that preterm birth modestly decreases an older sibling's test score.ConclusionsGain-scores are a promising strategy for identifying exposure-to-outcome spillover effects in sibling pairs while controlling for sibling-invariant unobserved confounding.
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Project description:This data article provides the summary data from tests comparing various Gaussian process software packages. Each spreadsheet represents a single function or type of function using a particular input sample size. In each spreadsheet, a row gives the results for a particular replication using a single package. Within each spreadsheet there are the results from eight Gaussian process model-fitting packages on five replicates of the surface. There is also one spreadsheet comparing the results from two packages performing stochastic kriging. These data enable comparisons between the packages to determine which package will give users the best results.
| S-EPMC5995745 | biostudies-literature