Matching Items (6)
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- All Subjects: Bayesian
- All Subjects: Psychology--Research--Methodology.
- Creators: Mackinnon, David P
- Creators: McCulloch, Robert
- Member of: ASU Electronic Theses and Dissertations
Description
Random Forests is a statistical learning method which has been proposed for propensity score estimation models that involve complex interactions, nonlinear relationships, or both of the covariates. In this dissertation I conducted a simulation study to examine the effects of three Random Forests model specifications in propensity score analysis. The results suggested that, depending on the nature of data, optimal specification of (1) decision rules to select the covariate and its split value in a Classification Tree, (2) the number of covariates randomly sampled for selection, and (3) methods of estimating Random Forests propensity scores could potentially produce an unbiased average treatment effect estimate after propensity scores weighting by the odds adjustment. Compared to the logistic regression estimation model using the true propensity score model, Random Forests had an additional advantage in producing unbiased estimated standard error and correct statistical inference of the average treatment effect. The relationship between the balance on the covariates' means and the bias of average treatment effect estimate was examined both within and between conditions of the simulation. Within conditions, across repeated samples there was no noticeable correlation between the covariates' mean differences and the magnitude of bias of average treatment effect estimate for the covariates that were imbalanced before adjustment. Between conditions, small mean differences of covariates after propensity score adjustment were not sensitive enough to identify the optimal Random Forests model specification for propensity score analysis.
ContributorsCham, Hei Ning (Author) / Tein, Jenn-Yun (Thesis advisor) / Enders, Stephen G (Thesis advisor) / Enders, Craig K. (Committee member) / Mackinnon, David P (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation covers several topics in machine learning and causal inference. First, the question of “feature selection,” a common byproduct of regularized machine learning methods, is investigated theoretically in the context of treatment effect estimation. This involves a detailed review and extension of frameworks for estimating causal effects and in-depth theoretical study. Next, various computational approaches to estimating causal effects with machine learning methods are compared with these theoretical desiderata in mind. Several improvements to current methods for causal machine learning are identified and compelling angles for further study are pinpointed. Finally, a common method used for “explaining” predictions of machine learning algorithms, SHAP, is evaluated critically through a statistical lens.
ContributorsHerren, Andrew (Author) / Hahn, P Richard (Thesis advisor) / Kao, Ming-Hung (Committee member) / Lopes, Hedibert (Committee member) / McCulloch, Robert (Committee member) / Zhou, Shuang (Committee member) / Arizona State University (Publisher)
Created2023
Description
In this work, I present a Bayesian inference computational framework for the analysis of widefield microscopy data that addresses three challenges: (1) counting and localizing stationary fluorescent molecules; (2) inferring a spatially-dependent effective fluorescence profile that describes the spatially-varying rate at which fluorescent molecules emit subsequently-detected photons (due to different illumination intensities or different local environments); and (3) inferring the camera gain. My general theoretical framework utilizes the Bayesian nonparametric Gaussian and beta-Bernoulli processes with a Markov chain Monte Carlo sampling scheme, which I further specify and implement for Total Internal Reflection Fluorescence (TIRF) microscopy data, benchmarking the method on synthetic data. These three frameworks are self-contained, and can be used concurrently so that the fluorescence profile and emitter locations are both considered unknown and, under some conditions, learned simultaneously. The framework I present is flexible and may be adapted to accommodate the inference of other parameters, such as emission photophysical kinetics and the trajectories of moving molecules. My TIRF-specific implementation may find use in the study of structures on cell membranes, or in studying local sample properties that affect fluorescent molecule photon emission rates.
ContributorsWallgren, Ross (Author) / Presse, Steve (Thesis advisor) / Armbruster, Hans (Thesis advisor) / McCulloch, Robert (Committee member) / Arizona State University (Publisher)
Created2019
Description
Bayesian Additive Regression Trees (BART) is a non-parametric Bayesian model
that often outperforms other popular predictive models in terms of out-of-sample error. This thesis studies a modified version of BART called Accelerated Bayesian Additive Regression Trees (XBART). The study consists of simulation and real data experiments comparing XBART to other leading algorithms, including BART. The results show that XBART maintains BART’s predictive power while reducing its computation time. The thesis also describes the development of a Python package implementing XBART.
that often outperforms other popular predictive models in terms of out-of-sample error. This thesis studies a modified version of BART called Accelerated Bayesian Additive Regression Trees (XBART). The study consists of simulation and real data experiments comparing XBART to other leading algorithms, including BART. The results show that XBART maintains BART’s predictive power while reducing its computation time. The thesis also describes the development of a Python package implementing XBART.
ContributorsYalov, Saar (Author) / Hahn, P. Richard (Thesis advisor) / McCulloch, Robert (Committee member) / Kao, Ming-Hung (Committee member) / Arizona State University (Publisher)
Created2019
Description
This dissertation examines a planned missing data design in the context of mediational analysis. The study considered a scenario in which the high cost of an expensive mediator limited sample size, but in which less expensive mediators could be gathered on a larger sample size. Simulated multivariate normal data were generated from a latent variable mediation model with three observed indicator variables, M1, M2, and M3. Planned missingness was implemented on M1 under the missing completely at random mechanism. Five analysis methods were employed: latent variable mediation model with all three mediators as indicators of a latent construct (Method 1), auxiliary variable model with M1 as the mediator and M2 and M3 as auxiliary variables (Method 2), auxiliary variable model with M1 as the mediator and M2 as a single auxiliary variable (Method 3), maximum likelihood estimation including all available data but incorporating only mediator M1 (Method 4), and listwise deletion (Method 5).
The main outcome of interest was empirical power to detect the mediated effect. The main effects of mediation effect size, sample size, and missing data rate performed as expected with power increasing for increasing mediation effect sizes, increasing sample sizes, and decreasing missing data rates. Consistent with expectations, power was the greatest for analysis methods that included all three mediators, and power decreased with analysis methods that included less information. Across all design cells relative to the complete data condition, Method 1 with 20% missingness on M1 produced only 2.06% loss in power for the mediated effect; with 50% missingness, 6.02% loss; and 80% missingess, only 11.86% loss. Method 2 exhibited 20.72% power loss at 80% missingness, even though the total amount of data utilized was the same as Method 1. Methods 3 – 5 exhibited greater power loss. Compared to an average power loss of 11.55% across all levels of missingness for Method 1, average power losses for Methods 3, 4, and 5 were 23.87%, 29.35%, and 32.40%, respectively. In conclusion, planned missingness in a multiple mediator design may permit higher quality characterization of the mediator construct at feasible cost.
The main outcome of interest was empirical power to detect the mediated effect. The main effects of mediation effect size, sample size, and missing data rate performed as expected with power increasing for increasing mediation effect sizes, increasing sample sizes, and decreasing missing data rates. Consistent with expectations, power was the greatest for analysis methods that included all three mediators, and power decreased with analysis methods that included less information. Across all design cells relative to the complete data condition, Method 1 with 20% missingness on M1 produced only 2.06% loss in power for the mediated effect; with 50% missingness, 6.02% loss; and 80% missingess, only 11.86% loss. Method 2 exhibited 20.72% power loss at 80% missingness, even though the total amount of data utilized was the same as Method 1. Methods 3 – 5 exhibited greater power loss. Compared to an average power loss of 11.55% across all levels of missingness for Method 1, average power losses for Methods 3, 4, and 5 were 23.87%, 29.35%, and 32.40%, respectively. In conclusion, planned missingness in a multiple mediator design may permit higher quality characterization of the mediator construct at feasible cost.
ContributorsBaraldi, Amanda N (Author) / Enders, Craig K. (Thesis advisor) / Mackinnon, David P (Thesis advisor) / Aiken, Leona S. (Committee member) / Tein, Jenn-Yun (Committee member) / Arizona State University (Publisher)
Created2015
Description
Time metric is an important consideration for all longitudinal models because it can influence the interpretation of estimates, parameter estimate accuracy, and model convergence in longitudinal models with latent variables. Currently, the literature on latent difference score (LDS) models does not discuss the importance of time metric. Furthermore, there is little research using simulations to investigate LDS models. This study examined the influence of time metric on model estimation, interpretation, parameter estimate accuracy, and convergence in LDS models using empirical simulations. Results indicated that for a time structure with a true time metric where participants had different starting points and unequally spaced intervals, LDS models fit with a restructured and less informative time metric resulted in biased parameter estimates. However, models examined using the true time metric were less likely to converge than models using the restructured time metric, likely due to missing data. Where participants had different starting points but equally spaced intervals, LDS models fit with a restructured time metric resulted in biased estimates of intercept means, but all other parameter estimates were unbiased, and models examined using the true time metric had less convergence than the restructured time metric as well due to missing data. The findings of this study support prior research on time metric in longitudinal models, and further research should examine these findings under alternative conditions. The importance of these findings for substantive researchers is discussed.
ContributorsO'Rourke, Holly P (Author) / Grimm, Kevin J. (Thesis advisor) / Mackinnon, David P (Thesis advisor) / Chassin, Laurie (Committee member) / Aiken, Leona S. (Committee member) / Arizona State University (Publisher)
Created2016