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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
Cryptocurrencies have become one of the most fascinating forms of currency and economics due to their fluctuating values and lack of centralization. This project attempts to use machine learning methods to effectively model in-sample data for Bitcoin and Ethereum using rule induction methods. The dataset is cleaned by removing entries with missing data. The new column is created to measure price difference to create a more accurate analysis on the change in price. Eight relevant variables are selected using cross validation: the total number of bitcoins, the total size of the blockchains, the hash rate, mining difficulty, revenue from mining, transaction fees, the cost of transactions and the estimated transaction volume. The in-sample data is modeled using a simple tree fit, first with one variable and then with eight. Using all eight variables, the in-sample model and data have a correlation of 0.6822657. The in-sample model is improved by first applying bootstrap aggregation (also known as bagging) to fit 400 decision trees to the in-sample data using one variable. Then the random forests technique is applied to the data using all eight variables. This results in a correlation between the model and data of 9.9443413. The random forests technique is then applied to an Ethereum dataset, resulting in a correlation of 9.6904798. Finally, an out-of-sample model is created for Bitcoin and Ethereum using random forests, with a benchmark correlation of 0.03 for financial data. The correlation between the training model and the testing data for Bitcoin was 0.06957639, while for Ethereum the correlation was -0.171125. In conclusion, it is confirmed that cryptocurrencies can have accurate in-sample models by applying the random forests method to a dataset. However, out-of-sample modeling is more difficult, but in some cases better than typical forms of financial data. It should also be noted that cryptocurrency data has similar properties to other related financial datasets, realizing future potential for system modeling for cryptocurrency within the financial world.
ContributorsBrowning, Jacob Christian (Author) / Meuth, Ryan (Thesis director) / Jones, Donald (Committee member) / McCulloch, Robert (Committee member) / Computer Science and Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This dissertation centers on Bayesian Additive Regression Trees (BART) and Accelerated BART (XBART) and presents a series of models that tackle extrapolation, classification, and causal inference challenges. To improve extrapolation in tree-based models, I propose a method called local Gaussian Process (GP) that combines Gaussian process regression with trained BART trees. This allows for extrapolation based on the most relevant data points and covariate variables determined by the trees' structure. The local GP technique is extended to the Bayesian causal forest (BCF) models to address the positivity violation issue in causal inference. Additionally, I introduce the LongBet model to estimate time-varying, heterogeneous treatment effects in panel data. Furthermore, I present a Poisson-based model, with a modified likelihood for XBART for the multi-class classification problem.
ContributorsWang, Meijia (Author) / Hahn, Paul (Thesis advisor) / He, Jingyu (Committee member) / Lan, Shiwei (Committee member) / McCulloch, Robert (Committee member) / Zhou, Shuang (Committee member) / Arizona State University (Publisher)
Created2024
Description
Spatial regression is one of the central topics in spatial statistics. Based on the goals, interpretation or prediction, spatial regression models can be classified into two categories, linear mixed regression models and nonlinear regression models. This dissertation explored these models and their real world applications. New methods and models were proposed to overcome the challenges in practice. There are three major parts in the dissertation.
In the first part, nonlinear regression models were embedded into a multistage workflow to predict the spatial abundance of reef fish species in the Gulf of Mexico. There were two challenges, zero-inflated data and out of sample prediction. The methods and models in the workflow could effectively handle the zero-inflated sampling data without strong assumptions. Three strategies were proposed to solve the out of sample prediction problem. The results and discussions showed that the nonlinear prediction had the advantages of high accuracy, low bias and well-performed in multi-resolution.
In the second part, a two-stage spatial regression model was proposed for analyzing soil carbon stock (SOC) data. In the first stage, there was a spatial linear mixed model that captured the linear and stationary effects. In the second stage, a generalized additive model was used to explain the nonlinear and nonstationary effects. The results illustrated that the two-stage model had good interpretability in understanding the effect of covariates, meanwhile, it kept high prediction accuracy which is competitive to the popular machine learning models, like, random forest, xgboost and support vector machine.
A new nonlinear regression model, Gaussian process BART (Bayesian additive regression tree), was proposed in the third part. Combining advantages in both BART and Gaussian process, the model could capture the nonlinear effects of both observed and latent covariates. To develop the model, first, the traditional BART was generalized to accommodate correlated errors. Then, the failure of likelihood based Markov chain Monte Carlo (MCMC) in parameter estimating was discussed. Based on the idea of analysis of variation, back comparing and tuning range, were proposed to tackle this failure. Finally, effectiveness of the new model was examined by experiments on both simulation and real data.
In the first part, nonlinear regression models were embedded into a multistage workflow to predict the spatial abundance of reef fish species in the Gulf of Mexico. There were two challenges, zero-inflated data and out of sample prediction. The methods and models in the workflow could effectively handle the zero-inflated sampling data without strong assumptions. Three strategies were proposed to solve the out of sample prediction problem. The results and discussions showed that the nonlinear prediction had the advantages of high accuracy, low bias and well-performed in multi-resolution.
In the second part, a two-stage spatial regression model was proposed for analyzing soil carbon stock (SOC) data. In the first stage, there was a spatial linear mixed model that captured the linear and stationary effects. In the second stage, a generalized additive model was used to explain the nonlinear and nonstationary effects. The results illustrated that the two-stage model had good interpretability in understanding the effect of covariates, meanwhile, it kept high prediction accuracy which is competitive to the popular machine learning models, like, random forest, xgboost and support vector machine.
A new nonlinear regression model, Gaussian process BART (Bayesian additive regression tree), was proposed in the third part. Combining advantages in both BART and Gaussian process, the model could capture the nonlinear effects of both observed and latent covariates. To develop the model, first, the traditional BART was generalized to accommodate correlated errors. Then, the failure of likelihood based Markov chain Monte Carlo (MCMC) in parameter estimating was discussed. Based on the idea of analysis of variation, back comparing and tuning range, were proposed to tackle this failure. Finally, effectiveness of the new model was examined by experiments on both simulation and real data.
ContributorsLu, Xuetao (Author) / McCulloch, Robert (Thesis advisor) / Hahn, Paul (Committee member) / Lan, Shiwei (Committee member) / Zhou, Shuang (Committee member) / Saul, Steven (Committee member) / Arizona State University (Publisher)
Created2020
Description
Geographically Weighted Regression (GWR) has been broadly used in various fields to
model spatially non-stationary relationships. Classic GWR is considered as a single-scale model that is based on one bandwidth parameter which controls the amount of distance-decay in weighting neighboring data around each location. The single bandwidth in GWR assumes that processes (relationships between the response variable and the predictor variables) all operate at the same scale. However, this posits a limitation in modeling potentially multi-scale processes which are more often seen in the real world. For example, the measured ambient temperature of a location is affected by the built environment, regional weather and global warming, all of which operate at different scales. A recent advancement to GWR termed Multiscale GWR (MGWR) removes the single bandwidth assumption and allows the bandwidths for each covariate to vary. This results in each parameter surface being allowed to have a different degree of spatial variation, reflecting variation across covariate-specific processes. In this way, MGWR has the capability to differentiate local, regional and global processes by using varying bandwidths for covariates. Additionally, bandwidths in MGWR become explicit indicators of the scale at various processes operate. The proposed dissertation covers three perspectives centering on MGWR: Computation; Inference; and Application. The first component focuses on addressing computational issues in MGWR to allow MGWR models to be calibrated more efficiently and to be applied on large datasets. The second component aims to statistically differentiate the spatial scales at which different processes operate by quantifying the uncertainty associated with each bandwidth obtained from MGWR. In the third component, an empirical study will be conducted to model the changing relationships between county-level socio-economic factors and voter preferences in the 2008-2016 United States presidential elections using MGWR.
model spatially non-stationary relationships. Classic GWR is considered as a single-scale model that is based on one bandwidth parameter which controls the amount of distance-decay in weighting neighboring data around each location. The single bandwidth in GWR assumes that processes (relationships between the response variable and the predictor variables) all operate at the same scale. However, this posits a limitation in modeling potentially multi-scale processes which are more often seen in the real world. For example, the measured ambient temperature of a location is affected by the built environment, regional weather and global warming, all of which operate at different scales. A recent advancement to GWR termed Multiscale GWR (MGWR) removes the single bandwidth assumption and allows the bandwidths for each covariate to vary. This results in each parameter surface being allowed to have a different degree of spatial variation, reflecting variation across covariate-specific processes. In this way, MGWR has the capability to differentiate local, regional and global processes by using varying bandwidths for covariates. Additionally, bandwidths in MGWR become explicit indicators of the scale at various processes operate. The proposed dissertation covers three perspectives centering on MGWR: Computation; Inference; and Application. The first component focuses on addressing computational issues in MGWR to allow MGWR models to be calibrated more efficiently and to be applied on large datasets. The second component aims to statistically differentiate the spatial scales at which different processes operate by quantifying the uncertainty associated with each bandwidth obtained from MGWR. In the third component, an empirical study will be conducted to model the changing relationships between county-level socio-economic factors and voter preferences in the 2008-2016 United States presidential elections using MGWR.
ContributorsLi, Ziqi (Author) / Fotheringham, A. Stewart (Thesis advisor) / Goodchild, Michael F. (Committee member) / Li, Wenwen (Committee member) / Arizona State University (Publisher)
Created2020