Physical Sciences and Mathematics Commons^™

Applications Of Independent And Identically Distributed (Iid) Random Processes In Polarimetry And Climatology, Dan Kestner

Dissertations, Master's Theses and Master's Reports

The unifying theme of this thesis is the characterization of “perfect randomness,” i.e., independent and identically distributed (IID) stochastic processes as these are applied in physical science. Two specific and mathematically distinct applications are chosen: (i) Radar and optical polarimetry; (ii) Analysis of time series in meteorology. In (i), IID process of a special kind, namely, with a distribution defined by symmetry, is used to link its multivariate Gaussian density to uniformity on the Poincaré sphere. This “statistical ellipsometry” approach is then used to relate polarimetric mismatches or imbalances to ellipsometric variables and suitably chosen cross-correlation measures. In (ii), recently …

Statistical Methods For Gene Selection And Genetic Association Studies, Xuewei Cao

Dissertations, Master's Theses and Master's Reports

This dissertation includes five Chapters. A brief description of each chapter is organized as follows.

In Chapter One, we propose a signed bipartite genotype and phenotype network (GPN) by linking phenotypes and genotypes based on the statistical associations. It provides a new insight to investigate the genetic architecture among multiple correlated phenotypes and explore where phenotypes might be related at a higher level of cellular and organismal organization. We show that multiple phenotypes association studies by considering the proposed network are improved by incorporating the genetic information into the phenotype clustering.

In Chapter Two, we first illustrate the proposed GPN …

Machine Learning Methods For Prediction Of Human Infectious Virus And Imputation Of Hla Alleles, Xiaoqing Gao

Dissertations, Master's Theses and Master's Reports

This dissertation contains three Chapters. The following is a concise description of each Chapters.

In Chapter 1, we introduced the Random Forest, a machine learning method, to foresee whether a virus is capable of infecting humans. The Covid pandemic informs us the importance of predicting the ability of a zoonotic virus that can infect humans from its genomic sequence. We used the -mer with and as features of a virus to predict if it can affect humans. We further employed the Boruta algorithm to select the important features, then fed those important features into the Random Forest method to train …

Additive P-Value Combination Test, Xing Ling

Dissertations, Master's Theses and Master's Reports

This dissertation includes four Chapters. A brief description of each chapter is organized as follows.

In Chapter 1, some developments on multiple hypotheses tests are introduced. Some preliminaries about the definition and the assumption are included.

In Chapter 2, a Stable Combination Test is proposed to combine $p$-values from multiple hypotheses tests. We show the proposed method controls the family-wise error rate at the target level and maintains asymptotically optimal power even when the elementary p-values from the individual hypotheses are dependent.

In Chapter 3, a deeper dig into the additive p-value combination test is performed. A common idea behind …

Joint Probability Analysis Of Extreme Precipitation And Water Level For Chicago, Illinois, Anna Li Holey

Dissertations, Master's Theses and Master's Reports

A compound flooding event occurs when there is a combination of two or more extreme factors that happen simultaneously or in quick succession and can lead to flooding. In the Great Lakes region, it is common for a compound flooding event to occur with a high lake water level and heavy rainfall. With the potential of increasing water levels and an increase in precipitation under climate change, the Great Lakes coastal regions could be at risk for more frequent and severe flooding. The City of Chicago which is located on Lake Michigan has a high population and dense infrastructure and …

Knowledge Discovery On The Integrative Analysis Of Electrical And Mechanical Dyssynchrony To Improve Cardiac Resynchronization Therapy, Zhuo He

Dissertations, Master's Theses and Master's Reports

Cardiac resynchronization therapy (CRT) is a standard method of treating heart failure by coordinating the function of the left and right ventricles. However, up to 40% of CRT recipients do not experience clinical symptoms or cardiac function improvements. The main reasons for CRT non-response include: (1) suboptimal patient selection based on electrical dyssynchrony measured by electrocardiogram (ECG) in current guidelines; (2) mechanical dyssynchrony has been shown to be effective but has not been fully explored; and (3) inappropriate placement of the CRT left ventricular (LV) lead in a significant number of patients.

In terms of mechanical dyssynchrony, we utilize an …

Investigating Collaborative Explainable Ai (Cxai)/Social Forum As An Explainable Ai (Xai) Method In Autonomous Driving (Ad), Tauseef Ibne Mamun

Dissertations, Master's Theses and Master's Reports

Explainable AI (XAI) systems primarily focus on algorithms, integrating additional information into AI decisions and classifications to enhance user or developer comprehension of the system's behavior. These systems often incorporate untested concepts of explainability, lacking grounding in the cognitive and educational psychology literature (S. T. Mueller et al., 2021). Consequently, their effectiveness may be limited, as they may address problems that real users don't encounter or provide information that users do not seek.

In contrast, an alternative approach called Collaborative XAI (CXAI), as proposed by S. Mueller et al (2021), emphasizes generating explanations without relying solely on algorithms. CXAI centers …

Searching For Anomalous Extensive Air Showers Using The Pierre Auger Observatory Fluorescence Detector, Andrew Puyleart

Dissertations, Master's Theses and Master's Reports

Anomalous extensive air showers have yet to be detected by cosmic ray observatories. Fluorescence detectors provide a way to view the air showers created by cosmic rays with primary energies reaching up to hundreds of EeV . The resulting air showers produced by these highly energetic collisions can contain features that deviate from average air showers. Detection of these anomalous events may provide information into unknown regions of particle physics, and place constraints on cross-sectional interaction lengths of protons. In this dissertation, I propose measurements of extensive air shower profiles that are used in a machine learning pipeline to distinguish …

Maximum Likelihood Estimator Method To Estimate Flaw Parameters For Different Glass Types, Nabhajit Goswami

Dissertations, Master's Theses and Master's Reports

Glass is commonly used in architectural applications, such as windows and in-fill panels and structural applications, such as beams and staircases. Despite the popularity of structural glass use in buildings, an engineering design standard to determine the required component or member strength for design loads does not exist. Glass is a brittle material that lacks a well-defined yield or ultimate stress, unlike ductile materials. The traditional engineering methods used to design a ductile material cannot be used to design a glass component. Glass fails in tension primarily due to the presence of microscopic flaws present on the surface that acts …

Impact Of Hemodynamic Vortex Spatial And Temporal Characteristics On Analysis Of Intracranial Aneurysms, Kevin W. Sunderland

Dissertations, Master's Theses and Master's Reports

Subarachnoid hemorrhage is a potentially devastating pathological condition in which bleeding occurs into the space surrounding the brain. One of the prominent sources of subarachnoid hemorrhage are intracranial aneurysms (IA): degenerative, irregular expansions of area(s) of the cerebral vasculature. In the event of IA rupture, the resultant subarachnoid hemorrhage ends in patient mortality occurring in ~50% of cases, with survivors enduring significant neurological damage with physical or cognitive impairment. The seriousness of IA rupture drives a degree of clinical interest in understanding these conditions that promote both the development and possible rupture of the vascular malformations. Current metrics for the …

A Transdisciplinary Analysis Of Just Transition Pathways To 100% Renewable Electricity, Adewale Aremu Adesanya

Dissertations, Master's Theses and Master's Reports

The transition to using clean, affordable, and reliable electrical energy is critical for enhancing human opportunities and capabilities. In the United States, many states and localities are engaging in this transition despite the lack of ambitious federal policy support. This research builds on the theoretical framework of the multilevel perspective (MLP) of sociotechnical transitions as well as the concept of energy justice to investigate potential pathways to 100 percent renewable energy (RE) for electricity provision in the U.S. This research seeks to answer the question: what are the technical, policy, and perceptual pathways, barriers, and opportunities for just transition to …

Superresolution Enhancement With Active Convolved Illumination, Anindya Ghoshroy

Dissertations, Master's Theses and Master's Reports

The first two decades of the 21st century witnessed the emergence of “metamaterials”. The prospect of unrestricted control over light-matter interactions was a major contributing factor leading to the realization of new technologies and advancement of existing ones. While the field certainly does not lack innovative applications, widespread commercial deployment may still be several decades away. Fabrication of sophisticated 3d micro and nano structures, specially for telecommunications and optical frequencies will require a significant advancement of current technologies. More importantly, the effects of absorption and scattering losses will require a robust solution since this renders any conceivable application of metamaterials …

Construction And Analysis Of Genetic Regulatory Networks With Rna-Seq Data From Arabidopsis Thaliana, Tessa Kriz

Dissertations, Master's Theses and Master's Reports

Reconstruction of gene regulatory networks (GRNs) is a fundamental aspect of genetic engineering and provides a deeper understanding of the biological processes of an organism. Two methods were implemented to reconstruct the gene regulatory networks of Arabidopsis thaliana under two treatments: methyl jasmonate (MeJa) and salicylic acid (SA). The Joint Reconstruction of multiple Gene Regulatory Networks (JRmGRN) method was utilized to construct a joint network for identifying hub genes common to both conditions in addition to networks specific to each condition. The Differential Network Analysis with False Discover Rate Control method constructed a network of connections unique to only one …

Statistical Methods In Genetic Studies, Cheng Gao

Dissertations, Master's Theses and Master's Reports

This dissertation includes three Chapters. A brief description of each chapter is organized as follows.

In Chapter 1, we proposed a new method, called MF-TOWmuT, for genome-wide association studies with multiple genetic variants and multiple phenotypes using family samples. MF-TOWmuT uses kinship matrix to account for sample relatedness. It is worth mentioning that in simulations, we considered hidden polygenic effects and varied the proportion of variance contributed by it to generate phenotypes. Simulation studies show that MF-TOWmuT can preserve the type I error rates and is more powerful than several existing methods in different simulation scenarios, MFTOWmuT is also quite …

Joint Simulation Of Continuous And Categorical Variables For Mineral Resource Modeling And Recoverable Reserves Calculation, Sentle Augustinus Hlajoane

Dissertations, Master's Theses and Master's Reports

Spatial variability and uncertainty of continuous variables (grade) and categorical variables (rock-types) in mineral evaluation significantly impact the economics of mining projects. The conventional approach of simulating grades using deterministic rock- types is problematic since spatial variability, and uncertainty of grades at rock-type contacts are not well captured in deposits where the grade changes gradually between rock-types. Therefore, jointly simulating these variables can improve confidence (reduce uncertainty) in a resource model. Also, resource classification and recoverable reserve calculation can significantly improve the understanding of the deposit and its economic viability. This research utilized the Plural-Gaussian geostatistical simulation to jointly simulate …

Statistical Methods For Mixed Frequency Data Sampling Models, Yun Liu

Dissertations, Master's Theses and Master's Reports

The MIDAS models are developed to handle different sampling frequencies in one regression model, preserving information in the higher sampling frequency. Time averaging has been the traditional parametric approach to handle mixed sampling frequencies. However, it ignores information potentially embedded in high frequency. MIDAS regression models provide a concise way to utilize additional information in HF variables. While a parametric MIDAS model provides a parsimonious way to summarize information in HF data, nonparametric models would maintain more flexibility at the expense of the computational complexity. Moreover, one parametric form may not necessarily be appropriate for all cross-sectional subjects. This thesis …

Statistical Methods For Joint Analysis Of Multiple Phenotypes And Their Applications For Phewas, Xueling Li

Dissertations, Master's Theses and Master's Reports

Genome-wide association studies (GWAS) have successfully detected tens of thousands of robust SNP-trait associations. Earlier researches have primarily focused on association studies of genetic variants and some well-defined functions or phenotypic traits. Emerging evidence suggests that pleiotropy, the phenomenon of one genetic variant affects multiple phenotypes, is widespread, especially in complex human diseases. Therefore, individual phenotype analyses may lose statistical power to identify the underlying genetic mechanism. Contrasting with single phenotype analyses, joint analysis of multiple phenotypes exploits the correlations between phenotypes and aggregates multiple weak marginal effects and is therefore likely to provide new insights into the functional consequences …

Bayesian Analysis For The Intraclass Model And For The Quantile Semiparametric Mixed-Effects Double Regression Models, Duo Zhang

Dissertations, Master's Theses and Master's Reports

This dissertation consists of three distinct but related research projects. The first two projects focus on objective Bayesian hypothesis testing and estimation for the intraclass correlation coefficient in linear models. The third project deals with Bayesian quantile inference for the semiparametric mixed-effects double regression models. In the first project, we derive the Bayes factors based on the divergence-based priors for testing the intraclass correlation coefficient (ICC). The hypothesis testing of the ICC is used to test the uncorrelatedness in multilevel modeling, and it has not well been studied from an objective Bayesian perspective. Simulation results show that the two sorts …

A Model To Predict Concentrations And Uncertainty For Mercury Species In Lakes, Ashley Hendricks

Dissertations, Master's Theses and Master's Reports

To increase understanding of mercury cycling, a seasonal mass balance model was developed to predict mercury concentrations in lakes and fish. Results indicate that seasonality in mercury cycling is significant and is important for a northern latitude lake. Models, when validated, have the potential to be used as an alternative to measurements; models are relatively inexpensive and are not as time intensive. Previously published mercury models have neglected to perform a thorough validation. Model validation allows for regulators to be able to make more informed, confident decisions when using models in water quality management. It is critical to quantify uncertainty; …

Statistical Methods For Detecting Causal Rare Variants And Analyzing Multiple Phenotypes, Xinlan Yang

Dissertations, Master's Theses and Master's Reports

This dissertation includes two papers with each distributed in one chapter. To date, genome-wide association studies (GWAS) have identified a large number of common variants that are associated with complex diseases successfully. However, the common variants identified by GWAS only account for a small proportion of trait heritability. Many studies showed that rare variants could explain parts of the missing heritability. Since the well-developed common variant detecting methods are underpowered for rare variant association tests unless sample sizes or effect sizes are very large, investigation the roles of rare variants in complex diseases presents substantial challenges. In chapter 1, we …

Offline And Online Density Estimation For Large High-Dimensional Data, Aref Majdara

Dissertations, Master's Theses and Master's Reports

Density estimation has wide applications in machine learning and data analysis techniques including clustering, classification, multimodality analysis, bump hunting and anomaly detection. In high-dimensional space, sparsity of data in local neighborhood makes many of parametric and nonparametric density estimation methods mostly inefficient.

This work presents development of computationally efficient algorithms for high-dimensional density estimation, based on Bayesian sequential partitioning (BSP). Copula transform is used to separate the estimation of marginal and joint densities, with the purpose of reducing the computational complexity and estimation error. Using this separation, a parallel implementation of the density estimation algorithm on a 4-core CPU is …

Joint Analysis Of Multiple Phenotypes In Association Studies, Xiaoyu Liang

Dissertations, Master's Theses and Master's Reports

Genome-wide association studies (GWAS) have become a very effective research tool to identify genetic variants of underlying various complex diseases. In spite of the success of GWAS in identifying thousands of reproducible associations between genetic variants and complex disease, in general, the association between genetic variants and a single phenotype is usually weak. It is increasingly recognized that joint analysis of multiple phenotypes can be potentially more powerful than the univariate analysis, and can shed new light on underlying biological mechanisms of complex diseases. Therefore, developing statistical methods to test for genetic association with multiple phenotypes has become increasingly important. …

Statistical Methods For Analyzing Multivariate Phenotypes And Detecting Rare Variant Associations, Huanhuan Zhu

Dissertations, Master's Theses and Master's Reports

This dissertation includes four papers with each distributed in one chapter.

In chapter 1, I compared the performance of eight multivariate phenotype association tests. The motivation to conduct this power comparison paper is as follows. For nearly 15 years, genome-wide association studies (GWAS) have been widely used to identify genetic variants associated with human diseases and traits. GWAS typically investigate genetic variants for a predefined phenotype, thus fail to identify weak but important effects. In recent years, many multivariate association tests have been developed. However, there is a lack of comprehensive summary of such kinds of approaches. To fill this …

Algorithms For Reconstruction Of Gene Regulatory Networks From High -Throughput Gene Expression Data, Wenping Deng

Dissertations, Master's Theses and Master's Reports

Understanding gene interactions in complex living systems is one of the central tasks in system biology. With the availability of microarray and RNA-Seq technologies, a multitude of gene expression datasets has been generated towards novel biological knowledge discovery through statistical analysis and reconstruction of gene regulatory networks (GRN). Reconstruction of GRNs can reveal the interrelationships among genes and identify the hierarchies of genes and hubs in networks. The new algorithms I developed in this dissertation are specifically focused on the reconstruction of GRNs with increased accuracy from microarray and RNA-Seq high-throughput gene expression data sets.

The first algorithm (Chapter 2) …

Joint Analysis For Multiple Traits, Zhenchuan Wang

Dissertations, Master's Theses and Master's Reports

This dissertation includes three papers with each distributed in one chapter.

In chapter 1, we proposed an Adaptive Weighting Reverse Regression (AWRR) method to test association between multiple traits and rare variants in a genomic region. AWRR is robust to the directions of effects of causal variants and is also robust to the directions of association of traits. Using extensive simulation studies, we compared the performance of AWRR with canonical correlation analysis (CCA), Single-TOW, and the Weighted Sum Reverse Regression (WSRR). Our results showed that, in all of the simulation scenarios, AWRR is consistently more powerful than CCA. In most …

Application Of Remote Sensing And Machine Learning Modeling To Post-Wildfire Debris Flow Risks, Priscilla Addison

Dissertations, Master's Theses and Master's Reports

Historically, post-fire debris flows (DFs) have been mostly more deadly than the fires that preceded them. Fires can transform a location that had no history of DFs to one that is primed for it. Studies have found that the higher the severity of the fire, the higher the probability of DF occurrence. Due to high fatalities associated with these events, several statistical models have been developed for use as emergency decision support tools. These previous models used linear modeling approaches that produced subpar results. Our study therefore investigated the application of nonlinear machine learning modeling as an alternative. Existing models …

Wildfire Emissions In The Context Of Global Change And The Implications For Mercury Pollution, Aditya Kumar

Dissertations, Master's Theses and Master's Reports

Wildfires are episodic disturbances that exert a significant influence on the Earth system. They emit substantial amounts of atmospheric pollutants, which can impact atmospheric chemistry/composition and the Earth’s climate at the global and regional scales. This work presents a collection of studies aimed at better estimating wildfire emissions of atmospheric pollutants, quantifying their impacts on remote ecosystems and determining the implications of 2000s-2050s global environmental change (land use/land cover, climate) for wildfire emissions following the Intergovernmental Panel on Climate Change (IPCC) A1B socioeconomic scenario.

A global fire emissions model is developed to compile global wildfire emission inventories for major atmospheric …

Analysis Of Data From A Study To Identify Potential Biomarkers To Indicate Renal Injury, Mitchell D. Tahtinen

Dissertations, Master's Theses and Master's Reports

Ureteropelvic junction obstruction is a disease in which flow from the kidney to the bladder is obstructed for extended periods of time causing irreversible damage to the kidney. Current tests to detect kidney damage caused by obstruction are not effective until significant damage occurs. The purpose of this report is to identify a panel of biomarkers in urine to detect kidney damage earlier by analyzing data collected from a two-part study. Currently, two established urinary biomarkers to indicate kidney damage are NGAL and KIM-1. Biomarkers of interest in this study are CD13, CD10, and CD26. Results from the linear mixed …

Gamma/Hadron Separation For The Hawc Observatory, Michael J. Gerhardt

Dissertations, Master's Theses and Master's Reports

The High-Altitude Water Cherenkov (HAWC) Observatory is a gamma-ray observatory sensitive to gamma rays from 100 GeV to 100 TeV with an instantaneous field of view of ~2 sr. It is located on the Sierra Negra plateau in Mexico at an elevation of 4,100 m and began full operation in March 2015. The purpose of the detector is to study relativistic particles that are produced by interstellar and intergalactic objects such as: pulsars, supernova remnants, molecular clouds, black holes and more. To achieve optimal angular resolution, energy reconstruction and cosmic ray background suppression for the extensive air showers detected by …

On The Equivalence Between Bayesian And Frequentist Nonparametric Hypothesis Testing, Qiuchen Hai

Dissertations, Master's Theses and Master's Reports

Testing of hypotheses about the population parameter is one of the most fundamental tasks in the empirical sciences and is often conducted by using parametric tests (e.g., the t-test and F-test), in which they assume that the samples are from populations that are normally distributed. When the normality assumption is violated, nonparametric tests are employed as alternatives for making statistical inference. In recent years, the Bayesian versions of parametric tests have been well studied in the literature, whereas in contrast, the Bayesian versions of nonparametric tests are quite scant (for exception, Yuan and Johnson (2008) ) in the literature, mainly …