Digital Commons Network^™

Phylogenetic Reconstruction Analysis On Gene Order And Copy Number Variation, Ruofan Xia

Theses and Dissertations

Genome rearrangement is known as one of the main evolutionary mechanisms on the genomic level. Phylogenetic analysis based on rearrangement played a crucial role in biological research in the past decades, especially with the increasing avail- ability of fully sequenced genomes. In general, phylogenetic analysis aims to solve two problems: Small Parsimony Problem (SPP) and Big Parsimony Problem (BPP). Maximum parsimony is a popular approach for SPP and BPP which relies on itera- tively solving a NP-hard problem, the median problem. As a result, current median solvers and phylogenetic inference methods based on the median problem all face se- rious …

Disinfection By-Products: Method Optimization For Quantification, Unknown Analysis, And Calculated Toxicity, Amy A. Cuthbertson

Theses and Dissertations

Disinfected drinking water contains hundreds of disinfection by-products (DBPs) that are formed by the reaction of disinfectants with natural and anthropogenic organic matter, bromide, and iodide. Understanding what these DBPs are is important because millions of people worldwide consume drinking water every day, and human epidemiologic studies have reported cancer, miscarriage, and birth defects from consuming such waters. While more than 700 DBPs are reported in the literature, very few studies quantify complete classes of chlorinated, brominated, and iodinated DBPs. The following document contains five chapters in the format designated for specific scientific journals on this subject. Chapter 1 describes …

Spatio-Temporal Analysis Of Precipitation And Flood Data From South Carolina, Haigang Liu

Theses and Dissertations

Spatio-temporal data are everywhere: we encounter them on TV, in newspapers, on computer screens, on tablets, and on plain paper maps. As a result, researchers in di- verse areas are increasingly faced with the task of modeling geographically-referenced and temporally-correlated data. In this dissertation, we propose two different spa- tiotemporal models to capture the behavior of rainfall and flood data in the state of South Carolina.

Both models are built using a Bayesian hierarchical framework, which involves specifying the true underlying process in the first level and the spatio-temporal ran- dom effect in the second level of the hierarchy. The …

An Instruction Embedding Model For Binary Code Analysis, Kimberly Michelle Redmond

Theses and Dissertations

Binary code analysis is important for understanding programs without access to the original source code, which is common with proprietary software. Analyzing binaries can be challenging given their high variability: due to growth in tech manufactur- ers, source code is now frequently compiled for multiple instruction set architectures (ISAs); however, there is no formal dictionary that translates between their assem- bly languages. The difficulty of analysis is further compounded by different compiler optimizations and obfuscated malware signatures. Such minutiae means that some vulnerabilities may only be detectable on a fine-grained level. Recent strides in ma- chine learning—particularly in Natural Language …