Physical Sciences and Mathematics Commons^™

Multidimensional Feature Engineering For Post-Translational Modification Prediction Problems, Norman Mapes Jr.

Doctoral Dissertations

Protein sequence data has been produced at an astounding speed. This creates an opportunity to characterize these proteins for the treatment of illness. A crucial characterization of proteins is their post translational modifications (PTM). There are 20 amino acids coded by DNA after coding (translation) nearly every protein is modified at an amino acid level. We focus on three specific PTMs. First is the bonding formed between two cysteine amino acids, thus introducing a loop to the straight chain of a protein. Second, we predict which cysteines can generally be modified (oxidized). Finally, we predict which lysine amino acids are …

Spatiotemporal Subspace Feature Tracking By Mining Discriminatory Characteristics, Richard D. Appiah

Doctoral Dissertations

Recent advancements in data collection technologies have made it possible to collect heterogeneous data at complex levels of abstraction, and at an alarming pace and volume. Data mining, and most recently data science seek to discover hidden patterns and insights from these data by employing a variety of knowledge discovery techniques. At the core of these techniques is the selection and use of features, variables or properties upon which the data were acquired to facilitate effective data modeling. Selecting relevant features in data modeling is critical to ensure an overall model accuracy and optimal predictive performance of future effects. The …

Anxiolytic Effects Of Propranolol And Diphenoxylate On Mice And Automated Stretch-Attend Posture Analysis, Kevin Scott Holly

Doctoral Dissertations

The prevention of social anxiety, performance anxiety, and social phobia via the combination of two generic drugs, diphenoxylate HC1 (opioid) plus atropine sulfate (anticholinergic) and propranolol HCl (beta blocker) was evaluated in mice through behavioral studies. A patent published on a September 8, 2011 by Benjamin D. Holly, US 2011/0218215 Al, prompted the research. The drug combination of diphenoxylate and atropine plus propranolol could be an immediate treatment for patients suffering from acute phobic and social anxiety disorders. Demonstrating the anxiolytic effects of the treatment on mice would validate a mouse model for neuroscientist to be used to detect the …

Sensitivity Of Mixed Models To Computational Algorithms Of Time Series Data, Gunaime Nevine

Doctoral Dissertations

Statistical analysis is influenced by implementation of the algorithms used to execute the computations associated with various statistical techniques. Over many years; very important criteria for model comparison has been studied and examined, and two algorithms on a single dataset have been performed numerous times. The goal of this research is not comparing two or more models on one dataset, but comparing models with numerical algorithms that have been used to solve them on the same dataset.

In this research, different models have been broadly applied in modeling and their contrasting which are affected by the numerical algorithms in different …

Dual Channel-Based Network Traffic Authentication, David Irakiza

Doctoral Dissertations

In a local network or the Internet in general, data that is transmitted between two computers (also known as network traffic or simply, traffic) in that network is usually classified as being of a malicious or of a benign nature by a traffic authentication system employing databases of previously observed malicious or benign traffic signatures, i.e., blacklists or whitelists, respectively. These lists typically consist of either the destinations (i.e., IP addresses or domain names) to which traffic is being sent or the statistical properties of the traffic, e.g., packet size, rate of connection establishment, etc. The drawback with the list-based …

Topology Dependence Of Ppm-Based Internet Protocol Traceback Schemes, Ankunda R. Kiremire

Doctoral Dissertations

Multiple schemes that utilize probabilistic packet marking (PPM) have been proposed to deal with Distributed Denial of Service (DDoS) attacks by reconstructing their attack graphs and identifying the attack sources.

In the first part of this dissertation, we present our contribution to the family of PPM-based schemes for Internet Protocol (IP) traceback. Our proposed approach, Prediction-Based Scheme (PBS), consists of marking and traceback algorithms that reduce scheme convergence times by dealing with the problems of data loss and incomplete attack graphs exhibited by previous PPM-based schemes.

Compared to previous PPM-based schemes, the PBS marking algorithm ensures that traceback is possible …

A Knowledge Discovery Approach For The Detection Of Power Grid State Variable Attacks, Nathan Wallace

Doctoral Dissertations

As the level of sophistication in power system technologies increases, the amount of system state parameters being recorded also increases. This data not only provides an opportunity for monitoring and diagnostics of a power system, but it also creates an environment wherein security can be maintained. Being able to extract relevant information from this pool of data is one of the key challenges still yet to be obtained in the smart grid. The potential exists for the creation of innovative power grid cybersecurity applications, which harness the information gained from advanced analytics. Such analytics can be based on the extraction …

Performance Modeling And Optimization Techniques For Heterogeneous Computing, Supada Laosooksathit

Doctoral Dissertations

Since Graphics Processing Units (CPUs) have increasingly gained popularity amoung non-graphic and computational applications, known as General-Purpose computation on GPU (GPGPU), CPUs have been deployed in many clusters, including the world's fastest supercomputer. However, to make the most efficiency from a GPU system, one should consider both performance and reliability of the system.

This dissertation makes four major contributions. First, the two-level checkpoint/restart protocol that aims to reduce the checkpoint and recovery costs with a latency hiding strategy in a system between a CPU (Central Processing Unit) and a GPU is proposed. The experimental results and analysis reveals some benefits, …

A Modeling And Simulation Framework For Electrokinetic Nanoparticle Treatment, James Phillips

Doctoral Dissertations

The focus of this research is to model and provide a simulation framework for the packing of differently sized spheres within a hard boundary. The novel contributions of this dissertation are the cylinders of influence (COI) method and sectoring method implementations. The impetus for this research stems from modeling electrokinetic nanoparticle (EN) treatment, which packs concrete pores with differently sized nanoparticles. We show an improved speed of the simulation compared to previously published results of EN treatment simulation while obtaining similar porosity reduction results. We mainly focused on readily, commercially available particle sizes of 2 nm and 20 nm particles, …

A Hybrid Finite Element-Finite Difference Method For Thermal Analysis In A Double-Layered Thin Film, Teng Zhu

Doctoral Dissertations

Thin film technology is of vital importance in microtechnology applications. For instance, thin films of metals, of dielectrics such as SiO2, or Si semiconductors are important components of microelectronic devices. The reduction of the device size to the microscale has the advantage of enhancing the switching speed of the device. The reduction, on the other hand, increases the rate of heat generation that leads to a high thermal load on the microdevice. Heat transfer at the microscale with an ultrafast pulsed-laser is also a very important process for thin films. Hence, studying the thermal behavior of thin films or of …

A Systematic Integration Of Register Allocation And Instruction Scheduling, Yukong Zhang

Doctoral Dissertations

In order to achieve high performance, processor architecture has become more and more complicated. As a result, compiler-time optimizations have become more and more important for the effective use of a complex processor. One of the promising compiler-time optimizations is the integration of register allocation and instruction scheduling based on register-reuse chains. In the previous approach, however, the generation of register-reuse chains was not completely systematic and consequently created many unnecessary dependencies that restrict instruction scheduling.

This research proposes a new register allocation technique based on a systematic generation of register-reuse chains. The first phase of the proposed technique is …