Physical Sciences and Mathematics Commons^™

Advanced Optimization Techniques For Monte Carlo Simulation On Graphics Processing Units, Eyad Hailat

Wayne State University Dissertations

The objective of this work is to design and implement a self-adaptive parallel GPU optimized Monte Carlo algorithm for the simulation of adsorption in porous materials. We focus on Nvidia's GPUs and CUDA's Fermi architecture specifically. The resulting package supports the different ensemble methods for the Monte Carlo simulation, which will allow for the simulation of multi-component adsorption in porous solids. Such an algorithm will have broad applications to the development of novel porous materials for the sequestration of CO2 and the filtration of toxic industrial chemicals.

The primary objective of this work is the release of a massively parallel …

Towards Personalized Medicine Using Systems Biology And Machine Learning, Calin Voichita

Wayne State University Dissertations

The rate of acquiring biological data has greatly surpassed our ability to interpret it. At the same time, we have started to understand that evolution of many diseases such as cancer, are the results of the interplay between the disease itself and the immune system of the host. It is now well accepted that cancer is not a single disease, but a “complex collection of distinct genetic diseases united by common hallmarks”. Understanding the differences between such disease subtypes is key not only in providing adequate treatments for known subtypes but also identifying new ones. These unforeseen disease subtypes are …

Performance Evaluation Of Voice Chat In Vechicular Ad-Hoc Networks, Vineeth Rakesh Mohan

Wayne State University Theses

Inter vehicle communication has emerged as an important area of research. With a rapid evolution of social networks, people are constantly looking for social interactions in all types of mobile environment. In this Thesis, we propose a voice chat model for Vehicle-to-Vehicle (V2V) communication that mimics a real-world group talk scenario, and measure its performance using Flood and Scalable broadcast (SBA) protocols. To evaluate the performance of the voice chat, we use different parameters such as group size, network density, transmission range and hop counts to show that our voice chat application is highly feasible in VANET environment. Furthermore, we …

Disulfide By Design 2.0: A Web-Based Tool For Disulfide Engineering In Proteins, Douglas B. Craig, Alan A. Dombkowski

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Disulfide engineering is an important biotechnological tool that has advanced a wide range of research. The introduction of novel disulfide bonds into proteins has been used extensively to improve protein stability, modify functional characteristics, and to assist in the study of protein dynamics. Successful use of this technology is greatly enhanced by software that can predict pairs of residues that will likely form a disulfide bond if mutated to cysteines.

Results

We had previously developed and distributed software for this purpose: Disulfide by Design (DbD). The original DbD program has been widely used; however, it has a number …

Visual Exploration And Information Analytics Of High-Dimensional Medical Images, Darshan Pai

Wayne State University Dissertations

Data visualization has transformed how we analyze increasingly large and complex data sets. Advanced visual tools logically represent data in a way that communicates the most important information inherent within it and culminate the analysis with an insightful conclusion. Automated analysis disciplines - such as data mining, machine learning, and statistics - have traditionally been the most dominant fields for data analysis. It has been complemented with a near-ubiquitous adoption of specialized hardware and software environments that handle the storage, retrieval, and pre- and postprocessing of digital data. The addition of interactive visualization tools allows an active human participant in …

Learning With An Insufficient Supply Of Data Via Knowledge Transfer And Sharing, Samir Al-Stouhi

Wayne State University Dissertations

As machine learning methods extend to more complex and diverse set of problems, situations arise where the complexity and availability of data presents a situation where the information source is not "adequate" to generate a representative hypothesis. Learning from multiple sources of data is a promising research direction as researchers leverage ever more diverse sources of information. Since data is not readily available, knowledge has to be transferred from other sources and new methods (both supervised and un-supervised) have to be developed to selectively share and transfer knowledge. In this dissertation, we present both supervised and un-supervised techniques to tackle …

Analyzing Environmental Change And Prehistoric Hunter Behavior Through A 3d Time-Lapsed Model With Level Auto-Generation And Cultural Algorithms, Samuel Dustin Stanley

Wayne State University Theses

This paper describes a system containing two portions whose purpose it is to help further the Alpena-Amberley Land Bridge research project and similar archaeological research. The first portion is a "time engine" which one can utilize to navigate through time in order to see how environmental conditions evolved as time passed, or to run experiments during a desired time period. The second portion is a hunting blind cultural algorithm, which is built on top of the time engine as well as Palazzolo's program. In this portion, the AI hunting blinds react to the goals that they are trying to achieve, …

On The Relationship Between The Vocabulary Of Bug Reports And Source Code, Amunugamage Buddhini Wathsala Bandara

Wayne State University Theses

The use of text retrieval techniques on concept location and bug localization yields remarkable benefits. The artifacts found in source code and bug reports contain important information related to the bug localization process. When locating the bugs, it is a programmer's task to formulate effective queries such that most of the predicted terms in the query appear in the relevant defect code, but not in most of the non-relevant source files. These queries are built based on the textual content found in the bug reports, especially the bug title and the description. A large body of research uses bug descriptions …

Regression Models For Readmission Prediction Using Electronic Medical Records, Yudi Niu

Wayne State University Theses

Hospital readmissions are not only expensive but are also potentially harmful, and most importantly, they are often preventable. Providing special care for a targeted group of patients who are at a high risk of readmission can significantly improve the chances of avoiding rehospitalization. Despite the significance of this problem, not many researchers have thoroughly investigated it due to the inherent complexities involved in analyzing and estimating the inherent predictive power of such complex hospitalization records. In this thesis, we propose using support vector machines and survival analysis methods to analyze data collected from Electronic Medical Records (EMR). We define the …

Opacity Of Discrete Event Systems: Analysis And Control, Majed Mohamed Ben Kalefa

Wayne State University Dissertations

The exchange of sensitive information in many systems over a network can be manipulated

by unauthorized access. Opacity is a property to investigate security and

privacy problems in such systems. Opacity characterizes whether a secret information

of a system can be inferred by an unauthorized user. One approach to verify security

and privacy properties using opacity problem is to model the system that may leak confidential

information as a discrete event system. The problem that has not investigated

intensively is the enforcement of opacity properties by supervisory control. In other

words, constructing a minimally restrictive supervisor to limit the system's …

Combinatorial Auction-Based Virtual Machine Provisioning And Allocation In Clouds, Sharrukh Zaman

Wayne State University Dissertations

Current cloud providers use fixed-price based mechanisms to allocate Virtual Machine (VM) instances to their users. But economic theory states that when there are large amount of resources to be allocated to large number of users, auctions are the most efficient allocation mechanisms. Auctions achieve efficiency of allocation and also maximize the providers' revenue, which a fixed-price based mechanism is unable to do. We argue that combinatorial auctions are best suited for the problem of VM provisioning and allocation in clouds, since they provide the users with the most flexible way to express their requirements. In combinatorial auctions, users bid …

Fault Management For Service-Oriented Systems, Amal Alhosban

Wayne State University Dissertations

Service Oriented Architectures (SOAs) enable the automatic creation of business applications from independently developed and deployed Web services. As Web services are inherently unreliable,

how to deliver reliable Web services composition over unreliable Web services is a significant and challenging problem. The process requires monitoring the system's behavior, determining when and why faults occur, and then applying fault prevention/recovery mechanisms to minimize the impact and/or recover from these faults. However, it is hard to apply a non-distributed management

approach to SOA, since a manager needs to communicate with the different components through authentications. In SOA, a business process can terminate …

Supporting Text Retrieval Query Formulation In Software Engineering, Sonia Cristina Haiduc

Wayne State University Dissertations

The text found in software artifacts captures important information. Text Retrieval (TR) techniques have been successfully used to leverage this information. Despite their advantages, the success of TR techniques strongly depends on the textual queries given as input. When poorly chosen queries are used, developers can waste time investigating irrelevant results.

The quality of a query indicates the relevance of the results returned by TR in response to the query and can give an indication if the results are worth investigating or a reformulation of the query should be sought instead. Knowing the quality of the query could lead to …