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  Partner: UNT Libraries
 Degree Discipline: Computer Science
 Degree Level: Doctoral
 Collection: UNT Theses and Dissertations
Exon/Intron Discrimination Using the Finite Induction Pattern Matching Technique

Exon/Intron Discrimination Using the Finite Induction Pattern Matching Technique

Date: December 1997
Creator: Taylor, Pamela A., 1941-
Description: DNA sequence analysis involves precise discrimination of two of the sequence's most important components: exons and introns. Exons encode the proteins that are responsible for almost all the functions in a living organism. Introns interrupt the sequence coding for a protein and must be removed from primary RNA transcripts before translation to protein can occur. A pattern recognition technique called Finite Induction (FI) is utilized to study the language of exons and introns. FI is especially suited for analyzing and classifying large amounts of data representing sequences of interest. It requires no biological information and employs no statistical functions. Finite Induction is applied to the exon and intron components of DNA by building a collection of rules based upon what it finds in the sequences it examines. It then attempts to match the known rule patterns with new rules formed as a result of analyzing a new sequence. A high number of matches predict a probable close relationship between the two sequences; a low number of matches signifies a large amount of difference between the two. This research demonstrates FI to be a viable tool for measurement when known patterns are available for the formation of rule sets.
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Exploring Trusted Platform Module Capabilities: A Theoretical and Experimental Study

Exploring Trusted Platform Module Capabilities: A Theoretical and Experimental Study

Date: May 2008
Creator: Gunupudi, Vandana
Description: Trusted platform modules (TPMs) are hardware modules that are bound to a computer's motherboard, that are being included in many desktops and laptops. Augmenting computers with these hardware modules adds powerful functionality in distributed settings, allowing us to reason about the security of these systems in new ways. In this dissertation, I study the functionality of TPMs from a theoretical as well as an experimental perspective. On the theoretical front, I leverage various features of TPMs to construct applications like random oracles that are impossible to implement in a standard model of computation. Apart from random oracles, I construct a new cryptographic primitive which is basically a non-interactive form of the standard cryptographic primitive of oblivious transfer. I apply this new primitive to secure mobile agent computations, where interaction between various entities is typically required to ensure security. I prove these constructions are secure using standard cryptographic techniques and assumptions. To test the practicability of these constructions and their applications, I performed an experimental study, both on an actual TPM and a software TPM simulator which has been enhanced to make it reflect timings from a real TPM. This allowed me to benchmark the performance of the applications and test ...
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Flexible Digital Authentication Techniques

Flexible Digital Authentication Techniques

Date: May 2006
Creator: Ge, He
Description: Abstract This dissertation investigates authentication techniques in some emerging areas. Specifically, authentication schemes have been proposed that are well-suited for embedded systems, and privacy-respecting pay Web sites. With embedded systems, a person could own several devices which are capable of communication and interaction, but these devices use embedded processors whose computational capabilities are limited as compared to desktop computers. Examples of this scenario include entertainment devices or appliances owned by a consumer, multiple control and sensor systems in an automobile or airplane, and environmental controls in a building. An efficient public key cryptosystem has been devised, which provides a complete solution to an embedded system, including protocols for authentication, authenticated key exchange, encryption, and revocation. The new construction is especially suitable for the devices with constrained computing capabilities and resources. Compared with other available authentication schemes, such as X.509, identity-based encryption, etc, the new construction provides unique features such as simplicity, efficiency, forward secrecy, and an efficient re-keying mechanism. In the application scenario for a pay Web site, users may be sensitive about their privacy, and do not wish their behaviors to be tracked by Web sites. Thus, an anonymous authentication scheme is desirable in this case. That is, a ...
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A Framework for Analyzing and Optimizing Regional Bio-Emergency Response Plans

A Framework for Analyzing and Optimizing Regional Bio-Emergency Response Plans

Date: December 2010
Creator: Schneider, Tamara
Description: The presence of naturally occurring and man-made public health threats necessitate the design and implementation of mitigation strategies, such that adequate response is provided in a timely manner. Since multiple variables, such as geographic properties, resource constraints, and government mandated time-frames must be accounted for, computational methods provide the necessary tools to develop contingency response plans while respecting underlying data and assumptions. A typical response scenario involves the placement of points of dispensing (PODs) in the affected geographic region to supply vaccines or medications to the general public. Computational tools aid in the analysis of such response plans, as well as in the strategic placement of PODs, such that feasible response scenarios can be developed. Due to the sensitivity of bio-emergency response plans, geographic information, such as POD locations, must be kept confidential. The generation of synthetic geographic regions allows for the development of emergency response plans on non-sensitive data, as well as for the study of the effects of single geographic parameters. Further, synthetic representations of geographic regions allow for results to be published and evaluated by the scientific community. This dissertation presents methodology for the analysis of bio-emergency response plans, methods for plan optimization, as well as methodology ...
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Framework for Evaluating Dynamic Memory Allocators Including a New Equivalence Class Based Cache-conscious Allocator

Framework for Evaluating Dynamic Memory Allocators Including a New Equivalence Class Based Cache-conscious Allocator

Date: August 2013
Creator: Janjusic, Tomislav
Description: Software applications’ performance is hindered by a variety of factors, but most notably by the well-known CPU-memory speed gap (often known as the memory wall). This results in the CPU sitting idle waiting for data to be brought from memory to processor caches. The addressing used by caches cause non-uniform accesses to various cache sets. The non-uniformity is due to several reasons, including how different objects are accessed by the code and how the data objects are located in memory. Memory allocators determine where dynamically created objects are placed, thus defining addresses and their mapping to cache locations. It is important to evaluate how different allocators behave with respect to the localities of the created objects. Most allocators use a single attribute, the size, of an object in making allocation decisions. Additional attributes such as the placement with respect to other objects, or specific cache area may lead to better use of cache memories. In this dissertation, we proposed and implemented a framework that allows for the development and evaluation of new memory allocation techniques. At the root of the framework is a memory tracing tool called Gleipnir, which provides very detailed information about every memory access, and relates it ...
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GPS CaPPture: a System for GPS Trajectory Collection, Processing, and Destination Prediction

GPS CaPPture: a System for GPS Trajectory Collection, Processing, and Destination Prediction

Date: May 2012
Creator: Griffin, Terry W.
Description: In the United States, smartphone ownership surpassed 69.5 million in February 2011 with a large portion of those users (20%) downloading applications (apps) that enhance the usability of a device by adding additional functionality. a large percentage of apps are written specifically to utilize the geographical position of a mobile device. One of the prime factors in developing location prediction models is the use of historical data to train such a model. with larger sets of training data, prediction algorithms become more accurate; however, the use of historical data can quickly become a downfall if the GPS stream is not collected or processed correctly. Inaccurate or incomplete or even improperly interpreted historical data can lead to the inability to develop accurately performing prediction algorithms. As GPS chipsets become the standard in the ever increasing number of mobile devices, the opportunity for the collection of GPS data increases remarkably. the goal of this study is to build a comprehensive system that addresses the following challenges: (1) collection of GPS data streams in a manner such that the data is highly usable and has a reduction in errors; (2) processing and reduction of the collected data in order to prepare it and ...
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Group-EDF: A New Approach and an Efficient Non-Preemptive Algorithm for Soft Real-Time Systems

Group-EDF: A New Approach and an Efficient Non-Preemptive Algorithm for Soft Real-Time Systems

Date: August 2006
Creator: Li, Wenming
Description: Hard real-time systems in robotics, space and military missions, and control devices are specified with stringent and critical time constraints. On the other hand, soft real-time applications arising from multimedia, telecommunications, Internet web services, and games are specified with more lenient constraints. Real-time systems can also be distinguished in terms of their implementation into preemptive and non-preemptive systems. In preemptive systems, tasks are often preempted by higher priority tasks. Non-preemptive systems are gaining interest for implementing soft-real applications on multithreaded platforms. In this dissertation, I propose a new algorithm that uses a two-level scheduling strategy for scheduling non-preemptive soft real-time tasks. Our goal is to improve the success ratios of the well-known earliest deadline first (EDF) approach when the load on the system is very high and to improve the overall performance in both underloaded and overloaded conditions. Our approach, known as group-EDF (gEDF), is based on dynamic grouping of tasks with deadlines that are very close to each other, and using a shortest job first (SJF) technique to schedule tasks within the group. I believe that grouping tasks dynamically with similar deadlines and utilizing secondary criteria, such as minimizing the total execution time can lead to new and more ...
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High Performance Architecture using Speculative Threads and Dynamic Memory Management Hardware

High Performance Architecture using Speculative Threads and Dynamic Memory Management Hardware

Date: December 2007
Creator: Li, Wentong
Description: With the advances in very large scale integration (VLSI) technology, hundreds of billions of transistors can be packed into a single chip. With the increased hardware budget, how to take advantage of available hardware resources becomes an important research area. Some researchers have shifted from control flow Von-Neumann architecture back to dataflow architecture again in order to explore scalable architectures leading to multi-core systems with several hundreds of processing elements. In this dissertation, I address how the performance of modern processing systems can be improved, while attempting to reduce hardware complexity and energy consumptions. My research described here tackles both central processing unit (CPU) performance and memory subsystem performance. More specifically I will describe my research related to the design of an innovative decoupled multithreaded architecture that can be used in multi-core processor implementations. I also address how memory management functions can be off-loaded from processing pipelines to further improve system performance and eliminate cache pollution caused by runtime management functions.
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Higher Compression from the Burrows-Wheeler Transform with New Algorithms for the List Update Problem

Higher Compression from the Burrows-Wheeler Transform with New Algorithms for the List Update Problem

Date: August 2001
Creator: Chapin, Brenton
Description: Burrows-Wheeler compression is a three stage process in which the data is transformed with the Burrows-Wheeler Transform, then transformed with Move-To-Front, and finally encoded with an entropy coder. Move-To-Front, Transpose, and Frequency Count are some of the many algorithms used on the List Update problem. In 1985, Competitive Analysis first showed the superiority of Move-To-Front over Transpose and Frequency Count for the List Update problem with arbitrary data. Earlier studies due to Bitner assumed independent identically distributed data, and showed that while Move-To-Front adapts to a distribution faster, incurring less overwork, the asymptotic costs of Frequency Count and Transpose are less. The improvements to Burrows-Wheeler compression this work covers are increases in the amount, not speed, of compression. Best x of 2x-1 is a new family of algorithms created to improve on Move-To-Front's processing of the output of the Burrows-Wheeler Transform which is like piecewise independent identically distributed data. Other algorithms for both the middle stage of Burrows-Wheeler compression and the List Update problem for which overwork, asymptotic cost, and competitive ratios are also analyzed are several variations of Move One From Front and part of the randomized algorithm Timestamp. The Best x of 2x - 1 family includes Move-To-Front, ...
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A Highly Fault-Tolerant Distributed Database System with Replicated Data

A Highly Fault-Tolerant Distributed Database System with Replicated Data

Date: December 1994
Creator: Lin, Tsai S. (Tsai Shooumeei)
Description: Because of the high cost and impracticality of a high connectivity network, most recent research in transaction processing has focused on a distributed replicated database system. In such a system, multiple copies of a data item are created and stored at several sites in the network, so that the system is able to tolerate more crash and communication failures and attain higher data availability. However, the multiple copies also introduce a global inconsistency problem, especially in a partitioned network. In this dissertation a tree quorum algorithm is proposed to solve this problem, imposing a logical tree structure along with dynamic system reconfiguration on all the copies of each data item. The proposed algorithm can be viewed as a dynamic voting technique which, with the help of an appropriate concurrency control algorithm, exhibits the major advantages of quorum-based replica control algorithms and of the available copies algorithm, so that a single copy is read for a read operation and a quorum of copies is written for a write operation. In addition, read and write quorums are computed dynamically and independently. As a result expensive read operations, like those that require several copies of a data item to be read in most ...
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