Physical Sciences and Mathematics Commons^™

Computer Methods For Pre-Microrna Secondary Structure Prediction, Dianwei Han

Theses and Dissertations--Computer Science

This thesis presents a new algorithm to predict the pre-microRNA secondary structure. An accurate prediction of the pre-microRNA secondary structure is important in miRNA informatics. Based on a recently proposed model, nucleotide cyclic motifs (NCM), to predict RNA secondary structure, we propose and implement a Modified NCM (MNCM) model with a physics-based scoring strategy to tackle the problem of pre-microRNA folding. Our microRNAfold is implemented using a global optimal algorithm based on the bottom-up local optimal solutions.

It has been shown that studying the functions of multiple genes and predicting the secondary structure of multiple related microRNA is more important …

Efficient Greedy-Face-Greedy Geographic Routing Protocols In Mobile Ad Hoc And Sensor Networks, Yan Sun

Theses and Dissertations--Computer Science

This thesis describes and develops two planarization algorithms for geographic routing and a geographic routing protocol for mobile ad hoc and sensor networks. As all nodes are mobile and there is no fixed infrastructure, the design of routing protocols is one of the most challenging issues in mobile ad hoc and sensor networks. In recent years, greedyface- greedy (GFG) geographic routing protocols have been widely used, which need nodes to construct planar graphs as the underlying graphs for face routing.

Two kinds of planarization algorithms have been developed, idealized and realistic planarization algorithms, respectively. The idealized planarization algorithms make the …

Novel Dense Stereo Algorithms For High-Quality Depth Estimation From Images, Liang Wang

Theses and Dissertations--Computer Science

This dissertation addresses the problem of inferring scene depth information from a collection of calibrated images taken from different viewpoints via stereo matching. Although it has been heavily investigated for decades, depth from stereo remains a long-standing challenge and popular research topic for several reasons. First of all, in order to be of practical use for many real-time applications such as autonomous driving, accurate depth estimation in real-time is of great importance and one of the core challenges in stereo. Second, for applications such as 3D reconstruction and view synthesis, high-quality depth estimation is crucial to achieve photo realistic results. …

Energy-Aware Optimization For Embedded Systems With Chip Multiprocessor And Phase-Change Memory, Jiayin Li

Theses and Dissertations--Electrical and Computer Engineering

Over the last two decades, functions of the embedded systems have evolved from simple real-time control and monitoring to more complicated services. Embedded systems equipped with powerful chips can provide the performance that computationally demanding information processing applications need. However, due to the power issue, the easy way to gain increasing performance by scaling up chip frequencies is no longer feasible. Recently, low-power architecture designs have been the main trend in embedded system designs.

In this dissertation, we present our approaches to attack the energy-related issues in embedded system designs, such as thermal issues in the 3D chip multiprocessor (CMP), …

A Reliability-Based Routing Protocol For Vehicular Ad-Hoc Networks, James Bernsen

University of Kentucky Master's Theses

Vehicular Ad hoc NETworks (VANETs), an emerging technology, would allow vehicles to form a self-organized network without the aid of a permanent infrastructure. As a prerequisite to communication in VANETs, an efficient route between communicating nodes in the network must be established, and the routing protocol must adapt to the rapidly changing topology of vehicles in motion. This is one of the goals of VANET routing protocols. In this thesis, we present an efficient routing protocol for VANETs, called the Reliable Inter-VEhicular Routing (RIVER) protocol. RIVER utilizes an undirected graph that represents the surrounding street layout where the vertices of …

Cluster-Based Term Weighting And Document Ranking Models, Keerthiram Murugesan

University of Kentucky Master's Theses

A term weighting scheme measures the importance of a term in a collection. A document ranking model uses these term weights to find the rank or score of a document in a collection. We present a series of cluster-based term weighting and document ranking models based on the TF-IDF and Okapi BM25 models. These term weighting and document ranking models update the inter-cluster and intra-cluster frequency components based on the generated clusters. These inter-cluster and intra-cluster frequency components are used for weighting the importance of a term in addition to the term and document frequency components. In this thesis, we …

Three Dimensional Modeling And Animation Of Facial Expressions, Alice J. Lin

University of Kentucky Doctoral Dissertations

Facial expression and animation are important aspects of the 3D environment featuring human characters. These animations are frequently used in many kinds of applications and there have been many efforts to increase the realism. Three aspects are still stimulating active research: the detailed subtle facial expressions, the process of rigging a face, and the transfer of an expression from one person to another. This dissertation focuses on the above three aspects.

A system for freely designing and creating detailed, dynamic, and animated facial expressions is developed. The presented pattern functions produce detailed and animated facial expressions. The system produces realistic …

Checkpointing And Recovery In Distributed And Database Systems, Jiang Wu

Theses and Dissertations--Computer Science

A transaction-consistent global checkpoint of a database records a state of the database which reflects the effect of only completed transactions and not the re- sults of any partially executed transactions. This thesis establishes the necessary and sufficient conditions for a checkpoint of a data item (or the checkpoints of a set of data items) to be part of a transaction-consistent global checkpoint of the database. This result would be useful for constructing transaction-consistent global checkpoints incrementally from the checkpoints of each individual data item of a database. By applying this condition, we can start from any useful checkpoint of …

On Simple But Hard Random Instances Of Propositional Theories And Logic Programs, Gayathri Namasivayam

University of Kentucky Doctoral Dissertations

In the last decade, Answer Set Programming (ASP) and Satisfiability (SAT) have been used to solve combinatorial search problems and practical applications in which they arise. In each of these formalisms, a tool called a solver is used to solve problems. A solver takes as input a specification of the problem – a logic program in the case of ASP, and a CNF theory for SAT – and produces as output a solution to the problem. Designing fast solvers is important for the success of this general-purpose approach to solving search problems. Classes of instances that pose challenges to solvers …

Modeling And Quantitative Analysis Of White Matter Fiber Tracts In Diffusion Tensor Imaging, Xuwei Liang

University of Kentucky Doctoral Dissertations

Diffusion tensor imaging (DTI) is a structural magnetic resonance imaging (MRI) technique to record incoherent motion of water molecules and has been used to detect micro structural white matter alterations in clinical studies to explore certain brain disorders. A variety of DTI based techniques for detecting brain disorders and facilitating clinical group analysis have been developed in the past few years. However, there are two crucial issues that have great impacts on the performance of those algorithms. One is that brain neural pathways appear in complicated 3D structures which are inappropriate and inaccurate to be approximated by simple 2D structures, …

Resource Allocation And Efficient Routing In Wireless Networks, Jianjun Yang

University of Kentucky Doctoral Dissertations

In wireless networks, devices (nodes) are connected by wireless links. An important issue is to set up high quality (high bandwidth) and efficient routing paths when one node wants to send packets to other nodes. Resource allocation is the foundation to guarantee high quality connections. In addition, it is critical to handle void areas in order to set up detour-free paths. Moreover, fast message broadcasting is essential in mobile wireless networks. Thus, my research includes dynamic channel allocation in wireless mesh networks, geographic routing in Ad Hoc networks, and message broadcasting in vehicular networks.

The quality of connections in a …

A Secure Online Payment System, Shristi Pant

Theses and Dissertations--Computer Science

An online payment system allows a customer to make a payment to an online merchant or a service provider. Payment gateways, a channel between customers and payment processors, use various security tools to secure a customer’s payment information, usually debit or credit card information, during an online payment. However, the security provided by a payment gateway cannot completely protect a customer’s payment information when a merchant also has the ability to obtain the payment information in some form. Furthermore, not all merchants provide a secure payment environment to their customers and, despite having a standard payment policy, adhere to it. …

Construction Of Efficient Authentication Schemes Using Trapdoor Hash Functions, Santosh Chandrasekhar

University of Kentucky Doctoral Dissertations

In large-scale distributed systems, where adversarial attacks can have widespread impact, authentication provides protection from threats involving impersonation of entities and tampering of data. Practical solutions to authentication problems in distributed systems must meet specific constraints of the target system, and provide a reasonable balance between security and cost. The goal of this dissertation is to address the problem of building practical and efficient authentication mechanisms to secure distributed applications. This dissertation presents techniques to construct efficient digital signature schemes using trapdoor hash functions for various distributed applications. Trapdoor hash functions are collision-resistant hash functions associated with a secret trapdoor …

High Accuracy Multiscale Multigrid Computation For Partial Differential Equations, Yin Wang

University of Kentucky Doctoral Dissertations

Scientific computing and computer simulation play an increasingly important role in scientific investigation and engineering designs, supplementing traditional experiments, such as in automotive crash studies, global climate change, ocean modeling, medical imaging, and nuclear weapons. The numerical simulation is much cheaper than experimentation for these application areas and it can be used as the third way of science discovery beyond the experimental and theoretical analysis. However, the increasing demand of high resolution solutions of the Partial Differential Equations (PDEs) with less computational time has increased the importance for researchers and engineers to come up with efficient and scalable computational techniques …

A Trusted Storage System For The Cloud, Sushama Karumanchi

University of Kentucky Master's Theses

Data stored in third party storage systems like the cloud might not be secure since confidentiality and integrity of data are not guaranteed. Though cloud computing provides cost-effective storage services, it is a third party service and so, a client cannot trust the cloud service provider to store its data securely within the cloud. Hence, many organizations and users may not be willing to use the cloud services to store their data in the cloud until certain security guarantees are made. In this thesis, a solution to the problem of securely storing the client’s data by maintaining the confidentiality and …

Single View Reconstruction For Human Face And Motion With Priors, Xianwang Wang

University of Kentucky Doctoral Dissertations

Single view reconstruction is fundamentally an under-constrained problem. We aim to develop new approaches to model human face and motion with model priors that restrict the space of possible solutions. First, we develop a novel approach to recover the 3D shape from a single view image under challenging conditions, such as large variations in illumination and pose. The problem is addressed by employing the techniques of non-linear manifold embedding and alignment. Specifically, the local image models for each patch of facial images and the local surface models for each patch of 3D shape are learned using a non-linear dimensionality reduction …

Analysis Of Security Measures For Sequences, Ramakanth Kavuluru

University of Kentucky Doctoral Dissertations

Stream ciphers are private key cryptosystems used for security in communication and data transmission systems. Because they are used to encrypt streams of data, it is necessary for stream ciphers to use primitives that are easy to implement and fast to operate. LFSRs and the recently invented FCSRs are two such primitives, which give rise to certain security measures for the cryptographic strength of sequences, which we refer to as complexity measures henceforth following the convention. The linear (resp. N-adic) complexity of a sequence is the length of the shortest LFSR (resp. FCSR) that can generate the sequence. Due …

A Protocol Suite For Wireless Personal Area Networks, Karl E. Persson

University of Kentucky Doctoral Dissertations

A Wireless Personal Area Network (WPAN) is an ad hoc network that consists of devices that surround an individual or an object. Bluetooth^® technology is especially suitable for formation of WPANs due to the pervasiveness of devices with Bluetooth^® chipsets, its operation in the unlicensed Industrial, Scientific, Medical (ISM) frequency band, and its interference resilience. Bluetooth^® technology has great potential to become the de facto standard for communication between heterogeneous devices in WPANs.

The piconet, which is the basic Bluetooth^® networking unit, utilizes a Master/Slave (MS) configuration that permits only a single master and up to …

3d Reconstruction Using Multi-View Imaging System, Conglin Huang

University of Kentucky Master's Theses

This thesis presents a new system that reconstructs the 3D representation of dental casts. To maintain the integrity of the 3D representation, a standard model is built to cover the blind spots that the camera cannot reach. The standard model is obtained by scanning a real human mouth model with a laser scanner. Then the model is simplified by an algorithm which is based on iterative contraction of vertex pairs. The simplified standard model uses a local parametrization method to obtain the curvature information. The system uses a digital camera and a square tube mirror in front of the camera …

Satisfaction Assessment Of Textual Software Engineering Artifacts, Elizabeth Ashlee Holbrook

University of Kentucky Doctoral Dissertations

A large number of software projects exist and will continue to be developed that have textual requirements and textual design elements where the design elements should fully satisfy the requirements. Current techniques to assess the satisfaction of requirements by corresponding design elements are largely manual processes that lack formal criteria and standard practices. Software projects that require satisfaction assessment are often very large systems containing several hundred requirements and design elements. Often these projects are within a high assurance project domain, where human lives and millions of dollars of funding are at stake. Manual satisfaction assessment is expensive in terms …

Accurate And Robust Preconditioning Techniques For Solving General Sparse Linear Systems, Eun-Joo Lee

University of Kentucky Doctoral Dissertations

Please download this dissertation to see the abstract.

Data Assimilation And Visualization For Ensemble Wildland Fire Models, Soham Chakraborty

University of Kentucky Master's Theses

This thesis describes an observation function for a dynamic data driven application system designed to produce short range forecasts of the behavior of a wildland fire. The thesis presents an overview of the atmosphere-fire model, which models the complex interactions between the fire and the surrounding weather and the data assimilation module which is responsible for assimilating sensor information into the model. Observation plays an important role in data assimilation as it is used to estimate the model variables at the sensor locations. Also described is the implementation of a portable and user friendly visualization tool which displays the locations …

Computer Simulation And Modeling Of Physical And Biological Processes Using Partial Differential Equations, Wensheng Shen

University of Kentucky Doctoral Dissertations

Scientific research in areas of physics, chemistry, and biology traditionally depends purely on experimental and theoretical methods. Recently numerical simulation is emerging as the third way of science discovery beyond the experimental and theoretical approaches. This work describes some general procedures in numerical computation, and presents several applications of numerical modeling in bioheat transfer and biomechanics, jet diffusion flame, and bio-molecular interactions of proteins in blood circulation.

A three-dimensional (3D) multilayer model based on the skin physical structure is developed to investigate the transient thermal response of human skin subject to external heating. The temperature distribution of the skin is …

Bidirectional Lao* Algorithm (A Faster Approach To Solve Goal-Directed Mdps), Venkata Deepti Kiran Bhuma

University of Kentucky Master's Theses

Uncertainty is a feature of many AI applications. While there are polynomial-time algorithms for planning in stochastic systems, planning is still slow, in part because most algorithms plan for all eventualities. Algorithms such as LAO* are able to find good or optimal policies more quickly when the starting state of the system is known.

In this thesis we present an extension to LAO*, called BLAO*. BLAO* is an extension of the LAO* algorithm to a bidirectional search. We show that BLAO* finds optimal or ^_E-optimal solutions for goal-directed MDPs without necessarily evaluating the entire state space. BLAO* …