Engineering Commons^™

Data Mining Of Protein Databases, Christopher Assi

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Data mining of protein databases poses special challenges because many protein databases are non-relational whereas most data mining and machine learning algorithms assume the input data to be a relational database. Protein databases are non-relational mainly because they often contain set data types. We developed new data mining algorithms that can restructure non-relational protein databases so that they become relational and amenable for various data mining and machine learning tools. We applied the new restructuring algorithms to a pancreatic protein database. After the restructuring, we also applied two classification methods, such as decision tree and SVM classifiers and compared their …

On Heterogeneous User Demands In Peer-To-Peer Video Streaming Systems, Zhipeng Ouyang

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

A Peer-to-Peer (P2P) video streaming system usually consists of a large number of peers, which have heterogeneous physical properties. Orthogonal to the physical heterogeneity, there is another type of heterogeneity called demand heterogeneity. Namely, peers have their own demands on the quality and type of the streaming service. The problem of demand heterogeneity has received little attention and as a result current P2P video streaming systems cannot achieve satisfactory performance due to demand heterogeneity. In this dissertation, we study how to design efficient P2P video streaming systems with heterogeneous user demands.

First, we study the problem of heterogeneous user demands …

An Enhanced Self-Adaptive Mapreduce Scheduling Algorithm, Xiaoyu Sun

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

MapReduce is a framework for processing huge amounts of data in a distributed environment and Hadoop is Apache’s open source implementation of MapReduce, which is widely used. However, Hadoop’s performance is currently limited by its default task scheduler, which assumes that cluster nodes are homogeneous when estimating the task progress and choosing slow tasks for re-execution. In practice, the homogeneity assumption does not always hold. Longest Approximate Time to End (LATE) is a scheduling algorithm that takes heterogeneity into account. It, however, still depends on a static method to estimate the task execution time. As a result, neither Hadoop default …

Probabilistic Qos Analysis In Wireless Sensor Networks, Yunbo Wang

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Emerging applications of wireless sensor networks (WSNs) require real-time quality of service (QoS) guarantees to be provided by the network. Traditional analysis work only focuses on the first-order statistics, such as the mean and the variance of the QoS performance. However, due to unique characteristics of WSNs, a cross-layer probabilistic analysis of QoS performance is essential. In this dissertation, a comprehensive cross-layer probabilistic analysis framework is developed to investigate the probabilistic evaluation and optimization of QoS performance provided by WSNs. In this framework, the distributions of QoS performance metrics are derived, which are natural tools to discover the probabilities to …

Cogtool-Helper: Leveraging Gui Functional Testing Tools To Generate Predictive Human Performance Models, Amanda Swearngin

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Numerous tools and techniques for human performance modeling have been introduced in the field of human-computer interaction. With such tools comes the ability to model legacy applications. Models can be used to compare design ideas to existing applications, or to evaluate products against those of competitors. One such mod- eling tool, CogTool, allows user interface designers and analysts to mock up design ideas, demonstrate tasks, and obtain human performance predictions for those tasks. This is one step towards a simple and complete analysis process, but it still requires a large amount of manual work. Graphical user interface (GUI) testing tools …

Supporting Developer-Onboarding With Enhanced Resource Finding And Visual Exploration, Jianguo Wang

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Understanding the basic structure of a code base and a development team are essential to get new developers up to speed in a software development project. Developers do so through the process of early experimentation with code and the creation of mental models of technical and social structures in a project. However, getting up-to-speed in a new project can be challenging due to difficulties in: finding the right place to begin explorations, expanding the focus to determine relevant resources for tasks, and identifying dependencies across project elements to gain a high-level overview of project structures. In this thesis, I first …

Improving Backup And Restore Performance For Deduplication-Based Cloud Backup Services, Stephen Mkandawire

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

The benefits provided by cloud computing and the space savings offered by data deduplication make it attractive to host data storage services like backup in the cloud. Data deduplication relies on comparing fingerprints of data chunks, and store them in the chunk index, to identify and remove redundant data, with an ultimate goal of saving storage space and network bandwidth.

However, the chunk index presents a bottleneck to the throughput of the backup operation. While several solutions to address deduplication throughput have been proposed, the chunk index is still a centralized resource and limits the scalability of both storage capacity …

Location Cheating: A Security Challenge To Location-Based Social Network Services, Mai Ren

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Location-based mobile social network services such as Foursquare and Gowalla have grown exponentially over the past several years. These location-based services utilize the geographical position to enrich user experiences in a variety of contexts, including location-based searching and location-based mobile advertising. To attract more users, the location-based mobile social network services provide real-world rewards to the user, when a user checks in at a certain venue or location. This gives incentives for users to cheat on their locations.

In this thesis, we investigate the threat of location cheating attacks, find the root cause of the vulnerability, and outline the possible …

Relational Neighborhood Inverse Consistency For Constraint Satisfaction: A Structure-Based Approach For Adjusting Consistency & Managing Propagation, Robert J. Woodward

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Freuder and Elfe [1996] introduced Neighborhood Inverse Consistency (NIC) as a local consistency property defined on the values in the variables' domains of a Constraint Satisfaction Problem (CSP). Debruyne and Bessiere [2011] showed that enforcing NIC on binary CSPs is ineffective on sparse graph and too costly on dense graphs. In this thesis, we propose Relational Neighborhood Inverse Consistency (RNIC), an extension of NIC defined as a local consistency property on the tuples of the relations of a CSP. We characterize RNIC for both binary and non-binary CSPs, and propose an algorithm for enforcing it whose complexity is bounded by …

Efficient Traffic Crash And Snow Complaint Gis System, Anthony B. Ngo

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

We describe the design and implementation of a traffic crash and snow complaint GIS system developed for the Lincoln Public Works department. We also describe a novel geocoding algorithm that was used to move data from the older Criminal Justice Information System, which is a relational database, to the new GIS system. In addition, we describe the implementation of several indexing algorithms that enable the system to efficiently answer rectangular range queries and queries about the relative locations of moving objects. Finally, in many applications (on-line analysis or mobile GIS), we need to execute spatial query efficiently (fast and small), …

Classification For Mass Spectra And Comprehensive Two-Dimensional Chromatograms, Xue Tian

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Mass spectra contain characteristic information regarding the molecular structure and properties of compounds. The mass spectra of compounds from the same chemically related group are similar. Classification is one of the fundamental methodologies for analyzing mass spectral data. The primary goals of classification are to automatically group compounds based on their mass spectra, to find correlation between the properties of compounds and their mass spectra, and to provide a positive identification of unknown compounds.

This dissertation presents a new algorithm for the classification of mass spectra, the most similar neighbor with a probability-based spectrum similarity measure (MSN-PSSM). Experimental results demonstrate …

Molecular Dynamics Simulation Based On Hadoop Mapreduce, Chen He

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Molecular Dynamics (MD) simulation is a computationally intensive application used in multiple fields. It can exploit a distributed environment due to inherent computational parallelism. However, most of the existing implementations focus on performance enhancement. They may not provide fault-tolerance for every time-step.

MapReduce is a framework first proposed by Google for processing huge amounts of data in a distributed environment. The simplicity of the programming model and fault- tolerance for node failure during run-time make it very popular not only for commercial applications but also in scientific computing.

In this thesis, we develop a novel communication-free and each time-step fault- …

Real-Time Divisible Load Scheduling For Cluster Computing, Anwar Mamat

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Cluster computing has become an important paradigm for solving large-scale problems. However, as the size of a cluster increases, so does the complexity of resource management and maintenance. Therefore, automated performance control and re- source management are expected to play critical roles in sustaining the evolution of cluster computing. The current cluster scheduling practice is similar in sophistication to early supercomputer batch scheduling algorithms, and no consideration is given to desired quality-of-service (QoS) attributes. To fully avail the power of computational clusters, new scheduling algorithms that provides high performance, QoS assurance, fault-tolerance, energy savings and streamlined management of the cluster …

A Reservation-Based Smart Parking System, Hongwei Wang

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

In metropolitan areas, parking management influences drivers search time and cost for parking spaces, parking revenue, and traffic congestion. The wide deployment of wireless parking meters with sensing and communications capabilities allows the parking authority to monitor the state of each parking space in real time and optimize the parking management.

In this thesis, we study state-of-the-art parking policies in smart parking systems, and show that the smart parking system needs to be "smarter". Our design goals of the smart parking systems include: (1) simplify the operations of parking systems, (2) improve drivers' satisfaction, (3) increase parking revenue, and (4) …

Campus Grids: A Framework To Facilitate Resource Sharing, Derek J. Weitzel

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

It is common at research institutions to maintain multiple clusters. These might fulfill different needs and policies, or represent different owners or generations of hard- ware. Many of these clusters are under utilized while researchers at other departments may require these resources. This may be solved by linking clusters with grid mid- dleware. This thesis describes a distributed high throughput computing framework to link clusters without changing security or execution environments. The framework initially keeps jobs local to the submitter, overflowing if necessary to the campus, and regional grid. The framework is implemented spanning two campuses at the Holland Computing …

Protein Structure – Based Method For Identification Of Horizontal Gene Transfer In Bacteria, Swetha Billa

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Horizontal Gene Transfer is defined as the movement of genetic material from one strain of species to another. Bacteria, being an asexual organism were always believed to transfer genes vertically. But recent studies provide evidence that shows bacteria can also transfer genes horizontally.

HGT plays a major role in evolution and medicine. It is the major contributor in bacterial evolution, enabling species to acquire genes to adapt to the new environments. Bacteria are also believed to develop drug resistance to antibiotics through the phenomenon of HGT. Therefore further study of HGT and its implications is necessary to understand the effects …

Ontology For Psychophysiological Dysregulation Of Anger/Aggression, Swathi Vasanthapuram

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

The advancement of Information Technology in the last four decades led to the use of computers in medicine. A new area called Medical Informatics has emerged. This area comprises the application of IT to healthcare with the aim of creating tools that help healthcare personnel diagnose and treat patients more accurately and efficiently. IT not only provides tools for storing, integrating, and updating patient information base but also for processing information efficiently. One of such tools is a Clinical Decision Support System. Ontologies are an integral part of clinical decision support systems because they help formalize and integrate domain knowledge. …

Multi-Channel Peer-To-Peer Streaming Systems As Resource Allocation Problems, Miao Wang

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

In the past few years, the Internet has witnessed the success of Peer-to-Peer (P2P) streaming technology, which has attracted millions of users. More recently, commercial P2P streaming systems have begun to support multiple channels and a user in such systems is allowed to watch more than one channel at a time. We refer to such systems as multi-channel P2P streaming systems. In this dissertation, we focus on designing multi-channel P2P streaming systems with the goal of providing optimal streaming quality for all channels, termed as system-wide optimal streaming quality. Specifically, we design the systems from the perspective of how to …

Offline Optimization Of Advance Reservation Of Bandwidth Over Dynamic Circuit Networks, Pragatheeswaran Angu

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

E-science projects require very high-speed and reliable networks to transfer data across various destinations in the world. Dynamic Circuit Network (DCN) is a networking service to make advance reservation of bandwidth between a source and a destination in a network. In this thesis we solve the problem of advance reservation of bandwidth in next-generation wavelength-division multiplexing (WDM) networks using a simulation based approach.
We implement a greedy algorithm and a genetic algorithm in parallel, in separate threads. The request for advance reservation is processed by both but the user gets the response only from the greedy algorithm. The genetic algorithm …

Polygonal Spatial Clustering, Deepti Joshi

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Clustering, the process of grouping together similar objects, is a fundamental task in data mining to help perform knowledge discovery in large datasets. With the growing number of sensor networks, geospatial satellites, global positioning devices, and human networks tremendous amounts of spatio-temporal data that measure the state of the planet Earth are being collected every day. This large amount of spatio-temporal data has increased the need for efficient spatial data mining techniques. Furthermore, most of the anthropogenic objects in space are represented using polygons, for example – counties, census tracts, and watersheds. Therefore, it is important to develop data mining …

Identifying Horizontal Gene Transfer Using Anomalies In Protein Structures And Sequences, Venkat Ram B. Santosh

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Genetics has traditionally focused on vertical gene transfer, which is the passing of the genetic material of an organism to its offspring. However, recent studies in genetics increased the awareness that horizontal gene transfer, which is the passing of the genetic material of an organism to another organism that is not its offspring, is also a significant phenomenon. Horizontal gene transfer is thought to play a major role in the natural evolution of bacteria, such as, when several different types of bacteria all suddenly develop the same drug resistance genes. Artificial horizontal gene transfer occurs in genetic engineering.

This thesis …

Testing Embedded System Applications, Tingting Yu

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Embedded systems are becoming increasingly ubiquitous, controlling a wide variety of popular and safety-critical devices. Testing is the most commonly used method for validating software systems, and effective testing techniques could be helpful for improving the dependability of these systems. However, there are challenges involved in developing such techniques. Embedded systems consist of layers of software – application layers utilize services provided by underlying system service and hardware support layers. A typical embedded application consists of multiple user tasks. Interactions between application layers and lower layers, and interactions between the various user tasks that are initiated by the application layer, …

Experimental Evaluation Of Transmission Link Characteristics In Body Area Networks, Apoorva Kiran Pandya

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Recent advances in digital electronics, embedded systems, and wireless communications have led the way to a new class of distributed Wireless Sensor Networks (WSNs). A Body Area Network (BAN) is a WSN consisting of miniaturized, low-power, autonomous, wireless biosensors, which are seamlessly placed or implanted in the human body to provide an adaptable and smart health care system. The possible applications of BAN are in health care services and medicine, assisting persons with disabilities, and entertainment and sports. The nodes in a BAN generally use IEEE 802.15.4 radios which have low- power consumption and are relatively immune to interference. In …

Managing Large Data Sets Using Support Vector Machines, Ranjini Srinivas

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Hundreds of Terabytes of CMS (Compact Muon Solenoid) data are being accumulated for storage day by day at the University of Nebraska-Lincoln, which is one of the eight US CMS Tier-2 sites. Managing this data includes retaining useful CMS data sets and clearing storage space for newly arriving data by deleting less useful data sets. This is an important task that is currently being done manually and it requires a large amount of time. The overall objective of this study was to develop a methodology to help identify the data sets to be deleted when there is a requirement for …

Simsight: A Virtual Machine Based Dynamic Call Graph Generator, Xueling Chen

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

One problem with using component-based software development approach is that once software modules are reused over generations of products, they form legacy structures that can be challenging to understand, making validating these systems difficult. Therefore, tools and methodologies that enable engineers to see interactions of these software modules will enhance their ability to make these software systems more dependable. To address this need, we propose SimSight, a framework to capture dynamic call graphs in Simics, a widely adopted commercial full-system simulator. Simics is a software system that simulates complete computer systems. Thus, it performs nearly identical tasks to …

Jvm-Based Techniques For Improving Java Observability, Peng Du

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Observability measures the support of computer systems to accurately capture, analyze, and present (collectively observe) the internal information about the systems. Observability frameworks play important roles for program understanding, troubleshooting, performance diagnosis, and optimizations. However, traditional solutions are either expensive or coarse-grained, consequently compromising their utility in accommodating today’s increasingly complex software systems. New solutions are emerging for VM-based languages due to the full control language VMs have over program executions. Existing such solutions, nonetheless, still lack flexibility, have high overhead, or provide limited context information for developing powerful dynamic analyses. In this thesis, we present a VM-based infrastructure, called …

A Framework For Automatically Repairing Gui Test Suites, Si Huang

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Testing is an effective means for assuring the quality of software. In programs with Graphical User Interfaces (GUIs), event sequences serve as test cases for executing system tests. To aid in the test generation process, researchers have developed methods that automatically derive graph models from GUIs, which can then be traversed to create sequences for testing. Recent advances using these graph models incorporate combinatorial interaction testing sampling techniques to generate longer GUI test cases, which exercise more event interactions and have been shown to improve fault detection. However, because the models extracted are only approximations of the actual event interactions, …

Designing Software Product Lines For Testability, Isis Cabral

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Software product line (SPL) engineering offers several advantages in the development of families of software products such as reduced costs, high quality and a short time to market. A software product line is a set of software intensive systems, each of which shares a common core set of functionalities, but also differs from the other products through customization tailored to fit the needs of individual groups of customers. The differences between products within the family are well-understood and organized into a feature model that represents the variability of the SPL. Products can then be built by generating and composing features …

Analysis And Transformation Of Pipe-Like Web Mashups For End User Programmers, Kathryn T. Stolee

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Mashups are becoming increasingly popular as end users are able to easily access, manipulate, and compose data from several web sources. To support end users, communities are forming around mashup development environments that facilitate sharing code and knowledge. We have observed, however, that end user mashups tend to suffer from several deficiencies, such as inoperable components or references to invalid data sources, and that those deficiencies are often propagated through the rampant reuse in these end user communities.

In this work, we identify and specify ten code smells indicative of deficiencies we observed in a sample of 8,051 pipe-like web …

Channel Characterization For Wireless Underground Sensor Networks, Agnelo R. Silva

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Wireless Underground Sensor Networks (WUSNs) are natural extensions of the established Wireless Sensor Network (WSN) phenomenon and consist of sensors buried underground which communicate through soil. WUSNs have the potential to impact a wide variety of applications including precision agriculture, environmental monitoring, border patrol, and infrastructure monitoring. The main difference between WUSNs and traditional wireless networks is the communication medium. However, a comprehensive wireless underground channel model for WUSNs has not been developed so far. In this thesis, the Soil Subsurface Wireless Communication (SSWC) channel model is developed based on an extensive empirical study in a large agriculture field. The …