Computer Sciences Commons^™

Statistical Software Properties: Definition, Inference And Monitoring, Javier A. Darsie

School of Computing: Dissertations, Theses, and Student Research

Software properties define how software systems should operate. Specifying correct properties, however, can be difficult and expensive as it requires deep knowledge of the system's expected behavior and the environment in which it operates. Automated analysis techniques to infer properties from code or code executions can mitigate that cost, but are still unable to go beyond state properties and the simplest patterns of temporal properties. This limitation renders properties that sacrifice fault detection power.

To address this problem, we introduce a new type of software properties called \textit{statistical properties}, which characterize significant statistical relationships among the values of variables across …

Data Mining Of Protein Databases, Christopher Assi

School of Computing: 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 …

A Wlan Fingerprinting Based Indoor Localization Technique, Landu Jiang

School of Computing: Dissertations, Theses, and Student Research

Satellite-based Global Positioning Systems (GPS) have enabled a variety of location-based services such as navigation systems, and become increasingly popular and important in our everyday life. However, GPS does not work well in indoor environments where walls, floors and other construction objects greatly attenuate satellite signals.

In this paper, we propose an Indoor Positioning System (IPS) based on widely deployed indoor WiFi systems. Our system uses not only the Received Signal Strength (RSS) values measured at the current location but also the previous location information to determine the current location of a mobile user. We have conducted a large number …

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

School of Computing: 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 …

The R Journal (June 2012) 4(1): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

Analysing Seasonal Data, Adrian G. Barnett, Peter Baker, and Annette J. Dobson

MARSS: Multivariate Autoregressive State-space Models for Analyzing Time-series Data, Elizabeth E. Holmes, Eric J. Ward, and Kellie Wills

openair: Data Analysis Tools for the Air Quality Community, Karl Ropkins and David C. Carslaw

Foreign Library Interface, Daniel Adler

Vdgraph: A Package for Creating Variance Dispersion Graphs, John Lawson

xgrid and R: Parallel Distributed Processing Using Heterogeneous Groups of Apple Computers, Sarah C. Anoke, Yuting Zhao, Rafael Jaeger, and Nicholas J. Horton

maxent: An R Package for Low-memory Multinomial Logistic Regression with Support for Semi-automated Text …

Who Did What? The Roles Of R Package Authors And How To Refer To Them, Kurt Hornik, Duncan Murdoch, Achim Zeileis

The R Journal

Computational infrastructure for rep resenting persons and citations has been avail able in R for several years, but has been restructured through enhanced classes "person" and "bibentry" in recent versions of R. The new features include support for the specification of the roles of package authors (e.g. maintainer, author, contributor, translator, etc.) and more flexible formatting/printing tools among various other improvements. Here, we introduce the new classes and their methods and indicate how this functionality is employed in the management of R packages. Specifically, we show how the authors of R packages can be specified along with their roles in …

Xgrid And R: Parallel Distributed Processing Using Heterogeneous Groups Of Apple Computers, Sarah C. Anoke, Yuting Zhao, Rafael Jaeger, Nicholas J. Horton

The R Journal

The Apple Xgrid system provides access to groups (or grids) of computers that can be used to facilitate parallel processing. We describe the xgrid package which facilitates access to this system to undertake independent simulations or other long-running jobs that can be divided into replicate runs within R. Detailed examples are provided to demonstrate the interface, along with results from a simulation study of the performance gains using a variety of grids. Use of the grid for “embarassingly parallel” independent jobs has the potential for major speedups in time to completion. Appendices provide guidance on setting up the workflow, utilizing …

Openair: Data Analysis Tools For The Air Quality Community, Karl Ropkins, David C. Carslaw

The R Journal

The openair package contains data analysis tools for the air quality community. This paper provides an overview of data importers, main functions, and selected utilities and workhorse functions within the package and the function output class, as of package version 0.4-14. It is intended as an explanation of the rationale for the package and a technical description for those wishing to work more inter actively with the main functions or develop additional functions to support ‘higher level’ use of openair and R.

Maxent: An R Package For Low-Memory Multinomial Logistic Regression With Support For Semi-Automated Text Classification, Timothy P. Jurka

The R Journal

maxent is a package with tools for data classification using multinomial logistic regression, also known as maximum entropy. The focus of this maximum entropy classifier is to minimize memory consumption on very large datasets, particularly sparse document-term matrices represented by the tm text mining pack age.

Marss: Multivariate Autoregressive State-Space Models For Analyzing Time-Series Data, Elizabeth E. Holmes, Eric J. Ward, Kellie Wills

The R Journal

MARSS is a package for fitting multivariate autoregressive state-space models to time-series data. The MARSS package implements state-space models in a maximum likelihood framework. The core functionality of MARSSis based on likelihood maximization using the Kalman filter/smoother, combined with an EM algorithm. To make comparisons with other packages available, parameter estimation is also permitted via direct search routines avail able in ’optim’. The MARSS package allows data to contain missing values and allows a wide variety of model structures and constraints to be specified (such as fixed or shared parameters). In addition to model-fitting, the package provides bootstrap routines for …

Vdgraph: A Package For Creating Variance Dispersion Graphs, John Lawson

The R Journal

This article introduces the package Vdgraph that is used form a king variance dispersion graphs of response surface designs.The package includes functions that make the variance dispersion graph of one design or compare variance dispersion graphs of two designs, which are stored in data frames or matrices.The package also contains several minimum run response surface designs (stored as matrices) that are not available in other R packages.

Analysing Seasonal Data, Adrian G. Barnett, Peter Baker, Annette J. Dobson

The R Journal

Many common diseases, such as the flu and cardiovascular disease, increase markedly in winter and dip in summer. These seasonal patterns have been part of life for millennia and were first noted in ancient Greece by both Hippocrates and Herodotus. Recent interest has focused on climate change, and the concern that seasons will become more extreme with harsher winter and summer weather. We describe a set of R functions designed to model seasonal pat terns in disease. We illustrate some simple descriptive and graphical methods, a more complex method that is able to model non-stationary patterns, and the case-crossover to …

Foreign Library Interface, Daniel Adler

The R Journal

We present an improved Foreign Function Interface (FFI) for R to call arbitary native functions without the need for C wrapper code. Further we discuss a dynamic linkage framework for binding standard C libraries to R across platforms using a universal type information format. The package rdyncall comprises the framework and an initial repository of cross platform bindings for standard libraries such as (legacy and modern) OpenGL, the family of SDL libraries and Expat. The package enables system level programming using the R language; sample applications are given in the article. We out line the underlying automation tool-chain that extracts …

Sumo: An Authenticating Web Application With An Embedded R Session, Timothy T. Bergsma, Michael S. Smith

The R Journal

Sumo is a web application intended as a template for developers. It is distributed as a Java ‘war’ file that deploys automatically when placed in a Servlet container’s ‘webapps’ directory. If a user supplies proper credentials, Sumocreates a session-specific Secure Shell connection to the host and a user-specific R session over that connection. Developers may write dynamic server pages that make use of the persistent R session and user-specific file space. The supplied example plots a data set conditional on preferences indicated by the user; it also displays some static text. A companion server page al lows the user to …

Solving The Search For Suitable Code: An Initial Implementation, Kathryn T. Stolee, Sebastian Elbaum

School of Computing: Technical Reports

Searching for code is a common task among programmers, with the ultimate goal of finding and reusing code or getting ideas for implementation. While the process of searching for code - issuing a query and selecting a relevant match - is straightforward, several costs must be balanced, including the costs of specifying the query, examining the results to find desired code, and not finding a relevant result. For the popular syntactic searches the query cost is quite low, but the results are often vague or irrelevant, so the examination cost is high and matches may not be found. Semantic searches …

A Scalable Inline Cluster Deduplication Framework For Big Data Protection, Yinjin Fu, Hong Jiang, Nong Xiao

School of Computing: Technical Reports

Cluster deduplication has become a widely deployed technology in data protection services for Big Data to satisfy the requirements of service level agreement (SLA). However, it remains a great challenge for cluster deduplica- tion to strike a sensible tradeoff between the conflicting goals of scalable dedu- plication throughput and high duplicate elimination ratio in cluster systems with low-end individual secondary storage nodes. We propose Σ-Dedupe, a scalable inline cluster deduplication framework, as a middleware deployable in cloud da- ta centers, to meet this challenge by exploiting data similarity and locality to op- timize cluster deduplication in inter-node and intra-node scenarios, …

An Enhanced Self-Adaptive Mapreduce Scheduling Algorithm, Xiaoyu Sun

School of Computing: 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 …

A Multi-Modal Sensing And Communication Platform For Continental-Scale Migratory Bird Tracking, David J. Anthony

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

This thesis presents a novel platform for tracking migratory birds on a continental scale. Cellular technology is used to augment the short-range radios that have traditionally been used in wireless sensor networks. The platform utilizes multiple sensors, including a GPS and solid state compass. By using these sensors, the platform is capable of not only tracking a bird’s migration path, but also provides information on a bird’s behavior during its life-cycle. Testing methodology utilizing simulations and aspect-oriented programming is used to reveal faults in the platform prior to deployment on wild animals. In collaboration with the International Crane Foundation, and …

Probabilistic Qos Analysis In Wireless Sensor Networks, Yunbo Wang

School of Computing: 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 …

Resonant Wireless Power Transfer To Ground Sensors From A Uav, Brent Griffin, Carrick Detweiler

School of Computing: Conference and Workshop Papers

Wireless magnetic resonant power transfer is an emerging technology that has many advantages over other wireless power transfer methods due to its safety, lack of interference, and efficiency at medium ranges. In this paper, we develop a wireless magnetic resonant power transfer system that enables unmanned aerial vehicles (UAVs) to provide power to, and recharge batteries of wireless sensors and other electronics far removed from the electric grid. We address the difficulties of implementing and outfitting this system on a UAV with limited payload capabilities and develop a controller that maximizes the received power as the UAV moves into and …

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

School of Computing: 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

School of Computing: 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

School of Computing: 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 …

Combinatorics Using Computational Methods, Derrick Stolee

Department of Mathematics: Dissertations, Theses, and Student Research

Computational combinatorics involves combining pure mathematics, algorithms, and computational resources to solve problems in pure combinatorics. This thesis provides a theoretical framework for combinatorial search, which is then applied to several problems in combinatorics. Some results in space-bounded computational complexity are also presented.

Sentence Recognition From Articulatory Movements For Silent Speech Interfaces, Jun Wang, Ashok Samal, Jordan R. Green, Frank Rudzicz

Department of Special Education and Communication Disorders: Faculty Publications

Recent research has demonstrated the potential of using an articulation-based silent speech interface for command-and-control systems. Such an interface converts articulation to words that can then drive a text-to-speech synthesizer. In this paper, we have proposed a novel near-time algorithm to recognize whole-sentences from continuous tongue and lip movements. Our goal is to assist persons who are aphonic or have a severe motor speech impairment to produce functional speech using their tongue and lips. Our algorithm was tested using a functional sentence data set collected from ten speakers (3012 utterances). The average accuracy was 94.89% with an average latency of …

Cross-Layer Analysis Of The End-To-End Delay Distribution In Wireless Sensor Networks, Yunbo Wang, Mehmet C. Vuran, Steve Goddard

School of Computing: Faculty Publications

Emerging applications of wireless sensor networks (WSNs) require real-time quality-of-service (QoS) guarantees to be provided by the network. Due to the nondeterministic impacts of the wireless channel and queuing mechanisms, probabilistic analysis of QoS is essential. One important metric of QoS in WSNs is the probability distribution of the end-to-end delay. Compared to other widely used delay performance metrics such as the mean delay, delay variance, and worst-case delay, the delay distribution can be used to obtain the probability to meet a specific deadline for QoS-based communication in WSNs. To investigate the end-to-end delay distribution, in this paper, a comprehensive …

An Approach To The Virtual Flora Of Mongolia – From A Data Repository To An Expert System, Http://Greif.Uni-Greifswald.De/Floragreif/, Jörg Hartleib, Martin Schnittler, Sabrina Rilke, Anne Zemmrich, Bernd Bobertz, Ulrike Najmi, Reinhard Zölitz, Susanne Starke

Erforschung biologischer Ressourcen der Mongolei / Exploration into the Biological Resources of Mongolia, ISSN 0440-1298

FloraGREIF is an internet accessible information system providing taxonomic, phytogeographic and ecological information on Mongolia’s flora in terms of descriptions, high-resolution plant images and an interactive WebGIS application. Organised along an updated checklist of the approx. 3000 Mongolian vascular plants that serves as a taxonomic backbone, information is split into the taxon level, referring to plant species, and the record level, referring to record or a collected plant specimen. At the latter level, images of living plants, scans of herbarium sheets, habitat photos and further notes can be found. Both data levels are linked by the name of the respective …

A Performance Comparison Of Mobile Wimax Spectrums: 2.5 Ghz Vs. 3.65 Ghz, Pradhumna Shrestha, Michael Hempel, Puttipong Mahasukhon, Tao Ma, Hamid Sharif

School of Computing: Conference and Workshop Papers

Mobile WiMAX is a popular broadband solution with diverse applications. In the United States, the Federal Communications Commission (FCC) currently issues licenses for Mobile WiMAX in several frequency bands, of which 2.5 GHz and 3.65 GHz are the most prevalent. A significant amount of research has been conducted in the domain of 2.5 GHz due to its widespread commercial use. However, no such work – academic or industrial – has been reported for 3.65 GHz, in spite of it being a more favorable option for many applications, particularly because of its licensing requirements. In this paper, we present a comprehensive …

Connecting Soil To The Cloud: A Wireless Underground Sensor Network Testbed, John Tooker, Xin Dong, Mehmet C. Vuran, Suat Irmak

School of Computing: Conference and Workshop Papers

In this demo, a novel underground communication system and an online underground sensor network testbed is demonstrated. The underground communication system, developed in the Cyber-physical Networking (CPN) Laboratory at the University of Nebraska-Lincoln, includes an underground antenna that is tailored to mitigate the adverse effects of soil on underground communication. An online connection is established with the CPN underground sensor network testbed that is located at Clay Center, Nebraska. The underground sensor network testbed consists of a network of underground communication systems equipped with soil moisture sensors and a mobile data harvesting unit equipped with cellular communication capabilities. Real-time soil …

Features For Non-Targeted Cross-Sample Analysis With Comprehensive Two-Dimensional Chromatography, Stephen E. Reichenbach, Xue Tian, Chiara Cordero, Qingping Tao

School of Computing: Faculty Publications

This review surveys different approaches for generating features from comprehensive two-dimensional chromatography for non-targeted cross-sample analysis. The goal of non-targeted cross-sample analysis is to discover relevant chemical characteristics (such as compositional similarities or differences) from multiple samples. In non-targeted analysis, the relevant characteristics are unknown, so individual features for all chemical constituents should be analyzed, not just those for targeted or selected analytes. Cross-sample analysis requires matching the corresponding features that characterize each constituent across multiple samples so that relevant characteristics or patterns can be recognized. Non-targeted, cross-sample analysis requires generating and matching all features across all samples. Applications of …