Engineering Commons^™

Suffix Tree, Minwise Hashing And Streaming Algorithms For Big Data Analysis In Bioinformatics, Sairam Behera

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

In this dissertation, we worked on several algorithmic problems in bioinformatics using mainly three approaches: (a) a streaming model, (b) sux-tree based indexing, and (c) minwise-hashing (minhash) and locality-sensitive hashing (LSH). The streaming models are useful for large data problems where a good approximation needs to be achieved with limited space usage. We developed an approximation algorithm (Kmer-Estimate) using the streaming approach to obtain a better estimation of the frequency of k-mer counts. A k-mer, a subsequence of length k, plays an important role in many bioinformatics analyses such as genome distance estimation. We also developed new methods that use …

A Novel Spatiotemporal Prediction Method Of Cumulative Covid-19 Cases, Junzhe Cai

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

Prediction methods are important for many applications. In particular, an accurate prediction for the total number of cases for pandemics such as the Covid-19 pandemic could help medical preparedness by providing in time a sufficient supply of testing kits, hospital beds and medical personnel. This thesis experimentally compares the accuracy of ten prediction methods for the cumulative number of Covid-19 pandemic cases. These ten methods include two types of neural networks and extrapolation methods based on best fit linear, best fit quadratic, best fit cubic and Lagrange interpolation, as well as an extrapolation method from Revesz. We also consider the …

Representational Learning Approach For Predicting Developer Expertise Using Eye Movements, Sumeet Maan

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

The thesis analyzes an existing eye-tracking dataset collected while software developers were solving bug fixing tasks in an open-source system. The analysis is performed using a representational learning approach namely, Multi-layer Perceptron (MLP). The novel aspect of the analysis is the introduction of a new feature engineering method based on the eye-tracking data. This is then used to predict developer expertise on the data. The dataset used in this thesis is inherently more complex because it is collected in a very dynamic environment i.e., the Eclipse IDE using an eye-tracking plugin, iTrace. Previous work in this area only worked on …

Formal Concept Analysis Applications In Bioinformatics, Sarah Roscoe

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

Bioinformatics is an important field that seeks to solve biological problems with the help of computation. One specific field in bioinformatics is that of genomics, the study of genes and their functions. Genomics can provide valuable analysis as to the interaction between how genes interact with their environment. One such way to measure the interaction is through gene expression data, which determines whether (and how much) a certain gene activates in a situation. Analyzing this data can be critical for predicting diseases or other biological reactions. One method used for analysis is Formal Concept Analysis (FCA), a computing technique based …

Investigating Factors Predicting Effective Learning In A Cs Professional Development Program For K-12 Teachers, Patrick Morrow

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

The demand for K-12 Computer Science (CS) education is growing and there is not an adequate number of educators to match the demand. Comprehensive research was carried out to investigate and understand the influence of a summer two-week professional development (PD) program on teachers’ CS content and pedagogical knowledge, their confidence in such knowledge, their interest in and perceived value of CS, and the factors influencing such impacts. Two courses designed to train K-12 teachers to teach CS, focusing on both concepts and pedagogy skills were taught over two separate summers to two separate cohorts of teachers. Statistical and SWOT …

Formal Language Constraints In Deep Reinforcement Learning For Self-Driving Vehicles, Tyler Bienhoff

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

In recent years, self-driving vehicles have become a holy grail technology that, once fully developed, could radically change the daily behaviors of people and enhance safety. The complexities of controlling a car in a constantly changing environment are too immense to directly program how the vehicle should behave in each specific scenario. Thus, a common technique when developing autonomous vehicles is to use reinforcement learning, where vehicles can be trained in simulated and real-world environments to make proper decisions in a wide variety of scenarios. Reinforcement learning models, however, have uncertainties in how the vehicle acts, especially in a previously …

Power-Over-Tether Uas Leveraged For Nearly-Indefinite Meteorological Data Acquisition, Daniel Rico, Carrick Detweiler, Francisco Muñoz-Arriola

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

Use of unmanned aerial systems (UASs) in agriculture has risen in the past decade. These systems are key to modernizing agriculture. UASs collect and elucidate data previously difficult to obtain and used to help increase agricultural efficiency and production. Typical commercial off-the-shelf (COTS) UASs are limited by small payloads and short flight times. Such limits inhibit their ability to provide abundant data at multiple spatiotemporal scales. In this paper, we describe the design and construction of the tethered aircraft unmanned system (TAUS), which is a novel power-over-tether UAS leveraging the physical presence of the tether to launch multiple sensors along …

Understanding Eye Gaze Patterns In Code Comprehension, Jonathan Saddler

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

Program comprehension is a sub-field of software engineering that seeks to understand how developers understand programs. Comprehension acts as a starting point for many software engineering tasks such as bug fixing, refactoring, and feature creation. The dissertation presents a series of empirical studies to understand how developers comprehend software in realistic settings. The unique aspect of this work is the use of eye tracking equipment to gather fine-grained detailed information of what developers look at in software artifacts while they perform realistic tasks in an environment familiar to them, namely a context including both the Integrated Development Environment (Eclipse or …

Emotional Awareness During Bug Fixes – A Pilot Study, Jada O. Loro, Abigail L. Schneff, Sarah J. Oran, Bonita Sharif

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

This study examines the effects of a programmer's emotional awareness on progress while fixing bugs. The goal of the study is to capitalize on emotional awareness to ultimately increase progress made during software development. This process could result in improved software maintenance.

An Eye Tracking Replication Study Of A Randomized Controlled Trial On The Effects Of Embedded Computer Language Switching, Cole Peterson

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

The use of multiple programming languages (polyglot programming) during software development is common practice in modern software development. However, not much is known about how the use of these different languages affects developer productivity. The study presented in this thesis replicates a randomized controlled trial that investigates the use of multiple languages in the context of database programming tasks. Participants in our study were given coding tasks written in Java and one of three SQL-like embedded languages: plain SQL in strings, Java methods only, a hybrid embedded language that was more similar to Java. In addition to recording the online …

A Memory Usage Comparison Between Jitana And Soot, Yuanjiu Hu

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

There are several factors that make analyzing Android apps to address dependability and security concerns challenging. These factors include (i) resource efficiency as analysts need to be able to analyze large code-bases to look for issues that can exist in the application code and underlying platform code; (ii) scalability as today’s cybercriminals deploy attacks that may involve many participating apps; and (iii) in many cases, security analysts often rely on dynamic or hybrid analysis techniques to detect and identify the sources of issues.

The underlying principle governing the design of existing program analysis engines is the main cause that prevents …

An Algorithm For Building Language Superfamilies Using Swadesh Lists, Bill Mutabazi

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

The main contributions of this thesis are the following: i. Developing an algorithm to generate language families and superfamilies given for each input language a Swadesh list represented using the international phonetic alphabet (IPA) notation. ii. The algorithm is novel in using the Levenshtein distance metric on the IPA representation and in the way it measures overall distance between pairs of Swadesh lists. iii. Building a Swadesh list for the author's native Kinyarwanda language because a Swadesh list could not be found even after an extensive search for it.

Adviser: Peter Revesz

Advanced Techniques To Detect Complex Android Malware, Zhiqiang Li

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

Android is currently the most popular operating system for mobile devices in the world. However, its openness is the main reason for the majority of malware to be targeting Android devices. Various approaches have been developed to detect malware.

Unfortunately, new breeds of malware utilize sophisticated techniques to defeat malware detectors. For example, to defeat signature-based detectors, malware authors change the malware’s signatures to avoid detection. As such, a more effective approach to detect malware is by leveraging malware’s behavioral characteristics. However, if a behavior-based detector is based on static analysis, its reported results may contain a large number of …

Open Dynamic Interaction Network: A Cell-Phone Based Platform For Responsive Ema, Gisela Font Sayeras

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

The study of social networks is central to advancing our understanding of a wide range of phenomena in human societies. Social networks co-evolve concurrently alongside the individuals within them. Selection processes cause network structure to change in response to emerging similarities/differences between individuals. At the same time, diffusion processes occur as individuals influence one another when they interact across network links. Indeed, each network link is a logical abstraction that aggregates many short-lived pairwise interactions of interest that are being studied. Traditionally, network co-evolution is studied by periodically taking static snapshots of social networks using surveys. Unfortunately, participation incentives …

An Anns Based Failure Detection Method For Onos Sdon Controller, Shideh Yavary Mehr

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

Network reachability is an important factor of an optical telecommunication network. In a wavelength-division-muliplexing (WDM) optical network, any failure can cause a large amount of loss and disruptions in network. Failures can occur in network elements, link, and component inside a node or etc. Since major network disruptions can caused network performance degradations, it is necessary that operators have solutions to prevent such those failures. This work examines a prediction model in optical networks and propose a protection plan using a Machine Learning (ML) algorithm called Artificial Neural Networks (ANN) using Mininet emulator. ANN is one of the best method …

Designing Shared Control Strategies For Teleoperated Robots Across Intrinsic User Qualities, Nancy Pham

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

Accounting for variance in human behavior is an integral part of interacting with robotic systems that share control between users and robots in order to reduce errors, improve performance, and maintain safety. In this work we focus on the shared control of a telepresence robot and how individual user traits may affect a person's performance while navigating the robot. This requires understanding which user qualities impact performance and cause conflicts -- with the ultimate goal of building shared controllers that adapt to those qualities. Toward this goal, we develop novel adaptive shared controllers and integrate the study of intrinsic user …