Engineering Commons^™

Clustering And Classification Of Multi-Domain Proteins, Neethu Shah

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

Rapid development of next-generation sequencing technology has led to an unprecedented growth in protein sequence data repositories over the last decade. Majority of these proteins lack structural and functional characterization. This necessitates design and development of fast, efficient, and sensitive computational tools and algorithms that can classify these proteins into functionally coherent groups.

Domains are fundamental units of protein structure and function. Multi-domain proteins are extremely complex as opposed to proteins that have single or no domains. They exhibit network-like complex evolutionary events such as domain shuffling, domain loss, and domain gain. These events therefore, cannot be represented in the …

Online Ecosystems In Software Development, Corey J. Jergensen

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

Software projects are no longer developed as individual, monolithic projects. In- stead, they exist as part of an ecosystem where related projects are developed together using a common underlying technical infrastructure and common project cultures.

This work explores characteristics of online software communities by comparing and contrasting two software ecosystems that are both related to programming, but provide different functions. The first is Stack Overflow, a programming question and answer forum. The second is Gnome, an open-source, Linux desktop environment. Both are examples of online communities because: (1) the communities are composed of smaller projects or topics, (2) users contributions …

Solving The Search For Source Code, Kathryn T. Stolee

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

Programmers frequently search for source code to reuse using keyword searches. When effective and efficient, a code search can boost programmer productivity, however, the search effectiveness depends on the programmer's ability to specify a query that captures how the desired code may have been implemented. Further, the results often include many irrelevant matches that must be filtered manually. More semantic search approaches could address these limitations, yet existing approaches either do not scale, are not flexible enough to find approximate matches, or require complex specifications.

We propose a novel approach to semantic search that addresses some of these limitations and …

Decentralized Collision Avoidance, Jayasri K. Janardanan

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

Autonomous Robots must carry out their tasks as independently as possible and each robot may be assigned different tasks at different locations. As these tasks are being performed, the robots have to navigate correctly such that the assigned tasks are completed efficiently, while also avoiding each other and other obstacles. To accomplish effective navigation, we must ensure that the robots are calibrated to avoid colliding with any kind of object on its path. Each robot has to sense the obstacles on its path and take necessary corrective measure to avoid those obstacles. In a situation with multiple robots, robots may …

User Modeling Via Machine Learning And Rule-Based Reasoning To Understand And Predict Errors In Survey Systems, Leonard Cleve Stuart

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

User modeling is traditionally applied to systems were users have a large degree of control over their goals, the content they view, and the manner in which they navigate through the system. These systems aim to both recommend useful goals to users and to assist them in achieving perceived goals. Systems such as online or telephone surveys are different in that users have only a singular goal of survey completion, extremely limited control over navigation, and content is restricted to prescribed set of survey tasks; changing the user modeling problem to one in which the best means of assisting users …

Improving Virtual Collaboration: Modeling For Recommendation Systems In A Classroom Wiki Environment, Derrick A. Lam

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

Collaboration is of increased importance in today’s society, with increased emphasis placed on working jointly with others, whether it is in the classroom, in the lab, in the workplace, or virtually across the world. The wiki is one particular virtual collaboration tool that is gaining particular prominence in recent years, enabling people – either in small project groups or as part of the wiki’s entire user base – to socially construct knowledge asynchronously on a wide variety of topics. However, there are few intelligent support tools for wikis available, particularly those providing recommendation-based support to users.

This thesis investigates the …

Fastlane: Flow-Based Channel Assignment In Dense Wireless Networks, Dane N. Seaberg

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

Wireless communication in dense networks is becoming more apparent and presents challenges in achieving reliable and near real-time communication. While some works have begun to address dense wireless networks, few address both reliability and latency. In this work we introduce FastLane, a method of ow-based channel assignment for dense wireless networks, which works to achieve reliable, near real-time communication in a dense environment with single-radio devices. FastLane uses an assignment mechanism that assigns channels at a ow-level granularity, rather than a tree-level or link-level granularity. Our scheme also takes into account channel quality and can adapt as the quality changes …

Energy-Efficient Failure Recovery In Hadoop Cluster, Weiyue Xu

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

Based on U.S. Environmental Protection Agency’s estimation, only in U.S., billions of dollars are spent on the electricity cost of data centers each year, and the cost is continually increasing very quickly. Energy efficiency is now used as an important metric for evaluating a computing system. However, saving energy is a big challenge due to many constraints. For example, in one of the most popular distributed processing frameworks, Hadoop, three replicas of each data block are randomly distributed in order to improve performance and fault tolerance, but such a mechanism limits the largest number of machine that can be turned …

Test Advising Framework, Yurong Wang

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

Test cases are represented in various formats depending on the process, the technique or the tool used to generate the tests. While different test case representations are necessary, this diversity challenges us in comparing test cases and leveraging strengths among them - a common test representation will help.

In this thesis, we define a new Test Case Language (TCL) that can be used to represent test cases that vary in structure and are generated by multiple test generation frameworks. We also present a methodology for transforming test cases of varying representations into a common format where they can be matched …

Directed Test Suite Augmentation, Zhihong Xu

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

Test suite augmentation techniques are used in regression testing to identify code elements affected by changes and to generate test cases to cover those elements. Whereas methods and techniques to find affected elements have been extensively researched in regression testing, the problem of generating new test cases to cover these elements cost-effectively has rarely been studied. We believe that reusing existing test cases will help us achieve this task. This research develops test suite augmentation techniques that reuse existing test cases to automatically generate new test cases to cost-effectively cover affected elements. We begin by using two dynamic test case …