Computer Engineering Commons^™

A New System For Human Microrna Functional Evaluation And Network, Jiachun Han

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

MicroRNAs are functionally important endogenous non-coding RNAs that silence host genes in animal and plant via destabilizing the mRNAs or preventing the translation. Given the far-reaching implication of microRNA regulation in human health, novel bioinformatics tools are desired to facilitate the mechanistic understanding of microRNA mediated gene regulation, their roles in biological processes, and the functional relevance among microRNAs. However, most state-of-the-art computational methods still focus on the functional study of microRNA targets and there is no e ective strategy to infer the functional similarity among microRNAs. In this study, we developed a new method to quantitatively measure the functional …

The Effect Of Frequency Resolution On Intelligibility Sentence And Its Relevance To Cochlear Implant Design, Seth H. Roy

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

The purpose of this study is to understand how electrical stimulation (as opposed to acoustical stimulation) of the auditory nerve is used in cochlear implants. Speech is a complex signal that changes rapidly in time and frequency domains. Since phonemes (the smallest unit of speech that distinguishes words) depend on nuanced differences in frequency patterns, it would be expected that a signal with drastically reduced frequency information would be of limited value for conveying speech. Such a frequency-poor signal is the object to be investigated in the present work. It is also the basis of the way speech is represented …

Design Of A Flexible Control Platform And Miniature In Vivo Robots For Laparo-Endoscopic Single-Site Surgeries, Lou P. Cubrich

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Minimally-invasive laparoscopic procedures have proven efficacy for a wide range of surgical procedures as well as benefits such as reducing scarring, infection, recovery time, and post-operative pain. While the procedures have many advantages, there are significant shortcomings such as limited instrument motion and reduced dexterity. In recent years, robotic surgical technology has overcome some of these limitations and has become an effective tool for many types of surgeries. These robotic platforms typically have an increased workspace, greater dexterity, improved ergonomics, and finer control than traditional laparoscopic methods. This thesis presents the designs of both a four degree-of-freedom (DOF) and 5-DOF …

On Path Consistency For Binary Constraint Satisfaction Problems, Christopher G. Reeson

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

Constraint satisfaction problems (CSPs) provide a flexible and powerful framework for modeling and solving many decision problems of practical importance. Consistency properties and the algorithms for enforcing them on a problem instance are at the heart of Constraint Processing and best distinguish this area from other areas concerned with the same combinatorial problems. In this thesis, we study path consistency (PC) and investigate several algorithms for enforcing it on binary finite CSPs. We also study algorithms for enforcing consistency properties that are related to PC but are stronger or weaker than PC.

We identify and correct errors in the literature …

Optimization Of Irrigation Decision In Cornsoywater, Dharmic Payyala

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

A crop simulation model is used to estimate crop production as a function of weather conditions, soil parameters, and plant related inputs. These crop simulation models are extensively used by farmers, corporations and policy makers for agronomical planning and decision making. CornSoyWater is one such application which provides irrigation recommendation for soy and corn farmers using hybrid maize and soy sim models. As this is a simulation technology, the accuracy of results depends on the quality of data provided to it. One such important input parameter is weather data. CornSoyWater simulates field and crop conditions by retrieving the updated weather …

Characterization Of Molecular Communication Based On Cell Metabolism Through Mutual Information And Flux Balance Analysis, Zahmeeth Sayed Sakkaff

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

Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit them for novel purposes, such as the development of ubiquitous and heterogeneous communication networks to interconnect biological cells with nano and biotechnology-enabled devices, i.e., the Internet of Bio-Nano Things. One major problem in realizing these goals stands in the development of reliable techniques to control the engineered cells and their behavior from the …

Semeo: A Semantic Equivalence Analysis Framework For Obfuscated Android Applications, Zhen Hu

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

Software repackaging is a common approach for creating malware. In this approach, malware authors inject malicious payloads into legitimate applications; then, to ren- der security analysis more difficult, they obfuscate most or all of the code. This forces analysts to spend a large amount of effort filtering out benign obfuscated methods in order to locate potentially malicious methods for further analysis. If an effective mechanism for filtering out benign obfuscated methods were available, the number of methods that must be analyzed could be reduced, allowing analysts to be more productive. In this thesis, we introduce SEMEO, a highly effective and …

Autonomous Uavs For Near Earth Environmental Sensing, David J. Anthony

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

Unmanned aerial vehicles (UAVs) are playing an increasing role in large scale environmental monitoring. Small UAVs are increasingly used to monitor agricultural fields, infrastructure projects, and disaster areas. The combination of their sensors, ease of use, and portability make them an ideal tool for collecting information on demand about geographic regions. These small UAVs do have several significant limitations. The UAVs have very limited autonomy and fly pre-determined flight paths far above the underlying terrain, limiting the spatial resolution of the collected data. Current battery technology severely limits their flight times, which in turn limits the temporal resolution of the …

Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan

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

Evolutionary studies usually assume that the genetic mutations are independent of each other. However, that does not imply that the observed mutations are independent of each other because it is possible that when a nucleotide is mutated, then it may be biologically beneficial if an adjacent nucleotide mutates too.

With a number of decoded genes currently available in various genome libraries and online databases, it is now possible to have a large-scale computer-based study to test whether the independence assumption holds for pairs of adjacent amino acids. Hence the independence question also arises for pairs of adjacent amino acids within …

Power Management In Heterogeneous Mapreduce Cluster, Rojee Sunuwar

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

The growing expenses of power in data centers as compared to the operation costs has been a concern for the past several decades. It has been predicted that without an intervention, the energy cost will soon outgrow the infrastructure and operation cost. Therefore, it is of great importance to make data center clusters more energy efficient which is critical for avoiding system overheating and failures. In addition, energy inefficiency causes not only the loss of capital but also environmental pollution. Various Power Management(PM) strategies have been developed over the years to make system more energy efficient and to counteract the …

Rectilinear Steiner Tree Construction, Zhiliu Zhang

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

The Minimum Rectilinear Steiner Tree (MRST) problem is to find the minimal spanning tree of a set of points (also called terminals) in the plane that interconnects all the terminals and some extra points (called Steiner points) introduced by intermediate junctions, and in which edge lengths are measured in the L1 (Manhattan) metric. This is one of the oldest optimization problems in mathematics that has been extensively studied and has been proven to be NP-complete, thus efficient approximation heuristics are more applicable than exact algorithms.

In this thesis, we present a new heuristic to construct rectilinear Steiner trees (RSTs) with …

Towards Building A Review Recommendation System That Trains Novices By Leveraging The Actions Of Experts, Shilpa Khanal

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

Online reviews increase consumer visits, increase the time spent on the website, and create a sense of community among the frequent shoppers. Because of the importance of online reviews, online retailers such as Amazon.com and eOpinions provide detailed guidelines for writing reviews. However, though these guidelines provide instructions on how to write reviews, reviewers are not provided instructions for writing product-specific reviews. As a result, poorly-written reviews are abound and a customer may need to scroll through a large number of reviews, which could be up to 6000 pixels down from the top of the page, in order to find …

Determination Of Plant Architecture And Component Phenotyping Based On Time-Lapse Image Analysis, Srinidhi Bashyam

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

Plant breeding and the development of new food production depend on accurate measurement of different phenotypes (observable physical traits) of a plant. The plant phenotypes play a very important role in the agronomic production. The successful computation of plant phenotypes largely depends on the determination of the architecture of the plant, i.e., the arrangement of its parts (leaves, stems, flowers, etc.) relative to each other, and how the size, shape, and positions of those parts change over time. Researchers and breeders extract valuable information from these types of data to make an informed decision on which individuals to advance to …

Finding Dna Motifs: A Probabilistic Suffix Tree Approach, Abhishek Majumdar

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

We address the problem of de novo motif identification. That is, given a set of DNA sequences we try to identify motifs in the dataset without having any prior knowledge about existence of any motifs in the dataset. We propose a method based on Probabilistic Suffix Trees (PSTs) to identify fixed-length motifs from a given set of DNA sequences. Our experiments reveal that our approach successfully discovers true motifs. We compared our method with the popular MEME algorithm, and observed that it detects a larger number of correct and statistically significant motifs than MEME. Our method is highly efficient as …

Overview Of Lte Spectrum Sharing Technologies, Yun Ye, Dalei Wu, Zhihui Shu, Yi Qian

Department of Electrical and Computer Engineering: Faculty Publications

Long-Term Evolution (LTE) communication systems feature advanced frequency reuse and interference coordination techniques providing faster and more secured mobile services. However, the network capacity in licensed spectrum is still behind market demands. Dynamic spectrum access or spectrum sharing in other frequently vacant or unlicensed frequency bands is considered an effective means to boost system throughput. Different from operations in licensed spectrum with exclusive access, LTE deployment needs to take into account the distinct regulations on channel access to each shared frequency band, in order to avoid interference to incumbent users, and to maintain fair play with peer operators in heterogeneous …

Recognizing And Combating Cybercrime, Marcia L. Dority Baker

Information Technology Services: Publications

Can You Spot the Scam?

Scams make great stories. Tales of Internet crime or other fraud make up some of Hollywood's most exciting thrillers. While cybercrime blockbusters are fun to watch on the big screen, cybercrime is a serious problem on campuses globally.

How many people do you know who are the victim of a scam (Internet or phone)? According to the FBI, cybercrime is a growing threat that affects individuals and businesses around the world. A recent Washington Post article reported that cybercrime cost the global economy $445 billion in 2014.

Eventflowslicer: A Goal-Based Test Case Generation Strategy For Graphical User Interfaces, Jonathan Saddler

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

Automated test generation techniques for graphical user interfaces include model-based approaches that generate tests from a graph or state machine model of the interface, capture-replay methods that require the user to specify and demonstrate each test case individually, and modeling-language approaches that provide templates for abstract test cases. There has been little work, however, in automated goal-based testing, where the goal is a realistic user task, a function, or an abstract behavior. Recent work in human performance regression testing (HPRT) has shown that there is a need for generating multiple test cases that execute the same user task in different …

Exploring Dynamic Memory Allocations For Bioinformatics Applications, Nitya Kovur

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

The progression of scientific data leads to an increase in the demand of powerful high performance computers (HPC) where data can be stored and analyzed. High performance computing is used in several research areas to solve large problems. However, efficient usage of supercomputing resources that are available is a major concern for most of the researchers. The user has to choose the amount of resources needed for execution before submitting the job. Over or under subscription of resources leads to low system utilization and/or low user satisfaction.

Bioinformatics is one such field that heavily relies on HPC. One of the …

Activity Analysis Of Spectator Performer Videos Using Motion Trajectories, Anish Timsina

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

Spectator Performer Space (SPS) is a frequently occurring crowd dynamics, composed of one or more central performers, and a peripheral crowd of spectators. Analysis of videos in this space is often complicated due to occlusion and high density of people. Although there are many video analysis approaches, they are targeted for individual actors or low-density crowd and hence are not suitable for SPS videos. In this work, we present two trajectory-based features: Histogram of Trajectories (HoT) and Histogram of Trajectory Clusters (HoTC) to analyze SPS videos. HoT is calculated from the distribution of length and orientation of motion trajectories in …

Improving The Efficiency Of Ci With Uber-Commits, Matias Waterloo

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

Continuous Integration (CI) is a software engineering practice where developers break their coding tasks into small changes that can be integrated with the shared code repository on a frequent basis. The primary objectives of CI are to avoid integration problems caused by large change sets and to provide prompt developer feedback so that if a problem is detected, it can be easily and quickly resolved. In this thesis, we argue that while keeping changes small and integrating often is a wise approach for developers, the CI server may be more efficient operating on a different scale. In our approach, the …

Use Of Clustering Techniques For Protein Domain Analysis, Eric Rodene

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

Next-generation sequencing has allowed many new protein sequences to be identified. However, this expansion of sequence data limits the ability to determine the structure and function of most of these newly-identified proteins. Inferring the function and relationships between proteins is possible with traditional alignment-based phylogeny. However, this requires at least one shared subsequence. Without such a subsequence, no meaningful alignments between the protein sequences are possible. The entire protein set (or proteome) of an organism contains many unrelated proteins. At this level, the necessary similarity does not occur. Therefore, an alternative method of understanding relationships within diverse sets of proteins …

Control Of Networked Systems With Engineering Applications, Housheng Su, Michael Z.Q. Chen, Qing Hui, Yuan Fan, Zhiwei Gao

Department of Electrical and Computer Engineering: Faculty Publications

Recently, control of networked systems problems has attracted much attention among researchers in biology, physics, control engineering, and computer science for decades, partially due to the broad applications of control of networked systems in many engineering areas including cooperative control of mobile robots and estimation of mobile sensor networks. The study of complex network topology and modeling is to understand the influence of network structure on its function and consequently to find effective ways to improve network performance.

This special issue focuses on theoretical and technological achievements in control of networked systems. The contents of the accepted papers are summarized …

Secure And Lightweight Hardware Authentication Using Isolated Physical Unclonable Function, Mehrdad Zaker Shahrak

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

As embedded computers become ubiquitous, mobile and more integrated in connectivity, user dependence on integrated circuits (ICs) increases massively for handling security sensitive tasks as well as processing sensitive information. During this process, hardware authentication is important to prevent unauthorized users or devices from gaining access to secret information. An effective method for hardware authentication is by using physical unclonable function (PUF), which is a hardware design that leverages intrinsic unique physical characteristics of an IC, such as propagation delay, for security authentication in real time. However, PUF is vulnerable to modeling attacks, as one can design an algorithm to …

Significant Permission Identification For Android Malware Detection, Lichao Sun

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

A recent report indicates that a newly developed malicious app for Android is introduced every 11 seconds. To combat this alarming rate of malware creation, we need a scalable malware detection approach that is effective and efficient. In this thesis, we introduce SigPID, a malware detection system based on permission analysis to cope with the rapid increase in the number of Android malware. Instead of analyzing all 135 Android permissions, our approach applies 3-level pruning by mining the permission data to identify only significant permissions that can be effective in distinguishing benign and malicious apps. Based on the identified significant …

On Optimizations Of Virtual Machine Live Storage Migration For The Cloud, Yaodong Yang

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

Virtual Machine (VM) live storage migration is widely performed in the data cen- ters of the Cloud, for the purposes of load balance, reliability, availability, hardware maintenance and system upgrade. It entails moving all the state information of the VM being migrated, including memory state, network state and storage state, from one physical server to another within the same data center or across different data centers. To minimize its performance impact, this migration process is required to be transparent to applications running within the migrating VM, meaning that ap- plications will keep running inside the VM as if there were …

Towards Building An Intelligent Integrated Multi-Mode Time Diary Survey Framework, Hariharan Arunachalam

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

Enabling true responses is an important characteristic in surveys; where the responses are free from bias and satisficing. In this thesis, we examine the current state of surveys, briefly touching upon questionnaire surveys, and then on time diary surveys (TDS). TDS are open-ended conversational surveys of a free-form nature with both, the interviewer and the respondent, playing a part in its progress and successful completion. With limited research available on how intelligent and assistive components can affect TDS respondents, we explore ways in which intelligent systems such as Computer Adaptive Testing, Intelligent Tutoring Systems, Recommender Systems, and Decision Support Systems …

Joint Resource Provisioning In Optical Cloud Networks, Pan Yi

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

Resource allocation is an evolving part of many Cloud computing and data center management problems. For infrastructure as a service (IaaS) in the Cloud, the Cloud service provider allocates virtual machines (VMs) to the customers with required CPU, memory and disk configurations. In addition to the computing infrastructures, the bandwidth resources would also be allocated to customers for data transmission between reserved VMs. In the near future, users may also want to reserve multiple virtual data centers (VDCs) to construct their own virtual Cloud, which could be called data center as a service (DCaaS). For these two types of services, …

Successful Female Students In Undergraduate Computer Science And Computer Engineering: Motivation, Self-Regulation, And Qualitative Characteristics, Melissa Patterson Hazley

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Computer Science (CS) and Computer Engineering (CE) fields typically have not been successful at recruiting or retaining women students. Research indicates several reasons for this shortage but mainly from three perspectives: social issues, exposure/prior knowledge and curriculum issues in K-12 settings. This mixed-methods research addresses a gap in the literature by investigating the motivation and self-regulation behaviors of successful female students who are studying computer science and computer engineering. The findings in phase one of this study indicated that learning and performance approach goals predicted adaptive strategic self-regulation behaviors including strategy use, knowledge building and engagement. Learning avoidance goals predicted …

Bridging The Communication Gap Successfully For Library/It Projects, Amanda Harlan, Dhanushka Samarakoon

Nebraska Library Association: Conferences

Have you ever had a difficult time describing a concept for a project? This can be especially true with collaborative projects between library and IT staff. Library and IT staff have historically been at odds concerning communication due to the use of jargon specific to their area, different working environments and styles, and conflicting best practices and standards that each follow. K-State Libraries and their internal IT department will share the communication issues with solutions from a librarian’s and developer’s perspective. We will also discuss how has influenced processes and methodologies used for collaborative projects between library and IT staff …

Reconfigurable Battery Techniques And Systems: A Survey, Song Ci, Ni Lin, Dalei Wu

Department of Electrical and Computer Engineering: Faculty Publications

Battery packs with a large number of battery cells are becoming more and more widely adopted in electronic systems, such as robotics, renewable energy systems, energy storage in smart grids, and electronic vehicles. Therefore, a well-designed battery pack is essential for battery applications. In the literature, the majority of research in battery pack design focuses on battery management system, safety circuit, and cell-balancing strategies. Recently, the reconfigurable battery pack design has gained increasing attentions as a promising solution to solve the problems existing in the conventional battery packs and associated battery management systems, such as low energy efficiency, short pack …