Physical Sciences and Mathematics Commons^™

Gmaim: An Analytical Pipeline For Microrna Splicing Profiling Using Generative Model, Kan Liu

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

MicroRNAs (miRNAs) are a class of short (~22 nt) single strand RNA molecules predominantly found in eukaryotes. Being involved in many major biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. The imprecise splicing of miRNA splicing which introduces severe variability in terms of sequences of miRNA products and their corresponding downstream gene expression regulation. For example, to study biogenesis of miRNAs, usually, biologists can deplete a gene in the miRNA biogenesis pathway and study the change of miRNA sequences, which can cause impression of miRNAs. Although high-throughput sequencing technologies such as …

Scale-Out Algorithm For Apache Storm In Saas Environment, Ravi Kiran Puttaswamy

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

The main appeal of the Cloud is in its cost effective and flexible access to computing power. Apache Storm is a data processing framework used to process streaming data. In our work we explore the possibility of offering Apache Storm as a software service. Further, we take advantage of the cgroups feature in Storm to divide the computing power of worker machine into smaller units to be offered to users. We predict that the compute bounds placed on the cgroups could be used to approximate the state of the workflow. We discuss the limitations of the current schedulers in facilitating …

Reducing The Tail Latency Of A Distributed Nosql Database, Jun Wu

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

The request latency is an important performance metric of a distributed database, such as the popular Apache Cassandra, because of its direct impact on the user experience. Specifically, the latency of a read or write request is defined as the total time interval from the instant when a user makes the request to the instant when the user receives the request, and it involves not only the actual read or write time at a specific database node, but also various types of latency introduced by the distributed mechanism of the database. Most of the current work focuses only on reducing …

Controller Evolution And Divergence: A Software Perspective, Balaji Balasubramaniam

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

Successful controllers evolve as they are refined, extended, and adapted to new systems and contexts. This evolution occurs in the controller design and also in its software implementation. Model-based design and controller synthesis can help to synchronize this evolution of design and software, but such synchronization is rarely complete as software tends to also evolve in response to elements rarely present in a control model, leading to mismatches between the control design and the software.

In this thesis, we perform a first-of-its-kind study on the evolution of two popular open-source safety-critical autopilot control software -- ArduPilot, and Paparazzi, to better …

Evoalloy: An Evolutionary Approach For Analyzing Alloy Specifications, Jianghao Wang

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

Using mathematical notations and logical reasoning, formal methods precisely define a program’s specifications, from which we can instantiate valid instances of a system. With these techniques, we can perform a variety of analysis tasks to verify system dependability and rigorously prove the correctness of system properties. While there exist well-designed automated verification tools including ones considered lightweight, they still lack a strong adoption in practice. The essence of the problem is that when applied to large real world applications, they are not scalable and applicable due to the expense of thorough verification process. In this thesis, I present a new …

Deploying, Improving And Evaluating Edge Bundling Methods For Visualizing Large Graphs, Jieting Wu

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

A tremendous increase in the scale of graphs has been witnessed in a wide range of fields, which demands efficient and effective visualization techniques to assist users in better understandings of large graphs. Conventional node-link diagrams are often used to visualize graphs, whereas excessive edge crossings can easily incur severe visual clutter in the node-link diagram of a large graph. Edge bundling can effectively remedy visual clutter and reveal high-level graph structures. Although significant efforts have been devoted to developing edge bundling, three challenging problems remain. First, edge bundling techniques are often computationally expensive and are not easy to deploy …

Supporting Diverse Customers And Prioritized Traffic In Next-Generation Passive Optical Networks, Naureen Hoque

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

The already high demand for more bandwidth usage has been growing rapidly. Access network traffic is usually bursty in nature and the present traffic trend is mostly video-dominant. This motivates the need for higher transmission rates in the system. At the same time, the deployment costs and maintenance expenditures have to be reasonable. Therefore, Passive Optical Networks (PON) are considered promising next-generation access technologies. As the existing PON standards are not suitable to support future-PON services and applications, the FSAN (Full Service Access Network) group and the ITU-T (Telecommunication Standardization Sector of the International Telecommunication Union) have worked on developing …

A Comprehensive Framework To Replicate Process-Level Concurrency Faults, Supat Rattanasuksun

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

Concurrency faults are one of the most damaging types of faults that can affect the dependability of today’s computer systems. Currently, concurrency faults such as process-level races, order violations, and atomicity violations represent the largest class of faults that has been reported to various Linux bug repositories. Clearly, existing approaches for testing such faults during software development processes are not adequate as these faults escape in-house testing efforts and are discovered during deployment and must be debugged.

The main reason concurrency faults are hard to test is because the conditions that allow these to occur can be difficult to replicate, …

Optical Wireless Data Center Networks, Abdelbaset S. Hamza

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

Bandwidth and computation-intensive Big Data applications in disciplines like social media, bio- and nano-informatics, Internet-of-Things (IoT), and real-time analytics, are pushing existing access and core (backbone) networks as well as Data Center Networks (DCNs) to their limits. Next generation DCNs must support continuously increasing network traffic while satisfying minimum performance requirements of latency, reliability, flexibility and scalability. Therefore, a larger number of cables (i.e., copper-cables and fiber optics) may be required in conventional wired DCNs. In addition to limiting the possible topologies, large number of cables may result into design and development problems related to wire ducting and maintenance, heat …

Amino Acid Pop-Set: Model File Name: Amino-Acid-Wgrp-Pop_Sc3.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model for protein primary structure. It consists of four amino acids (tryptophan, proline, arginine, and glycine) depicted in stick and space-fill representations, five peptide bonds depicted in space-fill, and an N-terminus and a C-terminus depicted in space-fill. It is designed so that students can make various peptides to explore the amount of space of the electron clouds of the amino acids and bonds, and explore the psi and phi angles for the peptides. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Amino acid pop-set”. This model has …

Lipoprotein Signal Peptidase Ii: Model File Name: 5dir-Lipoii-Reps_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of lipoprotein signal peptidase II (PDB: 5DIR). It is designed with different regions of the protein depicted in space-filling, ribbon, stick, and backbone-only representations to explore protein secondary structure and illustrate how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lipoprotein signal peptidase II” and is intended to accompany the “Crambin”, “Cytochrome c” and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in …

3 Water Molecules: Model File Name: 3hoh-Final.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of 3 water molecules depicted in space-fill. It is designed to the same scale as the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models to illustrate the amount of space taken up by proteins. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “3 water molecules” and is intended to accompany the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering …

Crambin: Model File Name: 2fd7-Crambin-Stick_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of cytochrome c (PDB: 2FD7). It is designed in a stick representation to explore protein secondary structure and how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Crambin” and is intended to accompany the “Lipoprotein signal peptidase II”, “Cytochrome c”, and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Cytochrome C: Model File Name: 1b7v-Cytc-Stick_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of cytochrome c (PDB: 1B7V). It is designed in a stick representation to explore protein secondary structure and how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Cytochrome c” and is intended to accompany the “Lipoprotein signal peptidase II”, “Crambin”, and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Girls Who Code 3rd-5th, Khristina Polivanov

Honors Expanded Learning Clubs

The goal of the club is to encourage girls to be confident in themselves and their abilities while teaching them basic concepts used in computer science.

Using Chronicling America’S Images To Explore Digitized Historic Newspapers & Imagine Alternative Futures, Elizabeth Lorang, Leen-Kiat Soh

University of Nebraska-Lincoln Libraries: Conference Presentations and Speeches

This presentation situates the work of the Aida team broadly as well as hinges this work on some very specific challenges for digital libraries. In doing so demonstrate the many types of questions and domains to be explored in digitized newspapers.

Minutes & Seconds: The Scientists, Patrick Aievoli

Zea E-Books Collection

Minutes & Seconds, is a captivating intelligible read for those who strive to understand where the “what if” moment has gone. Succeeding his other captivating books, Aievoli’s deep introspective lens dials his readers in to awaken the proverbial sleeping giant inside of our consciousness. He designs an insightful exciting romp through the surreal landscape of our society and illustrates how various pioneers have lead us to a crossroads. I’m truly impressed with Aievoli’s perspicacious comprehension of where digital has taken us through the hands of these select individuals. --Sequoyah Wharton

In creating Minutes & Seconds, Aievoli has assembled an interesting …

Human Hexokinase I - Allosteric Regulation: Model File Name: 1dgk-Editb22-Allostery_Sc06.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of human Hexokinase I in a surface representation with small molecules ADP and G6P included (PDB: 1DGK). It is designed to be hollow with a lever to mimic allosteric regulation. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Human Hexokinase I - Allosteric regulation model”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Higher-Level Consistencies: Where, When, And How Much, Robert J. Woodward

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

Determining whether or not a Constraint Satisfaction Problem (CSP) has a solution is NP-complete. CSPs are solved by inference (i.e., enforcing consistency), conditioning (i.e., doing search), or, more commonly, by interleaving the two mechanisms. The most common consistency property enforced during search is Generalized Arc Consistency (GAC). In recent years, new algorithms that enforce consistency properties stronger than GAC have been proposed and shown to be necessary to solve difficult problem instances.

We frame the question of balancing the cost and the pruning effectiveness of consistency algorithms as the question of determining where, when, and how much of a higher-level …

Scaling Up An Infrastructure For Controlled Experimentation With Testing Techniques, Wayne D. Motycka

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

Software testing research often involves reproducing previous experimental results. Previous work created a repository infrastructure for containment and dissemination of testable research subjects using a private centralized storage mechanism for hosting these test subject archives. While this is a good way to store these subjects it can be inefficient when the size of subjects increases or the number of versions of the subject’s source code is large. The delivery of these large subjects from a centralized repository can be quite large and on occasion may not succeed requiring the user to repeat the download request. Coupled with the limited resources …

Data Mining Ancient Script Image Data Using Convolutional Neural Networks, Shruti Daggumati, Peter Revesz

CSE Conference and Workshop Papers

The recent surge in ancient scripts has resulted in huge image libraries of ancient texts. Data mining of the collected images enables the study of the evolution of these ancient scripts. In particular, the origin of the Indus Valley script is highly debated. We use convolutional neural networks to test which Phoenician alphabet letters and Brahmi symbols are closest to the Indus Valley script symbols. Surprisingly, our analysis shows that overall the Phoenician alphabet is much closer than the Brahmi script to the Indus Valley script symbols.

Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam Mcdermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma

School of Computing: Faculty Publications

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to …

Applications Of Varying Leadership Structures For Software Engineering Teams, Elliot Sandfort

Honors Theses

This thesis explores the similarities and differences between applications of managing software engineering teams in Design Studio and the state of the practice. Information about the leadership structure of Design Studio teams was gathered over 3 semesters of Design Studio experiences with two companies: Hudl and TD Ameritrade. Information about leadership concepts in the state of the practice was gathered from experiences and observations with three different companies: Hudl, Garmin, and TD Ameritrade. From these experiences and observations, it can be concluded that the leadership structure of Design Studio is valuable as a student learning experience, and with proper consideration …

Application Of Cosine Similarity In Bioinformatics, Srikanth Maturu

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

Finding similar sequences to an input query sequence (DNA or proteins) from a sequence data set is an important problem in bioinformatics. It provides researchers an intuition of what could be related or how the search space can be reduced for further tasks. An exact brute-force nearest-neighbor algorithm used for this task has complexity O(m * n) where n is the database size and m is the query size. Such an algorithm faces time-complexity issues as the database and query sizes increase. Furthermore, the use of alignment-based similarity measures such as minimum edit distance adds an additional complexity to the …

Performance Evaluation Of V-Enodeb Using Virtualized Radio Resource Management, Sai Keerti Teja Boddepalli

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

With the demand upsurge for high bandwidth services, continuous increase in the number of cellular subscriptions, adoption of Internet of Things (IoT), and marked growth in Machine-to-Machine (M2M) traffic, there is great stress exerted on cellular network infrastructure. The present wireline and wireless networking technologies are rigid in nature and heavily hardware-dependent, as a result of which the process of infrastructure upgrade to keep up with future demand is cumbersome and expensive.

Software-defined networks (SDN) hold the promise to decrease network rigidity by providing central control and flow abstraction, which in current network setups are hardware-based. The embrace of SDN …

Effectively Enforcing Minimality During Backtrack Search, Daniel J. Geschwender

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

Constraint Processing is an expressive and powerful framework for modeling and solving combinatorial decision problems. Enforcing consistency during backtrack search is an effective technique for reducing thrashing in a large search tree. The higher the level of the consistency enforced, the stronger the pruning of inconsistent subtrees. Recently, high-level consistencies (HLC) were shown to be instrumental for solving difficult instances. In particular, minimality, which is guaranteed to prune all inconsistent branches, is advantageous even when enforced locally. In this thesis, we study two algorithms for computing minimality and propose three new mechanisms that significantly improve performance. Then, we integrate the …

Assessing The Quality And Stability Of Recommender Systems, David Shriver

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

Recommender systems help users to find products they may like when lacking personal experience or facing an overwhelmingly large set of items. However, assessing the quality and stability of recommender systems can present challenges for developers. First, traditional accuracy metrics, such as precision and recall, for validating the quality of recommendations, offer only a coarse, one-dimensional view of the system performance. Second, assessing the stability of a recommender systems requires generating new data and retraining a system, which is expensive. In this work, we present two new approaches for assessing the quality and stability of recommender systems to address these …

Consensus Ensemble Approaches Improve De Novo Transcriptome Assemblies, Adam Voshall

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

Accurate and comprehensive transcriptome assemblies lay the foundation for a range of analyses, such as differential gene expression analysis, metabolic pathway reconstruction, novel gene discovery, or metabolic flux analysis. With the arrival of next-generation sequencing technologies it has become possible to acquire the whole transcriptome data rapidly even from non-model organisms. However, the problem of accurately assembling the transcriptome for any given sample remains extremely challenging, especially in species with a high prevalence of recent gene or genome duplications, those with alternative splicing of transcripts, or those whose genomes are not well studied. This thesis provides a detailed overview of …

Cost-Effective Techniques For Continuous Integration Testing, Jingjing Liang

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

Continuous integration (CI) development environments allow software engineers to frequently integrate and test their code. While CI environments provide advantages, they also utilize non-trivial amounts of time and resources. To address this issue, researchers have adapted techniques for test case prioritization (TCP) and regression test selection (RTS) to CI environments.

To date, current TCP techniques under CI environments have operated on test suites, and have not achieved substantial improvements. In this thesis, we use a lightweight approach based on test suite failure and execution history, and “continuously” prioritizes commits that are waiting for execution in response to the arrival of …

Modular Scheduling System For Westside School District, Tyler Bienhoff

Honors Theses

Westside School district offers a modular scheduling system for their high school that is more similar to a college schedule than the typical high school system. Due to the complexity of their master schedule each semester, there are no commercially available products that can assist in creating a schedule. Hence, this thesis discusses a scheduling algorithm and management system that was built specifically for Westside High School with the potential to be expanded for use by other interested schools. The first part of the paper is focused on gathering input from students and faculty for which courses and how many …