Digital Commons Network^™

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 …

Using Software Testing Techniques To Infer Biological Models, Mikaela Cashman

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

Years of research in software testing has given us novel ways to reason about and test the behavior of complex software systems that contain hundreds of thousands of lines of code. Many of these techniques have been inspired by nature such as genetic algorithms, swarm intelligence, and ant colony optimization. However, they use a unidirectional analogy – taking from nature without giving back.

In this thesis we invert this view and ask if we can utilize techniques from testing and modeling of highly-configurable software systems to aid in the emerging field of systems biology which aims to model and predict …

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 …

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 …

Connecting Program Synthesis And Reachability: Automatic Program Repair Using Test-Input Generation, Thanhvu Nguyen, Westley Weimer, Deepak Kapur, Stephanie Forrest

CSE Technical Reports

We prove that certain formulations of program synthesis and reachability are equivalent. Specifically, our constructive proof shows the reductions between the template-based synthesis problem, which generates a program in a pre-specified form, and the reachability problem, which decides the reachability of a program location. This establishes a link between the two research fields and allows for the transfer of techniques and results between them.

To demonstrate the equivalence, we develop a program repair prototype using reachability tools. We transform a buggy program and its required specification into a specific program containing a location reachable only when the original program can …

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.

White Paper, Hd-51897-14, Image Analysis For Archival Discovery (Aida), October 2016, Elizabeth M. Lorang, Leen-Kiat Soh

CDRH Grant Reports

With its Office of Digital Humanities Start-up Grant, the Image Analysis for Archival Discovery (Aida) team set out to further develop image analysis as a methodology for the identification and retrieval of items of relevance within digitized collections of historic materials.1 Specifically, we sought to identify poetic content within historic newspapers, using Chronicling America's newspapers (http://chroniclingamerica.loc.gov/) as our test case. The project activities we undertook—both those completed and those in process—support this goal and align well with the activities proposed in our original funding application and as approved by NEH. To achieve our goal of creating an image processing-based system …

Final Report, Hd-51897-14, Image Analysis For Archival Discovery (Aida), October 2016, Elizabeth M. Lorang, Leen-Kiat Soh

CDRH Grant Reports

With its Office of Digital Humanities Start-up Grant, the Image Analysis for Archival Discovery (Aida) team set out to further develop image analysis as a methodology for the identification and retrieval of items of relevance within digitized collections of historic materials. Specifically, we sought to identify poetic content within historic newspapers, using Chronicling America's newspapers (http://chroniclingamerica.loc.gov/) as our test case. The project activities we undertook—both those completed and those in process—support this goal and align well with the activities proposed in our original funding application and as approved by NEH. To achieve our goal of creating an image processing-based system …

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 …

An Extendable Visualization And User Interface Design For Time-Varying Multivariate Geoscience Data, Yanfu Zhou

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

Geoscience data has unique and complex data structures, and its visualization has been challenging due to a lack of effective data models and visual representations to tackle the heterogeneity of geoscience data. In today’s big data era, the needs of visualizing geoscience data become urgent, especially driven by its potential value to human societies, such as environmental disaster prediction, urban growth simulation, and so on. In this thesis, I created a novel geoscience data visualization framework and applied interface automata theory to geoscience data visualization tasks. The framework can support heterogeneous geoscience data and facilitate data operations. The interface automata …

Incremental Phylogenetics By Repeated Insertions: An Evolutionary Tree Algorithm, Peter Revesz, Zhiqiang Li

School of Computing: Faculty Publications

We introduce the idea of constructing hypothetical evolutionary trees using an incremental algorithm that inserts species one-by-one into the current evolutionary tree. The method of incremental phylogenetics by repeated insertions lead to an algorithm that can be used on DNA, RNA and amino acid sequences. According to experimental results on both synthetic and biological data, the new algorithm generates more accurate evolutionary trees than the UPGMA and the Neighbor Joining algorithms.

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 …

Spica: Stereographic Projection For Interactive Crystallographic Analysis, Xingzhong Li

Nebraska Center for Materials and Nanoscience: Faculty Publications

In numerous research fields, especially the applications of electron and X-ray diffraction, stereographic projection represents a powerful tool for researchers. SPICA is a new computer program for stereographic projection in interactive crystallographic analysis, which inherits features from the previous JECP/SP and includes more functions for extensive crystallographic analysis. SPICA provides fully interactive options for users to plot stereograms of crystal directions and crystal planes, traces, and Kikuchi maps for an arbitrary crystal structure; it can be used to explore the orientation relationships between two crystalline phases with a composite stereogram; it is also used to predict the tilt angles of …

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 …

Examining Bridges Between Informal And Formal Learning Environments: A Sequential Mixed Method Design, Dagen L. Valentine

Department of Agricultural Leadership, Education and Communication: Dissertations, Theses, and Student Scholarship

The purpose of this sequential mixed method study was to identify schools implementing a technology-based engineering design intervention in a way that connects or bridges formal learning environments of the school-day to informal learning environments such as afterschool programs. Further, this study investigated educators’ decisions that enabled or facilitated bridging between formal and informal learning environments. This cooperation and/or linking between informal and formal learning time is bridging. Participants included public schools (n=16) in Eastern Nebraska that incorporated the Nebraska Wearables Technology (WearTec) program at their school, club or Out-of-School-Time program during the 2015-2016 school year. Three of the schools …

Why Do Record/Replay Tests Of Web Applications Break?, Mouna Hammoudi

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

Software engineers often use record/replay tools to enable the automated testing of web applications. Tests created in this manner can then be used to regression test new versions of the web applications as they evolve. Web application tests recorded by record/replay tools, however, can be quite brittle; they can easily break as applications change. For this reason, researchers have begun to seek approaches for automatically repairing record/replay tests. To date, however, there have been no comprehensive attempts to characterize the causes of breakages in record/replay tests for web applications. In this work, we present a taxonomy classifying the ways in …

Sonifying Git History, Kevin J. North

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

Version control is a technique that software developers use in industry to manage their source code artifacts. One benefit of using version control is that it produces a history of every change made to a codebase, which developers frequently analyze in order to aid the software development process. However, version control history contains highly multidimensional and temporal data. State of the art techniques can show several of these dimensions, but they cannot show a large number of dimensions simultaneously without becoming difficult to understand. An alternative technique to understand temporal data with high dimensionality is sonification. Sonification maps information to …

A Roadmap To Safe And Reliable Engineered Biological Nano-Communication Networks, Justin W. Firestone

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

Synthetic biology has the potential to benefit society with novel applications that can improve soil quality, produce biofuels, grow customized biological tissue, and perform intelligent drug delivery, among many other possibilities. Engineers are creating techniques to program living cells, inserting new logic, and leveraging cell-to-cell communication, which result in changes to a cell's core functionality. Using these techniques, we can now create synthetic biological organisms (SBOs) with entirely new (potentially unseen) behaviors, which, similar to silicon devices, can sense, actuate, perform computation, and interconnect with other networks at the nanoscale level. SBOs are programmable evolving entities, and can be likened …

Chipathlon: A Competitive Assessment For Gene Regulation Tools., Avi Knecht, Adam Caprez, Istvan Ladunga

UCARE Research Products

When gene regulation of the cell cycle malfunctions, it frequently causes cancer.

Adult, differentiated cells can be reprogrammed to induced pluripotent stem cell; which can then be reprogrammed to heart muscle, skin, etc, to repair damaged tissue (to limited extent in clinical practice).

ChIPathlon: Evaluate the performance of all transcription factor mapping (peak calling) methods. To this end, we will develop a scalable and easy to use super computing pipeline to stage data, compare many different peak calling and differential binding site tools, and store all results into a single database.

Flying By Fire: Making Controlled Burns Safer For Humans And Uavs, Rebecca Horzewski, Carrick Detweiler

UCARE Research Products

A temperature sensing circuit board was developed that will allow Nimbus Lab's controlled burn starting UAV to react to the temperatures around it.

Alignment For Comprehensive Two-Dimensional Gas Chromatography (Gcxgc) With Global, Low-Order Polynomial Transformations, Davis Rempe, Stephen Reichenbach, Stephen Scott

UCARE Research Products

As columns age and differ between systems, retention times for GC x GC may vary between runs. In order to properly analyze chromatograms, it is often desirable to align chromatographic features between chromatograms. This alignment can be characterized by a mapping of retention times from one chromatogram to the retention times of another chromatogram. Alignment methods can be classified as global or local, i.e., whether the geometric differences between chromatograms are characterized by a single function for the entire chromatogram or by a combination of many functions for different regions of the chromatogram. Previous work has shown that global, low-degree …

Past Meets Future: Combining Gis, 3d Technologies, And Legacy Data To Reanalyze Ceramics At Copan, Honduras, Stephanie Sterling, Heather Richards-Rissetto, René Viel

UCARE Research Products

The archaeological site of Copán—a UNESCO World Heritage Site in Honduras—was a primary center for cultural and economic exchange in the Maya world from the fifth to ninth centuries. Our research investigates the sociopolitical climate of the city immediately preceding this collapse. This poster presents the results of a pilot study intended to evaluate the potential of using a combination of digital technologies and legacy data to reanalyze a subset of diagnostic ceramics from select sites outside of Copan’s urban core. Our methods involved:

(1) Applying photogrammetry to generate 3D models for approximately 30 potentially temporally-diagnostic ceramic types

(2) Digitizing, …

A Mitochondrial Dna-Based Computational Model Of The Spread Of Human Populations, Peter Revesz

School of Computing: Faculty Publications

This paper presents a mitochondrial DNA-based computational model of the spread of human populations. The computation model is based on a new measure of the relatedness of two populations that may be both heterogeneous in terms of their set of mtDNA haplogroups. The measure gives an exponentially increasing weight for the similarity of two haplogroups with the number of levels shared in the mtDNA classification tree. In an experiment, the computational model is applied to the study of the relatedness of seven human populations ranging from the Neolithic through the Bronze Age to the present. The human populations included in …

A Systems Approach To Animal Communication, Eileen A. Hebets, Andrew B. Barron, Christopher N. Balakrishnan, Mark E. Hauber, Paul H. Mason, Kim L. Hoke

Eileen Hebets Publications

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication—an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and how function …

Table Headers: An Entrance To The Data Mine, George Nagy, Sharad C. Seth

CSE Conference and Workshop Papers

Algorithmic methods are demonstrated for information extraction from table header elements, including data categories and data hierarchies. The table headers are found with the Minimum Index Point Search algorithm. The header-path alignment and header completion algorithms yield database-ready table content and configuration statistics on a random sample of 400 diverse tables with ground truth and 1120 tables without ground truth from international statistical data sites.

Impacts Of Soil Type And Moisture On The Capacity Of Multi-Carrier Modulation In Internet Of Underground Things, Abdul Salam, Mehmet C. Vuran

CSE Conference and Workshop Papers

Unique interactions between soil and communication components in wireless underground communications necessitate revisiting fundamental communication concepts from a different perspective. In this paper, capacity profile of wireless underground (UG) channel for multi-carrier transmission techniques is analyzed based on empirical antenna return loss and channel frequency response models in different soil types and moisture values. It is shown that data rates in excess of 124 Mbps are possible for distances up to 12 m. For shorter distances and lower soil moisture conditions, data rates of 362 Mbps can be achieved. It is also shown that due to soil moisture variations, UG …

Learning Hierarchically Decomposable Concepts With Active Over-Labeling, Yuji Mo, Stephen Scott, Doug Downey

CSE Conference and Workshop Papers

Many classification tasks target high-level concepts that can be decomposed into a hierarchy of finer-grained subconcepts. For example, some string entities that are Locations are also Attractions, some Attractions are Museums, etc. Such hierarchies are common in named entity recognition (NER), document classification, and biological sequence analysis. We present a new approach for learning hierarchically decomposable concepts. The approach learns a high-level classifier (e.g., location vs. non-location) by seperately learning multiple finer-grained classifiers (e.g., museum vs. non-museum), and then combining the results. Soliciting labels at a finer level of granularity than that of the target concept is a new approach …

The Unforeseen Evolution Of Technology, Dylan White

Nebraska College Preparatory Academy: Senior Capstone Projects

Technology has evolved in the past two decades to alter how countries and their people live in the present day. Said technology has also both solved and created new problems for world powers (i.e. the U.S. and China) to face. Issues of cyber security and cyber surveillance are already potential problems that need to be addressed, where topics like cyber warfare need to be closely monitored with time. All of these are potentially underestimated threats to civil liberties, and to countries in their entirety.

I agree with the findings in my project… • The United States is a model to …

Image Harvest: An Open-Source Platform For High-Throughput Plant Image Processing And Analysis, Avi C. Knecht, Malachy T. Campbell, Adam Caprez, David R. Swanson, Harkamal Walia

Holland Computing Center: Faculty Publications

High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources …

Interim Report, Hd-51897-14, Image Analysis For Archival Discovery (Aida), January 2016, Elizabeth M. Lorang, Leen-Kiat Soh

CDRH Grant Reports

In the third six months of work on "Image Analysis for Archival Discovery," the project team has made progress toward the goals outlined in our report from June 2015. As we reported in June 2015, we realized that our original plan to analyze 7 million pages from Chronicling America was overly ambitious for the grant period, and we revised our goal to complete a thorough case study of our methodology and code for all newspaper images in Chronicling America from the period 1836-1840. Activities undertaken, toward this and other grant goals, from June 2015–December 2015:

• Publication of the article, "Developing …

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