Computer Sciences Commons^™

Dynamic Data Management In A Data Grid Environment, Björn Barrefors

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

A data grid is a geographically distributed set of resources providing a facility for computationally intensive analysis of large datasets to a large number of geographically distributed users. In the scientific community, data grids have become increasingly popular as scientific research is driven by large datasets. Until recently, developments in data management for data grids have focused on management of data at lower layers in the data grid architecture. With dataset sizes expected to approach exabyte scale in coming years, data management in data grids are facing a new set of challenges. In particularly, the problem of automatically placing and …

Routing Optimization In Interplanetary Networks, Sara El Alaoui

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

Interplanetary Internet or Interplanetary Networking (IPN) is envisaged as a space network which interconnects spacecrafts, satellites, rovers and orbiters of different planets and comets for efficient exchange of scientific data such as telemetry and images. IPNs are classified among challenged networks because of the unpredictable changes in the network and the large varying delays in communication. These networks are hard to model using static graphs and do not behave optimally when operated using the standards and techniques of static networks. Delay Tolerant Networking (DTN), in its different implementations, is one of the suggested solutions to overcome these challenges. DTN has …

Transforming C Openmp Programs For Verification In Civl, Michael Rogers

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

There are numerous way to express parallelism which can make it challenging for developers to verify these programs. Many tools only target a single dialect but the Concurrency Intermediate Verification Language (CIVL) targets MPI, Pthreads, and CUDA. CIVL provides a general concurrency model that can represent pro- grams in a variety of concurrency dialects. CIVL includes a front-end that support all of the dialects mentioned above. The back-end is a verifier that uses model checking and symbolic execution to check standard properties.

In this thesis, we have designed and implemented a transformer that will take C OpenMP programs and transform …

The Digital Incunabula: Rock • Paper • Pixels, Patrick Aievoli

Zea E-Books Collection

“The Digital Incunabula is Patrick Aievoli’s personal sonnet through media, interaction and communication design. He carefully crafts each evolutionary step into ripples that are supported by his own storied professional and academic experiences. It’s full of facts, terms and historical information which makes it perfect for anyone looking to flat out learn!” ● James Pannafino, Professor, Millersville University & Interaction Design

“This is a serious work that will find a broad community of readers. The depth and breadth of Aievoli’s experience in the publication industry give his voice and ideas credibility in the extreme. This book will inspire deep reflection.” …

Chemometric And Bioinformatic Analyses Of Cellular Biochemistry, Bradley Worley

Department of Chemistry: Dissertations, Theses, and Student Research

The amount of information collected and analyzed in biochemical and bioanalytical research has exploded over the last few decades, due in large part to the increasing availability of analytical instrumentation that yields information-rich spectra. Datasets from Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), infrared (IR) or Raman spectroscopy may easily carry tens to hundreds of thousands of potentially correlated variables observed from only a few samples, making the application of classical statistical methods inappropriate, if not impossible. Drawing useful biochemical conclusions from these unique sources of data requires the use of specialized multivariate data handling techniques.

Unfortunately, proper implementation of …

Mutations Of Adjacent Amino Acid Pairs Are Not Always Independent, Jyotsna Ramanan, Peter Revesz

CSE Conference and Workshop Papers

Evolutionary studies usually assume that the genetic mutations are independent of each other. This paper tests the independence hypothesis for genetic mutations with regard to protein coding regions. According to the new experimental results the independence assumption generally holds, but there are certain exceptions. In particular, the coding regions that represent two adjacent amino acids seem to change in ways that sometimes deviate significantly from the expected theoretical probability under the independence assumption.

A Computational Translation Of The Phaistos Disk, Peter Revesz

CSE Conference and Workshop Papers

For over a century the text of the Phaistos Disk remained an enigma without a convincing translation. This paper presents a novel semi-automatic translation method that uses for the first time a recently discovered connection between the Phaistos Disk symbols and other ancient scripts, including the Old Hungarian alphabet. The connection between the Phaistos Disk script and the Old Hungarian alphabet suggested the possibility that the Phaistos Disk language may be related to Proto-Finno-Ugric, Proto-Ugric, or Proto-Hungarian. Using words and suffixes from those languages, it is possible to translate the Phaistos Disk text as an ancient sun hymn, possibly connected …

A Computational Model Of The Spread Of Ancient Human Populations Based On Mitochondrial Dna Samples, Peter Revesz

CSE Conference and Workshop Papers

The extraction of mitochondrial DNA (mtDNA) from ancient human population samples provides important data for the reconstruction of population influences, spread and evolution from the Neolithic to the present. This paper presents a mtDNA-based similarity measure between pairs of human populations and a computational model for the evolution of human populations. In a computational experiment, the paper studies the mtDNA information from five Neolithic and Bronze Age populations, namely the Andronovo, the Bell Beaker, the Minoan, the Rössen and the Únětice populations. In the past these populations were identified as separate cultural groups based on geographic location, age and the …

A-Maze-D: Advanced Maze Development Kit Using Constraint Databases, Shruti Daggumarti, Peter Revesz, Corey Svehla

CSE Conference and Workshop Papers

In this paper, we describe the A-Maze-D system which shows that constraint databases can be applied conveniently and efficiently to the design of maze games. A-Maze-D provides a versatile set of features by a combination of a MATLAB library and the MLPQ constraint database system. A-Maze-D is the first system that uses constraint databases to build maze games and opens new ideas in video game development.

An Incremental Phylogenetic Tree Algorithm Based On Repeated Insertions Of Species, Peter Revesz, Zhiqiang Li

CSE Conference and Workshop Papers

In this paper, we introduce a new phylogenetic tree algorithm that generates phylogenetic trees by repeatedly inserting species one-by-one. The incremental phylogenetic tree algorithm can work on proteins or DNA sequences. Computer experiments show that the new algorithm is better than the commonly used UPGMA and Neighbor Joining algorithms.

A Computational Study Of The Evolution Of Cretan And Related Scripts, Peter Revesz

CSE Conference and Workshop Papers

Crete was the birthplace of several ancient writings, including the Cretan Hieroglyphs, the Linear A and the Linear B scripts. Out of these three only Linear B is deciphered. The sound values of the Cretan Hieroglyph and the Linear A symbols are unknown and attempts to reconstruct them based on Linear B have not been fruitful. In this paper, we compare the ancient Cretan scripts with four other Mediterranean and Black Sea scripts, namely Phoenician, South Arabic, Greek and Old Hungarian. We provide a computational study of the evolution of the three Cretan and four other scripts. This study encompasses …

Bioinformatics Approaches To Single-Cell Analysis In Developmental Biology, Dicle Yalcin, Zeynep M. Hakguder, Hasan H. Otu

Department of Electrical and Computer Engineering: Faculty Publications

Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging …

A Visual Analysis Of Articulated Motion Complexity Based On Optical Flow And Spatial-Temporal Features, Beau Michael Christ

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

The understanding of motion is an important problem in computer vision with applications including crowd-flow analysis, video surveillance, and estimating three-dimensional structure. A less-explored problem is the visual characterization and quantification of motion complexity. An important motion class that is prevalent in living beings is articulated motion (segments connected by joints). At present, no known standardized measure for quantifying the complexity of articulated motion exists. Such a measure could facilitate advanced motion analysis with applications including video indexing, motion comparison, and advanced biological study of visual signals in organisms.

This dissertation presents an in-depth study of the development of several …

Discovery Over Application: A Case Study Of Misaligned Incentives In Software Engineering, Eric F. Rizzi

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

In this thesis, we present evidence that there is an under-emphasis on the application of software systems in Software Engineering research, affecting the advancement of the field as a whole. Specifically, we perform a case-study on KLEE, a tool with over 1000 citations. We made improvements that consisted of fixing performance bugs and implementing optimizations that have become common practice, increasing KLEE's performance by 2-11X. To understand how techniques proposed in the literature would be affected by these improvements, we analyzed 100 papers that cited the original KLEE paper. From this analysis we found two things. First, it is clear …

Distributed Caching Using The Htcondor Cached, Derek J. Weitzel, Brian Bockelman, David Swanson

Holland Computing Center: Faculty Publications

A batch processing job in a distributed system has three clear steps, stage-in, execution, and stage-out. As data sizes have increased, the stage-in time has also increased. In order to optimize stage-in time for shared inputs, we propose the CacheD, a caching mechanism for high throughput computing. Along with caching on worker nodes for rapid transfers, we also introduce a novel transfer method to distribute shared caches to multiple worker nodes utilizing BitTorrent. We show that our caching method significantly improves workflow completion times by minimizing stage-in time while being non-intrusive to the computational resources, allowing for opportunistic resources to …

Enabling Distributed Scientific Computing On The Campus, Derek J. Weitzel

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

Campus research computing has evolved from many small decentralized resources, such as individual desktops, to fewer, larger centralized resources, such as clusters. This change has been necessitated by the increasing size of researcher's workloads, but this change has harmed the researcher's user experience. We propose to improve the user experience on the computational resources by creating an overlay cluster they are able to control. This overlay should transparently scale to national cyberinfrastructure as the user's demands increase.

We explore methods for improving the user experience when submitting jobs on a campus grid. To this end, we created a remote submission …

Dietary Microrna Database (Dmd): An Archive Database And Analytic Tool For Food-Borne Micrornas, Kevin Chiang, Jiang Shu, Janos Zempleni, Juan Cui

School of Computing: Faculty Publications

With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs discovered in dietary resources. Currently there are fifteen types of dietary species, such as apple, grape, cow milk, and cow fat, included in the database originating from 9 plant and 5 animal species. Annotation for each entry, a mature microRNA indexed as DM0000*, covers information of the mature sequences, genome locations, hairpin structures of parental …

Robust And Real-Time Stereo Matching On Parallel Graphics Hardware Using Gradient-Based Disparity Refinement, Jedrzej Kowalczuk

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

Computer vision attempts to provide camera-equipped machines with visual perception, i.e., the capability to comprehend their surroundings through the analysis and understanding of images. The ability to perceive depth is a vital component of visual perception that enables machines to interpret the three-dimensional structure of their surroundings and allows them to navigate through the environment. In computer vision, depth perception is achieved via stereo matching, a process that identifies correspondences between pixels in images acquired using a pair of horizontally offset cameras. It is possible to calculate depths from correspondences or, more specifically, the positional offsets (disparities) between pixels in …

Reflective, Deliberative Agent-Based Information Gathering, Adam D. Eck

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

As computational devices and entities become further established as routine, omnipresent components of our everyday lives (e.g., wearable sensors, smart homes, cyber-physical systems, embodied agents, human-robot interactions), such systems face an increased pressure to perpetually understand the complex, noisy, uncertain world around them in real-time. This environmental knowledge enables computational systems to intelligently decide how to best behave in response to the current situation, adapt to the ever-changing conditions of the dynamic world, and accomplish system goals that ultimately aim to improve our daily experience. However, achieving and maintaining such knowledge is very complicated due to the complexities and challenging …

Visual Analytics For Large Communication Trace Data, Jieting Wu

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

Executions of modern parallel programs often yield complex communications among compute nodes of large-scale clusters of workstations or supercomputers. Analyzing communication patterns is becoming increasingly critical to performance optimiza- tion. As the scale and complexity of parallel applications drastically increases, visu- alization has become a feasible means to conduct analysis of massive communication patterns. However, most visualization tools fall short in showing comprehensive dy- namic communication graph and addressing the scalability issue. Our solution for analyzing dynamic communication patterns is based on an analytics framework cou- pled with a new visualization technique, named CommGram [29], that provides a flexible solution …

Developing An Image-Based Classifier For Detecting Poetic Content In Historic Newspaper Collections, Elizabeth M. Lorang, Leen-Kiat Soh, Maanas Varma Datla, Spencer Kulwicki

UNL Libraries: Faculty Publications

"Developing an Image-Based Classifier for Detecting Poetic Content in Historic Newspaper Collections" details and analyzes the first stage of work of the Image Analysis for Archival Discovery project team. Our team is is investigating the use of image analysis to identify poetic content in historic newspapers. The project seeks both to augment the study of literary history by drawing attention to the magnitude of poetry published in newspapers and by making the poetry more readily available for study, as well as to advance work on the use of digital images in facilitating discovery in digital libraries and other digitized collections. …

Clustering Header Categories Extracted From Web Tables, George Nagy, David W. Embley, Mukkai Krishnamoorthy, Sharad C. Seth

CSE Conference and Workshop Papers

Revealing related content among heterogeneous web tables is part of our long term objective of formulating queries over multiple sources of information. Two hundred HTML tables from institutional web sites are segmented and each table cell is classified according to the fundamental indexing property of row and column headers. The categories that correspond to the multi-dimensional data cube view of a table are extracted by factoring the (often multi-row/column) headers. To reveal commonalities between tables from diverse sources, the Jaccard distances between pairs of category headers (and also table titles) are computed. We show how about one third of our …

A Middleware Framework For Application-Aware And User-Specific Energy Optimization In Smart Mobile Devices, Sudeep Pasricha, Brad K. Donohoo, Chris Ohlsen

U.S. Air Force Research

munication, and social interaction. In addition to the demand for an acceptable level of performance and a comprehensive set of features, users often desire extended battery lifetime. In fact, limited battery lifetime is one of the biggest obstacles facing the current utility and future growth of increasingly sophisticated ‘‘smart’’ mobile devices. This paper proposes a novel application-aware and user-interaction aware energy optimization middleware framework (AURA) for pervasive mobile devices. AURA optimizes CPU and screen backlight energy consumption while maintaining a minimum acceptable level of performance. The proposed framework employs a novel Bayesian application classifier and management strategies based on Markov …

Metadata And Linked Data In Word Sense Disambiguation, Matthew Corsmeier

Library Philosophy and Practice (e-journal)

Word Sense Disambiguation (WSD) can be assisted by taking advantage of the metadata embedded in the various ontologies, lexica, databases, etc… that exist in the Semantic Web. Automated processes that exploit the links already present in the Semantic Web can strengthen parsing of word senses by using user-contributed and semantically-linked data. These processes are only possible because of a commitment to interoperability and the creation of shared standards. This paper will review some of the most heavily used Linguistic Linked Open Data (LLOD) tools and models which show the most promise for using metadata to alleviate problems caused by polysemous …