Computer Sciences Commons^™

Multiblock Discriminant Analysis For Integrative Genomic Study, Mingon Kang, Dong-Chul Kim, Chunyu Liu, Jean Gao

Computer Science Faculty Publications

Human diseases are abnormal medical conditions in which multiple biological components are complicatedly involved. Nevertheless, most contributions of research have been made with a single type of genetic data such as Single Nucleotide Polymorphism (SNP) or Copy Number Variation (CNV). Furthermore, epigenetic modifications and transcriptional regulations have to be considered to fully exploit the knowledge of the complex human diseases as well as the genomic variants. We call the collection of the multiple heterogeneous data “multiblock data.” In this paper, we propose a novel Multiblock Discriminant Analysis (MultiDA) method that provides a new integrative genomic model for the multiblock analysis …

A Stabilized Finite Element Method For Calculating Balance Velocities In Ice Sheets, Douglas Brinkerhoff, Jesse Johnson

Computer Science Faculty Publications

We present a numerical method for calculating vertically averaged velocity fields using a mass conservation approach, commonly known as balance velocities. This allows for an unstructured grid, is not dependent on a heuristic flow routing algorithm, and is both parallelizable and efficient. We apply the method to calculate depth-averaged velocities of the Greenland Ice Sheet, and find that the method produces grid-independent velocity fields for a sufficient parameterization of horizontal plane stresses on flow directions. We show that balance velocity can be used as the forward model for a constrained optimization problem that can be used to fill gaps and …

Compression Of Video Tracking And Bandwidth Balancing Routing In Wireless Multimedia Sensor Networks, Yin Wang, Jianjun Yang, Ju Shen, Bryson Payne, Juan Guo, Kun Hua

Computer Science Faculty Publications

There has been a tremendous growth in multimedia applications over wireless networks. Wireless Multimedia Sensor Networks(WMSNs) have become the premier choice in many research communities and industry. Many state-of-art applications, such as surveillance, traffic monitoring, and remote heath care are essentially video tracking and transmission in WMSNs. The transmission speed is constrained by the big file size of video data and fixed bandwidth allocation in constant routing paths. In this paper, we present a CamShift based algorithm to compress the tracking of videos. Then we propose a bandwidth balancing strategy in which each sensor node is able to dynamically select …

Leading Undergraduate Students To Big Data Generation, Jianjun Yang, Ju Shen

Computer Science Faculty Publications

People are facing a flood of data today. Data are being collected at unprecedented scale in many areas, such as networking, image processing, virtualization, scientific computation, and algorithms. The huge data nowadays are called Big Data. Big data is an all encompassing term for any collection of data sets so large and complex that it becomes difficult to process them using traditional data processing applications. In this article, the authors present a unique way which uses network simulator and tools of image processing to train students abilities to learn, analyze, manipulate, and apply Big Data. Thus they develop students hands-on …

Hole Detection And Shape-Free Representation And Double Landmarks Based Geographic Routing In Wireless Sensor Networks, Jianjun Yang, Zongming Fei, Ju Shen

Computer Science Faculty Publications

In wireless sensor networks, an important issue of geographic routing is “local minimum” problem, which is caused by a “hole” that blocks the greedy forwarding process. Existing geographic routing algorithms use perimeter routing strategies to find a long detour path when such a situation occurs. To avoid the long detour path, recent research focuses on detecting the hole in advance, then the nodes located on the boundary of the hole advertise the hole information to the nodes near the hole. Hence the long detour path can be avoided in future routing. We propose a heuristic hole detecting algorithm which identifies …

Serve Or Skip: The Power Of Rejection In Online Bottleneck Matching, Barbara M. Anthony, Christine Chung

Computer Science Faculty Publications

We consider the online matching problem, where n server-vertices lie in a metric space and n request-vertices that arrive over time each must immediately be permanently assigned to a server-vertex.We focus on the egalitarian bottleneck objective, where the goal is to minimize the maximum distance between any request and its server. It has been demonstrated that while there are effective algorithms for the utilitarian objective (minimizing total cost) in the resource augmentation setting where the offline adversary has half the resources, these are not effective for the egalitarian objective. Thus, we propose a new Serve-or-Skip bicriteria analysis model, where the …

Quick Git Setup, Joseph Lawrence, Seikyung Jung

Computer Science Faculty Publications

Version control is widely adopted in industry because it enables software development in groups, yet few students gain sufficient experience through their undergraduate courses. Even though version control is ideal for work submission, faculty may avoid it in favor of course management systems used only in academia. This tutorial introduces software to automate setting up version control with cloud project hosting services, and gives experience with version control as a side-effect of work submission and collection. This tutorial assumes no prior experience.

Pedagogical Possibilities For The 2048 Puzzle Game, Todd W. Neller

Computer Science Faculty Publications

In this paper, we describe an engaging puzzle game called 2048 and outline a variety of exercises that can leverage the game’s popularity to engage student interest, reinforce core CS concepts, and excite student curiosity towards undergraduate research. Exercises range in difficulty from CS1-level exercises suitable for exercising and assessing 1D and 2D array skills to empirical undergraduate research in Monte Carlo Tree Search methods and skilled heuristic evaluation design.

Perfect Graphs, Chinh T. Hoang, R. Sritharan

Computer Science Faculty Publications

This chapter is a survey on perfect graphs with an algorithmic flavor. Our emphasis is on important classes of perfect graphs for which there are fast and efficient recognition and optimization algorithms. The classes of graphs we discuss in this chapter are chordal, comparability, interval, perfectly orderable, weakly chordal, perfectly contractile, and chi-bound graphs. For each of these classes, when appropriate, we discuss the complexity of the recognition algorithm and algorithms for finding a minimum coloring, and a largest clique in the graph and its complement.

Salient Object Detection Via Objectness Proposals, Tam Nguyen

Computer Science Faculty Publications

Salient object detection has gradually become a popular topic in robotics and computer vision research. This paper presents a real-time system that detects salient objects by integrating objectness, foreground, and compactness measures. Our algorithm consists of four basic steps. First, our method generates the objectness map via object proposals. Based on the objectness map, we estimate the background margin and compute the corresponding foreground map which prefers the foreground objects. From the objectness map and the foreground map, the compactness map is formed to favor the compact objects. We then integrate those cues to form a pixel-accurate saliency map which …

Universal Computation With Arbitrary Polyomino Tiles In Non-Cooperative Self-Assembly, Sándor P. Fekete, Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers

Computer Science Faculty Publications

In this paper we explore the power of geometry to overcome the limitations of non-cooperative self-assembly. We define a generalization of the abstract Tile Assembly Model (aTAM), such that a tile system consists of a collection of polyomino tiles, the Polyomino Tile Assembly Model (polyTAM), and investigate the computational powers of polyTAM systems at temperature 1, where attachment among tiles occurs without glue cooperation (i.e., without the enforcement that more than one tile already existing in an assembly must contribute to the binding of a new tile). Systems composed of the unit-square tiles of the aTAM at temperature 1 …

What Is Answer Set Programming To Propositional Satisfiability, Yuliya Lierler

Computer Science Faculty Publications

Propositional satisfiability (or satisfiability) and answer set programming are two closely related subareas of Artificial Intelligence that are used to model and solve difficult combinatorial search problems. Satisfiability solvers and answer set solvers are the software systems that find satisfying interpretations and answer sets for given propositional formulas and logic programs, respectively. These systems are closely related in their common design patterns. In satisfiability, a propositional formula is used to encode problem specifications in a way that its satisfying interpretations correspond to the solutions of the problem. To find solutions to a problem it is then sufficient to use a …

Reminiscing About 15 Years Of Interoperability Efforts, Herbert Van De Sompel, Michael L. Nelson

Computer Science Faculty Publications

Over the past fifteen years, our perspective on tackling information interoperability problems for web-based scholarship has evolved significantly. In this opinion piece, we look back at three efforts that we have been involved in that aptly illustrate this evolution: OAI-PMH, OAI-ORE, and Memento. Understanding that no interoperability specification is neutral, we attempt to characterize the perspectives and technical toolkits that provided the basis for these endeavors. With that regard, we consider repository-centric and web-centric interoperability perspectives, and the use of a Linked Data or a REST/HATEAOS technology stack, respectively. We also lament the lack of interoperability across nodes that play …

Making Sense Of Video Analytics: Lessons Learned From Clickstream Interactions, Attitudes, And Learning Outcome In A Video-Assisted Course, Michail N. Giannakos, Konstantinos Chorianopoulos, Nikos Chrisochoides

Computer Science Faculty Publications

Online video lectures have been considered an instructional media for various pedagogic approaches, such as the flipped classroom and open online courses. In comparison to other instructional media, online video affords the opportunity for recording student clickstream patterns within a video lecture. Video analytics within lecture videos may provide insights into student learning performance and inform the improvement of video-assisted teaching tactics. Nevertheless, video analytics are not accessible to learning stakeholders, such as researchers and educators, mainly because online video platforms do not broadly share the interactions of the users with their systems. For this purpose, we have designed an …

Deep Convolutional Neural Networks For Annotating Gene Expression Patterns In The Mouse Brain, Tao Zeng, Rongjian Li, Ravi Mukkamala, Jieping Ye, Shuiwang Ji

Computer Science Faculty Publications

Background: Profiling gene expression in brain structures at various spatial and temporal scales is essential to understanding how genes regulate the development of brain structures. The Allen Developing Mouse Brain Atlas provides high-resolution 3-D in situ hybridization (ISH) gene expression patterns in multiple developing stages of the mouse brain. Currently, the ISH images are annotated with anatomical terms manually. In this paper, we propose a computational approach to annotate gene expression pattern images in the mouse brain at various structural levels over the course of development.

Results: We applied deep convolutional neural network that was trained on a large set …

Scalable 3d Hybrid Parallel Delaunay Image-To-Mesh Conversion Algorithm For Distributed Shared Memory Architectures, Daming Feng, Christos Tsolakis, Andrey N. Chernikov, Nikos P. Chrisochoides

Computer Science Faculty Publications

In this paper, we present a scalable three dimensional hybrid parallel Delaunay image-to-mesh conversion algorithm (PDR.PODM) for distributed shared memory architectures. PDR.PODM is able to explore parallelism early in the mesh generation process because of the aggressive speculative approach employed by the Parallel Optimistic Delaunay Mesh generation algorithm (PODM). In addition, it decreases the communication overhead and improves data locality by making use of a data partitioning scheme offered by the Parallel Delaunay Refinement algorithm (PDR). PDR.PODM utilizes an octree structure to decompose the initial mesh and to distribute the bad elements to different octree leaves (subregions). A set of …

Tetrahedral Image-To-Mesh Conversion Software For Anatomic Modeling Of Arteriovenous Malformations, Fotis Drakopoulos, Ricardo Ortiz, Andinet Enquobahrie, Deanna Sasaki-Adams, Nikos Chrisochoides

Computer Science Faculty Publications

We describe a new implementation of an adaptive multi-tissue tetrahedral mesh generator targeting anatomic modeling of Arteriovenous Malformation (AVM) for surgical simulations. Our method, initially constructs an adaptive Body-Centered Cubic (BCC) mesh of high quality elements. Then, it deforms the mesh surfaces to their corresponding physical image boundaries, hence, improving the mesh fidelity and smoothness. Our deformation scheme, which builds upon the ITK toolkit, is based on the concept of energy minimization, and relies on a multi-material point-based registration. It uses non-connectivity patterns to implicitly control the number of the extracted feature points needed for the registration, and thus, adjusts …

Saccharomyces Boulardii And Bismuth Subsalicylate As Low-Cost Interventions To Reduce The Duration And Severity Of Cholera, Johnathan Sheele, Jessica Cartowski, Angela Dart, Arjun Poddar, Shikha Gupta, Ajay Gupta

Computer Science Faculty Publications

We conducted a randomised single-blinded clinical trial of 100 cholera patients in Port-au-Prince, Haiti to determine if the probiotic Saccharomyces cerevisiae var. boulardii and the anti-diarrhoeal drug bismuth subsalicylate (BS) were able to reduce the duration and severity of cholera. Subjects received either: S. boulardii 250 mg, S. boulardii 250 mg capsule plus BS 524 mg tablet, BS 524 mg, or two placebo capsules every 6 hours alongside standard treatment for cholera. The length of hospitalisation plus the number and volume of emesis, stool and urine were recorded every 6 hours until the study subject was discharged (n=83), left against …

Characteristics Of Social Media Stories, Yasmin Ainoamany, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

An emerging trend in social media is for users to create and publish "stories", or curated lists of web resources with the purpose of creating a particular narrative of interest to the user. While some stories on the web are automatically generated, such as Facebook’s "Year in Review", one of the most popular storytelling services is "Storify", which provides users with curation tools to select, arrange, and annotate stories with content from social media and the web at large. We would like to use tools like Storify to present automatically created summaries of archival collections. To support automatic story creation, …

Scaffolding To Improve Writing Skills In A Computer Science Literacy Course, Wu He, Harris Wu, Li Xu, Kurt Maly

Computer Science Faculty Publications

Writing has been recognized as an important skill in the technology field. This paper reports a study that uses a scaffolding approach to improve student writing skills in a computer science literacy course. While the quantitative results do not show a significant impact of scaffolding in individual paper assignment on the subsequent group wiki assignment, the student feedback in end-of-semester evaluations strongly indicated that scaffolding indeed helped improve their writing.

Extreme-Scale Parallel Mesh Generation: Telescopic Approach, Nikos Chrisochoides, Andrey Chernikov, Daming Feng, Christos Tsolakis

Computer Science Faculty Publications

In this poster we focus and present our preliminary results pertinent to the integration of multiple parallel Delaunay mesh generation methods into a coherent hierarchical framework. The goal of this project is to study our telescopic approach and to develop Delaunay-based methods to explore concurrency at all hardware layers using abstractions at (a) medium-grain level for many cores within a single chip and (b) coarse-grain level, i.e., sub-domain level using proper error metric- and application-specific continuous decomposition methods.

Profiling Web Archives For Efficient Memento Query Routing, Sawood Alam, Michael L. Nelson, Herbert Van De Sompel, Lyudmila L. Balakireva, Harihar Shankar, David S. H. Rosenthal

Computer Science Faculty Publications

No abstract provided.

A Dynamic Programming Algorithm For Finding The Optimal Placement Of A Secondary Structure Topology In Cryo-Em Data, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He

Computer Science Faculty Publications

The determination of secondary structure topology is a critical step in deriving the atomic structures from the protein density maps obtained from electron cryomicroscopy technique. This step often relies on matching the secondary structure traces detected from the protein density map to the secondary structure sequence segments predicted from the amino acid sequence. Due to inaccuracies in both sources of information, a pool of possible secondary structure positions needs to be sampled. One way to approach the problem is to first derive a small number of possible topologies using existing matching algorithms, and then find the optimal placement for each …

Flow Dynamics Of Byrd Glacier, East Antarctica, C. J. Van Der Veen, L. A. Stearns, Jesse Johnson, B. Csatho

Computer Science Faculty Publications

Force-balance calculations on Byrd Glacier, East Antarctica, reveal large spatial variations in the along-flow component of driving stress with corresponding sticky spots that are stationary over time. On the large scale, flow resistance is partitioned between basal (�80%) and lateral (�20%) drag. Ice flow is due mostly to basal sliding and concentrated vertical shear in the basal ice layers, indicating the bed is at or close to the pressure-melting temperature. There is a significant component of driving stress in the across-flow direction resulting in nonzero basal drag in that direction. This is an unrealistic result and we propose that there …

Aspccgtk: Towards Syntactic Parsing With Semantic Disambiguation, Yuliya Lierler, Peter Schueller

Computer Science Faculty Publications

Natural language expressions are often ambiguous, allowing multiple interpretations. In this note we describe an approach that integrates syntactic analysis with semantic constraints in a system called ASPCCGTK. This system is based on Answer Set Programming — a popular declarative constraint programming paradigm.

A Specific Type Of Cyclin-Like F-Box Domain Gene Is Involved In The Cryogenic Autolysis Of Volvariella Volvacea, Ming Gong, Mingjie Chen, Hong Wang, Qiuming Zhu, Qi Tan

Computer Science Faculty Publications

Cryogenic autolysis is a typical phenomenon of abnormal metabolism in Volvariella volvacea. Recent studies have identified 20 significantly upregulated genes via high-throughput sequencing of the mRNAs expressed in the mycelia of V. volvacea after cold exposure. Among these significantly upregulated genes, 15 annotated genes were used for functional annotation cluster analysis. Our results showed that the cyclin-like F-box domain (FBDC) formed the functional cluster with the lowest P-value. We also observed a significant expansion of FBDC families in V. volvacea. Among these, the FBDC3 family displayed the maximal gene expansion in V. volvacea. Gene expression profiling analysis revealed …

Theoretical Analysis Of Steady State Genetic Algorithms, Alexandru Agapie, Alden H. Wright

Computer Science Faculty Publications

Evolutionary Algorithms, also known as Genetic Algorithms in a former terminology, are probabilistic algorithms for optimization, which mimic operators from natural selection and genetics. The paper analyses the convergence of the heuristic associated to a special type of Genetic Algorithm, namely the Steady State Genetic Algorithm (SSGA), considered as a discrete-time dynamical system non-generational model. Inspired by the Markov chain results in finite Evolutionary Algorithms, conditions are given under which the SSGA heuristic converges to the population consisting of copies of the best chromosome.

Evaluation Of Microarray-Based Dna Methylation Measurement Using Technical Replicates: The Atherosclerosis Risk In Communities (Aric) Study, Maitreyee Bose, Chong Wu, James S. Pankow, Ellen W. Demerath, Jan Bressler, Myriam Fornage, Megan L. Grove, Thomas H. Mosley, Chindo Hicks, Kari North, Wen Hong Kao, Yu Zhang, Eric Boerwinkle, Weihua Guan

Computer Science Faculty Publications

Background: DNA methylation is a widely studied epigenetic phenomenon; alterations in methylation patterns influence human phenotypes and risk of disease. As part of the Atherosclerosis Risk in Communities (ARIC) study, the Illumina Infinium HumanMethylation450 (HM450) BeadChip was used to measure DNA methylation in peripheral blood obtained from ~3000 African American study participants. Over 480,000 cytosine-guanine (CpG) dinucleotide sites were surveyed on the HM450 BeadChip. To evaluate the impact of technical variation, 265 technical replicates from 130 participants were included in the study.

Results: For each CpG site, we calculated the intraclass correlation coefficient (ICC) to compare variation of methylation levels …

On The Approximability Of The Exemplar Adjacency Number Problem For Genomes With Gene Repetitions, Zhinxiag Chen, Bin Fu, Randy Goebel, Guohui Lin, Weitian Tong, Jinhui Xu, Boting Yang, Zhiyu Zhao, Binhai Zhu

Computer Science Faculty Publications

In this paper, we apply a measure, exemplar adjacency number, which complements and extends the well-studied breakpoint distance between two permutations, to measure the similarity between two genomes (or in general, between any two sequences drawn from the same alphabet). For two genomes and drawn from the same set of n gene families and containing gene repetitions, we consider the corresponding Exemplar Adjacency Number problem (EAN), in which we delete duplicated genes from and such that the resultant exemplar genomes (permutations) G and H have the maximum adjacency number. We obtain the following results. First, we prove that the one-sided …

Piecing The Puzzle Together: A Revisit To Transcript Reconstruction Problem In Rna-Seq, Yan Huang, Yin Hu, Jinze Liu

Computer Science Faculty Publications

The advancement of RNA sequencing (RNA-seq) has provided an unprecedented opportunity to assess both the diversity and quantity of transcript isoforms in an mRNA transcriptome. In this paper, we revisit the computational problem of transcript reconstruction and quantification. Unlike existing methods which focus on how to explain the exons and splice variants detected by the reads with a set of isoforms, we aim at reconstructing transcripts by piecing the reads into individual effective transcript copies. Simultaneously, the quantity of each isoform is explicitly measured by the number of assembled effective copies, instead of estimated solely based on the collective read …