Physical Sciences and Mathematics Commons^™

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 …

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 …

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 …

Seeing Human Weight From A Single Rgb-D Image, Tam Nguyen, Jiashi Feng, Shuicheng Yan

Computer Science Faculty Publications

Human weight estimation is useful in a variety of potential applications, e.g., targeted advertisement, entertainment scenarios and forensic science. However, estimating weight only from color cues is particularly challenging since these cues are quite sensitive to lighting and imaging conditions. In this article, we propose a novel weight estimator based on a single RGB-D image, which utilizes the visual color cues and depth information. Our main contributions are three-fold.

First, we construct the W8-RGBD dataset including RGB-D images of different people with ground truth weight.

Second, the novel sideview shape feature and the feature fusion model are proposed to facilitate …

Digital Scholarship: Applying Digital Tools To Undergraduate Student Research Papers, A Proposal For A Freshman Seminar. Part I: Definition Of Student Research Methodology, Charles W. Kann

Computer Science Faculty Publications

There are many digital tools that can be used for research and presentation in nearly every college discipline, including the social sciences and humanities. These tools hold the promise to radically change both the process and products of research. But in their application these tools have failed miserably to live up to their promise.

This paper is based on the hypothesis that one reason these tools do reach their potential is that there is no systemic way to include them in research process, resulting in the tools being seen as ways to improve the final research product. This results in …

Distributed Power-Line Outage Detection Based On Wide Area Measurement System, Liang Zhao, Wen-Zhan Song

Computer Science Faculty Publications

In modern power grids, the fast and reliable detection of power-line outages is an important functionality, which prevents cascading failures and facilitates an accurate state estimation to monitor the real-time conditions of the grids. However, most of the existing approaches for outage detection suffer from two drawbacks, namely: (i) high computational complexity; and (ii) relying on a centralized means of implementation. The high computational complexity limits the practical usage of outage detection only for the case of single-line or double-line outages. Meanwhile, the centralized means of implementation raises security and privacy issues. Considering these drawbacks, the present paper proposes a …

Structure Preserving Large Imagery Reconstruction, Ju Shen, Jianjun Yang, Sami Taha Abu Sneineh, Bryson Payne, Markus Hitz

Computer Science Faculty Publications

With the explosive growth of web-based cameras and mobile devices, billions of photographs are uploaded to the internet. We can trivially collect a huge number of photo streams for various goals, such as image clustering, 3D scene reconstruction, and other big data applications. However, such tasks are not easy due to the fact the retrieved photos can have large variations in their view perspectives, resolutions, lighting, noises, and distortions. Furthermore, with the occlusion of unexpected objects like people, vehicles, it is even more challenging to find feature correspondences and reconstruct realistic scenes. In this paper, we propose a structure-based image …

Accurate Viral Population Assembly From Ultra-Deep Sequencing Data, Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alexander Zelikovskiy, Ren Sun, Eleazar Eskin

Computer Science Faculty Publications

Motivation: Next-generation sequencing technologies sequence viruses with ultra-deep coverage, thus promising to revolutionize our understanding of the underlying diversity of viral populations. While the sequencing coverage is high enough that even rare viral variants are sequenced, the presence of sequencing errors makes it difficult to distinguish between rare variants and sequencing errors. Results: In this article, we present a method to overcome the limitations of sequencing technologies and assemble a diverse viral population that allows for the detection of previously undiscovered rare variants. The proposed method consists of a high-fidelity sequencing protocol and an accurate viral population assembly method, referred …

Optimal Acceleration Thresholds For Non-Holonomic Agents, Brian Ricks, Parris K. Egbert

Computer Science Faculty Publications

Finding optimal trajectories for non-accelerating, non-holonomic agents is a well-understood problem. However, in video games, robotics, and crowd simulations non-holonomic agents start and stop frequently. With the vision of improving crowd simulation, we find optimal paths for virtual agents accelerating from a standstill. These paths are designed for the “ideal”, initial stage of planning when obstacles are ignored. We analytically derive paths and arrival times using arbitrary acceleration angle thresholds. We use these paths and arrival times to find an agent’s optimal ideal path. We then numerically calculate the decision surface that can be used by an application at run-time …

Cloud Computing For Detecting High-Order Genome-Wide Epistatic Interaction Via Dynamic Clustering, Xuan Guo, Yu Meng, Ning Yu, Yi Pan

Computer Science Faculty Publications

Backgroud: Taking the advan tage of high-throughput single nucleotide polymorphism (SNP) genotyping technology, large genome-wide association studies (GWASs) have been considered to hold promise for unravelling complex relationships between genotype and phenotype. At present, traditional single-locus-based methods are insufficient to detect interactions consisting of multiple-locus, which are broadly existing in complex traits. In addition, statistic tests for high order epistatic interactions with more than 2 SNPs propose computational and analytical challenges because the computation increases exponentially as the cardinality of SNPs combinations gets larger. Results: In this paper, we provide a simple, fast and powerful method using dynamic clustering and …

Automatic Objects Removal For Scene Completion, Jianjun Yang, Yin Wang, Honggang Wang, Kun Hua, Wei Wang, Ju Shen

Computer Science Faculty Publications

With the explosive growth of Web-based cameras and mobile devices, billions of photographs are uploaded to the Internet. We can trivially collect a huge number of photo streams for various goals, such as 3D scene reconstruction and other big data applications. However, this is not an easy task due to the fact the retrieved photos are neither aligned nor calibrated. Furthermore, with the occlusion of unexpected foreground objects like people, vehicles, it is even more challenging to find feature correspondences and reconstruct realistic scenes. In this paper, we propose a structure-based image completion algorithm for object removal that produces visually …

Pointing Devices For Wearable Computers, Saverio Perugini, Andres A. Calvo

Computer Science Faculty Publications

We present a survey of pointing devices for wearable computers, which are body-mounted devices that users can access at any time. Since traditional pointing devices (i.e., mouse, touchpad, and trackpoint) were designed to be used on a steady and flat surface, they are inappropriate for wearable computers. Just as the advent of laptops resulted in the development of the touchpad and trackpoint, the emergence of wearable computers is leading to the development of pointing devices designed for them. However, unlike laptops, since wearable computers are operated from different body positions under different environmental conditions for different uses, researchers have developed …

Unstructured P2p Link Lifetimes Redux, Zhongmei Yao, Daren B. H. Cline

Computer Science Faculty Publications

We revisit link lifetimes in random P2P graphs under dynamic node failure and create a unifying stochastic model that generalizes the majority of previous efforts in this direction. We not only allow nonexponential user lifetimes and age-dependent neighbor selection, but also cover both active and passive neighbor-management strategies, model the lifetimes of incoming and outgoing links, derive churn-related message volume of the system, and obtain the distribution of transient in/out degree at each user. We then discuss the impact of design parameters on overhead and resilience of the network.

Relating Constraint Answer Set Programming Languages And Algorithms, Yuliya Lierler

Computer Science Faculty Publications

Recently a logic programming language AC was proposed by Mellarkod et al. (2008) to integrate answer set programming and constraint logic programming. Soon after that, a CLINGCON language integrating answer set programming and finite domain constraints, as well as an EZCSP language integrating answer set programming and constraint logic programming were introduced. The development of these languages and systems constitutes the appearance of a new AI subarea called constraint answer set programming. All these languages have something in common. In particular, they aim at developing new efficient inference algorithms that combine traditional answer set programming procedures and other methods in …

An Infrastructure-Less Vehicle Counting Without Disruption, Jie Wu, Paul Sabatino, Jennifer Tsan, Zhen Jiang

Computer Science Faculty Publications

No abstract provided.

Mqvc: Measuring Quranic Verses Similarity And Sura Classification Using N-Gram, M. Akour, Izzat M. Alsmadi, I. Alazzam

Computer Science Faculty Publications

Extensive research efforts in the area of Information Retrieval were concentrated on developing retrieval systems related to Arabic language for the different natural language and information retrieval methodologies. However, little effort was conducted in those areas for knowledge extraction from the Holly Muslim book, the Quran. In this paper, we present an approach (MQVC) for retrieving the most similar verses in comparison with a user input verse as a query. To demonstrate the accuracy of our approach, we performed a set of experiments and compared the results with an evaluation from a Quran Specialist who manually identified all relevant chapters …

Gui: Gps-Less Traffic Congestion Avoidance In Urban Areas With Inter-Vehicular Communication, Zhen Jiang, Jie Wu, Paul Sabatino

Computer Science Faculty Publications

No abstract provided.

Approaches For Testing And Evaluation Of Xacml Policies, Izzat M. Alsmadi

Computer Science Faculty Publications

Security services are provided through: The applications, operating systems, databases, and the network. There are many proposals to use policies to define, implement and evaluate security services. We discussed a full test automation framework to test XACML based policies. Using policies as input the developed tool can generate test cases based on the policy and the general XACML model. We evaluated a large dataset of policy implementations. The collection includes more than 200 test cases that represent instances of policies. Policies are executed and verified, using requests and responses generated for each instance of policies. WSO2 platform is used to …

Issues Related To The Detection Of Source Code Plagiarism In Students Assignments, Izzat M. Alsmadi, I. Alhami, S. Kazakzeh

Computer Science Faculty Publications

Detecting similarity or plagiarism in the academic research publications, source code, etc. has been a long time complex and time consuming task. Several algorithms, tools and websites exist that try to find plagiarism or possible plagiarism in those human creative products. In this paper we used source code plagiarism detection tools to assess the level of plagiarism in source codes. We also investigated issues related to accuracy and challenges in detecting possible plagiarism in students' assignments. In a second study, we evaluated some tools against detecting possible plagiarism in research papers. Results showed that such process or decision is not …

Test Cases Selection Based On Source Code Features Extraction, I. Alazzam, Izzat M. Alsmadi, M. Akour

Computer Science Faculty Publications

Extracting valuable information from source code automatically was the subject of many research papers. Such information can be used for document traceability, concept or feature extraction, etc. In this paper, we used an Information Retrieval (IR) technique: Latent Semantic Indexing (LSI) for the automatic extraction of source code concepts for the purpose of test cases' reduction. We used and updated the open source FLAT Eclipse add on to try several code stemming approaches. The goal is to check the best approach to extract code concepts that can improve the process of test cases' selection or reduction.

Identifying Dynamic Protein Complexes Based On Gene Expression Profiles And Ppi Networks, Min Li, Weijie Chen, Jianxin Wang, Fang-Xiang Wu, Yi Pan

Computer Science Faculty Publications

Identification of protein complexes fromprotein-protein interaction networks has become a key problem for understanding cellular life in postgenomic era. Many computational methods have been proposed for identifying protein complexes. Up to now, the existing computational methods are mostly applied on static PPI networks. However, proteins and their interactions are dynamic in reality. Identifying dynamic protein complexes is more meaningful and challenging. In this paper, a novel algorithm, named DPC, is proposed to identify dynamic protein complexes by integrating PPI data and gene expression profiles. According to Core-Attachment assumption, these proteins which are always active in the molecular cycle are regarded …

A Novel Algorithm For Detecting Protein Complexes With The Breadth First Search, Xiwei Tang, Jianxin Wang, Min Li, Yiming He, Yi Pan

Computer Science Faculty Publications

Most biological processes are carried out by protein complexes. A substantial number of false positives of the protein-protein interaction (PPI) data can compromise the utility of the datasets for complexes reconstruction. In order to reduce the impact of such discrepancies, a number of data integration and affinity scoring schemes have been devised. The methods encode the reliabilities (confidence) of physical interactions between pairs of proteins. The challenge now is to identify novel and meaningful protein complexes fromthe weighted PPI network. To address this problem, a novel protein complex mining algorithm ClusterBFS (Cluster with Breadth-First Search) is proposed. Based on the …

Deliberate Barriers To User Participation On Metafilter, Hannah Pileggi, Briana B. Morrison, Amy Bruckman

Computer Science Faculty Publications

This descriptive study explores deliberate barriers to user participation on the long-lived discussion site Metafilter.com. Metafilter has been in continuous operation since its founding in 1999, and at the time of this writing has around 12,000 active users. While many newer online sites appear eager to eliminate barriers to participation and recruit as many new members as possible, Metafilter charges a $5 fee to join and has a mandatory one-week waiting period before new users are allowed to post. In this paper, we explore both why these barriers were imposed and why some users choose to surmount the barriers to …

The Effects Of Using Chaotic Map On Improving The Performance Of Multiobjective Evolutionary Algorithms, Hui Lu, Xiaoteng Wang, Zongming Fei, Meikang Qiu

Computer Science Faculty Publications

Chaotic maps play an important role in improving evolutionary algorithms (EAs) for avoiding the local optima and speeding up the convergence. However, different chaotic maps in different phases have different effects on EAs. This paper focuses on exploring the effects of chaotic maps and giving comprehensive guidance for improving multiobjective evolutionary algorithms (MOEAs) by series of experiments. NSGA-II algorithm, a representative of MOEAs using the nondominated sorting and elitist strategy, is taken as the framework to study the effect of chaotic maps. Ten chaotic maps are applied in MOEAs in three phases, that is, initial population, crossover, and mutation operator. …

Moved But Not Gone: An Evaluation Of Real-Time Methods For Discovering Replacement Web Pages, Martin Klein, Michael L. Nelson

Computer Science Faculty Publications

Inaccessible Web pages and 404 “Page Not Found” responses are a common Web phenomenon and a detriment to the user’s browsing experience. The rediscovery of missing Web pages is, therefore, a relevant research topic in the digital preservation as well as in the Information Retrieval realm. In this article, we bring these two areas together by analyzing four content- and link-based methods to rediscover missing Web pages. We investigate the retrieval performance of the methods individually as well as their combinations and give an insight into how effective these methods are over time. As the main result of this work, …

Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information And Context-Based Features, Ashraf Yaseen, Yaohang Li

Computer Science Faculty Publications

Background: Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models.

Methods: In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. …

Automated Identification Of Cell Type Specific Genes In The Mouse Brain By Image Computing Of Expression Patterns, Rongjian Li, Wenlu Zhang, Shuiwang Ji

Computer Science Faculty Publications

Background: Differential gene expression patterns in cells of the mammalian brain result in the morphological, connectional, and functional diversity of cells. A wide variety of studies have shown that certain genes are expressed only in specific cell-types. Analysis of cell-type-specific gene expression patterns can provide insights into the relationship between genes, connectivity, brain regions, and cell-types. However, automated methods for identifying cell-type-specific genes are lacking to date.

Results: Here, we describe a set of computational methods for identifying cell-type-specific genes in the mouse brain by automated image computing of in situ hybridization (ISH) expression patterns. We applied invariant image feature …

Toward A Real Time Multi-Tissue Adaptive Physics Based Non-Rigid Registration Framework For Brain Tumor Resection, Fotis Drakopoulos, Panagiotis Foteinos, Yixun Liu, Nikos Chrisochoides

Computer Science Faculty Publications

This paper presents an adaptive non-rigid registration method for aligning pre-operative MRI with intra-operative MRI (iMRI) to compensate for brain deformation during brain tumor resection. This method extends a successful existing Physics-Based Non-Rigid Registration (PBNRR) technique implemented in ITKv4.5. The new method relies on a parallel adaptive heterogeneous biomechanical Finite Element (FE) model for tissue/tumor removal depicted in the iMRI. In contrast the existing PBNRR in ITK relies on homogeneous static FE model designed for brain shift only (i.e., it is not designed to handle brain tumor resection). As a result, the new method (1) accurately captures the intra-operative deformations …