Computer Sciences Commons^™

Designing Software Product Lines For Testability, Isis Cabral

School of Computing: Dissertations, Theses, and Student Research

Software product line (SPL) engineering offers several advantages in the development of families of software products such as reduced costs, high quality and a short time to market. A software product line is a set of software intensive systems, each of which shares a common core set of functionalities, but also differs from the other products through customization tailored to fit the needs of individual groups of customers. The differences between products within the family are well-understood and organized into a feature model that represents the variability of the SPL. Products can then be built by generating and composing features …

The R Journal (June 2010) 2(1): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

IsoGene: An R Package for Analyzing Dose-response Studies in Microarray Experiments, Setia Pramana, Dan Lin, Philippe Haldermans, Ziv Shkedy, Tobias Verbeke, Hinrich Göhlmann, An De Bondt, Willem Talloen, and Luc Bijnens

MCMC for Generalized Linear Mixed Models with glmmBUGS, Patrick Brown and Lutong Zhou

Mapping and Measuring Country Shapes, Nils B. Weidmann and Kristian Skrede Gleditsch

tmvtnorm: A Package for the Truncated Multivariate Normal Distribution, Stefan Wilhelm and B. G. Manjunath

neuralnet: Training of Neural Networks, Frauke Günther and Stefan Fritsch

glmperm: A Permutation of Regressor Residuals Test for Inference in Generalized Linear Models, Wiebke Werft and …

Isogene: An R Package For Analyzing Dose-Response Studies In Microarray Experiments, Setia Pramana, Dan Lin, Philippe Haldermans, Ziv Shkedy, Tobias Verbeke, Hinrich Göhlmann, An De Bondt, Williem Talloen, Luc Bijnens

The R Journal

IsoGene is an R package for the analysis of dose-response microarray experiments to identify gene or subsets of genes with a mono tone relationship between the gene expression and the doses. Several testing procedures (i.e., the likelihood ratio test, Williams, Marcus, the M, and Modified M), that take into account the order restriction of the means with respect to the increasing doses are implemented in the package. The inference is based on resampling methods, both permutations and the Significance Analysis of Microarrays (SAM).

Two-Sided Exact Tests And Matching Confidence Intervals For Discrete Data, Michael P. Fay

The R Journal

There is an inherent relationship between two-sided hypothesis tests and confidence intervals. A series of two-sided hypothesis tests may be inverted to obtain the matching 100(1-)% confidence interval defined as the smallest interval that contains all point null parameter values that would not be rejected at the α level. Unfortunately, for discrete data there are several different ways of defining two-sided exact tests and the most commonly used two sided exact tests are defined one way, while the most commonly used exact confidence intervals are inversions of tests defined another way. This can lead to inconsistencies where the exact test …

Neuralnet: Training Of Neural Networks, Franke Günther, Stefan Fritsch

The R Journal

Artificial neural networks are applied in many situations. neuralnet is built to train multi-layer perceptrons in the context of regression analyses, i.e. to approximate functional relationships between covariates and response variables. Thus, neural networks are used as extensions of generalized linear models. neuralnet is a very flexible package. The back propagation algorithm and three versions of resilient back-propagation are implemented and it provides a custom-choice of activation and error function. An arbitrary number of covariates and response variables as well as of hidden layers can theoretically be included. The paper gives a brief introduction to multi-layer perceptrons and resilient back-propagation …

Mcmc For Generalized Linear Mixed Models With Glmmbugs, Patrick Brown, Lutong Zhou

The R Journal

The glmmBUGS package is a bridging tool between Generalized Linear Mixed Models (GLMMs) in R and the BUGS language. It provides a simple way of performing Bayesian inference using Markov Chain Monte Carlo (MCMC) methods, taking a model formula and data frame in R and writing a BUGS model file, data file, and initial values files. Functions are provided to reformat and summarize the BUGS results. A key aim of the package is to provide files and objects that can be modified prior to calling BUGS, giving users a platform for customizing and extending the models to accommodate a wide …

Glmperm: A Permutation Of Regressor Residuals Test For Inference In Generalized Linear Models, Wiebke Werft, Axel Benner

The R Journal

We introduce a new R package called glmperm for inference in generalized linear models especially for small and moderate-sized data sets. The inference is based on the per mutation of regressor residuals test introduced by Potter (2005). The implementation of glmperm outperforms currently available permutation test software as glmperm can be applied in situations where more than one covariate is involved.

Tmvtnorm: A Package For The Truncated Multivariate Normal Distribution, Stefan Wilhelm, B. G. Manjunath

The R Journal

In this article we present tmvtnorm, an R package implementation for the truncated multivariate normal distribution. We consider random number generation with rejection and Gibbs sampling, computation of marginal densities as well as computation of the mean and co variance of the truncated variables. This contribution brings together latest research in this field and provides useful methods for both scholars and practitioners when working with truncated normal variables.

Analysis And Transformation Of Pipe-Like Web Mashups For End User Programmers, Kathryn T. Stolee

School of Computing: Dissertations, Theses, and Student Research

Mashups are becoming increasingly popular as end users are able to easily access, manipulate, and compose data from several web sources. To support end users, communities are forming around mashup development environments that facilitate sharing code and knowledge. We have observed, however, that end user mashups tend to suffer from several deficiencies, such as inoperable components or references to invalid data sources, and that those deficiencies are often propagated through the rampant reuse in these end user communities.

In this work, we identify and specify ten code smells indicative of deficiencies we observed in a sample of 8,051 pipe-like web …

Automated Extraction Of Structures From Sketches Of Biological Specimens, Jamie Joseph Schirf

School of Computing: Dissertations, Theses, and Student Research

The goal of this study was to develop automated techniques to extract biological structures from sketches of biological specimens. This will form the basis for a searchable database of information about the specimens. Having such a database enables researchers to efficiently search for specimens with particular qualities or identify unknown specimens. After some preprocessing of the images, the important internal organs of the specimen are extracted using image analysis techniques. The shape, size, and organization of the organs are used to categorize and then to reorganize them in the image. Results using a large database of sketches of trematodes, in …

Rapport: Semantic-Sensitive Namespace Management In Large-Scale File Systems, Yu Hua, Hong Jiang, Yifeng Zhu, Dan Feng

School of Computing: Technical Reports

Explosive growth in volume and complexity of data exacerbates the key challenge to effectively and efficiently manage data in a way that fundamentally improves the ease and efficacy of their use. Existing large-scale file systems rely on hierarchically structured namespace that leads to severe performance bottlenecks and renders it impossible to support real-time queries on multi-dimensional attributes. This paper proposes a novel semantic-sensitive scheme, called Rapport, to provide dynamic and adaptive namespace management and support complex queries. The basic idea is to build files’ namespace by utilizing their semantic correlation and exploiting dynamic evolution of attributes to support namespace management. …

Channel Characterization For Wireless Underground Sensor Networks, Agnelo Rocha Da Silva

School of Computing: Dissertations, Theses, and Student Research

Wireless Underground Sensor Networks (WUSNs) are natural extensions of the established Wireless Sensor Network (WSN) phenomenon and consist of sensors buried underground which communicate through soil. WUSNs have the potential to impact a wide variety of applications including precision agriculture, environmental monitoring, border patrol, and infrastructure monitoring. The main difference between WUSNs and traditional wireless networks is the communication medium. However, a comprehensive wireless underground channel model for WUSNs has not been developed so far. In this thesis, the Soil Subsurface Wireless Communication (SSWC) channel model is developed based on an extensive empirical study in a large agriculture field. The …

Dsfs: Decentralized Security For Large Parallel File Systems, Zhongying Niu, Hong Jiang, Ke Zhou, Dan Feng, Tianming Yang, Dongliang Lei, Anli Chen

School of Computing: Technical Reports

This paper describes DSFS, a decentralized security system for large parallel file system. DSFS stores global access control lists (ACLs) in a centralized decisionmaking server and pushes pre-authorization lists (PALs) into storage devices. Thus DSFS allows users to flexibly set any access control policy for the global ACL or even change the global ACL system without having to upgrade the security code in their storage devices. With pre-authorization lists, DSFS enables a networkattached storage device to immediately authorize I/O, instead of demanding a client to acquire an authorization from a centralized authorization server at a crucial time. The client needs …

Service-Differentiated And Reliable Communication In Event-Based Wireless Sensor Networks, Yuyan Xue

School of Computing: Dissertations, Theses, and Student Research

Wireless Sensor Networks (WSNs) consist of low-power embedded devices with integrated sensing, computing and wireless communication capabilities. These devices, called sensor nodes or motes, are often battery-powered and deployed in a distributed manner to provide observations on the physical world. Reliably and promptly collecting the sensing data to convey the features of a surveillance area, especially the events of interest, to the sink is one of the most critical requirements of WSN design. However, dynamic wireless channel conditions and the constrained energy resources make it a challenging task to provide the end-to-end performance guarantees in multi-hop WSNs. The objective of …

New Integrated Data Analyses Software Components, Ronald Conze, Frank Krysiak, Josh Reed, Yu-Chung Chen, Hans-Joachim Wallrabe-Adams, Colin Graham, New Jersey Shallow Shelf Science Team, Volker Wennrich, Lake El’Gygytgyn Science Team

ANDRILL Research and Publications

Data management in scientific drilling programs such as the Integrated Ocean Drilling Program (IODP), the International Continental Scientific Drilling Program (ICDP), and the Antarctic Drilling Program (ANDRILL) performs two functions: firstly, the capture of drilling and scientific data during an expedition, and secondly, the long-term storage and dissemination of these data. Here we describe the progress in linking data management with stand-alone data capture and visualization applications. This provides a two-way flow of data between the database and the applications, and a more integrated data environment for scientists. The new system has been tested, so far, with cores from the …

Coset: Cooperative Set Last Level Caches, Dongyuan Zhan, Hong Jiang, Sharad Seth

School of Computing: Technical Reports

The speed gap between processors and DRAM remains a crit-ical performance bottleneck for contemporary computer systems, which necessitates an effective management of last level caches (LLC) to minimize expensive off-chip accesses. However, because all sets in a conventional set-associative cache design are statically assigned an equal number of blocks, the LLC capacity utilization can drastically diminish when the cache actually exhibits non-uniform capacity demands across the sets. To reveal the wide exis-tence of set-level non-uniformity of capacity demand in real appli-cations, this technical report first establishes an accurate metric for measuring individual sets’ capacity demands by developing a group of …

Communication-Aware Load Balancing For Parallel Applications On Clusters, Xiao Qin, Hong Jiang, Adam Manzanares, Xiaojun Ruan, Shu Yin

School of Computing: Faculty Publications

Cluster computing has emerged as a primary and cost-effective platform for running parallel applications, including communication-intensive applications that transfer a large amount of data among the nodes of a cluster via the interconnection network. Conventional load balancers have proven effective in increasing the utilization of CPU, memory, and disk I/O resources in a cluster. However, most of the existing load-balancing schemes ignore network resources, leaving an opportunity to improve the effective bandwidth of networks on clusters running parallel applications. For this reason, we propose a communication-aware load-balancing technique that is capable of improving the performance of communication-intensive applications by increasing …

Classroomwiki: A Collaborative Wiki For Instructional Use With Multiagent Group Formation, Nobel Khandaker, Leen-Kiat Soh

School of Computing: Faculty Publications

Abstract—Wikis today are being used as a tool to conduct collaborative writing assignments in classrooms. However, typical Wikis do not adequately address the assessment of individual student contributions toward their groups or provide any automated group formation mechanism. To improve these aspects, we have designed and implemented ClassroomWiki – a Web-based collaborative Wiki writing tool. For the students, ClassroomWiki provides a Web interface for writing and revising their group’s Wiki and a topic-based forum for discussing their ideas during collaboration. When the students collaborate, ClassroomWiki tracks all student activities and builds detailed student models that represent their contributions toward their …

Communication With Aboveground Devices In Wireless Underground Sensor Networks: An Empirical Study, Agnelo R. Silva, Mehmet C. Vuran

School of Computing: Conference and Workshop Papers

Wireless Underground Sensor Networks (WUSNs) consist of wirelessly connected underground sensor nodes that communicate untethered through soil. WUSNs have the potential to impact a wide variety of novel applications including intelligent irrigation, environment monitoring, border patrol, and assisted navigation. Although its deployment is mainly based on underground sensor nodes, a WUSN still requires aboveground devices for data retrieval, management, and relay functionalities. Therefore, the characterization of the bi-directional communication between a buried node and an aboveground device is essential for the realization of WUSNs. In this work, empirical evaluations of underground-to-aboveground (UG2AG) and aboveground-to-underground (AG2UG) communication are presented. More specifically, …

A Partial Taxonomy Of Substitutability & Interchangeability, Shant Karakashian, Robert J. Woodward, Berthe Y. Choueiry, Steven D. Prestwich, Eugene C. Freuder

School of Computing: Conference and Workshop Papers

•Introduction

–Basic form & extensions

–Features & use

–Further developments

•Taxonomy using a partial order

–One example

•Relation to

–General forms of symmetry

–Symmetry breaking during search

•Future research & conclusions

A Unified Solution To Scan Test Volume, Time, And Power Minimization, Zhen Chen, Sharad C. Seth, Dong Xiang, Bhargab B. Bhattacharya

School of Computing: Conference and Workshop Papers

The double-tree scan-path architecture, originally proposed for low test power, is adapted to simultaneously reduce the test application time and test data volume under external testing. Experimental results show significant performance improvements over other existing scan architectures.

Cost Efficiency Of Anycast-Based Forwarding In Duty-Cycled Wsns With Lossy Channel, Yuyan Xue, Mehmet C. Vuran, Byrav Ramamurthy

School of Computing: Conference and Workshop Papers

Anycasting has been proposed recently as an efficient communication method for asynchronous duty-cycled wireless sensor networks. However, the interdependencies between end-toend communication cost and the anycasting design parameters have not been systematically studied. In this paper, a statistical endtoend cost model is presented to capture the end-to-end latency and energy consumption of anycasting operation under a realistic wireless channel model. By exploring the relationship between the end-to-end cost efficiency and the forwarding decision dependent anycasting design parameters, two anycasting forwarding metrics are proposed for fully distributed forwarding decision. By exploring the relationship among the preamble length, the size of the …

Stochastic Analysis Of Energy Consumption In Wireless Sensor Networks, Yunbo Wang, Mehmet C. Vuran, Steve Goddard

School of Computing: Conference and Workshop Papers

Limited energy resources in increasingly sophisticated wireless sensor networks (WSNs) call for a comprehensive crosslayer analysis of energy consumption in a multi-hop network. For reliability analysis in such networks, the statistical information about energy consumption and lifetime is required. However, traditional energy analysis approaches only focus on the average energy consumed. In this paper, instead, we provide a stochastic analysis of the energy consumption in a random network environment. Accordingly, a comprehensive cross-layer analysis framework, which employs a stochastic queueing model, is developed. Using this framework, the distribution of energy consumption for nodes in WSNs during a given time period …

Preface, Berthe Y. Choueiry, Bob Givan

School of Computing: Conference and Workshop Papers

The Tenth International Symposium on Artificial Intelligence and Mathematics (ISAIM 2008) gathered a fine and distinguished crowd of researchers active in mathematics, theoretical computer science, and artificial intelligence. The three-day meeting, held from January 2 to 4, 2008, in Fort Lauderdale, featured invited talks by keynote speakers David McAllester, Francesca Rossi and Naftali Tishby. The program also included special sessions on “Computation and Social Choice” (organized by Toby Walsh), “Effective Exploration in Active Learning and Reinforcement Learning” (organized by Pascal Poupart), and “Logic in Artificial Intelligence” (organized by Michael Kaminski and Miroslaw Truszczynski, and the subject of a separate special …

A First Practical Algorithm For High Levels Of Relational Consistency, Shant Karakashian, Robert J. Woodward, Christopher Reeson, Berthe Y. Choueiry, Christian Bessiere

School of Computing: Conference and Workshop Papers

•Introduction

•Relational Consistency R(*,m)C :

–Definition, Naïve algorithm, Properties

•Preliminaries: Dual CSP

•Our Approach

–Algorithm

–Index-Tree Data Structure

–Advantages

•A weakened version of R(*,m)C: wR(*,m)C

•Experimental Evaluations

•Conclusions & Future Work

Genbank, Dennis A. Benson, Ilene Karasch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers

Harold W. Manter Laboratory of Parasitology: Library Materials

GenBank(R) is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data …

A Novel Weighted-Graph-Based Grouping Algorithm For Metadata Prefetching, Peng Gu, Jun Wang, Yifeng Zhu, Hong Jiang, Pengju Shang

School of Computing: Faculty Publications

Although data prefetching algorithms have been extensively studied for years, there is no counterpart research done for metadata access performance. Existing data prefetching algorithms, either lack of emphasis on group prefetching, or bearing a high level of computational complexity, do not work well with metadata prefetching cases. Therefore, an efficient, accurate, and distributed metadata-oriented prefetching scheme is critical to leverage the overall performance in large distributed storage systems. In this paper, we present a novel weighted-graph-based prefetching technique, built on both direct and indirect successor relationship, to reap performance benefit from prefetching specifically for clustered metadata servers, an arrangement envisioned …

Xlp: A Cross-Layer Protocol For Efficient Communication In Wireless Sensor Networks, Mehmet C. Vuran, Ian F. Akyildiz

School of Computing: Faculty Publications

Severe energy constraints of battery-powered sensor nodes necessitate energy-efficient communication in Wireless Sensor Networks (WSNs). However, the vast majority of the existing solutions is based on classical layered protocols approach, which leads to significant overhead. It is much more efficient to have a unified scheme which blends common protocol layer functionalities into a cross-layer module. In this paper, a cross layer protocol (XLP) is introduced, which achieves congestion control, routing, and medium access control in a cross-layer fashion. The design principle of XLP is based on the cross-layer concept of initiative determination, which enables receiver-based contention, initiative-based forwarding, local …

Linear Programming Models For Multi-Channel P2p Streaming Systems, Miao Wang, Lisong Xu, Byrav Ramamurthy

School of Computing: Conference and Workshop Papers

Most of the commercial P2P video streaming deployments support hundreds of channels and are referred to as multichannel systems. Measurement studies show that bandwidth resources of different channels are highly unbalanced and thus recent research studies have proposed various protocols to improve the streaming qualities for all channels by enabling cross-channel cooperation among multiple channels. However, there is no general framework for comparing existing and potential designs for multi-channel P2P systems. The goal of this paper is to establish tractable models for answering the fundamental question in multi-channel system designs: Under what circumstances, should a particular design be used to …

Spatio-Temporal Soil Moisture Measurement With Wireless Underground Sensor Networks, Xin Dong, Mehmet C. Vuran

School of Computing: Conference and Workshop Papers

In this paper, the estimation distortion of distributed soil moisture measurement using Wireless Underground Sensor Networks (WUSNs) is investigated. The main focus of this paper is to analyze the impact of the environment and network parameters on the estimation distortion of the soil moisture.More specifically, the effects of rainfall, soil porosity, and vegetation root zone are investigated by exploiting a rainfall model, in addition to the effects of sampling rate, network topology, and measurement signal noise ratio. Spatio-temporal correlation is characterized to develop a measurement distortion model with respect to these factors. The evaluations reveal that with porous soil and …