Computer Sciences Commons^™

Chemalign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties, Hyrum Carroll, Mark J. Clement, Quinn O. Snell, David Mcclellan

Faculty Publications

We present a new algorithm, ChemAlign, that uses physicochemical properties and secondary structure elements to create biologically relevant multiple sequence alignments (MSAs). Additionally, we introduce the Physicochemical Property Difference (PPD) score for the evaluation of MSAs. This score is the normalized difference of physicochemical property values between a calculated and a reference alignment. It takes a step beyond sequence similarity and measures characteristics of the amino acids to provide a more biologically relevant metric. ChemAlign is able to produce more biologically correct alignments and can help to identify potential drug docking sites.

User Interfaces For Visual Analysis And Monitoring In Business Intelligence, Lars Grammel, Margaret-Anne Storey, Christoph Treude

Research Collection School Of Computing and Information Systems

Business intelligence is concerned with understanding and leveraging the vast amounts of information stored in the databases of modern enterprises. Visualization techniques have been used to make sense of this data for a long time, first in the form of simple charts, and nowadays in the form of interactive visualizations. By leveraging the strengths of the human perceptual system and incorporating user interaction, they support the flexible analysis of data as well as data monitoring by users. The recent progress in the fields of information and data visualization as well as new hardware developments and trends in business intelligence have …

Ensemble And Individual Noise Reduction Method For Induction-Motor Signature Analysis, Zhaoxia Wang, C.S. Chang, Tw Chua, W.W Tan

Research Collection School Of Computing and Information Systems

Unlike a fixed-frequency power supply, the voltagesupplying an inverter-fed motor is heavily corrupted by noises,which are produced from high-frequency switching leading tonoisy stator currents. To extract useful information from statorcurrentmeasurements, a theoretically sound and robust denoisingmethod is required. The effective filtering of these noisesis difficult with certain frequency-domain techniques, such asFourier transform or Wavelet analysis, because some noises havefrequencies overlapping with those of the actual signals, andsome have high noise-to-frequency ratios. In order to analyze thestatistical signatures of different types of signals, a certainnumber is required of the individual signals to be de-noisedwithout sacrificing the individual characteristic and quantity ofthe …

What Makes Categories Difficult To Classify?, Aixin Sun, Ee Peng Lim, Ying Liu

Research Collection School Of Computing and Information Systems

In this paper, we try to predict which category will be less accurately classified compared with other categories in a classification task that involves multiple categories. The categories with poor predicted performance will be identified before any classifiers are trained and additional steps can be taken to address the predicted poor accuracies of these categories. Inspired by the work on query performance prediction in ad-hoc retrieval, we propose to predict classification performance using two measures, namely, category size and category coherence. Our experiments on 20-Newsgroup and Reuters-21578 datasets show that the Spearman rank correlation coefficient between the predicted rank of …

Trust Relationship Prediction Using Online Product Review Data, Nan Ma, Ee Peng Lim, Viet-An Nguyen, Aixin Sun

Research Collection School Of Computing and Information Systems

Trust between users is an important piece of knowledge that can be exploited in search and recommendation.Given that user-supplied trust relationships are usually very sparse, we study the prediction of trust relationships using user interaction features in an online user generated review application context. We show that trust relationship prediction can achieve better accuracy when one adopts personalized and cluster-based classification methods. The former trains one classifier for each user using user-specific training data. The cluster-based method first constructs user clusters before training one classifier for each user cluster. Our proposed methods have been evaluated in a series of experiments …

Static Validation Of C Preprocessor Macros, Andreas Saebjornsen, Lingxiao Jiang, Daniel Quinlan, Zhendong Su

Research Collection School Of Computing and Information Systems

The widely used C preprocessor (CPP) is generally considered a source of difficulty for understanding and maintaining C/C++ programs. The main reason for this difficulty is CPP’s purely lexical semantics, i.e., its treatment of both input and output as token streams. This can easily lead to errors that are difficult to diagnose, and it has been estimated that up to 20% of all macros are erroneous. To reduce such errors, more restrictive, replacement languages for CPP have been proposed to limit expanded macros to be valid C syntactic units. However, there is no practical tool that can effectively validate CPP …

Minimum Latency Broadcasting In Multiradio, Multichannel, Multirate Wireless Meshes, Junaid Qadir, Chuntung Chou, Archan Misra, Joo Ghee Lim

Research Collection School Of Computing and Information Systems

We address the problem of minimizing the worst-case broadcast delay in multi-radio multi-channel multi-rate (MR2-MC) wireless mesh networks (WMN). The problem of 'efficient' broadcast in such networks is especially challenging due to the numerous interrelated decisions that have to be made. The multi-rate transmission capability of WMN nodes, interference between wireless transmissions, and the hardness of optimal channel assignment adds complexity to our considered problem. We present four heuristic algorithms to solve the minimum latency broadcast problem for such settings and show that the 'best' performing algorithms usually adapt themselves to the available radio interfaces and channels. We also study …

Vireo/Dvmm At Trecvid 2009: High-Level Feature Extraction, Automatic Video Search, And Content-Based Copy Detection, Chong-Wah Ngo, Yu-Gang Jiang, Xiao-Yong Wei, Wanlei Zhao, Yang Liu, Jun Wang, Shiai Zhu, Shih-Fu Chang

Research Collection School Of Computing and Information Systems

This paper presents overview and comparative analysis of our systems designed for 3 TRECVID 2009 tasks: high-level feature extraction, automatic search, and content-based copy detection.

Mining Communities In Networks: A Solution For Consistency And Its Evaluation, Haewoon Kwak, Yoonchan Choi, Young-Ho Eom, Hawoong Jeong, Sue Moon

Research Collection School Of Computing and Information Systems

Online social networks pose significant challenges to computer scientists, physicists, and sociologists alike, for their massive size, fast evolution, and uncharted potential for social computing. One particular problem that has interested us is community identification. Many algorithms based on various metrics have been proposed for communities in networks [18, 24], but a few algorithms scale to very large networks. Three recent community identification algorithms, namely CNM [16], Wakita [59], and Louvain [10], stand out for their scalability to a few millions of nodes. All of them use modularity as the metric of optimization. However, all three algorithms produce inconsistent communities …

A Cisco-Based Proposal For Arne Core Routing Infrastructure, Ingrimar James

Regis University Student Publications (comprehensive collection)

Systems Engineering and Application Development (SEAD) Practicum provides opportunities for students to engage in proposing, designing, building and testing various projects related to information technology. There are several ongoing projects designed to upgrade, improve or revamp some aspect of the Academic Research Network, generally referred to as ARNe, and services or applications that are a part of its architecture. Regis University is in the process of replacing their current architecture and equipment that forms the core of ARNe in order to facilitate further upgrades and new projects within various aspects of ARNe. This paper examines and proposes a Cisco-based routing …

Breaking From Tradition: India And The Path To Development, Angel M. Newsom

Regis University Student Publications (comprehensive collection)

"How could a country with more than 300 million illiterate people also have the kind of scientific human resources that bring some of the world's largest corporations to base their R&D labs in India?" (Tripathi, 2007, p.68). This question acknowledges the coexistence of two vastly different worlds within one country. On one hand, India is making significant progress on the path to becoming a developed country;one that can provide the basic fundamentals of living for its citizens while sustaining progressive economic growth; on the other hand, it must overcome challenges to this goal that relate to a crumbling infrastructure, poverty, …

3d Reconstruction And Visualization Of A Hovering Dragonfly, Christopher Koehler, Thomas Wischgoll, Haibo Dong, Zachary Gaston, Hui Wan

Computer Science and Engineering Faculty Publications

No abstract provided.

A Survey Of The Semantic Specification Of Sensors, Michael Compton, Cory Andrew Henson, Laurent Lefort, Holger Neuhaus, Amit P. Sheth

Kno.e.sis Publications

Semantic sensor networks use declarative descriptions of sensors promote reuse and integration, and to help solve the difficulties of installing, querying and maintaining complex, heterogeneous sensor networks. This paper reviews the state of the art for the semantic specification of sensors, one of the fundamental technologies in the semantic sensor network vision. Twelve sensor ontologies are reviewed and analysed for the range and expressive power of their concepts. The reasoning and search technology developed in conjunction with these ontologies is also reviewed, as is technology for annotating OGC standards with links to ontologies. Sensor concepts that cannot be expressed accurately …

Database System Architecture For Fault Tolerance And Disaster Recovery, Anthony Nguyen

Regis University Student Publications (comprehensive collection)

Application systems being used today rely heavily on the availability of the database system. Disruption of database system can be damaging and catastrophic to the organization that depends on the availability of the database system for its business and service operations. To ensure business continuity under foreseeable and unforeseeable man-made or natural disasters, the database system has to be designed and built with fault tolerance and disaster recovery capabilities. This project explored existing technologies and solutions to design, build, and implement database system architecture for fault tolerance and disaster recovery using Oracle database software products. The project goal was to …

Working Session: Using Eye-Tracking To Understand Program Comprehension, Yann Gaël Guéhéneuc, Huzefa Kagdi, Jonathan I. Maletic

Computer Science Faculty Research & Creative Works

The working session focuses on the use of eye-tracking technology to assess, understand, and evaluate tools and techniques for program comprehension. an introduction to the technology and tools of eye-tracking will be presented. a discussion of how these tools augment existing evaluation mechanism in the context of program comprehension will follow. Research directions and open problems will be a main topic. © 2009 IEEE.

Contribution Based Priority Assessment In A Web-Based Intelligent Argumentation Network For Collaborative Software Development, Xiaoqing Frank Liu, Maithili Satyavolu, Ming-Chuan Leu

Computer Science Faculty Research & Creative Works

Decision making is an important aspect in a collaborative software development process which involves a complex process of conflict resolution. the priority of the participants plays a vital role in conflict resolution as the decision-making process involves many participants from multiple perspectives. the priority assessment methods used in the process so far are usually static in nature, i.e., the priorities of the participants remain constant throughout the decision-making process. in order to make the collaborative system closer to real world scenarios, we incorporate dynamic priority assessment into a web-Based collaborative system based on intelligent computational argumentation, which was developed in …

Integration And Deployment Techniques In Combination With Development Methodologies, Brian E. Nesbitt

Regis University Student Publications (comprehensive collection)

Efficient and inefficient pairings of software development methodologies and software integration and deployment techniques exist. Often times the automation of code integration and deployment is chosen but the full benefit of these technologies are throttled by the incorporation of a development methodology. It can be hypothesized that the evolution of software development created this situation along with the latency of implementing development methodologies. This work examines four scenarios comprised of traditional and conventional development methodologies with manual and automated software integration and deployment techniques. Similar web-based software applications were selected from waterfall (traditional) and agile (conventional) run project development teams. …

Provenir Ontology: Towards A Framework For Escience Provenance Management, Satya S. Sahoo, Amit P. Sheth

Kno.e.sis Publications

Provenance metadata describes the 'lineage' or history of an entity and necessary information to verify the quality of data, validate experiment protocols, and associate trust value with scientific results. eScience projects generate data and the associated provenance metadata in a distributed environment (such as myGrid) and on a very large scale that often precludes manual analysis. Given this scenario, provenance information should be, (a) interoperable across projects, research groups, and application domains, and (b) support analysis over large datasets using reasoning to discover implicit information. In this paper, we introduce an ontology-driven framework for eScience provenance management underpinned by an …

Fantom - Lessons Learned From Design, Implementation, Administration, And Use Of A Visualization System For Over 10 Years, Alexander Wiebel, Christoph Garth, Mario Hlawitschka, Thomas Wischgoll, Gerik Scheuermann

Computer Science and Engineering Faculty Publications

No abstract provided.

Altruistic Task Allocation Despite Unbalanced Relationships Within Multi-Robot Communities, Ryan Morton, George A. Bekey, Christopher M. Clark

Computer Science and Software Engineering

Typical Multi-Robot Systems consist of robots cooperating to maximize global fitness functions. However, in some scenarios, the set of interacting robots may not share common goals and thus the concept of a global fitness function becomes invalid. This work examines Multi-Robot Communities(MRC), in which individual robots have independent goals. Within the MRC context, we present a task allocation architecture that optimizes individual robot fitness functions over long time horizons using reciprocal altruism.

Previous work has shown that reciprocating altruistic relationships can evolve between two willing robots, using market-based task auctions, while still protecting against selfish robots aiming to exploit …

(Re-) Discovering Lost Web Pages, Martin Klein, Michael L. Nelson

Computer Science Presentations

PDF of a powerpoint presentation from a Mathematics & Computer Science Seminar at Emory University, Atlanta, Georgia, October 2, 2009. Also available on Slideshare.

Stochastic Stability In Internet Router Congestion Games, Christine Chung, Evangelia Pyrga

Computer Science Faculty Publications

No abstract provided.

Voshm: A Velocity Optimized Seamless Handover Mechanism For Wimax Networks, Chi Ma, Enda Fallon, Yansong Qiao

9th. IT & T Conference

For seamless handover in heterogeneous wireless networks, service continuity and minimal handover disruption time are the primary requirements. The emerging Media Independent Handover (MIH) standard proposes to address these requirements through the introduction of link performance prediction features. In particular the MIH Event Service introduces a Link_Going_Down event which utilizes L2 performance characteristics to trigger predictive events. While the MIH standard proposes a framework by which L2 events can be communicated to the upper layer, it does provide detail on the performance characteristics which trigger these events. In this paper, we design a MIH based Velocity Optimized Seamless Handover Mechanism …

Building Fire Emergency Detection And Response Using Wireless Sensor Networks, Yuanyuan Zeng, Sean Og Murphy, Lanny Sitanayah, Tatiana Tabirca, Thuy Truong, Ken Brown, Cormac Sreenan

9th. IT & T Conference

Wireless sensor networks (WSNs) provide a low cost solution with respect to maintenance and installation and in particular, building refurbishment and retrofitting are easily accomplished via wireless technologies. Fire emergency detection and response for building environments is a novel application area for the deployment of wireless sensor networks. In such a critical environment, timely data acquisition, detection and response are needed for successful building automation. This paper presents an overview of our recent research activity in this area. Firstly we explain research on communication protocols that are suitable for this problem. Then we describe work on the use of WSNs …

Venn, A Tool For Titrating Sequence Conservation Onto Protein Structures, Jay Vyas, Michael R. Gryk, Martin R. Schiller

Life Sciences Faculty Research

Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/.

Suggestions For Owl 3, Pascal Hitzler

Computer Science and Engineering Faculty Publications

With OWL 2 about to be completed, it is the right time to start discussions on possible future modifications of OWL. We present here a number of suggestions in order to discuss them with the OWL user community. They encompass expressive extensions on polynomial OWL 2 profiles, a suggestion for an OWL Rules language, and expressive extensions for OWL DL.

Writing A Supercomputer Proposal For The National Science Foundation's Major Research Instrumentation Solicitation, Amy Apon

Presentations

No abstract provided.

Performance Optimisation Of The Ait Campus Wireless Mesh Network Deployment, Eduardo Brito, Robert Stewart, John Allen, M. H. Hassan

9th. IT & T Conference

The deployment of an 802.11x wireless mesh network in urban areas is a complex task and is traditionally based on an exhaustive site survey, rules-of-thumb or past experiences. In this research we propose exploring the spatial distribution of the clients, the topology and the clutter using software tools from Motorola in a VoWiFi mesh network before deployment. The objective is to obtain the optimal position for the wireless access points that allows an increase in the overall capacity and performance. The cost savings inherent in running real-time applications over IP based wireless mesh networks will be of interest to industry, …

Beyond Home Automation: Designing More Effective Smart Home Systems, Paolo Carner

9th. IT & T Conference

This paper outlines a Smart Home Proof-of-Concept system that uses a Bayesian Network to predict the likelihood of a monitored event to occur. Firstly, this paper will provide an introduction to the concept of a smart home system; then it will outline how Artificial Intelligence concepts can be used to make such systems more effective. Finally, it will detail the implementation of a smart home system, which uses an inference engine to determine the likelihood of a fire. The system prototype has implemented using a LonWorks™ hardware kit and a Netica™ Bayesian Network engine from Norsys.

Error Rate Based Analytical Switchover Approach For Multi-Homed Body Sensor Networks, Sadik Armagan, Enda Fallon, Yuansong Qiao

9th. IT & T Conference

For patients who have undergone cardiovascular surgery it is necessary to monitor vital signs such as respiration, oxygen in the blood, temperature, and electrocardiogram (ECG) in real time. As well as the sensor device, many existing solutions need a bulky coordinating unit like a PDA located on the patient for network communication. In this paper we investigate an infrastructure mode based approach in which the wireless sensor, communicates directly with the wireless access point. Our investigation particularly focuses on how the emerging technology, Media Independent Handover (MIH) can be used by the wireless sensor to manage path migration. Since MIH …