Computer Sciences Commons^™

A Running Time Improvement For Two Thresholds Two Divisors Algorithm, Bingchun Chang

Master's Projects

Chunking algorithms play an important role in data de-duplication systems. The Basic Sliding Window (BSW) algorithm is the first prototype of the content-based chunking algorithm which can handle most types of data. The Two Thresholds Two Divisors (TTTD) algorithm was proposed to improve the BSW algorithm in terms of controlling the variations of the chunk-size. In this project, we investigate and compare the BSW algorithm and TTTD algorithm from different factors by a series of systematic experiments. Up to now, no paper conducts these experimental evaluations for these two algorithms. This is the first value of this paper. According to …

Intrusion Alerts Analysis Using Attack Graphs And Clustering, Hardik Patel

Master's Projects

Network and information security is very crucial in keeping large information infrastructures safe and secure. Many researchers have been working on different issues to strengthen and measure security of a network. An important problem is to model security in order to apply analysis schemes efficiently to that model. An attack graph is a tool to model security of a network which considers individual vulnerabilities in a global view where individual hosts are interconnected. The analysis of intrusion alert information is very important for security evaluation of the system. Because of the huge number of alerts raised by intrusion detection systems, …

Objective Measurement Of Speech Quality In Voip Over Wireless Lan During Handoff, Nidhi Marwaha Gambhir

Master's Projects

Quality of Service is a very important factor to determine the quality of a VoIP call. Different subjective and objective models exist for evaluating the speech quality in VoIP. E-model is one of the objective methods of measuring the speech quality; it considers various factors like packet loss, delay and codec impairments. The calculations of Emodel are not very accurate in case of handovers – when a VoIP call moves from one wireless LAN to another. This project conducted experimental evaluation of performance of E-model during handovers and proposes a new approach to accurately calculate the speech quality of VoIP …

Analysis Of An Openmp Program For Race Detection, Dhaval Shah

Master's Projects

The race condition in a shared memory parallel program is subtle and harder to find than in a sequential program. The race conditions cause non-deterministic and unexpected results from the program. It should be avoided in the parallel region of OpenMP programs. The proposed OpenMP Race Avoidance Tool statically analyzes the parallel region. It gives alerts regarding possible data races in that parallel region. The proposed tool has the capability to analyze the basic frequently occurring non-nested ‘for loop(s)’. We are comparing the results of the proposed tool with the commercially available static analysis tool named Intel Parallel Lint and …

Expert Finding Using Social Networking, Parin Shah

Master's Projects

In today’s world, knowledge transfer is considered an important and essential activity for the success of an enterprise. Large corporations have realized the need to reuse existing knowledge rather than spend time and effort on solving the same problems again. For these reasons, most corporations now have knowledge repositories. These repositories are visited for possible solutions whenever there is a problem that cannot be easily resolved by using the expertise of the existing team. Apart from this, the problems faced by the people in the company can also be resolved by asking for help from expert in that problem domain. …

Chinese Wall Security Policy, Varun Gupta

Master's Projects

This project establishes a Chinese wall security policy model in the environment of cloud computing. In 1988 Brewer and Nash proposed a very nice commercial security policy in British financial world. Though the policy was well accepted, but the model was incorrect. A decade later, Dr. Lin provided a model in 2003 that meets Brewer & Nash’s Policy. One of the important components in Cloud computing is data center. In order for any company to store data in the center, a trustable security policy model is a must; Chinese wall security policy model will provide this assurance. The heart of …

Online Circular Calendar, Praveen Athmanathan Panneerselvam

Master's Projects

A calendar is a system to organize days for social, commercial or administrative purpose. Many calendar systems are available today. The calendar system helps the user in scheduling his/her events or tasks over a time period. This period may be an hour, a day, or even months. Due to increase in user’s activities, events that need to be scheduled in the calendar grow tremendously. Moreover, there are events that occur every year which require a good visualization for mental manipulation. As a result there is a difficulty in organizing these events in the current calendar system. The main idea of …

Triggering Of Just-In-Time Compilation In The Java Virtual Machine, Rouhollah Gougol

Master's Projects

The Java Virtual Machine (Standard Edition) normally interprets Java byte code but also compiles Java methods that are frequently interpreted and runs them natively. The purpose is to take advantage of native execution without having too much overhead for Just-In-Time compilation. A former SJSU thesis tried to enhance the standard policy by predicting frequently called methods ahead of their actual frequent interpretation. The project also tried to increase the compilation throughput by prioritizing the method compilations, if there is more than one hot method to compile at the same time. The paper claimed significant speedup. In this project, we tried …

Protein-Protein Docking Using Region-Based 3d Zernike Descriptors., Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur.

Results

We present a novel protein docking algorithm based …

Application Of 3d Zernike Descriptors To Shape-Based Ligand Similarity Searching, Vishwesh Venkatraman, Padmasini Ramji Chakravarthy, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed.

Results

In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, …

Stepping Off The Stage, Brian Mac Namee, John D. Kelleher

Conference papers

Mixed-reality virtual agents are an attractive solution to the problems associated with human-robot interaction, allowing all the expressiveness of virtual characters to be married with the advantages of a physical artifact which exists in a shared environment with the user. However, common approaches to achieving this restrict the virtual characters appearing on top of, or encompassing the robot. This paper describes the Stepping Off the Stage system in which mixed-reality agents are allowed to step off the robot stage and move to other parts of the environment, offering compelling new interaction possibilities.

Enabling Adaptation In Trust Computations, Luca Longo, Pierpaolo Dondio, Bresciani Riccardo, Andrew Butterfield, Stephen Barrett

Conference papers

Digital systems have been rapidly evolving within highly dynamic and unstructured environments, where the lack of a central authority forces entities to interact with each other through collaboration and negotiation. Digital agents often use Trust models in order to compute the level of trustworthiness of the partner they want to collaborate with. Unfortunately, due to the evolution speed of open and collaborative environments, the trustworthiness of an agent varies over time, and as a result, Trust models must be continuously adapted to the changing context. In this work we address the problem by presenting a self-adaptive model for Trust computations. …

Storage, Manipulation, And Visualization Of Lidar Data, Bianca Schoen-Phelan, M. Bertolotto, D. F. Laefer, Sean W. Corish

Conference papers

In recent years, three-dimensional (3D) data has become increasingly available, in part as a result of significant technological progresses in Light Detection and Ranging (LiDAR). LiDAR provides longitude and latitude information delivered in conjunction with a GPS device, and elevation information generated by a pulse or phase laser scanner, which together provide an effective way of acquiring accurate 3D information of a terrestrial or manmade feature. The main advantages of LiDAR over conventional surveying methods lie in the high accuracy of the data and the relatively little time needed to scan large geographical areas. LiDAR scans provide a vast amount …

Real-Time Regularized Ultrasound Elastography, Hassan Rivaz

Link Foundation Modeling, Simulation and Training Fellowship Reports

This paper introduces two real-time elastography techniques based on analytic minimization (AM) of regularized cost functions. The first method (1D AM) produces axial strain and integer lateral displacement, while the second method (2D AM) produces both axial and lateral strains. The cost functions incorporate similarity of RF data intensity and displacement continuity, making both AM methods robust to small decorrelations present throughout the image. We also exploit techniques from robust statistics to make the methods resistant to large local decorrelations. We further introduce Kalman filtering for calculating the strain field from the displacement field given by the AM methods. Simulation …

Appropriate Prosodic Variation Is Valued By Users, Rafael Escalante-Ruiz

Open Access Theses & Dissertations

Spoken dialog systems today do not vary the prosody of their utterances, although prosody is known to have many useful expressive functions. In a corpus of memory quizzes, I identified eleven dimensions of prosodic variation, each with its own expressive function. I identified the situations in which each was used, and how to detect these situations from the dialog context and the prosody of the interlocutor's previous utterance. I implemented the resulting response rules and had 21 users interact with two versions of the system. Overall they preferred the version in which the prosodic forms of the acknowledgments were chosen …

Identification Of Human Gait Using Genetic Algorithm Tuned Fuzzy Logic, Abdallah Abdel-Rahman Hassan Mahmoud

Open Access Theses & Dissertations

Data mining is concerned with the discovery of useful hidden information in large databases. Classification is a data mining task producing rules in which a set of attributes in data predict the value of a class attribute. Classifiers usually produce a large number of rules, most of which are not interesting to the user. Rule interestingness is a decisive factor. However, evaluating rule interestingness is challenging as it involves both objective (data-driven) and subjective (user-driven) aspects.

In this research, a fuzzy genetic algorithm is proposed to discover classification rules that are both accurate and interesting. Continuous attributes are fuzzified so …

Towards More Reliable Extrapolation Algorithms With Applications To Organic Chemistry, Jaime Nava

Open Access Theses & Dissertations

One of the main objectives of science and engineering is to predict the results of different situations. For example, in Newton's mechanics, we want to predict the positions and velocities of different objects (e.g., planets) at future moments of time.

In this Thesis, as a case study, we take the problem of predicting the properties of new chemical substances. One of the main objectives of chemistry is to design new molecules (and, more generally, new chemical compounds) which are useful for various practical tasks. New substances have already resulted in new materials for buildings and for spaceships, new explosives and …

Shadowing Chaos Via Optimization, Henrik Haakonsen

Mathematics, Statistics, and Computer Science Honors Projects

A prominent idea in the theory of chaos is that of shadowing, which says that, in many cases, the numerical results one sees after accuracy is lost are not total nonsense, but are in fact very close to the exact trajectory for an initial value that is near the one used. Using high-precision computation, I have researched the use of optimization as a way of finding exact shadows for several chaotic systems, such as the quadratic map r x (1 - x) and a billiard problem from the SIAM 100-Digit Challenge.

Computational Analysis Of Metabolomic Toxicological Data Derived From Nmr Spectroscopy, Benjamin J. Kelly

Browse all Theses and Dissertations

Nuclear magnetic resonance (NMR) spectroscopy is a non-invasive method of acquiring metabolic profiles from biofluids. The most informative metabolomic features, or biomarkers, may provide keys to the early detection of changes within an organism such as those that result from exposure to a toxin. One major difficulty with typical NMR data, whether it come from a toxicological, medical or other source, is that it features a low sample size relative to the number of variables measured. Thus, traditional pattern recognition techniques are not always feasible. The "curse of dimensionality" is an important consideration in selecting appropriate statistical and pattern recognition …

Tyflos: A Wearable Navigation Prototype For Blind & Visually Impaired; Design, Modelling And Experimental Results, Dimitrios Dakopoulos

Browse all Theses and Dissertations

The need for assistive devices has, had and will have a large merit in many engineering research arenas. This dissertation deals with the design, modeling, implementation and experimentation of the navigation component of a wearable assistive system for blind and visually impaired people, called TYFLOS (ΤΥΦΛΟΣ) which is the Greek word for "Blind".

The current prototype consists of two mini cameras attached to a pair of conventional eye-glasses, a 2D tactile display vibration array) which consists of 16 vibrating elements arranged in a 4x4 manner, attached to an elastic vest worn on the user's abdomen, a portable computer, an ear-speaker …

Investigation And Quantification Of Codon Usage Bias Trends In Prokaryotes, Amanda L. Hanes

Browse all Theses and Dissertations

Organisms construct proteins out of individual amino acids using instructions encoded in the nucleotide sequence of a DNA molecule. The genetic code associates combinations of three nucleotides, called codons, with every amino acid. Most amino acids are associated with multiple synonymous codons, but although they result in the same amino acid and thus have no effect on the final protein, synonymous codons are not present in equal amounts in the genomes of most organisms. This phenomenon is known as codon usage bias, and the literature has shown that all organisms display a unique pattern of codon usage. Research also suggests …

Semantics Enriched Service Environments, Karthik Rajagopal Gomadam

Browse all Theses and Dissertations

During the past seven years services centric computing has emerged as the preferred approach to architect complex software. Software is increasingly developed by integrating remotely existing components, popularly called services. This architectural paradigm, also called Service Oriented Architecture (SOA), brings with it the benefits of interoperability, agility and flexibility to software design and development. One can easily add or change new features to existing systems, either by the addition of new services or by replacing existing ones. Two popular approaches have emerged for realizing SOA. The first approach is based on the SOAP protocol for communication and the Web Service …

A Software Framework For The Design, Testing And Deployment Of Control Systems For Autonomous Robotics, Duane Stanley Bolick Jr.

Browse all Theses and Dissertations

Simulation and control of robotic agents are common enough tasks among computer science and engineering researchers that there exists a large variety of software applications, toolkits, and programming frameworks designed to facilitate such research. The intent of this project is to provide an autonomous robotics simulation and control framework with sufficiently useful tools and reference implementations so as to be immediately useful to basic users, as well as easily understood and extended by software developers and robotics researchers.

As such, this document describes the implementation of a general networking toolkit, an autonomous robotics extension framework, and an autonomous robotics simulator …

Burst Scheduling, Grooming And Qos Provisioning In Optical Burst-Switched Networks, Yuqi Fan

Browse all Theses and Dissertations

The demand of network capacity has been increasing steadily with more users than ever connected to the Internet through broadband access and the popularity of video based applications, such as YouTube. Optical wavelength division multiplexing (WDM) networks are expected to form the next-generation backbone network and to fulfill the insatiable appetite for bandwidth.

Wavelength routed WDM optical networks offer the granularity of switching at a fiber, waveband, or a wavelength level. The finest granularity offered is at a wavelength level by provisioning lightpaths for different clients/services. All-optical packet switching is still deemed technically infeasible and its competitiveness as a backbone …

Improving Remote Homology Detection Using A Sequence Property Approach, Gina Marie Cooper

Browse all Theses and Dissertations

Understanding the structure and function of proteins is a key part of understanding biological systems. Although proteins are complex biological macromolecules, they are made up of only 20 basic building blocks known as amino acids. The makeup of a protein can be described as a sequence of amino acids. One of the most important tools in modern bioinformatics is the ability to search for biological sequences (such as protein sequences) that are similar to a given query sequence. There are many tools for doing this (Altschul et al., 1990, Hobohm and Sander, 1995, Thomson et al., 1994, Karplus and Barrett, …

Design And Performance Analysis Of A Secure Proces-Sor Scan-Sp With Crypto-Biometric Capabilities, Raghudeep Kannavara

Browse all Theses and Dissertations

Secure computing is gaining importance in recent times as computing capability is increasingly becoming distributed and information is everywhere. Prevention of piracy and digital rights management has become very important. Information security is mandatory rather than an additional feature. Numerous software techniques have been proposed to provide certain level of copyright and intellectual property protection. Techniques like obfuscation attempt to transform the code into a form that is harder to reverse engineer. Tamper-proofing causes a program to malfunction when it detects that it has been modified. Software watermarking embeds copyright notice in the software code to allow the owners of …

Semantic And Role-Based Access Control For Data Grid Systems, Vineela Muppavarapu

Browse all Theses and Dissertations

A Grid is an integration infrastructure for sharing and coordinated use of diverseresources in dynamic, distributed virtual organizations (VOs). A Data Grid is an architecture for the access, exchange, and sharing of data in the Grid environment. Distributed data resources can be diverse in their formats, schema, quality, access mechanisms, ownership, access policies, and capabilities. In recent years, several organizations have started utilizing Grid technologies to deploy data-intensive and/or computation-intensive applications. As more and more organizations are sharing data resources and participating in Data Grids, the complexity and heterogeneity of the systems is increasing constantly, but their management techniques are …

Automated Transforms Of Software Models: A Design Pattern Approach, Brandon Adam Gump

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In the realm of software development, projects are plagued by continuous maintenance at the source code level as well as tedious transformations from formal specifications to source code. Such work consumes a large amount of time only to create complicated, un-intelligible, and un-reusable code that is completely detached from initial design rational. To cope with these problems, The Air Force Institute of Technology (AFIT) Wide Spectrum Object Modeling Environment (AWSOME) was designed to generate specifications that can be transformed into abstract designs and finally into source code. The specifications are written in the AFIT Wide-spectrum Language (AWL) and parsed in …

A Dynamic Insertion Approach For Multi-Dimensional Data Using Index Structures, Yong Shi

Faculty Articles

Nowadays large volumes of data with high dimensionality are being generated in many fields. Most existing indexing techniques degrade rapidly when dimensionality goes higher. A large amount of data sets are time related, and the existence of the obsolete data in the data sets may seriously degrade the data processing. In our previous work[7], we proposed ClusterTree⁺, a new indexing approach representing clusters generated by any existing clustering approach. It is a hierarchy of clusters and subclusters which incorporates the cluster representation into the index structure to achieve effective and efficient retrieval. It also has features from the …

Animated Courseware Support For Teaching Database Design, Meg C. Murray, Mario Guimaraes

Faculty Articles

Database technologies are a core component of computing technology curricula. Their importance will only continue to expand as more and more data are retained in database systems. An effective database system is predicated on a good data model. Database design is the conceptualization of an underlying data model that progresses from identifying user requirements to graphically depicting those requirements and finally mapping the graphical models to a set of tables implemented in a physical database system. The abstract nature of much of database design makes it challenging to teach. This paper presents a set of software animations designed to support …