Computer Sciences Commons^™

A Qos Aware Framework For Wireless Sensor Networks In Industrial Environments, Berta Carballido Villaverde

Theses

Wireless Sensor Networks (WSNs) are a key enabling technology for industrial monitoring applications where the use of wireless infrastructure allows high adaptivity and low cost in terms of installation and retrofitting. Although WSNs present several advantages over traditional wired monitoring systems, there is significant concern as to the reliability of wireless communications due to the unpredictability of the wireless channel, which is inhibiting the widespread adoption of the technology. Furthermore, due to the diverse range of monitoring applications that are found in industrial environments and their differing requirements, there is a need for quality of service (QoS) provisioning so that …

A Machine-Learning Approach For Workflow Identification From Low-Level Monitoring Information, Thorsten Stein

Theses

Knowing which workflows are executed within Service Oriented Architectures (SOA) is essential for successful IT management. In many cases, SOAs grew out of previous existing IT architectures; existing components are used as single services and therefore as parts of newly created workflows. Since such workflows consist of newly developed and legacy services, traditional workflow management systems often cannot be applied. This thesis presents a method for gathering information about the executed workflows within such heterogeneous environments. An implementation of a framework is presented. This framework allows the training of machine-learning algorithms with workflow models and the mapping of low-level monitoring …

Type-1 Diabetes Risk Prediction Using Multiple Kernel Learning, Paras Garg

Theses

This thesis presents an analysis of multiple kernel learning (MKL) for type-1 diabetes risk prediction. MKL combines different models and representation of data to find a linear combination of these representations of the data. MKL has been successfully been implemented in image detection, splice site detection, ribosomal and membrane protein prediction, etc. In this thesis, this method was applied for Genome-wide association study (GWAS) for classifying cases and controls.

This thesis has shown that combined kernel does not perform better than the individual kernels and that MKL does not select the best model for this problem. Also, the effect of …

In Silico Prediction Of Non-Coding Rnas Using Supervised Learning And Feature Ranking Methods, Stephen J. Griesmer

Theses

This thesis presents a novel method, RNAMultifold, for development of a non-coding RNA (ncRNA) classification model based on features derived from folding the consensus sequence of multiple sequence alignments using different folding programs: RNAalifold, CentroidFold, and RSpredict. The method ranks these folding features according to a Class Separation Measure (CSM) that quantifies the ability of the features to differentiate between samples from positive and negative test sets. The set of top-ranked features is then used to construct classification models: Naive Bayes, Fisher Linear Discriminant, and Support Vector Machine (SVM). These models are compared to the performance of the same models …

Social Group Discovery Using Using Co-Location Traces, Steve Mardenfeld

Theses

Social information can be used to enhance existing applications and services or can be utilized to devise entirely new applications. Examples of such applications include recommendation systems, peer-to-peer networks, opportunistic data dissemination in ad hoc networks, or mobile friend finder. Social information can be collected from either online or mobile sources.

This thesis focuses on identifying social groups based on data collected from mobile phones. These data can be either location or co-location traces. Unfortunately, location traces require a localization system for every mobile device, and users are reluctant to share absolute location due to privacy concerns. On the other …

Automated Interpretation Of The Tandem Mass Spectra Of Peptides Using Artificial Neural Networks, Timothy Patrick Manning

Theses

The manual interpretation of mass spectra is a complex and time consuming task. The problem of manually interpreting this data is further exacerbated by the large numbers of mass spectra which can potentially be produced in a single proteoniics experiment. This shows the need for high throughput approaches to the interpretation of mass spectra. Existing automated approaches are however error prone due to the complexity of the task. Accordingly, this thesis discusses and evaluates the application of neural networks to improving the sensitivity, specificity and robustness of current approaches to the automated interpretation of such mass spectral data.

Several neural …

Game Engine Architecture : A Comprehensive View, Donald Kehoe

Theses

Game development is an ever growing interdisciplinary field. A variety of different skill sets need to come together to create a professional game. These range from art, audio and design through programming and development. It is difficult to isolate the different disciplines in game development since every aspect of the game is co-dependent on everything else. Even in the programming domain there are a number of sub-disciplines that a game can require such as physics programming, environmental programming, artificial intelligence and programming the core game engine, A game can even be developed in a number of different ways depending on …

Road-Based Proactive Routing Protocols For Vehicular Networks, Neeraj Mahadevrao Rajgure

Theses

Vehicular networks are formed by vehicles communicating in an ad hoc manner or through cellular and IEEE 802.11 base stations. Routing in vehicular networks is challenging due to highly dynamic network topologies. Previous research done at the UbiNetS lab at NJIT has proposed the idea of Road-Based using Vehicular Traffic information (RBVT) routing. In RBVT, routes are sequences of road intersections, and geographical forwarding is used for sending packets between the intersections.

This thesis proposes two proactive RBVT protocols (RBVT-P and RBVT-PS) for city-based Vehicular Ad hoc NETworks (VANETs). RBVT-P is a completely distributed protocol that unicasts connectivity packets in …

Rna Secondary Structure Detection Programs With An Emphasis On Covariance Models, Justin Slotman

Theses

RNA secondary structure prediction requires a different approach from traditional alignment methods. Functional RNAs often have their secondary structure better conserved than their primary structure. Covariance models, probabilistic models that utilize stochastic-context-free grammars, are one approach. CMs allow for homology to be detected where purely sequence-based methods would fail. A background on CMs is given, as well as a background of the major classes of non-coding RNAs (ncRNAs). Comparisons are made between some CM-using tools (the Infernal suite and CMfinder) and some other RNA secondary structure tools (CARNAC, miRNAminer, Pfold, Mfold) as well as between Infernal and the primary alignment …

Information Brokerage - A New Approach Using Knowledge Management, Robert Loew

Theses

Traditional knowledge management attempts to store the total enterprise knowledge into IT related structures, but knowledge management strategies should focus also on people and organisations and not just on technology.

This can be addressed in part by communicating knowledge between people, in and across organisations. Such communication focuses on the development and exchange of people’s experience.

This thesis introduces a hybrid knowledge management solution consisting of an automated system that includes people: employees, experts and Knowledge Brokers (KB). The hybrid concept supports the identification of suitable people for certain topics of discussion. Further, it supports the knowledge communication process by …

Automated Network Planning For Industrial Ethernet Networks, Holger Machens

Theses

Engineers usually use computer aided methods to ease the increasingly complex planning task of automation plants. One such computer aided method for automated planning of Industrial Ethernet networks under given network QoS requirements is presented in this thesis. The method is based on partitioning the given set of network nodes according to specified communication relationships between the nodes, thereby creating subsets of nodes which are joined using given networking algorithms. Several networking algorithms may be applicable for each subset of nodes and any complete solution is a combination of several partial solutions, one for each subset of nodes. Enumeration through …

Developing A Virtual City For Emergency Preparedness Planning And Training, Jon K. Morgan

Theses

Existing techniques for emergency preparedness planning and training fail or lack the ability to convey training on a broad scale and timely fashion. Skill sets that are required for planning, mitigation, response and recovery issues are lost through information overload or failure to identify other channels in which to convey the information. In order to resolve some of the issues with currently existing methods such as tabletop training exercises (TTX), instructional video learning and full-scale exercises we can turn to virtual environments.

In a virtual environment teams can interact with their surroundings from the comfort of the office without having …

Rna Genome Annotation With A Focus On T. Brucei, Brett Bucci

Theses

The goal of this project is to identify untranslated regions (UTRs) and UTR-indicating patterns in the genome of T. brucei. T. brucei is an interesting organism, and as the cause of African sleeping sickness -- which infects 300,000-500,000 people and a significant number of cattle annually -- is currently the subject of considerable research. Using existing algorithms, several patterns have been found that may lead to more complete UTR annotations in the T. brucei genome. The most encouraging sequence is the 11-base sequence GAGGGIICG]TGGGG, which appears in five hypothetical genes near the tail. Discovery of several such sequences could guide …

Utr Prediction Programs For Trypanosoma Brucei, Maria Moutafis

Theses

In the past few years, the field of bioinformatics has seen a rapid increase in the need for use of various sequence analysis tools. As we advance in the fields of science and technology, new programs and software are constantly being developed in this field. Rapidly expanding gene sequence databases and rapidly evolving sequence analysis tools are providing researchers with ways to search for highly similar query sequences whether they are nucleotide, protein, or gene databases. This thesis will focus on sequence alignment tools, specifically concentrating on tools that help determine/predict non-coding regions of sequences also known as untranslated regions …

Lightweight Objective Quality Of Voice Estimation Through Machine Learning, Daniel Riordan

Theses

Communication systems are undergoing constant and rapid innovation, both at the design stage and in the field. This in turn has led to an inereasing need for fast, efficient, portable and economic methods for the testing of these systems. For voice carrying communication systems the quality of the transmitted voice that the system produces is a large factor in the overall performance rating of the system. This measure is known as the ‘Quality of Voice’ (QoV) and can be evaluated either subjectively or objectively.

Speech quality is a complex subjective phenomenon that can be best quantified by subjective testing. A …

Optimization In Multi-Agent Systems : Structures And Procedures, Ingo Stengel

Theses

The main advantage for the use of agent technology is in the capacity of agents to represent the interests of individual entities and to act autonomously on their behalf. In multi-agent systems this involves communication, coordination and negotiation.

The focus of this dissertation is to find ways to optimize multi-agent systems at different levels by taking into consideration their structure and the procedures used. As optimization depends to a large extent on the problem to be solved, group forming scenarios, in which self-interested agents compete to form and join groups, have been selected here for consideration. Optimization issues are discussed …

Management Framework For Hybrid Wireless Networks, Chong Shen

Theses

The objective of the Hybrid Wireless Network with dedicated Relay Nodes (HWN*) architecture is to interface the Base Station (BS) Oriented Mobile Network (BSON) and the 802.fix based Mobile Ad hoc Wireless Network (MANET) so that one system can be utilised as an alternative radio access network for data transmissions, while the incorporation of Relay Nodes (RN) is to extend the communication coverage, optimise medium resource sharing, increase spatial reuse opportunity, stabilise MANET link and create more micro-cells. The HWN* keeps the existing cellular infrastructure and a Mobile Terminal (MT) can borrow radio resources from other cells via secure multi-hop …

Amvc: A Loosely-Coupled Architecture For Component-Based Clients, Brendan Lawlor

Theses

There is an architectural deficit in most currently undertaken rich client applications: In n-tier applications the presentation layer is represented as a single layer. This is as true of browser-based rich clients (Rich Internet Applications) as of rich desktop clients since both are designed along component-based, event-driven lines. The result of creating rich clients without sufficient application architecture underpinning is often tightly-coupled code of unnecessary complexity, with the associated high cost of maintenance. No commonly understood pattern is currently evident that would allow rich client components to be combined into a loosely coupled application. This paper describes the theory and …

Model-Based Instrumentation Of Distributed Applications, Jan Schäfer

Theses

Problems such as inconsistent or erroneous instrumentation often plague applications whose source code is manually instrumented during the implementation phase. Integrating performance instrumentation capabilities into the Model Driven Software Development (MDSD) process would greatly assist software engineers who do not have detailed knowledge of source code instrumentation technologies. This thesis presents an approach that offers instrumentation support to software designers and developers. A collection of instrumentation patterns is defined to represent typical instrumentation scenarios for distributed applications. A UML profile derived from these patterns is then used to annotate UML models. Based on suitable code generation templates, the annotated models …

Elliptic Curve Cryptography Security On Restricted Mobile Devices, Debbie Mccann

Theses

Mobile technologies with limited resources, such as smart phones or PDAs, have increased dramatically in popularity. However, the level of security provided for these technologies has not kept pace with the value of the data that they contain or transmit.

Wireless networks usually provide some security, in the form of encryption. GSM and GPRS use different forms of the A5 algorithm, and Wi-Fi uses WEP or WPA. These encryption algorithms have proven weaknesses and in some cases have been efficiently cracked. To improve the security of wireless networks, stronger encryption algorithms need to be developed. One of the most attractive …

A Distributed Ai Approach For Large-Scale Wlan Design, Alan Mcgibney

Theses

The recent dramatic trend towards always-on-connectivity has driven the need for mobile ubiquitous computing environments with the advent of the Wireless Local Area Network (WLAN) seeing a shift from traditional wired networks to wireless networking. A WLAN typically contains a number of access points that allow wireless enabled clients access information and network resources such as the internet without the need for wires, offering flexibility and mobility to the users. Initial wireless networks were convenience based allowing users access to the primary wired network, and involved little planning prior to roll-out. The proliferation of low cost wireless devices combined wdth …

Personal Information Management. A Framework For Development Of Personalisable Web Based Services, Christopher Fuchs

Theses

The thesis research proposed herein will model, analyse and implement strategies for the development of personalised services. The goal of the research work is to design and implement a framework which supports developers by minimising the effort required in implementing personalised services. This includes the ability to react to localisation changes and to present proper information. An overall design goal is the independency of most components from each other which will be attained through the use of standard technologies and protocols and the consistent use of a component model. The result will include the proposed framework and the analyses of …

Anaerobic Digestion: Decision Support Software, Marco Poliafico

Theses

Ireland has significant quantities of livestock; meat exportation is a vibrant sector of the economy. Environmental management of animal wastes has therefore become an important concern. On the other hand in the last decade, national and EU policy debate has highlighted the need to investigate alternative energy: in particular energy for transport.

This study investigates the quantities of animal wastes produced in Ireland and their potential treatment using Anaerobic Digestion technologies. In 2005 Ireland had over 8 millions animals (cattle and pigs) and the annual slaughter accounted for over 4.2 million of these creatures. These animals have been responsible for …

Separation Of Ssl Protocol Phases Across Process Boundaries, Kirthikar Anantharam

Theses

Secure Sockets Layer is the de-facto standard used in the industry today for secure communications through web sites. An SSL connection is established by performing a Handshake, which is followed by the Record phase. While the SSL Handshake is computationally intensive and can cause of bottlenecks on an application server, the Record phase can cause similar bottlenecks while encrypting large volumes of data.

SSL Accelerators have been used to improve the performance of SSL-based application servers. These devices are expensive, complex to configure and inflexible to customizations. By separating the SSL Handshake and the Record phases into separate software processes, …

Dynamic Recomposition Of Documents From Distributed Data Sources, Abhishek Verma

Theses

Dynamic recomposition of documents refers to the process of on-the-fly creation of documents. A document can be generated from several documents that are stored at distributed data sites. The source can be queried and results obtained in the form of XML. These XML documents can be combined after a series of transformation operations to obtain the target document. The resultant document can be stored statically or in the form of a command, which can be invoked later to recompose this document dynamically. Also, in case a change is made to a document, then only the change can be stored, instead …

A Data Gathering Toolkit For Biological Information Integration, Munira Lokhandwala

Theses

SYSTERS is a biological information integration system containing protein sequences from many protein databases such as Swiss-Prot and TrEMBL and also protein sequences from complete genomes available at Ensembl, The Arabidopsis Information Resource, SGD and GeneDB. For some protein sequences their encoding nucleotide sequences can be found in their corresponding websites. However, for some protein sequences their encoding nucleotide sequences are missing.

The goal of this thesis is to. collect all nucleotide sequences for the protein sequences in SYSTERS and store them in a common database. There are two cases. The first case is that if the nucleotide sequences can …

Network Activity Arising From Optimal Diameters Of Neuronal Processes, Juliane Gansert

Theses

Electrical coupling provides an important pathway for signal transmission between neurons. In several regions of the mammalian brain electrical synapses have been detected, and their role in the synchronization of neural networks and the generation of oscillations has been studied theoretically. Recently, it has been found that the amplitude of the postsynaptic potential is maximized for a specific diameter of the postsynaptic fiber.

In this thesis, the impact of the fiber's diameter on the success or failure of the action potential initiation and propagation is studied theoretically. Systems of two coupled neurons, as well as small networks, are investigated. The …

Finding Role Errors Of The Ncit Gene Hierarchy Using The Ncbi, Marc Oren

Theses

Due to the knowledge discovery process of gene information, details such as organism and chromosomal location should be known. Furthermore, the extensive biomedical research in genomics led to discovery of processes and diseases in which a gene plays a role. In the Gene hierarchy of the NCI Thesaurus (NCIT) such knowledge is represented by appropriate roles. However, upon review of the Gene hierarchy of the NCIT, many role errors are found. Realizing that such details are provided by another knowledge repository of NIH, the NCBI gene database, a methodology is presented to use NCBI to discover role errors for the …

Comparative Analysis Of Parametric, Nonparametric And Permutation Methods For Differential Expression, Rahul Patil

Theses

DNA microarrays permit us to study the expression of thousands of genes simultaneously. They are now used in many different contexts to compare mRNA levels between two or more samples of cells. Microarray experiments typically give us expression measurements on a large number of genes. Increasing popularity of microarray technology has resulted in a number of tests being proposed to detect differentials expression.

The purpose of study is to compare the parametric, non parametric and permutation tests when applied to microarray data for differential expression analysis. t test (parametric), Mann Whitney test (nonparametric) and Significance of analysis (permutation ) test …

The Effects Of Limited Rebuild Buffer And Track Buffers On Rebuild Time In Raid5, Chintan Shah

Theses

Redundant Arrays of Independent Disks (RAID) are very popular for creating large, reliable storage systems. A RAID array consists of multiple independent disks that achieve fault tolerance by parity coding. The contents on a failed disk can be reconstructed on demand by reading and exciusive-ORing the corresponding blocks on surviving disks. Upon disk failure, the array enters rebuild mode when it begins to systematically reconstruct the data of the failed disk on a spare disk, provided one is available. The fundamental element of rebuild is the Rebuild Unit (RU).

Surviving disks engaged in rebuild, process user requests at a higher …