Physical Sciences and Mathematics Commons^™

A New Algorithm For Protein-Protein Interaction Prediction, Yiwei Li

Electronic Thesis and Dissertation Repository

Protein-protein interactions (PPI) are vital processes in molecular biology. However, the current understanding of PPIs is far from satisfactory. Improved methods of pre- dicting PPIs are very much needed. Since experimental methods are labour and time consuming and lack accuracy, the improvement is expected to come from the area of computational methods. We designed and implemented a new algorithm based on protein primary structure to predict PPIs using C++ and OpenMP for parallel computing. We compared our method with four leading methods. Our results are better than the competition for most of the important values. Furthermore, it succeeds in surpassing …

New Algorithms For Structural Variation Detection By De Novo Genome Assembly, Ehsan Haghshenas

Electronic Thesis and Dissertation Repository

Structural variations (SVs) are changes in the human genome that are reported in several studies to be associated with some diseases. Therefore, designing methods to find these types of variations would help us for early detection of those diseases and utilizing new treatment methods such as personalized medicine. Currently computational methods are applied to find structural variations from short reads obtained by Next Generation Sequencing (NGS) platforms. Usually each method has more power in finding particular types or sizes of SVs and limitations in finding others. Thus, still new approaches and methods are on demand for SV discovery.

In this …

Color Separation For Image Segmentation, Meng Tang

Electronic Thesis and Dissertation Repository

Image segmentation is a fundamental problem in computer vision that has drawn intensive research attention during the past few decades, resulting in a variety of segmentation algorithms. Segmentation is often formulated as a Markov random field (MRF) and the solution corresponding to the maximum a posteriori probability (MAP) is found using energy minimiza- tion framework. Many standard segmentation techniques rely on foreground and background appearance models given a priori. In this case the corresponding energy can be efficiently op- timized globally. If the appearance models are not known, the energy becomes NP-hard, and many methods resort to iterative schemes that …

On The Interoperability Of Programming Languages Based On The Fork-Join Parallelism Model, Sushek Shekar

Electronic Thesis and Dissertation Repository

This thesis describes the implementation of MetaFork, a meta-language for concurrency platforms targeting multicore architectures. First of all, MetaFork is a multithreaded language based on the fork-join model of concurrency: it allows the programmer to express parallel algorithms assuming that tasks are dynamically scheduled at run-time. While MetaFork makes no assumption about the run-time system, it formally defines the serial C-elision of a MetaFork program. In addition, MetaFork is a suite of source-to-source compilers permitting the automatic translation of multithreaded programs between programming languages based on the fork-join model. Currently, this compilation framework supports the OpenMP and CilkPlus concurrency platforms. …

Disaster Data Management In Cloud Environments, Katarina Grolinger

Electronic Thesis and Dissertation Repository

Facilitating decision-making in a vital discipline such as disaster management requires information gathering, sharing, and integration on a global scale and across governments, industries, communities, and academia. A large quantity of immensely heterogeneous disaster-related data is available; however, current data management solutions offer few or no integration capabilities and limited potential for collaboration. Moreover, recent advances in cloud computing, Big Data, and NoSQL have opened the door for new solutions in disaster data management.

In this thesis, a Knowledge as a Service (KaaS) framework is proposed for disaster cloud data management (Disaster-CDM) with the objectives of 1) facilitating information gathering …

Missing Requirements Information And Its Impact On Software Architectures: A Case Study, Md Rounok Salehin

Electronic Thesis and Dissertation Repository

[Context & motivation] In the development of large, software-intensive systems, the system’s requirements are seldom, if ever, concluded upon prior to commencing with systems architecture. Research shows that, in order to manage development and domain complexities, instances of requirements engineering (RE) and systems architecting (SA) processes tend to inter-weave. [Question/problem] However, missing requirements information can cause one to create (or recreate) the needed information during different SA activities. While backtracking in the software development process is known to be costly, the costs associated with missing requirements in the SA process have not been investigated empirically. [Principal ideas/results] We …

Performance Comparison Of 3d Sinc Interpolation For Fmri Motion Correction By Language Of Implementation And Hardware Platform, Andrew B. Kope

Electronic Thesis and Dissertation Repository

Substantial effort is devoted to improving neuroimaging data processing; this effort however, is typically from the algorithmic perspective only. I demonstrate that substantive running time performance improvements to neuroscientific data processing algorithms can be realized by considering their implementation. Focusing specifically on 3D sinc interpolation, an algorithm used for processing functional magnetic resonance imaging (fMRI) data, I compare the performance of Python, C and OpenCL implementations of this algorithm across multiple hardware platforms. I also benchmark the performance of a novel implementation of 3D sinc interpolation on a field programmable gate array (FPGA). Together, these comparisons demonstrate that the performance …

An Access Control Model For Nosql Databases, Motahera Shermin

Electronic Thesis and Dissertation Repository

Current development platforms are web scale, unlike recent platforms which were just network scale. There has been a rapid evolution in computing paradigm that has created the need for data storage as agile and scalable as the applications they support. Relational databases with their joins and locks influence performance in web scale systems negatively. Thus, various types of non-relational databases have emerged in recent years, commonly referred to as NoSQL databases. To fulfill the gaps created by their relational counter-part, they trade consistency and security for performance and scalability. With NoSQL databases being adopted by an increasing number of organizations, …

A Modular Approach To The Development Of Interactive Augmented Reality Applications., Nelson J. Andre

Electronic Thesis and Dissertation Repository

Augmented reality (AR) technologies are becoming increasingly popular as a result of the increase in the power of mobile computing devices. Emerging AR applications have the potential to have an enormous impact on industries such as education, healthcare, research, training and entertainment. There are currently a number of augmented reality toolkits and libraries available for the development of these applications; however, there is currently no standard tool for development. In this thesis we propose a modular approach to the organization and development of AR systems in order to enable the creation novel AR experiences. We also investigate the incorporation of …

Detecting Multilingual Lines Of Text With Fusion Moves, Igor Milevskiy

Electronic Thesis and Dissertation Repository

This thesis proposes an optimization-based algorithm for detecting lines of text in images taken by hand-held cameras. The majority of existing methods for this problem assume alphabet-based texts (e.g. in Latin or Greek) and they use heuristics specific to such texts: proximity between letters within one line, larger distance between separate lines, etc. We are interested in a more challenging problem where images combine alphabet and logographic characters from multiple languages where typographic rules vary a lot (e.g. English, Korean, and Chinese). Significantly higher complexity of fitting multiple lines of text in different languages calls for an energy-based formulation combining …

Redesign Of Johar: A Framework For Developing Accessible Applications, Oladapo Oyebode

Electronic Thesis and Dissertation Repository

As the population of disabled people continues to grow, designing accessible applications is still a challenge, since most applications are incompatible with assistive technologies used by disabled people to interact with the computer. This accessibility issue is usually caused by the reluctance of software engineers or developers to include complete accessibility features in their applications, which in turn is often due to the extra cost and development effort required to dynamically adapt applications to a wide range of disabilities. Our aim to resolve accessibility issues led to the design and implementation of the "Johar" framework, which facilitates the development of …

Representation, Recognition And Collaboration With Digital Ink, Rui Hu

Electronic Thesis and Dissertation Repository

Pen input for computing devices is now widespread, providing a promising interaction mechanism for many purposes. Nevertheless, the diverse nature of digital ink and varied application domains still present many challenges. First, the sampling rate and resolution of pen-based devices keep improving, making input data more costly to process and store. At the same time, existing applications typically record digital ink either in proprietary formats, which are restricted to single platforms and consequently lack portability, or simply as images, which lose important information. Moreover, in certain domains such as mathematics, current systems are now achieving good recognition rates on individual …

Hardware Acceleration Technologies In Computer Algebra: Challenges And Impact, Sardar Anisul Haque

Electronic Thesis and Dissertation Repository

The objective of high performance computing (HPC) is to ensure that the computational power of hardware resources is well utilized to solve a problem. Various techniques are usually employed to achieve this goal. Improvement of algorithm to reduce the number of arithmetic operations, modifications in accessing data or rearrangement of data in order to reduce memory traffic, code optimization at all levels, designing parallel algorithms to reduce span are some of the attractive areas that HPC researchers are working on. In this thesis, we investigate HPC techniques for the implementation of basic routines in computer algebra targeting hardware acceleration technologies. …

Application Of Computer Algebra In List Decoding, Muhammad Foizul Islam Chowdhury

Electronic Thesis and Dissertation Repository

The amount of data that we use in everyday life (social media, stock analysis, satellite communication etc.) are increasing day by day. As a result, the amount of data needs to be traverse through electronic media as well as to store are rapidly growing and there exist several environmental effects that can damage these important data during travelling or while in storage devices. To recover correct information from noisy data, we do use error correcting codes. The most challenging work in this area is to have a decoding algorithm that can decode the code quite fast, in addition with the …

Cognitive Activity Support Tools: Design Of The Visual Interface, Paul Parsons

Electronic Thesis and Dissertation Repository

This dissertation is broadly concerned with interactive computational tools that support the performance of complex cognitive activities, examples of which are analytical reasoning, decision making, problem solving, sense making, forecasting, and learning. Examples of tools that support such activities are visualization-based tools in the areas of: education, information visualization, personal information management, statistics, and health informatics. Such tools enable access to information and data and, through interaction, enable a human-information discourse. In a more specific sense, this dissertation is concerned with the design of the visual interface of these tools. This dissertation presents a large and comprehensive theoretical framework to …

Reinforcement Learning With Motivations For Realistic Agents, Jacquelyne T. Forgette

Electronic Thesis and Dissertation Repository

Believable virtual humans have important applications in various fields, including computer based video games. The challenge in programming video games is to produce a non-player controlled character that is autonomous, and capable of action selections that appear human. In this thesis, motivations are used as a basis for learning using reinforcements. With motives driving the decisions of the agents, their actions will appear less structured and repetitious, and more human in nature. This will also allow developers to easily create game agents with specific motivations, based mostly on their narrative purposes. With minimum and maximum desirable motive values, the agents …

Vehicular Instrumentation And Data Processing For The Study Of Driver Intent, Taha Kowsari

Electronic Thesis and Dissertation Repository

The primary goal of this thesis is to provide processed experimental data needed to determine whether driver intentionality and driving-related actions can be predicted from quantitative and qualitative analysis of driver behaviour. Towards this end, an instrumented experimental vehicle capable of recording several synchronized streams of data from the surroundings of the vehicle, the driver gaze with head pose and the vehicle state in a naturalistic driving environment was designed and developed. Several driving data sequences in both urban and rural environments were recorded with the instrumented vehicle. These sequences were automatically annotated for relevant artifacts such as lanes, vehicles …

Collaborative Policy-Based Autonomic Management In Iaas Clouds, Omid Mola

Electronic Thesis and Dissertation Repository

With the increasing number of "machines" (either virtual or physical) in a computing environment, it is becoming harder to monitor and manage these resources. Relying on human administrators, even with tools, is expensive and the growing complexity makes management even harder. The alternative is to look for automated approaches that can monitor and manage computing resources in real time with no human intervention. One of the approaches to this problem is policy-based autonomic management. However, in large systems having one single autonomic manager to manage everything is almost impossible. Therefore, multiple autonomic managers will be needed and these will need …

Hierarchical Classification And Its Application In University Search, Xiao Li

Electronic Thesis and Dissertation Repository

Web search engines have been adopted by most universities for searching webpages in their own domains. Basically, a user sends keywords to the search engine and the search engine returns a flat ranked list of webpages. However, in university search, user queries are usually related to topics. Simple keyword queries are often insufficient to express topics as keywords. On the other hand, most E-commerce sites allow users to browse and search products in various hierarchies. It would be ideal if hierarchical browsing and keyword search can be seamlessly combined for university search engines. The main difficulty is to automatically classify …

Reliability Models Applied To Smartphone Applications, Sonia Meskini

Electronic Thesis and Dissertation Repository

Smartphones have become the most used electronic devices. They carry out most of the functionalities of desktops, offering various useful applications that suit the user’s needs. Therefore, instead of the operator, the user has been the main controller of the device and its applications, therefore its reliability has become an emergent requirement. As a first step, based on collected smartphone applications failure data, we investigated and evaluated the efficacy of Software Reliability Growth Models (SRGMs) when applied to these smartphone data in order to check whether they achieve the same accuracy as in the desktop/laptop area. None of the selected …

Maps Of Lessons Learnt In Requirements Engineering, Ibtehal Noorwali

Electronic Thesis and Dissertation Repository

Both researchers and practitioners have emphasized the importance of learning from past experiences and its consequential impact on project time, cost, and quality. However, from the survey we conducted of requirements engineering (RE) practitioners, over 70\% of the respondents stated that they seldom use RE lessons in the RE process, though 85\% of these would use such lessons if readily available. Our observation, however, is that RE lessons are scattered, mainly implicitly, in the literature and practice, which obviously, does not help the situation. We, therefore, present ``maps” of RE lessons which would highlight weak (dark) and strong (bright) areas …

Localizing State-Dependent Faults Using Associated Sequence Mining, Shaimaa Ali

Electronic Thesis and Dissertation Repository

In this thesis we developed a new fault localization process to localize faults in object oriented software. The process is built upon the "Encapsulation'' principle and aims to locate state-dependent discrepancies in the software's behavior. We experimented with the proposed process on 50 seeded faults in 8 subject programs, and were able to locate the faulty class in 100% of the cases when objects with constant states were taken into consideration, while we missed 24% percent of the faults when these objects were not considered. We also developed a customized data mining technique "Associated sequence mining'' to be used in …

Representing Game Dialogue As Expressions In First-Order Logic, Kaylen Fj Wheeler

Electronic Thesis and Dissertation Repository

Despite advancements in graphics, physics, and artificial intelligence, modern video games are still lacking in believable dialogue generation. The more complex and interactive stories in modern games may allow the player to experience different paths in dialogue trees, but such trees are still required to be manually created by authors. Recently, there has been research on methods of creating emergent believable behaviour, but these are lacking true dialogue construction capabilities. Because the mapping of natural language to meaningful computational representations (logical forms) is a difficult problem, an important first step may be to develop a means of representing in-game dialogue …

An Architecture For Believable Socially Aware Agents, Arvand Dorgoly

Electronic Thesis and Dissertation Repository

The main focus of this thesis is to solve the believability problem in video game agents by integrating necessary psychological and sociological foundations by means of role based architecture. Our design agent also has the capability to reason and predict the decisions of other actors by using its own mental model. The agent has a separate mental model for every actor.

Integrated Development And Parallelization Of Automated Dicentric Chromosome Identification Software To Expedite Biodosimetry Analysis, Yanxin Li

Electronic Thesis and Dissertation Repository

Manual cytogenetic biodosimetry lacks the ability to handle mass casualty events. We present an automated dicentric chromosome identification (ADCI) software utilizing parallel computing technology. A parallelization strategy combining data and task parallelism, as well as optimization of I/O operations, has been designed, implemented, and incorporated in ADCI. Experiments on an eight-core desktop show that our algorithm can expedite the process of ADCI by at least four folds. Experiments on Symmetric Computing, SHARCNET, Blue Gene/Q multi-processor computers demonstrate the capability of parallelized ADCI to process thousands of samples for cytogenetic biodosimetry in a few hours. This increase in speed underscores the …

Nfa Reduction Via Hypergraph Vertex Cover Approximation, Timothy Ng

Electronic Thesis and Dissertation Repository

In this thesis, we study in minimum vertex cover problem on the class of k-partite k-uniform hypergraphs. This problem arises when reducing the size of nondeterministic finite automata (NFA) using preorders, as suggested by Champarnaud and Coulon. It has been shown that reducing NFAs using preorders is at least as hard as computing a minimal vertex cover on 3-partite 3-uniform hypergraphs, which is NP-hard. We present several classes of regular languages for which NFAs that recognize them can be optimally reduced via preorders. We introduce an algorithm for approximating vertex cover on k-partite k-uniform hypergraphs based on a theorem by …

Ratio-Based Edge Detection Inspired Speckle Reducing Anisotropic Diffusion, Asaduzzaman Babu

Electronic Thesis and Dissertation Repository

Speckle Reducing Anisotropic Diffusion, SRAD, is a multiplicative speckle noise reduction method. In highly speckled environment, SRAD occasionally produces over-smoothed, dislocated/broadened edge lines and inadequate de-noising on homogeneous image regions where the speckles are well developed. Moreover, the performance of SRAD is highly dependent on the initial selection of a good homogeneous area. To overcome these weaknesses, we propose two different ratio-based edge detection inspired extensions to SRAD. One of the proposed extensions incorporates an edge-sensitive boosting factor to guide the gradient and Laplacian operator based edge detector of SRAD. The edge-sensitive boosting factor is defined by the global edge …

Fuzzy Expert-Cocomo Risk Assessment And Effort Contingency Model In Software Project Management, Ekananta Manalif

Electronic Thesis and Dissertation Repository

Software development can be considered to be the most uncertain project when compared to other types of projects due to the uncertainty in the customer requirements, the complexity of the process, and the intangible nature of the product. In order to increase the likelihood of success in managing a software project, the project manager(s) must invest more time and effort in the project planning phase. The two main activities in project planning phase are effort estimation and risk management which has to be executed together because the accuracy of the effort estimation is highly dependent on the size and nature …

Util-Dss: Utilization-Based Dynamic Strategy Switching For Improvement In Data Centre Operation, Graham Foster

Electronic Thesis and Dissertation Repository

Applications are shifting into large scale, virtualized data centres that provide resources on a pay-per-usage basis. With power consumption representing a major operational cost, data centres must prioritize efficiency while still providing enough resources to meet application requirements. To meet variable application demands, a dynamic approach to virtual machine (VM) management is required. This requires: (i) placing newly arrived VMs, (ii) migrating VMs from highly utilized machines to avoid performance degradation, and (iii) migrating VMs from underutilized machines so that they may be deactivated to save power. Here, a management strategy is considered to be policy-set that guides these three …

Multi-Point Stride Coverage: A New Genre Of Test Coverage Criteria, Mohammad Mahdi Hassan

Electronic Thesis and Dissertation Repository

We introduce a family of coverage criteria, called Multi-Point Stride Coverage (MPSC). MPSC generalizes branch coverage to coverage of tuples of branches taken from the execution sequence of a program. We investigate its potential as a replacement for dataflow coverage, such as def-use coverage. We find that programs can be instrumented for MPSC easily, that the instrumentation usually incurs less overhead than that for def-use coverage, and that MPSC is comparable in usefulness to def-use in predicting test suite effectiveness. We also find that the space required to collect MPSC can be predicted from the number of branches in the …