Other Computer Sciences 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 …

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. …

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 …

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 …

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 …