Digital Commons Network^™

Algorithms For Transcriptome Quantification And Reconstruction From Rna-Seq Data, Serghei Mangul

Computer Science Dissertations

Massively parallel whole transcriptome sequencing and its ability to generate full transcriptome data at the single transcript level provides a powerful tool with multiple interrelated applications, including transcriptome reconstruction, gene/isoform expression estimation, also known as transcriptome quantification. As a result, whole transcriptome sequencing has become the technology of choice for performing transcriptome analysis, rapidly replacing array-based technologies. The most commonly used transcriptome sequencing protocol, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. RNA-Seq protocol reduces the sequencing cost and significantly increases data throughput, but is computationally challenging to reconstruct …

Connected Dominating Set Based Topology Control In Wireless Sensor Networks, Jing S. He

Computer Science Dissertations

Wireless Sensor Networks (WSNs) are now widely used for monitoring and controlling of systems where human intervention is not desirable or possible. Connected Dominating Sets (CDSs) based topology control in WSNs is one kind of hierarchical method to ensure sufficient coverage while reducing redundant connections in a relatively crowded network. Moreover, Minimum-sized Connected Dominating Set (MCDS) has become a well-known approach for constructing a Virtual Backbone (VB) to alleviate the broadcasting storm for efficient routing in WSNs extensively. However, no work considers the load-balance factor of CDSsin WSNs. In this dissertation, we first propose a new concept — the Load-Balanced …

Simulation Software As A Service And Service-Oriented Simulation Experiment, Song Guo

Computer Science Dissertations

Simulation software is being increasingly used in various domains for system analysis and/or behavior prediction. Traditionally, researchers and field experts need to have access to the computers that host the simulation software to do simulation experiments. With recent advances in cloud computing and Software as a Service (SaaS), a new paradigm is emerging where simulation software is used as services that are composed with others and dynamically influence each other for service-oriented simulation experiment on the Internet.

The new service-oriented paradigm brings new research challenges in composing multiple simulation services in a meaningful and correct way for simulation experiments. To …

Resource Management In Survivable Multi-Granular Optical Networks, Yang Wang

Computer Science Dissertations

The last decade witnessed a wild growth of the Internet traffic, promoted by bandwidth-hungry applications such as Youtube, P2P, and VoIP. This explosive increase is expected to proceed with an annual rate of 34% in the near future, which leads to a huge challenge to the Internet infrastructure. One foremost solution to this problem is advancing the optical networking and switching, by which abundant bandwidth can be provided in an energy-efficient manner. For instance, with Wavelength Division Multiplexing (WDM) technology, each fiber can carry a mass of wavelengths with bandwidth up to 100 Gbits/s or higher. To keep up with …

Innovative Algorithms And Evaluation Methods For Biological Motif Finding, Wooyoung Kim

Computer Science Dissertations

Biological motifs are defined as overly recurring sub-patterns in biological systems. Sequence motifs and network motifs are the examples of biological motifs. Due to the wide range of applications, many algorithms and computational tools have been developed for efficient search for biological motifs. Therefore, there are more computationally derived motifs than experimentally validated motifs, and how to validate the biological significance of the ‘candidate motifs’ becomes an important question. Some of sequence motifs are verified by their structural similarities or their functional roles in DNA or protein sequences, and stored in databases. However, biological role of

network motifs is still …

Di-Sec: Distributed Security Framework For Heterogeneous Wireless Sensor Networks, Marco Valero

Computer Science Dissertations

Wireless Sensor Networks (WSNs) are deployed for monitoring in a range of critical domains (e.g., health care, military, critical infrastructure). Accordingly, these WSNs should be resilient to attacks. The current approach to defending against malicious threats is to develop and deploy a specific defense mechanism for a specific attack. However, the problem with this traditional approach to defending sensor networks is that the solution for one attack (i.e., Jamming attack) does not defend against other attacks (e.g., Sybil and Selective Forwarding). This work addresses the challenges with the traditional approach to securing sensor networks and presents a comprehensive framework, Di-Sec, …

Protein Tertiary Model Assessment Using Granular Machine Learning Techniques, Anjum A. Chida

Computer Science Dissertations

The automatic prediction of protein three dimensional structures from its amino acid sequence has become one of the most important and researched fields in bioinformatics. As models are not experimental structures determined with known accuracy but rather with prediction it’s vital to determine estimates of models quality. We attempt to solve this problem using machine learning techniques and information from both the sequence and structure of the protein. The goal is to generate a machine that understands structures from PDB and when given a new model, predicts whether it belongs to the same class as the PDB structures (correct or …

Shadow Price Guided Genetic Algorithms, Gang Shen

Computer Science Dissertations

The Genetic Algorithm (GA) is a popular global search algorithm. Although it has been used successfully in many fields, there are still performance challenges that prevent GA’s further success. The performance challenges include: difficult to reach optimal solutions for complex problems and take a very long time to solve difficult problems. This dissertation is to research new ways to improve GA’s performance on solution quality and convergence speed. The main focus is to present the concept of shadow price and propose a two-measurement GA. The new algorithm uses the fitness value to measure solutions and shadow price to evaluate components. …