Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2002. / Includes bibliographical references (leaves 105-110). Also available in electronic version. Access restricted to campus users.

Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2004. / Includes bibliographical references (leaves 67-68). Also available in electronic version. Access restricted to campus users.

Thesis (M. S.)--Computing, Georgia Institute of Technology, 2009. / Committee Chair: Pande, Santosh; Committee Member: Clark, Nate; Committee Member: Yalamanchili, Sudhakar. Part of the SMARTech Electronic Thesis and Dissertation Collection.

With the rapid development of next-generation sequencing NGS technology, we are able to investigate various aspects biological problems, including genome and transcriptome sequencing, genomic structural variation and the mechanism of regulatory small RNAs, etc. An enormous number of associated computational methods have been proposed to study the biological problems using NGS reads, at a low cost of expense and time. Regulatory small RNAs and genomic structure variations are two main problems that we have studied. In the area of regulatory small RNA, various computational tools have been designed from the prediction of small RNA to target prediction. Regulatory small RNAs play essential roles in plants and bacteria such as in responses to environmental stresses. We focused on sRNAs that in act by base pairing with target mRNA in complementarity. A comprehensive analysis workflow that is able to integrate sRNA-Seq and RNA-Seq analysis and generate regulatory network haven't been designed yet. Thus, we proposed and implemented two small RNA analysis workflow for plants and bacteria respectively. In the area of genomic structural variations (SV), two types of disease-related SVs have been investigated, including complex low copy repeats (LCRs, also termed as segmental duplications) and tandem duplication (TD). LCRs provide structural basis to form a combination of other SVs which may in turn lead to some serious genetic diseases and TDs of specific areas have been reported for patients. Locating LCRs and TDs in human genome can help researchers to further interrogate the mechanism of related diseases. Therefore, we proposed two computational methods to predict novel LCRs and TDs in human genome. / published_or_final_version / Computer Science / Doctoral / Doctor of Philosophy

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A performance evaluation of CSTC (Cooperative Space Time Coding) with spatially cor-related fading and imperfect channel estimation in Gaussian as well as impulsive noise is presented. Closed form expressions for the pairwise error probability conditioned on the estimated channel gains are derived by assuming the components of the received vector are independent given the estimated channel gains. An expurgated union bound using the limiting before averaging technique given the estimated channel gains is then obtained. Although this assumption is not strictly valid, simulation results show that the bound is accurate in estimating the diversity order as long the channel estimation is not very poor. It is found that CSTC with block fading channels can reduce the frame error rate (FER) relative to SUSTC (Single User Space Time Coding) with quasi-static fading channels, even when the channel gains for each user are strongly correlated and when the channel estimations are very poor. A decision metric for CSTC with spatially correlated fading, imperfect channel estimation, and impulsive mixture Gaussian noise is derived which yields lower FERs than the Gaussian noise decision metric. Simulation results show that the FER performance of CSTC with mixture Gaussian noise outperforms CSTC with Gaussian noise at low SNR. At high SNR, the FER performance of CSTC with Gaussian noise is better than the FER performance of CSTC with mixture Gaussian noise due to the heavy tail of the mixture Gaussian noise.

The increasing demand on multimedia communication over wired and wireless networks imposes a continuous pressure on developing more robust coding schemes. Recently, joint source-channel coding with multiple description codes has become an attractive solution to ensure robust communication over noisy channels. In this thesis, we conduct analysis and design of multiple description codes for wired and wireless communication channels. First, a multiple description quantizer (MDQ) design method based on channel optimized quantization is developed. The proposed multiple channel optimized quantizer design scheme does not require index assignment and offers the benefit of resilience to both symbol and erasure errors. Low complexity MDQ is further explored and used to build a multiple description audio coder. Next, the advantages of employing multiple description coding over multiple-input multiple-output wireless channels are investigated. Information theoretical analysis is conducted and practical MDQ codes are designed. Finally, a new E-model based performance measure accounting for both rate-distortion performance and delay impairment is proposed to compare multiple description coding and layered coding for communication over packet networks. / Thesis (Ph.D, Electrical & Computer Engineering) -- Queen's University, 2007-09-28 15:07:27.322

The rapid adoption of the internet has occurred despite the lack of a ubiquitous identity meta-system. The status quo is a patchwork of proprietary security systems. A number of security issues have arisen as a result which threaten to lead to a loss of trust in the internet, and may limit the scope of applications built on it; effectively constraining the potential of the internet as a platform for business and services. Current initiatives by a broad consortium of industry leaders promise a vastly improved landscape with a set of interoperable protocols and systems, built on open specifications, and guided by a set of core identity principles, enabling a more secure online experience. Simultaneously there have arisen a large number of location aware web application and services which detect and use a user’s location to enhance their application experience. These advances, although useful, present new security and privacy issues. This paper investigates the operation of one of the new identity technologies, information cards, and proposes extensions to the existing supported schemas to incorporate recent advances in geo-location technology. The proposal is supported by reference to existing o pen source implementations.

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