Computer Engineering Commons^™

A Hierarchical Framework For Phylogenetic And Ancestral Genome Reconstruction On Whole Genome Data, Lingxi Zhou

Theses and Dissertations

Gene order gets evolved under events such as rearrangements, duplications, and losses, which can change both the order and content along the genome, through the long history of genome evolution. Recently, the accumulation of genomic sequences provides researchers with the chance to handle long-standing problems about the phylogenies, or evolutionary histories, of sets of species, and ancestral genomic content and orders. Over the past few years, such problems have been proven so interesting that a large number of algorithms have been proposed in the attempt to resolve them, following different standards. The work presented in this dissertation focuses on algorithms …

Hydro-Geological Flow Analysis Using Hidden Markov Models, Chandrahas Raj Venkat Gurram

Theses and Dissertations

Hidden Markov Models a class of statistical models used in various disciplines for understanding speech, finding different types of genes responsible for cancer and much more. In this thesis, Hidden Markov Models are used to obtain hidden states that can correlate the flow changes in the Wakulla Spring Cave. Sensors installed in the tunnels of Wakulla Spring Cave have recorded huge correlated changes in the water flows at numerous tunnels. Assuming the correlated flow changes are a consequence of system being in a set of discrete states, a Hidden Markov Model is calculated. This model comprising all the sensors installed …

Revealing Malicious Contents Hidden In The Internet, Muhammad Nazmus Sakib

Theses and Dissertations

In this age of ubiquitous communication in which we can stay constantly connected with the rest of the world, for most of the part, we have to be grateful for one particular invention - the Internet. But as the popularity of Internet connectivity grows, it has become a very dangerous place where objects of malicious content and intent can be hidden in plain sight. In this dissertation, we investigate different ways to detect and capture these malicious contents hidden in the Internet. First, we propose an automated system that mimics high-risk browsing activities such as clicking on suspicious online ads, …

Regular Expression Synthesis For Blast Two-Hit Filtering, Jordan Bradshaw

Theses and Dissertations

Genomic databases are exhibiting a growth rate that is outpacing Moore's Law, which has made database search algorithms a popular application for use on emerging processor technologies. NCBI BLAST is the standard tool for performing searches against these databases, which operates by transforming each database query into a filter that is subsequently applied to the database. This requires a database scan for every query, fundamentally limiting its performance by I/O bandwidth. In this dissertation we present a functionally-equivalent variation on the NCBI BLAST algorithm that maps more suitably to an FPGA implementation. This variation of the algorithm attempts to reduce …

Efficient Partitioning And Allocation Of Data For Workflow Compositions, Annamaria Victoria Kish

Theses and Dissertations

Our aim is to provide efficient partitioning and allocation of data for web service compositions. Web service compositions are represented as partial order database transactions. We accommodate a variety of transaction types, such as read-only and write-oriented transactions, to support workloads in cloud environments. We introduce an approach that partitions and allocates small units of data, called micropartitions, to multiple database nodes. Each database node stores only the data needed to support a specific workload. Transactions are routed directly to the appropriate data nodes. Our approach guarantees serializability and efficient execution.

In Phase 1, we cluster transactions based on data …

Positioning Commuters And Shoppers Through Sensing And Correlation, Rufeng Meng

Theses and Dissertations

Positioning is a basic and important need in many scenarios of human daily activities. With position information, multifarious services could be vitalized to benefit all kinds of users, from individuals to organizations. Through positioning, people are able to obtain not only geo-location but also time related information. By aggregating position information from individuals, organizations could derive statistical knowledge about group behaviors, such as traffic, business, event, etc.

Although enormous effort has been invested in positioning related academic and industrial work, there are still many holes to be filled. This dissertation proposes solutions to address the need of positioning in people’s …