Peptide-based hidden Markov model for peptide fingerprint mapping.

Peptide-based hidden Markov model for peptide fingerprint mapping.

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Date: December 2004
Creator: Yang, Dongmei
Description: Peptide mass fingerprinting (PMF) was the first automated method for protein identification in proteomics, and it remains in common usage today because of its simplicity and the low equipment costs for generating fingerprints. However, one of the problems with PMF is its limited specificity and sensitivity in protein identification. Here I present a method that shows potential to significantly enhance the accuracy of peptide mass fingerprinting, using a machine learning approach based on a hidden Markov model (HMM). This method is applied to improve differentiation of real protein matches from those that occur by chance. The system was trained using 300 examples of combined real and false-positive protein identification results, and 10-fold cross-validation applied to assess model discrimination. The model can achieve 93% accuracy in distinguishing correct and real protein identification results versus false-positive matches. The receiver operating characteristic (ROC) curve area for the best model was 0.833.
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Mediation on XQuery Views

Mediation on XQuery Views

Date: December 2006
Creator: Peng, Xiaobo
Description: The major goal of information integration is to provide efficient and easy-to-use access to multiple heterogeneous data sources with a single query. At the same time, one of the current trends is to use standard technologies for implementing solutions to complex software problems. In this dissertation, I used XML and XQuery as the standard technologies and have developed an extended projection algorithm to provide a solution to the information integration problem. In order to demonstrate my solution, I implemented a prototype mediation system called Omphalos based on XML related technologies. The dissertation describes the architecture of the system, its metadata, and the process it uses to answer queries. The system uses XQuery expressions (termed metaqueries) to capture complex mappings between global schemas and data source schemas. The system then applies these metaqueries in order to rewrite a user query on a virtual global database (representing the integrated view of the heterogeneous data sources) to a query (termed an outsourced query) on the real data sources. An extended XML document projection algorithm was developed to increase the efficiency of selecting the relevant subset of data from an individual data source to answer the user query. The system applies the projection algorithm ...
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Analysis of Web Services on J2EE Application Servers

Analysis of Web Services on J2EE Application Servers

Date: May 2004
Creator: Gosu, Adarsh Kumar
Description: The Internet became a standard way of exchanging business data between B2B and B2C applications and with this came the need for providing various services on the web instead of just static text and images. Web services are a new type of services offered via the web that aid in the creation of globally distributed applications. Web services are enhanced e-business applications that are easier to advertise and easier to discover on the Internet because of their flexibility and uniformity. In a real life scenario it is highly difficult to decide which J2EE application server to go for when deploying a enterprise web service. This thesis analyzes the various ways by which web services can be developed & deployed. Underlying protocols and crucial issues like EAI (enterprise application integration), asynchronous messaging, Registry tModel architecture etc have been considered in this research. This paper presents a report by analyzing what various J2EE application servers provide by doing a case study and by developing applications to test functionality.
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A Netcentric Scientific Research Repository

A Netcentric Scientific Research Repository

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Date: December 2006
Creator: Harrington, Brian
Description: The Internet and networks in general have become essential tools for disseminating in-formation. Search engines have become the predominant means of finding information on the Web and all other data repositories, including local resources. Domain scientists regularly acquire and analyze images generated by equipment such as microscopes and cameras, resulting in complex image files that need to be managed in a convenient manner. This type of integrated environment has been recently termed a netcentric sci-entific research repository. I developed a number of data manipulation tools that allow researchers to manage their information more effectively in a netcentric environment. The specific contributions are: (1) A unique interface for management of data including files and relational databases. A wrapper for relational databases was developed so that the data can be indexed and searched using traditional search engines. This approach allows data in databases to be searched with the same interface as other data. Fur-thermore, this approach makes it easier for scientists to work with their data if they are not familiar with SQL. (2) A Web services based architecture for integrating analysis op-erations into a repository. This technique allows the system to leverage the large num-ber of existing tools by wrapping them ...
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Adaptive planning and prediction in agent-supported distributed collaboration.

Adaptive planning and prediction in agent-supported distributed collaboration.

Date: December 2004
Creator: Hartness, Ken T. N.
Description: Agents that act as user assistants will become invaluable as the number of information sources continue to proliferate. Such agents can support the work of users by learning to automate time-consuming tasks and filter information to manageable levels. Although considerable advances have been made in this area, it remains a fertile area for further development. One application of agents under careful scrutiny is the automated negotiation of conflicts between different user's needs and desires. Many techniques require explicit user models in order to function. This dissertation explores a technique for dynamically constructing user models and the impact of using them to anticipate the need for negotiation. Negotiation is reduced by including an advising aspect to the agent that can use this anticipation of conflict to adjust user behavior.
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Automatic Tagging of Communication Data

Automatic Tagging of Communication Data

Date: August 2012
Creator: Hoyt, Matthew Ray
Description: Globally distributed software teams are widespread throughout industry. But finding reliable methods that can properly assess a team's activities is a real challenge. Methods such as surveys and manual coding of activities are too time consuming and are often unreliable. Recent advances in information retrieval and linguistics, however, suggest that automated and/or semi-automated text classification algorithms could be an effective way of finding differences in the communication patterns among individuals and groups. Communication among group members is frequent and generates a significant amount of data. Thus having a web-based tool that can automatically analyze the communication patterns among global software teams could lead to a better understanding of group performance. The goal of this thesis, therefore, is to compare automatic and semi-automatic measures of communication and evaluate their effectiveness in classifying different types of group activities that occur within a global software development project. In order to achieve this goal, we developed a web-based component that can be used to help clean and classify communication activities. The component was then used to compare different automated text classification techniques on various group activities to determine their effectiveness in correctly classifying data from a global software development team project.
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A Pattern Oriented Data Structure for Interactive Computer Music

A Pattern Oriented Data Structure for Interactive Computer Music

Date: May 2011
Creator: Lockhart, Adam
Description: This essay describes a pattern oriented data structure, or PODS, as a system for storing computer music data. It organizes input by sequences or patterns that recur, while extensively interlinking the data. The interlinking process emulates cognitive models, while the pattern processing draws specifically from music cognition. The project aims at creating open source external objects for the Max/MSP software environment. The computer code for this project is in the C and Objective-C computer programming languages.
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Investigating the Extractive Summarization of Literary Novels

Investigating the Extractive Summarization of Literary Novels

Date: December 2011
Creator: Ceylan, Hakan
Description: Abstract Due to the vast amount of information we are faced with, summarization has become a critical necessity of everyday human life. Given that a large fraction of the electronic documents available online and elsewhere consist of short texts such as Web pages, news articles, scientific reports, and others, the focus of natural language processing techniques to date has been on the automation of methods targeting short documents. We are witnessing however a change: an increasingly larger number of books become available in electronic format. This means that the need for language processing techniques able to handle very large documents such as books is becoming increasingly important. This thesis addresses the problem of summarization of novels, which are long and complex literary narratives. While there is a significant body of research that has been carried out on the task of automatic text summarization, most of this work has been concerned with the summarization of short documents, with a particular focus on news stories. However, novels are different in both length and genre, and consequently different summarization techniques are required. This thesis attempts to close this gap by analyzing a new domain for summarization, and by building unsupervised and supervised systems ...
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Ocean of Forms: for Soprano and Computer

Ocean of Forms: for Soprano and Computer

Date: May 2012
Creator: Price, Lee Scott
Description: Ocean of Forms is a cycle of five songs for solo soprano voice and electronic/computer music accompaniment on poems by noted Bengali poet, musician, philosopher, and author Rabindranath Tagore. This work approaches the song cycle as a vehicle for expressing and highlighting the poet's words. Word and syllabic stress, text painting, melodic development, and formal structure all function in relation to the text and its meaning. the replacement of the traditional piano accompaniment with electronic accompaniment provides further possibilities for new timbral structures and transformations, expressive microtonal intonation, algorithmic and aleatoric formal structures, acousmatic and spatialized sound, and a broad sonic palette. This work strives to provide a more fully developed expression of the text as afforded by these expanded musical means. the critical essay primarily explores the interaction between text and music in the work. the first chapter explores the historical precedents for the genre of the song cycle and other texted music as well as specific influences on the work. the following chapters explore the connections between the text and the vocal line and electronic/computer music, respectively. the final chapter deals with the formal structure of the work, especially the justly-tuned harmonic scheme and its relation to the ...
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The Impact of Predisposition Towards Group Work on Intention to Use a CSCW System

The Impact of Predisposition Towards Group Work on Intention to Use a CSCW System

Date: May 2005
Creator: Reyna, Josephine
Description: Groupware packages are increasingly being used to support content delivery, class discussion, student to student and student to faculty interactions and group work on projects. This research focused on groupware packages that are used to support students who are located in different places, but who are assigned group projects as part of their coursework requirements. In many cases, students are being asked to use unfamiliar technologies that are very different from those that support personal productivity. For example, computer-assisted cooperative work (CSCW) technology is different from other more traditional, stand-alone software applications because it requires the user to interact with the computer as well as other users. However, familiarity with the technology is not the only requirement for successful completion of a group assigned project. For a group to be successful, it must also have a desire to work together on the project. If this pre-requisite is not present within the group, then the technology will only create additional communication and coordination barriers. How much of an impact does each of these factors have on the acceptance of CSCW technology? The significance of this study is threefold. First, this research contributed to how a user's predisposition toward group work affects ...
Contributing Partner: UNT Libraries
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