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Browsing Math & Computer Science by Author "Lu, Zhiyong"

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    Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations
    (Oxford University Press, 2004) Szafron, Duane; Lu, Paul; Greiner, Russell; Wishart, David S.; Poulin, Brett; Eisner, Roman; Lu, Zhiyong; Anvik, John; Macdonell, Cam; Fyshe, Alona; Meeuwis, David
    Proteome Analyst (PA) (http://www.cs.ualberta.ca/~bioinfo/PA/) is a publicly available, high-throughput, web-based system for predicting various properties of each protein in an entire proteome. Using machine-learned classifiers, PA can predict, for example, the GeneQuiz general function and Gene Ontology (GO) molecular function of a protein. In addition, PA is currently the most accurate and most comprehensive system for predicting subcellular localization, the location within a cell where a protein performs its main function. Two other capabilities of PA are notable. First, PA can create a custom classifier to predict a new property, without requiring any programming, based on labeled training data (i.e. a set of examples, each with the correct classification label) provided by a user. PA has been used to create custom classifiers for potassium-ion channel proteins and other general function ontologies. Second, PA provides a sophisticated explanation feature that shows why one prediction is chosen over another. The PA system produces a Naïve Bayes classifier, which is amenable to a graphical and interactive approach to explanations for its predictions; transparent predictions increase the user's confidence in, and understanding of, PA.