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Simple and Effective Visual Models for Gene Expression Cancer Diagnostics

Gregor Leban and Minca Mramor and Ivan Bratko and Blaz Zupan (2005) Simple and Effective Visual Models for Gene Expression Cancer Diagnostics. In: ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, August 21-24, 2005, Chicago, IL, USA.

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    In the paper we show that diagnostic classes in cancer gene expression data sets, which most often include thousands of features (genes), may be effectively separated with simple two-dimensional plots such as scatterplot and radviz graph. The principal innovation proposed in the paper is a method called VizRank, which is able to score and identify the best among possibly millions of candidate projections for visualizations. Compared to recently much applied techniques in the field of cancer genomics that include neural networks, support vector machines and various ensemble-based approaches, VizRank is fast and finds visualization models that can be easily examined and interpreted by domain experts. Our experiments on a number of gene expression data sets show that VizRank was always able to find data visualizations with a small number of (two to seven) genes and excellent class separation. In addition to providing grounds for gene expression cancer diagnosis, VizRank and its visualizations also identify small sets of relevant genes, uncover interesting gene interactions and point to outliers and potential misclassifications in cancer data sets.

    Item Type: Conference or Workshop Item (Paper)
    Keywords: Gene Expression Analysis, Cancer Diagnosis, Machine Learning, Data Mining, Data Visualization
    Language of Content: English
    Related URLs:
    URLURL Type
    http://www.cobiss.si/scripts/cobiss?command=search&base=50070&select=(id=4939604)Alternative location
    Institution: University of Ljubljana
    Department: Faculty of Computer and Information Science
    Divisions: Faculty of Computer and Information Science > Artificial Intelligence Laboratory
    Item ID: 211
    Date Deposited: 09 Jun 2006
    Last Modified: 06 Dec 2013 11:35
    URI: http://eprints.fri.uni-lj.si/id/eprint/211

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