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Rank-based classifiers for extremely high-dimensional gene expression data

Author

Listed:
  • Ludwig Lausser

    (Ulm University)

  • Florian Schmid

    (Ulm University)

  • Lyn-Rouven Schirra

    (Ulm University
    Ulm University)

  • Adalbert F. X. Wilhelm

    (Jacobs University)

  • Hans A. Kestler

    (Ulm University
    Leibniz Institute on Aging–Fritz Lipmann Institute)

Abstract

Predicting phenotypes on the basis of gene expression profiles is a classification task that is becoming increasingly important in the field of precision medicine. Although these expression signals are real-valued, it is questionable if they can be analyzed on an interval scale. As with many biological signals their influence on e.g. protein levels is usually non-linear and thus can be misinterpreted. In this article we study gene expression profiles with up to 54,000 dimensions. We analyze these measurements on an ordinal scale by replacing the real-valued profiles by their ranks. This type of rank transformation can be used for the construction of invariant classifiers that are not affected by noise induced by data transformations which can occur in the measurement setup. Our 10 $$\times $$ × 10 fold cross-validation experiments on 86 different data sets and 19 different classification models indicate that classifiers largely benefit from this transformation. Especially random forests and support vector machines achieve improved classification results on a significant majority of datasets.

Suggested Citation

  • Ludwig Lausser & Florian Schmid & Lyn-Rouven Schirra & Adalbert F. X. Wilhelm & Hans A. Kestler, 2018. "Rank-based classifiers for extremely high-dimensional gene expression data," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 12(4), pages 917-936, December.
    • Handle: RePEc:spr:advdac:v:12:y:2018:i:4:d:10.1007_s11634-016-0277-3
    DOI: 10.1007/s11634-016-0277-3
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    References listed on IDEAS

    as
    1. Adrien Jamain & David Hand, 2009. "Where are the large and difficult datasets?," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 3(1), pages 25-38, June.
    2. Hans Kestler & Ludwig Lausser & Wolfgang Lindner & Günther Palm, 2011. "On the fusion of threshold classifiers for categorization and dimensionality reduction," Computational Statistics, Springer, vol. 26(2), pages 321-340, June.
    3. Müssel, Christoph & Lausser, Ludwig & Maucher, Markus & Kestler, Hans A., 2012. "Multi-Objective Parameter Selection for Classifiers," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 46(i05).
    4. François Bavaud, 2009. "Aggregation invariance in general clustering approaches," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 3(3), pages 205-225, December.
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