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The Influence of Multi-class Feature Selection on the Prediction of Diagnostic Phenotypes

  • Ludwig Lausser
  • Robin Szekely
  • Lyn-Rouven Schirra
  • Hans A. Kestler
Article

Abstract

In this work, we evaluate two schemes for incorporating feature selection processes in multi-class classifier systems on high-dimensional data of low cardinality. These schemes operate on the level of the systems’ individual base classifiers and therefore do not perfectly fit in the traditional categories of filter, wrapper and embedded feature selection strategies. They can be seen as two examples of feature selection networks that are only loosely related to the structure of the multi-class classifier system. The architectures are tested for their application in predicting diagnostic phenotypes from gene expression profiles. Their selection stability and the overall generalization ability are evaluated in \(10 \times 10\) cross-validation experiments with support vector machines, random forests and nearest neighbor classifiers on eight publicly available multi-class microarray datasets. Overall the feature selecting multi-class classifier systems were able to outperform their counterparts on at least five of eight datasets.

Keywords

Multi-class classification Classifier fusion Feature selection High-dimensional data Low cardinality 

Notes

Acknowledgements

The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under Grant Agreement No. 602783, the German Research Foundation (DFG, SFB 1074 project Z1), and the Federal Ministry of Education and Research (BMBF, Gerontosys II, Forschungskern SyStaR, ID 0315894A and e:Med, SYMBOL-HF, ID 01ZX1407A) all to HAK.

Supplementary material

11063_2017_9706_MOESM1_ESM.pdf (1.3 mb)
Supplementary material 1 (pdf 1326 KB)

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Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  1. 1.Institute of Medical Systems BiologyUlm UniversityUlmGermany
  2. 2.Institute of Number Theory and Probability TheoryUlm UniversityUlmGermany
  3. 3.Leibniz Institute on Aging – Fritz Lipmann InstituteJenaGermany

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