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Predicting breast cancer using an expression values weighted clinical classifier
BMC Bioinformatics
  • Minta Thomas, KU Leuven
  • Kris De Brabanter, Iowa State University
  • Johan AK Suykens, KU Leuven
  • Bart De Moor, KU Leuven
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Background: Clinical data, such as patient history, laboratory analysis, ultrasound parameters-which are the basis of day-to-day clinical decision support-are often used to guide the clinical management of cancer in the presence of microarray data. Several data fusion techniques are available to integrate genomics or proteomics data, but only a few studies have created a single prediction model using both gene expression and clinical data. These studies often remain inconclusive regarding an obtained improvement in prediction performance. To improve clinical management, these data should be fully exploited. This requires efficient algorithms to integrate these data sets and design a final classifier. Results: We compared and evaluated the proposed methods on five breast cancer case studies. Compared to LS-SVM classifier on individual data sets, generalized eigenvalue decomposition (GEVD) and kernel GEVD, the proposed weighted LS-SVM classifier offers good prediction performance, in terms of test area under ROC Curve (AUC), on all breast cancer case studies. Conclusions: Thus a clinical classifier weighted with microarray data set results in significantly improved diagnosis, prognosis and prediction responses to therapy. The proposed model has been shown as a promising mathematical framework in both data fusion and non-linear classification problems.

This article is from BMC Bioinformatics 15 (2014): article no. 411, doi: 10.1186/s12859-014-0411-1. Posted with permission.

Copyright 2014 Thomas et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Thomas et al
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Minta Thomas, Kris De Brabanter, Johan AK Suykens and Bart De Moor. "Predicting breast cancer using an expression values weighted clinical classifier" BMC Bioinformatics Vol. 15 Iss. 1 (2014) p. 411
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