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This article is part of the supplement: IEEE 7th International Conference on Bioinformatics and Bioengineering at Harvard Medical School

Open Access Research

Biomarker discovery across annotated and unannotated microarray datasets using semi-supervised learning

Cole Harris1* and Noushin Ghaffari12

Author affiliations

1 Exagen Diagnostics, Inc. Houston, TX, USA

2 Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA

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Citation and License

BMC Genomics 2008, 9(Suppl 2):S7  doi:10.1186/1471-2164-9-S2-S7

Published: 16 September 2008

Abstract

The growing body of DNA microarray data has the potential to advance our understanding of the molecular basis of disease. However annotating microarray datasets with clinically useful information is not always possible, as this often requires access to detailed patient records. In this study we introduce GLAD, a new Semi-Supervised Learning (SSL) method for combining independent annotated datasets and unannotated datasets with the aim of identifying more robust sample classifiers.

In our method, independent models are developed using subsets of genes for the annotated and unannotated datasets. These models are evaluated according to a scoring function that incorporates terms for classification accuracy on annotated data, and relative cluster separation in unannotated data. Improved models are iteratively generated using a genetic algorithm feature selection technique.

Our results show that the addition of unannotated data into training, significantly improves classifier robustness.