title: Biomarker discovery across annotated and unannotated microarray datasets using semi-supervised learning.
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.
authors.affiliation: Exagen Diagnostics, Inc, Houston, TX, USA. charris@exagen.com
authors.forename: Cole
authors.initials: C
authors.lastname: Harris
authors.forename: Noushin
authors.initials: N
authors.lastname: Ghaffari
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D014408:Biomarkers, Tumor; D016000:Cluster Analysis; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D008954:Models, Biological; D009369:Neoplasms / Q000145:classification; D020411:Oligonucleotide Array Sequence Analysis; D010363:Pattern Recognition, Automated / Q000379:methods*
chemical_list: D014408:Biomarkers, Tumor