Balanced Supervised Non-Negative Matrix Factorization for Childhood Leukaemia Patients

Supervised feature extraction methods have received considerable attention in the data mining community due to their capability to improve the classification performance of the unsupervised dimensionality reduction methods. With increasing dimensionality, several methods based on supervised feature extraction are proposed to achieve a feature ranking especially on microarray gene expression data. This paper proposes a method with twofold objectives: it implements a balanced supervised non-negative matrix factorization (BSNMF) to handle the class imbalance problem in supervised non-negative matrix factorization techniques. Furthermore, it proposes an accurate gene ranking method based on our proposed BSNMF for microarray gene expression datasets. To the best of our knowledge, this is the first work to handle the class imbalance problem in supervised feature extraction methods. This work is part of a Human Genome project at The Children's Hospital at Westmead (TB-CHW), Australia. Our experiments indicate that the factorized components using supervised feature extraction approach have more classification capability than the unsupervised one, but it drastically fails at the presence of class imbalance problem. Our proposed method outperforms the state-of-the-art methods and shows promise in overcoming this concern.