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A New Unsupervised Feature Ranking Method for Gene Expression Data Based on Consensus Affinity

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4 Author(s)
Shaohong Zhang ; Dept. of Comput. Sci., Guangzhou Univ., Guangzhou, China ; Hau-San Wong ; Ying Shen ; Dongqing Xie

Feature selection is widely established as one of the fundamental computational techniques in mining microarray data. Due to the lack of categorized information in practice, unsupervised feature selection is more practically important but correspondingly more difficult. Motivated by the cluster ensemble techniques, which combine multiple clustering solutions into a consensus solution of higher accuracy and stability, recent efforts in unsupervised feature selection proposed to use these consensus solutions as oracles. However, these methods are dependent on both the particular cluster ensemble algorithm used and the knowledge of the true cluster number. These methods will be unsuitable when the true cluster number is not available, which is common in practice. In view of the above problems, a new unsupervised feature ranking method is proposed to evaluate the importance of the features based on consensus affinity. Different from previous works, our method compares the corresponding affinity of each feature between a pair of instances based on the consensus matrix of clustering solutions. As a result, our method alleviates the need to know the true number of clusters and the dependence on particular cluster ensemble approaches as in previous works. Experiments on real gene expression data sets demonstrate significant improvement of the feature ranking results when compared to several state-of-the-art techniques.

Published in:

Computational Biology and Bioinformatics, IEEE/ACM Transactions on  (Volume:9 ,  Issue: 4 )