Abstract
We propose an effective Recursive Feature Elimination based on Linear Discriminant Analysis (RFELDA) method for gene selection and classification of diseases obtained from DNA microarray technology. LDA is proposed not only as an LDA classifier, but also as an LDA’s discriminant coefficients to obtain ranks for each gene. The performance of the proposed algorithm was tested against four well-known datasets from the literature and compared with recent state of the art algorithms. The experiment results on these datasets show that RFELDA outperforms similar methods reported in the literature, and obtains high classification accuracies with a relatively small number of genes.
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References
Alon, U., Barkai, N., et al.: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Nat. Acad. Sci. USA (1999)
Alizadeh, A., Eisen, M.B., et al.: Distinct types of diffuse large (b)–cell lymphoma identified by gene expression profiling. Nature, 503–511 (2000)
Golub, T., Slonim, D., et al.: Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 537, 286 (1999)
Dudoit, S., Fridlyand, J., Speed, T.: Comparison of discrimination methods for the classification of tumors using gene expression data. Journal of the American Statistical Association 97, 77–87 (2002)
Ye, J., Li, T., Xiong, T., Janardan, R.: Using uncorrelated discriminant analysis for tissue classification with gene expression data. IEEE/ACM Trans. Comput. 1(4), 181–190 (2004)
Yue, F., Wang, K., Zuo, W.: Informative gene selection and tumor classification by null space LDA for microarray data. In: Chen, B., Paterson, M., Zhang, G. (eds.) ESCAPE 2007. LNCS, vol. 4614, pp. 435–446. Springer, Heidelberg (2007)
Guyon, I., Weston, J., Barnhill, S., Vapnik, V.: Gene selection for cancer classification using support vector machines. Machine Learning 46(1-3), 389–422 (2002)
Tang, Y., Zhang, Y.-Q., Huang, Z.: Fcmsv- rfe gene feature selection algorithm for leukemia classification from microarray gene expression data. In: IEEE International Conference on Fuzzy Systems, pp. 97–10 (2005)
Luo, L.-K., Feng, D., Ye, L.-J., Zhou, Q.-F., Shao, G.-F., Peng, H.: Improving the computational efficiency of recursive cluster elimination for gene selection. IEEE/ACMTransactions on Computational Biology and Bioinformatics 8(1), 122–129 (2011)
Liu, Q., Sung, H.: Gene selection and classification for cancer microarray data based on machine learning and similarity measures. BMC Genomics 12(5), 1–12 (2011)
Yang, F., Mao, K.: Robust feature selection for microarray based on multicreterion fusion. IEEE/ACMTrans. Comput. Biology 8(4), 1080–1092 (2011)
Li, Z., Zeng, X.-Q., Yang, J.-Y., Yang, M.-Q.: Partial Least Squares based dimension reduction with gene selection for tumor classification. In: BIBE 2007, pp. 1439–1444 (2007)
Deng, L., Pei, J., Ma, J., Lee, D.L.: Rank sum test method for informative gene discovery. In: 10th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2004), pp. 410–419 (2004)
Mishra, D., Sahu, B.: Feature selection for cancer classification: A signal-to-noise ratio approach. International Journal of Scientific & Engineering Research 2(4), 1–7 (2011)
Pomeroy, S.-L., Tamayo, P., et al.: Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415, 436–442 (2002)
Singh, D., Febbo, P., Ross, K., Jackson, D., Manola, J., Ladd, C., Tamayo, P., Renshaw, A., D’Amico, A., Richie, J.: Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 1, 203–209 (2002)
Cho, S.-B., Won, H.-H.: Cancer classification using ensemble of neural networks with multiple significant gene subsets. Applied Intelligence 26(3), 243–250 (2007)
Li, S., Wu, X., Hu, X.: Gene selection using genetic algorithm and support vectors machines. Soft Computing 12(7), 693–698 (2008)
Alba, E., García-Nieto, J., Jourdan, L., Talbi, E.-G.: Gene selection in cancer classification using PSO/SVM and GA/SVM hybrid algorithms. In: Congress on Evolutionary Computation, pages, pp. 284–290 (2007)
Satoshi, N., Okuno, Y.: Lapalacian linear discriminant analysis to unsupervised feature selection. IEEE/Transactions on Biology and Bioinformatics 6(4), 605–614 (2009)
Li, X., Peng, S., Zhan, X., Zhang, J., Xu, Y.: Comparison of feature selection methods for multiclass cancer classification based on microarray data. In: 4th International Conference on Biomedical Engineering and Informatics (BMEI), pp. 1692–1696 (2011)
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Huerta, E.B., Caporal, R.M., Arjona, M.A., Hernández, J.C.H. (2013). Recursive Feature Elimination Based on Linear Discriminant Analysis for Molecular Selection and Classification of Diseases. In: Huang, DS., Jo, KH., Zhou, YQ., Han, K. (eds) Intelligent Computing Theories and Technology. ICIC 2013. Lecture Notes in Computer Science(), vol 7996. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39482-9_28
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DOI: https://doi.org/10.1007/978-3-642-39482-9_28
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