吉林大学学报(工学版) ›› 2013, Vol. 43 ›› Issue (01): 192-197.

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Tumor gene selection based on double regularized support vector machine

QIN Chuan-dong1,2, LIU San-yang3   

  1. 1. School of Computer Seience and Technology, Xidian University, Xi'an 710071, China;
    2. School of Information and Computation Science, Beifang University of Nationalities, Yinchuan 750021, China;
    3. College of Mathematic Science, Xidian University, Xi'an 710071, China
  • Received:2011-07-26 Online:2013-01-01 Published:2013-01-01

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Abstract: According to the strengths and weaknesses of the L2-norm Support Vector Machine (SVM) and the L1-norm SVM in the classification analysis of cancer gene, a Doubly Regularized Support Vector Machine (DRSVM) is applied to the DNA microarray classification based on the Bhattacharyya distance, which is used to eliminate most of the unimportant genes and gain a few highly correlated important genes for classification. A quadratic polynomial loss function changes the constrained optimization into unconstrained and differentiable optimization, which can be computed by Brogden-Fltcher-Goldfarb-Shanno (BFGS) algorithm. Experiment results on two kinds of tumor gene data sets show that this method is effective and feasible.

Key words: computer application, gene expression profiles, Bhattacharyya distance, doubly regularized support vector machine, quadratic polynomial loss function, BFGS algorithm

CLC Number: 

  • TP391
[1] Ramaswamy S, Golub T R. DNA micr oar rays in clinical oncology[J]. Journal of Clinical on Cology, 2002, 20(7): 1932-1941.

[2] Wang Y, Makedon F, Ford J C,et al. Hygiene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data[J]. Bioinformatics,2005, 21(8):1530-1537.

[3] 于化龙,顾国昌,赵靖,等. 基于DNA微阵列数据的特征子空间集成分类[J]. 吉林大学学报:工学版,2011,41(4):1071-1076. Yu Hua-long,Gu Guo-chang,Zhao Jing et al. Feature subspace ensemble classification based on DNA microarray data[J]. Joural of Jilin University (Engineering and Technolog Edition),2011,41(4): 1071-1076.

[4] Cho Sung-Bae, Won Hong-Hee. Machine learning in DNA microarray analysis for cancer classification//Proceedings of the First Asia Pacific Bioinformatics Conference on Bioinformatics, 2003: 189-198.

[5] 李建中,杨昆,高宏,等. 考虑样本不均衡的模型无关的基因选择方法[J]. 软件学报,2006,17(7):1485-1493. Li Jian-zhong,Yang Kun,Gao Hong,et al. Model-free gene selection method by considering unbalanced samples[J]. Journal of Software 2006,17(7):1485-1493.

[6] 李颖新,阮晓钢. 基于支持向量机的肿瘤分类特征基因选取[J]. 计算机研究与发展,2005,42(10): 1796-1801. Li Ying-xin,Ruan Xiao-gang. Feature selection for cancer classification based on support vector machine[J]. Journal of Computer Research and Development,2005,42(10): 1796-1801.

[7] Guyon Isabelle, Weston Jason, Barnhill Stephen, et al. Gene selection for cancer classification using support vector machines[J]. Mach Learn, 2002, 46:389-422.

[8] Zhu J, Rosset S, Hastie T, et al. 1-norm support vector machines//Advances in Neural Information Processing Systems 16, New York: MIT Press, 2004:49-56.

[9] 李颖新,刘全金,阮晓钢. 一种肿瘤基因表达数据的知识提取方法[J]. 电子学报,2004,32(9):1479-1482. Li Ying-xin, Liu Quan-jin,Ruan Xiao-gang. A method for extracting knowledge from tumor gene expression data[J]. Acta Electronica Sinica, 2004,32(9):1479-1482.

[10] 边肇祺,张学工. 模式识别[M]. 2版.北京:清华大学出版社,2000.

[11] Bradley P, Mangasarian O. Feature selection via concave minimization and support vector machines//Proceedings of the 15th International Conference on Machine Learning,1998.

[12] Wang Li, Zhu Ji, Zou Hui. Hybrid huberized support vector machines for microarray classification and gene selection[J]. Data and Text Mining,2008, 24(3):412-419.

[13] Li Jun-tao, Jia Ying-min. An improved elastic net for cancer classification and gene selection[J]. Acta Automatica Sinica, 2010,36(7):976-981.

[14] 袁玉波,严杰, 徐成贤. 多项式光滑的支撑向量机[J]. 计算机学报,2005, 28 (1):9-17. Yuan Yu-bo,Yan Jie,Xu Cheng-xian. Polynomial smooth support vector machine[J]. Chinese Journal of Computers,2005, 28 (1):9-17.

[15] 陈宝林. 最优化理论与算法[M]. 北京:清华大学出版社,2005:314-315.

[16] Massachusetts Institute of Technology... http://www.broad.mit.edu/cgi-bin/cancer/datasets.

[17] Princeton University...http://www.molbio.princeton.edu/colondata.

[18] Tatsuta M, Iishi H, Baba M, et al. Attenuation of vasoactive intestinal peptide enhancement of colon carcinogenesis by ornithine decarboxylase inhibitor[J]. Cancer Lett, 1995, 93(2): 219-225.

[19] Yang Ai-jun, Song Xin-yuan. Bayesian variable selection for disease classification using gene expression data[J]. Bioinformatics, 2010,26(2): 215-222.

[20] Simmons D, Seed B. Isolation of a cDNA encoding CD33, a differentiation antigen of myeloid progenitor cells[J]. Journal of Immunology, 1988, 141(8):2797-2800.

[21] Sounak Chakrabortya, Ruixin Guob. A Bayesian hybrid Huberized support vector machine and its applications in high-dimensional medical data[J]. Computational Statistics and Data Analysis, 2011,55: 1342-1356.
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