Citation: DAI Zhi-Jun, ZHOU Wei, YUAN Zhe-Ming. A Novel Method of Nonlinear Rapid Feature Selection for High Dimensional Data and Its Application in Peptide QSAR Modeling Based on Support Vector Machine[J]. Acta Physico-Chimica Sinica, ;2011, 27(07): 1654-1660. doi: 10.3866/PKU.WHXB20110735 shu

A Novel Method of Nonlinear Rapid Feature Selection for High Dimensional Data and Its Application in Peptide QSAR Modeling Based on Support Vector Machine

DAI Zhi-Jun ^1,2 ,
ZHOU Wei ¹ ,
YUAN Zhe-Ming ^1,2,

1.
1. College of Bio-safety Science and Technology, Hunan Agricultural University, Changsha 410128, P. R. China;
2. Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Changsha 410128, P. R. China

Received Date: 24 March 2011
Available Online: 3 June 2011
Fund Project: 湖南省杰出青年科学基金(10JJ1005) (10JJ1005) 高等学校博士点基金(200805370002) (200805370002)

Each amino acid residue of one peptide was characterized directly by 531 physicochemical property parameters. Based on support vector regression (SVR) we developed a new nonlinear rapid feature selection method for high dimensional data, which was applied to a quantitative sequence- activity relationship (QSAR) study of two peptide systems (bitter tasting thresholds and angiotensin converting enzyme inhibitors). In both systems, 10 descriptors with clear meaning were reserved. We established a SVR model for both peptide systems using the reserved descriptors of the peptides. For both models the accuracies of fitting, the leave-one-out cross validation, and the external prediction improved significantly compared with the results reported in literature. To enhance the interpretability of the models, significance tests of the nonlinear regression model, single-factor relative importance, and a single-factor effect analysis were carried out. The new method has broad application prospects for regression forecasting of high dimensional data such as QSAR modeling of peptide or proteins.
- High dimensional feature,
- Feature selection,
- Peptide,
- Quantitative sequence-activity relationship,
- Support vector machine
1. [1]
  
  (1) Ding, J. L.; Ho, B. Drug Dev. Res. 2004, 62 (4), 317.
2. [2]
  (2) Sneath, P. H. A. J. Theor. Biol. 1966, 12 (2), 157.
3. [3]
  (3) Kidera, A.; Konishi, Y.; Oka, M.; Ooi, T.; Scheraga, H. A. J. Protein Chem. 1985, 4 (1), 23.
4. [4]
  (4) Hellberg, S.; Eriksson, L.; Jonsson, J.; Lindgren, F.; Sjöström, M.; Skagerberg, B.;Wold, S.; Andrews, P. Int. J. Pept. Protein Res. 1991, 37 (5), 414.
5. [5]
  (5) Sandberg, M.; Eriksson, L.; Jonsson, J.; Sjöström, M.;Wold, S. J. Med. Chem. 1998, 41 (14), 2481.
6. [6]
  (6) Liang, G. Z.; Mei, H.; Zhou, P.; Zhou, Y.; Li, Z. L. Acta Phys. -Chim. Sin. 2006, 22 (3), 388. [梁桂兆, 梅虎, 周鹏, 周原, 李志良. 物理化学学报, 2006, 22 (3), 388.]
7. [7]
  (7) Zhou, Y.; Mei, H.; Yang, L.; Zhou, P.; Yang, S. B.; Li, Z, L. Chem. J. Chin. Univ. 2007, 28 (7), 1263. [周原, 梅虎, 杨力, 周鹏, 杨善斌, 李志良. 高等学校化学学报, 2007, 28 (7), 1263.]
8. [8]
  (8) Yang, S. B.; Xia, Z. N.; Shu, M.; Mei, H.; Lü, F. L.; Zhang, M.; Wu, Y. Q.; Li, Z. L. Chem. J. Chin. Univ. 2008, 29 (11), 2213. [杨善彬, 夏之宁, 舒茂, 梅虎, 吕凤林, 张梅, 吴玉乾, 李志良. 高等学校化学学报, 2008, 29 (11), 2213.]
9. [9]
  (9) Liang, G. Z.; Zhou, P.; Zhou, Y.; Zhang, Q. X.; Li, Z. L. Acta Chim. Sin. 2006, 64 (5), 393. [梁桂兆, 周鹏, 周原, 张巧霞, 李志良. 化学学报, 2006, 64 (5), 393.]
10. [10]
  (10) Li, Z. L.; Li, G. R.; Shu, M.; Sun, J. Y.; Yang, S. B.; Mei, H.; Zhang, M. J.; Zhou, P.;Wu, S. R.; Chen, G. H.; Lü, F. L.; Lü, T. T. Sci. China Ser. B: Chem. 2008, 38 (8), 745. [李志良, 李根容, 舒茂, 孙家英, 杨善斌, 梅虎, 张梦军, 周萍, 吴世荣, 陈国华, 吕凤林, 吕廷亭. 中国科学B辑: 化学, 2008, 38 (8), 745.]
11. [11]
  (11) Kawashima, S.; Pokarowski, P.; Pokarowska, M.; Kolinski, A.; Katayama, T.; Kanehisa, M. Nucleic Acids Res. 2008, 36, D202.
12. [12]
  (12) Dash, M.; Liu, H. Intell. Data Anal. 1997, 1 (3), 131.
13. [13]
  (13) Kohavi, R.; John, G. H. Artif. Intel. 1997, 97 (1-2), 273.
14. [14]
  (14) Cover, T. M. IEEE Trans. Syst. Man Cybern. 1974, 4 (2), 116.
15. [15]
  (15) Colannino, J.; Juban, J. The Best K Measurements are Not the K Best. http://cgm.cs.mcgill.ca/-athens/cs644/Projects/2004/ JustinColannino-JeremieJuban/best.html, (accessed Mar 22, 2011).
16. [16]
  (16) Cortes, C.; Vapnik, V. Mach. Learn. 1995, 20 (3), 273.
17. [17]
  (17) Hou, T. J.; Xu, Z.; Zhang,W.; McLaughlin, A,W.; Case, D. A.; Xu, Y.;Wang,W. Mol. Cell. Proteomics 2009, 8, 639.
18. [18]
  (18) Hou, T. J.; Zhang,W.; Case, D. A.;Wang,W. J. Mol. Biol. 2008, 376, 1201.
19. [19]
  (19) Wang, H.; Zhang, B. J.; Liu, X. Z.; Luo, D. Z.; Zhong, S. B. Adv. Mater. Res. 2011, 143, 1254.
20. [20]
  (20) Zhang, Y. M.; Jin, Q.;Wang, S. T.; Ren, R. Comput. Biol. Med. 2011, 41 (5), 271.
21. [21]
  (21) Yuan, Z. M.; Zhang, Y. S.; Xiong, J. Y. Scientia Agricultura Sinica 2008, 41 (8), 2485. [袁哲明, 张永生, 熊洁仪. 中国农业科学, 2008, 41 (8), 2485.]
22. [22]
  (22) Zhang, Y. S.; Yuan, Z. M.; Xiong, J. Y.; Zhou, T. J. Acta Ecologica Sinica 2007, 27 (6), 2419. [张永生, 袁哲明, 熊洁仪, 周铁军. 生态学报, 2007, 27 (6), 2419.]
23. [23]
  (23) Tan, X. S.;Wang, Z. M.; Tan, S. Q.; Yuan, Z. M.; Xiong, X. Y.; Journal of System Simulation 2009, 21 (24), 7795. [谭显胜, 王志明, 谭泗桥, 袁哲明, 熊兴耀. 系统仿真学报, 2009, 21(24), 7795.]
24. [24]
  (24) Yuan, Z. M.; Tan, X. S. Acta Agronomica Sinica 2010, 36 (7), 1176. [袁哲明, 谭显胜. 作物学报, 2010, 36 (7), 1176.]
25. [25]
  (25) Tan, X. S.; Yuan, Z. M.; Zhou, T. J.;Wang, C. J.; Xiong, J. Y. Chem. J. Chin. Univ. 2008, 29 (1), 95. [谭显胜, 袁哲明, 周铁军, 王春娟, 熊洁仪. 高等学校化学学报, 2008, 29 (1), 95.]
26. [26]
  (26) Tropsha, A.; Gramatica, P.; mbar, V. K. QSAR Comb. Sci. 2003, 22 (1), 69.
27. [27]
  (27) Cocchi, M.; Johansson, E. Quant. Struct. -Act. Relat. 1993, 12(1), 1.
28. [28]
  (28) Collantes, E. R.; Dunn,W. J. J. Med. Chem. 1995, 38 (14), 2705.
29. [29]
  (29) Mei, H.; Zhou, Y.; Sun, L. L.; Li, Z. L. Chemistry 2005, (7), 534. [梅虎, 周原, 孙立力, 李志良. 化学通报, 2005, (7), 534.]
30. [30]
  (30) Mei, H.; Liang, G. Z.; Zhou, Y.; Li, Z. L. Chin. Sci. Bull. 2005, 50 (16), 1703. [梅虎, 梁桂兆, 周原, 李志良. 科学通报, 2005, 50 (16), 1703.]
31. [31]
  (31) Richardson, J. S.; Richardson, D. C. Science 1988, 240 (4859), 1648.
32. [32]
  (32) Cornette, J. L.; Cease, K. B.; Margalit, H.; Spouge, J. L.; Berzofsky, J. A.; DeLisi, C. J. Mol. Biol. 1987, 195 (3), 659.
33. [33]
  (33) Pliška, V.; Schmidt, M.; Fauchère, J. L. J. Chromatogr. A 1981, 216, 79.
34. [34]
  (34) Hassell, C. H.; Krohn, A.; Moody, C. J.; Thomas,W. A. J. Chem. Soc. Perkin. Trans. 1 1984, 23, 155.
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