Efficient selection of discriminative genes from microarray gene expression data for cancer diagnosis

IEEE Transactions on Circuits and Systems I: Regular Papers

Volumn 52, Issue 9, 2005, Pages 1909-1918

  Huang, Di ^a   Chow, Tommy W S ^a   Ma, Eden W M ^a   Li, Jinyan ^b  

^a CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^b INSTITUTE FOR INFOCOMM RESEARCH   (Singapore)

Author keywords

Cancer diagnosis; Feature selection; Grid based redundancy elimination; Microarray gene expression data; Quadratic mutual information (QMI)

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; GENES; INFORMATION THEORY; ONCOLOGY; REDUNDANCY;

CANCER DIAGNOSIS; FEATURE SELECTION; GRID BASED REDUNDANCY ELIMINATION; MICROARRAY GENE EXPRESSION DATA; QUADRATIC MUTUAL INFORMATION;

FEATURE EXTRACTION;

EID: 27144471473     PISSN: 10577122     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCSI.2005.852013     Document Type: Article

References (27)

1. T. R. Golub, D. K. Slonim, P. Tamayo, C. Huard, M, Gaasenbeek, J. P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, C. D. Bloomfield, and E. S. Lander, "Molecular classification of cancer: class discovery and class prediction by gene expression monitoring," Science, vol. 286, pp. 531-537, Oct. 1999.
2. G. J. Gordon, R. V. Jensen, L.-L. Hsiao, S. R. Guillans, J. E. Blumenstock, S. Ramaswamy, W. G. Richards, D. J. Sugarbaker, and R. Bueno, "Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma," Cancer Res., vol. 62, pp. 4963-4967, 2002.
3. J. Li, H. Liu, J. R. Downing, A. E. Yeoh, and L. Wong, "Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients," Bioinform., vol. 19, pp. 71-78, 2003.
4. E. F. Petricoin, A. M. Ardekani, B. A. Hitt, P. J. Levine, V. A. Fusaro, S. M. Steinberg, G. B. Mills, C. Simone, D. A. Fishman, E. C. Kohn, and L. A. Liotta, "Use of proteomic patterns in serum to identify ovarian cancer," Lancet, vol. 359, pp. 572-577, 2002.
5. D. Singh, P. G. Febbol, K. Ross, D, G. Jackson, J. Manola, C. Ladd, P. Tamayo, A. A. Renshaw, A. V. D'Amico, J. P. Richie, E. S. Lander, M. Loda, P. W. Kantoff, T. R. Golub, and W. R. Sellers, "Gene expression correlates of clinical prostate cancer behavior," Cancer Cell, vol. 1, pp. 203-209, Mar. 2002.
6. E. Yeoh, M. E. Ross, S. A. Shurtleff, W. K. Williams, D. Patel, R. Mahfouz, F. G. Behm, S. C. Raimondi, M. V. Relling, A, Patel, C. Cheng, D. Campana, D. Wilkins, X. Zhou, J. Li, H. Liu, C, Pai, W. E. Evans, C. Naeve, L. Wong, and J. R. Downing, "Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling," Cancer Cell, vol. 1, pp. 133-143, Mar. 2002.
7. I. Guyon, J. Weston, and S. Barnhill, "Gene selection for cancer classification using support vector machines," Mach. Learn., vol. 46, pp. 389-422, 2002.
8. E. P. Xing, M. I. Jordan, and R. M. Karp, "Feature selection for high-dimensional genomic microarry data," in Proc. 18th Int. Conf. Machine Learning, Williamstown, MA, 2001,..
9. T. M. Cover and J. A. Thomas, Elements of Information Theory. New York: Wiley, 1994.
10. A. M. Fraser and H. L. Swinney, "Independent coordinates for strange attractors from mutual information," Phys. Rev. A, vol. 33, no, 2, pp. 1134-1140, 1986.
11. K. Torkkola, "Feature extraction by nonparametric mutual information maximization" J. Mach. Learn. Res., pp. 1415-1438, Mar. 2003.
12. J. C. Principe, J. W. Fisher III, and D. Xu, "Information theoretic learning," in In Unsupervised Adaptive Filtering, S. Haykin, Ed. New York: Wiley, 2000.
13. E. Parzen, "On the estimation of a probability density function and mode," Ann. Math. Statist., vol. 33, pp. 1064-1076, 1962.
14. B. W. Silverman, Density Estimation for Statistics and Data Analysis. London, U.K.: Chapman & Hall, 1986,
15. R. Battiti, "Using mutual information for selecting features in supervised neural net learning," IEEE Trans. Neur. Netw., vol. 5, no. 4, pp. 537-550; 1994.
16. N. Kwak and C.-H. Choi, "Input feature selection by mutual information based on Parzen window," IEEE Trans. Neur. Netw., vol. 13, no. 1, pp. 143-159, 2002.
17. J. W. Han and M. Kamber, Data Mining: Concepts and Techniques. San Mateo, CA: Morgan Kaufmann, 2001.
18. T. W. S. Chow and D. Huang, "Estimating the optimal features subset using efficient estimate of high dimensional mutual information," IEEE Trans. Neur, Netw., vol. 16, no. 1, pp. 213-224, Jan. 2005.
19. D. Huang and T. W. S. Chow, "Effective feature-selection scheme using mutual information," Neurocomp., vol. 63, pp. 325-343, Aug. 2004.
20. B. Bonnlander, "Nonparametric Selection of Input Variables for Connectionist Learning," Ph.D. dissertation, University of Colorado at Boulder, Boulder, CO, 1996.
21. G. D. Tourassi, E. D. Frederick, M. K. Markey, and C. E. Floyd Jr., "Application of the mutual information criterion for feature selection in computer-aided diagnosis," Med, Phys., vol. 28, no. 12, pp. 2394-2402, 2001.
22. P. A. Devijver and J. Kittler, Pattern Recognition: A Statistical Approach. Englewood Cliffs, NJ: Prentice Hall, 1982.
23. U. Alon, N. Barkar, D. A. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine, "Broad pattern of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays," Proc. Natl. Acad. Sci. U.S.A., vol. 96, no. 12, pp. 6745-6750, 1999.
24. M. Young, B. Rajagopalan, and U. Lall, "Estimation of mutual information using kernel density estimators," Phys. Rev. E, vol. 52, no. 3 (B), pp. 2318-2321, Sep. 1995.
25. M. Schena, D. Shalon, R. W. Davis, and P. O. Brown, "Quantitive monitoring of gene expression with a complementary DNA microarray," Science, vol. 270, pp. 467-471, 1995.
26. G. C. Tseng, "A comparative review of gene clustering in expression profile," in Proc. 8th Int. Conf. on Control, Automation, Robotics and Vision (ICARCV), 2004, pp. 1320-1324.
27. D. Huang, "Searching the salient features and samples for pattern recognition," Ph.D. dissertation, Dept. Electron. Eng., City University of Hong Kong, Hong Kong, 2005.