Robust classification method of tumor subtype by using correlation filters

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 2, 2012, Pages 580-591

  Wang, Shu Lin ^a   Zhu, Yi Hai ^b   Jia, Wei ^b   Huang, De Shuang ^c  

^a HUNAN UNIVERSITY   (China)

^b INSTITUTE OF INTELLIGENT MACHINES   (China)

^c TONGJI UNIVERSITY   (China)

Author keywords

Correlation filters; gene expression profiles; model based method; template based method; tumor classification

Indexed keywords

CORRELATION FILTERS; GENE EXPRESSION PROFILES; MODEL-BASED METHOD; TEMPLATE-BASED METHOD; TUMOR CLASSIFICATION;

CORRELATION METHODS; GENE EXPRESSION; TUMORS;

FACE RECOGNITION;

AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; NEOPLASM; PROCEDURES; ARTICLE; METHODOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; MODELS, GENETIC; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED;

EID: 84863018899     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.135     Document Type: Article

References (42)

1. J.J. Hornberg et al., "Cancer: A Systems Biology Disease," Biosystems, vol. 83, nos. 2/3, pp. 81-90, 2006. (Pubitemid 43199809)
2. J.P.A. Ioannidis, "Is Molecular Profiling Ready for Use in Clinical Decision Making?," Oncologist, vol. 12, no. 3, pp. 301-311, 2007. (Pubitemid 46556796)
3. T.R. Golub et al., "Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring," Science, vol. 286, no. 5439, pp. 531-537, 1999.
4. D.S. Huang and C.H. Zheng, "Independent Component Analysis-Based Penalized Discriminant Method for Tumor Classification Using Gene Expression Data," Bioinformatics, vol. 22, no. 15, pp. 1855-1862, 2006.
5. M.H. Asyali et al., "Gene Expression Profile Classification: A Review," Current Bioinformatics, vol. 1, no. 1, pp. 55-73, 2006.
6. U. Alon et al., "Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Arrays," Proc. Nat'l Academy of Sciences USA, vol. 96, no. 12, pp. 6745-6750, 1999. (Pubitemid 29274954)
7. I. Guyon, J. Weston, and V. Vapnik, "Gene Selection for Cancer Classification Using Support Vector Machine," Machine Learning, vol. 46, nos. 1-3, pp. 389-422, 2002. (Pubitemid 34129977)
8. E. Bair and R. Tibshirani, "Semi-Supervised Methods to Predict Patient Survival from Gene Expression Data," Plos Biology, vol. 2, no. 4, pp. 511-522, 2004.
9. J.P. Brunet et al., "Metagenes and Molecular Pattern Discovery Using Matrix Factorization," Proc. Nat'l Academy of Sciences USA, vol. 101, no. 12, pp. 4164-4169, 2004.
10. C.H. Zheng et al., "Tumor Clustering Using Nonnegative Matrix Factorization with Gene Selection," IEEE Trans. Information Technology in Biomedicine, vol. 13, no. 4, pp. 599-607, July 2009.
11. M. West, "Bayesian Factor Regression Models in the "Large p, Small n" paradigm," Bayesian Statistics, vol. 7, pp. 733-742, 2003.
12. L.P. Wang, F. Chu, and W. Xie, "Accurate Cancer Classification Using Expressions of Very Few Genes," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 4, no. 1, pp. 40-53, Jan.-Mar. 2007. (Pubitemid 46375815)
13. C. Ambroise and G.J. McLachlan, "Selection Bias in Gene Extraction on the Basis of Microarray Gene-Expression Data," Proc. Nat'l Academy of Sciences USA, vol. 99, no. 10, pp. 6562-6566, 2002. (Pubitemid 34526172)
14. D.F. Ransohoff, "Bias as a Threat to the Validity of Cancer Molecular-Marker Research," Nature Rev. Cancer, vol. 5, no. 2, pp. 142-149, 2005. (Pubitemid 40215862)
15. D.F. Ransohoff, "Rules of Evidence for Cancer Molecular-Marker Discovery and Validation," Nature Rev. Cancer, vol. 4, no. 4, pp. 309-314, 2004. (Pubitemid 38525286)
16. J. Nilsson et al., "Approximate Geodesic Distances Reveal Biologically Relevant Structures in Microarray Data," Bioinformatics, vol. 20, no. 6, pp. 874-880, 2004. (Pubitemid 38559727)
17. A.R. Dabney, "Classification of Microarrays to Nearest Centroids," Bioinformatics, vol. 21, no. 22, pp. 4148-4154, 2005. (Pubitemid 41672105)
18. B.V.K. Vijaya Kumar, A. Mahalanobis, and R.D. Juday, Correlation Pattern Recognition. Cambridge Univ. Press, 2005.
19. S.L. Wang and Y.H. Zhu, "A Novel Method to Robust Tumor Classification Based on MACE Filter," Proc. Intelligent Computing Fifth Int'l Conf. Emerging Intelligent Computing Technology and Applications, pp. 945-954, 2009.
20. A. Mahalanobis, B.V.K. Vijaya Kumar, and D. Casasent, "Minimum Average Correlation Energy Filters," Applied Optics, vol. 26, no. 17, pp. 3633-3640, 1987.
21. P. Refregier, "Filter Design for Optical Pattern Recognition: Multicriteria Optimization Approach," Optics Letters, vol. 15, no. 15, pp. 854-856, 1990.
22. J.R. Nevins and A. Potti, "Mining Gene Expression Profiles: Expression Signatures as Cancer Phenotypes," Nature Rev. Genetics, vol. 8, no. 8, pp. 601-609, 2007. (Pubitemid 47077277)
23. I. Kononenko, "Estimating Attributes: Analysis and Extensions of Relief," Proc. European Conf. Machine Learning, pp. 171-182, 1994.
24. P.H. Hennings-Yeomans, B. Kumar, and M. Savvides, "Palmprint Classification Using Multiple Advanced Correlation Filters and Palm-Specific Segmentation," IEEE Trans. Information Forensics and Security, vol. 2, no. 3, pp. 613-622, Sept. 2007. (Pubitemid 47290593)
25. B.V.K. Vijaya Kumar et al., "Biometric Verification with Correlation Filters," Applied Optics, vol. 43, no. 2, pp. 391-402, 2004.
26. B.V.K. Kumar Vijaya, "Tutorial Survey of Composite Filter Designs for Optical Correlators," Applied Optics vol. 31, no. 23, pp. 4773-4801, 1992.
27. B.V.K. Vijaya Kumar, "Minimum-Variance Synthetic Discriminant Functions," J. Optical Soc. of Am. A, vol. 3, no. 10, pp. 1579-1584, 1986.
28. S.A. Armstrong et al., "MLL Translocations Specify a Distinct Gene Expression Profile that Distinguishes a Unique Leukemia," Nature Genetics, vol. 30, no. 1, pp. 41-47, 2002.
29. C.L. Nutt et al., "Gene Expression-Based Classification of Malignant Gliomas Correlates Better with Survival than Histological Classification," Cancer Research, vol. 63, no. 7, pp. 1602-1607, 2003. (Pubitemid 36373650)
30. M.A. Shipp et al., "Diffuse Large B-Cell Lymphoma Outcome Prediction by Gene-Expression Profiling and Supervised Machine Learning," Nature Medicine, vol. 8, no. 1, pp. 68-74, 2002. (Pubitemid 34101731)
31. E.J. Yeoh et al., "Classification, Subtype Discovery, and Prediction of Outcome in Pediatric Acute Lymphoblastic Leukemia by Gene Expression Profiling," Cancer Cell, vol. 1, no. 2, pp. 133-143, 2002.
32. J. Khan et al., "Classification and Diagnostic Prediction of Cancers Using Gene Expression Profiling and Artificial Neural Networks," Nature Medicine, vol. 7, no. 6, pp. 673-679, 2001. (Pubitemid 32588022)
33. P.A. Futreal et al., "A Census of Human Cancer Genes," Nature Rev. Cancer, vol. 4, no. 3, pp. 177-183, 2004. (Pubitemid 38337497)
34. Y. Leung and Y. Hung, "A Multiple-Filter-Multiple-Wrapper Approach to Gene Selection and Microarray Data Classification," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 7, no. 1, pp. 108-117, Jan.-Mar. 2010.
35. P.N. Belhumeur, J.P. Hespanha, and D.J. Kriegman, "Eigenfaces versus Fisherfaces: Recognition Using Class Specific Linear Projection," IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 19, no. 7, pp. 711-720, July 1997. (Pubitemid 127762263)
36. M.S. Bartlett, J.R. Movellan, and T.J. Sejnowski, "Face Recognition by Independent Component Analysis," IEEE Trans. Neural Networks, vol. 13, no. 6, pp. 1450-1464, Nov. 2002. (Pubitemid 35428531)
37. V.N. Vapnik, Statistical Learning Theory, Wiley-Interscience, 1998.
38. D.F. Specht, "Probabilistic Neural Networks for Classification, Mapping, or Associative Memory," Proc. IEEE Int'l Conf. Neural Networks, pp. 525-532, 1988.
39. C.H. Zheng et al., "Tumor Classification Based on Independent Component Analysis," Int'l J. Pattern Recognition and Artificial Intelligence, vol. 20, no. 2, pp. 297-310, 2006.
40. D.M. Rocke et al., "Papers on Normalization, Variable Selection, Classification or Clustering of Microarray Data," Bioinformatics, vol. 25, no. 6, pp. 701-702, 2009.
41. A.K. Jain, R.P.W. Duin, and J.C. Mao, "Statistical Pattern Recognition: A Review," IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 22, no. 1, pp. 4-37, Jan. 2000. (Pubitemid 32132953)
42. B. Kumar et al., "Spatial Frequency Domain Image Processing for Biometric Recognition," Proc. Int'l Conf. Image Processing, pp. 53-56, 2002.