Direct classification of high-dimensional data in low-dimensional projected feature spaces-Comparison of several classification methodologies

Journal of Biomedical Informatics

Volumn 40, Issue 2, 2007, Pages 131-138

  Somorjai, R L ^a   Dolenko, B ^a   Mandelzweig, M ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

Comparison of classifiers; Direct classification; RDP mapping; Relative distance plane mapping; Transvariation

Indexed keywords

BIOMEDICAL ENGINEERING; CLASSIFICATION (OF INFORMATION); COMPUTATION THEORY; CONFORMAL MAPPING; DATA REDUCTION; DATA STRUCTURES;

DIRECT CLASSIFICATION; LINEAR DISCRIMINANT ANALYSIS (LDA); RDP MAPPING; RELATIVE DISTANCE PLANE MAPPING; TRANSVARIATION;

BIOINFORMATICS;

ACCURACY; ARTICLE; AUTOMATED PATTERN RECOGNITION; CALCULATION; CLASSIFICATION; DATA ANALYSIS; DISCRIMINANT ANALYSIS; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MEASUREMENT; PRIORITY JOURNAL; PROBABILITY; STANDARD;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTER GRAPHICS; COMPUTER SIMULATION; MODELS, BIOLOGICAL; PATTERN RECOGNITION, AUTOMATED; USER-COMPUTER INTERFACE;

EID: 33847677992     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2006.04.001     Document Type: Article

References (28)

1. Lean C.L., Somorjai R.L., Smith I.C.P., Russell P., and Mountford C.E. Accurate diagnosis and prognosis of human cancers by proton MRS and a three stage classification strategy. Annu Rep NMR Spectrosc 48 (2002) 71-111
2. Somorjai R.L., Dolenko B., Nikulin A., Nickerson P., Rush D., Shaw A., et al. Distinguishing normal from rejecting renal allografts: application of a three-stage classification strategy MR and IR spectra of urine. Vib Spectrosc 28 (2002) 97-102
3. Vlahou A., Schellhammer P.F., Mendrinos S., Patel K., Kondylis F.I., Gong L., et al. Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am J Pathol 158 (2001) 1491-1502
4. Li J., Zhang Zh., Rosenzweig J., Wang Y.Y., and Chan D.W. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 48 (2002) 1296-1304
5. Petricoin III E.F., Ardekani A.M., Hitt B.A., Levine P.J., Fusaro V.A., Steinberg S.M., et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359 (2002) 572-577
6. Alon U., Barkai N., Notterman D.A., Gish K., Ybarra S., Mack D., et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96 (1999) 6745-6750
7. Khan J., Wei J.S., Ringnér M., Saal H., Ladanyi M., Westermann F., et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 7 (2001) 1-10
8. Ibrahim J.G., Chen M.-H., and Gray R.J. Bayesian models for gene expression with DNA microarray data. J Am Stat Assoc-Application and Case Studies 97 (2002) 88-99
9. Pomeroy S.L., Tamayo P., Gaasenbeek M., Sturla L.M., Angelo M., McLaughlin M.E., et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415 (2002) 436-442
10. Somorjai R.L., Dolenko B., and Baumgartner R. Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions. Bioinformatics 19 (2003) 1484-1491
11. Somorjai R.L., Demko A., Mandelzweig M., Dolenko B., Nikulin A.E., Baumgartner R., et al. Mapping high-dimensional data onto a relative distance plane-A novel, exact method for visualizing and characterizing high-dimensional patterns. J Biomed Inform 37 (2004) 366-379
12. Lee R.C.T., Slagle J.R., and Blum H. A triangulation method for the sequential mapping of points from N-space to two-space. IEEE Trans Comput (1977) 288-292
13. Friedman J., and Tukey J.W. A projection pursuit algorithm for exploratory data analysis. IEEE Trans Computing C-23 (1974) 881-889
14. Huber P.J. Projection pursuit. Ann Stat 13 (1985) 435-475
15. Pekalska E., and Duin R.P.W. Dissimilarity representations allow for building good classifiers. Pattern Recognit Lett 23 (2002) 943-956
16. Pekalska E., and Duin R.P.W. Automatic pattern recognition by similarity representations. Electron Lett 37 (2001) 159-160
17. Pekalska E, Duin RPW. Classifiers for dissimilarity-based pattern recognition. In Sanfeliu A, Villanueva JJ, Vanrell M, Alquezar R, Eklundh JO, Aloimonos Y, editors. Proceedings of the 15th international conference on pattern recognition, ICPR 2000, vol. 2, Los Alamitos, CA, USA, 2000. p. 12-6.
18. Faragó A., Linder T., and Lugosi G. Fast nearest-neighbor search in dissimilarity spaces. IEEE Trans Pattern Anal Mach Intell 15 9 (1993) 957-962
19. Anderson T.W., and Bahadur R.R. Classification into two multivariate normal distributions with different covariance matrices. Ann Math Statist 33 (1962) 420-431
20. Gini C. Transvariazione (1959), Libreria Goliardica, Roma
21. Montanari A. Linear discriminant analysis and transvariation. J Classification 21 (2004) 71-88
22. Paclik P., and Duin R.P.W. Dissimilarity-based classification of spectra: computational issues. Real-Time Imaging 9 (2003) 237-244
23. Peltonen J., and Kaski S. Discriminative components of data. IEEE Trans Neural Netw 16 1 (2005) 68-83
24. Cowen L.J., and Priebe C.E. Randomized nonlinear projections uncover high-dimensional structure. Adv Appl Math 19 (1997) 319-331
25. Cannon AH, Cowen LJ, Priebe CE. Approximate distance classification. In: Proceedings of the 1998 symposium on the interface between computer science and statistics. vol. 30, no. (1), 1999. p. 544-9.
26. Priebe C.E. Olfactory classification via interpoint distance analysis. IEEE Trans Pattern Anal Mach Intell 23 (2001) 404-413
27. Metchev S.A., and Grindlay J.E. A two-dimensional Kolmogorov-Smirnov test for crowded field source detection: ROSAT sources in NGC 6397. Mon Not R Astron Soc 335 (2002) 73-83
28. Nikulin A.E., Dolenko B., Bezabeh T., and Somorjai R.L. Near-optimal region selection for feature space reduction: novel preprocessing methods for classifying MR spectra. NMR Biomed 11 (1998) 209-217