Clustering algorithms: On learning, validation, performance, and applications to genomics

Current Genomics

Volumn 10, Issue 6, 2009, Pages 430-445

  Dalton, Lori ^a   Ballarin, Virginia ^b   Brun, Marcel ^b  

^a Texas AandM University   (United States)

^b UNIVERSIDAD NACIONAL DE MAR DEL PLATA   (Argentina)

Author keywords

Clustering; Genomics; Microarray; Profiling; Validation index

Indexed keywords

ACUTE GRANULOCYTIC LEUKEMIA; ALGORITHM; ANALYTICAL ERROR; CANCER CLASSIFICATION; CLASSIFICATION; CLUSTER ANALYSIS; CLUSTERING ALGORITHM; DUNN VALIDATION INDEX; EXPECTATION MAXIMIZATION CLUSTERING; FIGURE OF MERIT INDEX; FUZZY C MEANS; FUZZY LOGIC; GENE EXPRESSION PROFILING; GENOMICS; HIERARCHICAL CLUSTERING; HUBERT CORRELATION; HUMAN; K MEANS ALGORITHM; KIDNEY CARCINOMA; LARGE CELL LYMPHOMA; MATHEMATICAL MODEL; PARTITIONING ALGORITHM; PATTERN RECOGNITION; RAND STATISTICS; RELATIVE VALIDATION INDEX; REVIEW; SELF ORGANIZING MAP CLUSTERING; SILHOUETTE INDEX; STATISTICS; THEORY; VALIDATION PROCESS;

EID: 70549111674     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920209789177601     Document Type: Review

References (57)

1. Andenberg, M.R. Cluster Analysis for Applications; Academic Press: New York, 1973.
2. Jain, A.K.; Murty, M.N.; Flynn, P.J. Data clustering: a review. ACM Comput. Surveys, 1999, 31, 264-323.
3. Jain, A.K.; Topchy, A.; Law, M.H.C.; Buhmann, J.M. Landscape of clustering algorithms. In Proc. 17th Int. Conf. Pattern Recognit. (ICPR '04), 2004, 1, 260-263.
4. Somogyi, R.; Fuhrman, S.; Askenazi, M.; Wuensche, A. The gene expression matrix: towards the extraction of genetic network architectures. Nonlinear Anal., 1997, 30, 1815-1824. (Pubitemid 127423798)
5. Eisen, M.B.; Spellman, P.T.; Brown, P.O.; Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 1998, 95, 14863-14868. (Pubitemid 29003722)
6. Ben-Dor, A.; Shamir, R.; Yakhini, Z. Clustering gene expression patterns. J. Comput. Biol., 1999, 6, 281-297.
7. Golub, T.R.; Slonim, D.K.; Tamayo, P.; Huard, C.; Gaasenbeek, M.; Mesirov, J.P.; Coller, H.; Loh, M.L.; Downing, J.R.; Caligiuri, M.A.; Bloomfield, C.D.; Lander, E.S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 1999, 286, 531-537.
8. Tamayo, P.; Slonim, D.; Mesirov, J.; Zhu, Q.; Kitareewan, S.; Dmitrovsky, E.; Lander, E.S.; Golub, T.R. Interpreting patterns of gene expression with self-organizing maps: methods and applications to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA, 1999, 96, 2907-2912.
9. Tavazoie, S.; Hughes, J.D.; Campbell, M.J.; Cho, R.J.; Church, G.M. Systematic determination of genetic network architecture. Nat. Genet., 1999, 22, 281-285.
10. Sharan, R.; Shamir, R. CLICK: A clustering algorithm with applications to gene expression analysis. In Proc. Int. Conf. Intell. Syst. Mol. Biol., 2000, 8, 307-316.
11. Yeung, K.Y.; Fraley, C.; Murua, A.; Raftery, A.E.; Ruzzo, W.L. Model-based clustering and data transformation for gene expression data. Bioinformatics, 2001, 17, 977-987. (Pubitemid 32998635)
12. Dougherty, E.R.; Barrera, J.; Brun, M.; Kim, S.; Cesar, R.M.; Chen, Y.; Bittner, M.L.; Trent, J.M. Inference from clustering with application to gene-expression microarrays. J. Comput. Biol., 2002, 9, 105-126.
13. Dembélé, D.; Kastner, P. Fuzzy c-means method for clustering microarray data. Bioinformatics, 2003, 19, 973-980. (Pubitemid 36675818)
14. Brunet, J.P.; Tamayo, P.; Golub, T.R.; Mesirov, J.P. Metagenes and molecular pattern discovery using matrix factorization. Proc. Natl. Acad. Sci. USA, 2004, 101, 4164-4169. (Pubitemid 38405900)
15. Chipman, H.; Hastie, T.; Tibshirani, R. Clustering microarray data. In Statistical Analysis of Gene Expression Microarray Data; Speed, T., Ed.; Chapman & Hall/CRC: Boca Raton, FL, 2003; pp. 159-200.
16. Brun, M.; Johnson, C.D.; Ramos, K.S. Clustering: revealing intrinsic dependencies in microarray data. In Genomic Signal Processing and Statistics; Dougherty, E.R., Shmulevich, I., Chen, J., Wang, Z.J., Eds.; EURASIP Book Series on Signal Processing and Communications; Hindawi Publishing Corporation: New York, 2005, pp. 129-162.
17. Kalton, A.; Langley, P.; Wagstaff, K.; Yoo, J. Generalized clustering, supervised learning, and data assignment. In Proc. 7th Int. Conf. on Knowl. Discov. and Data Min., 2001, 299-304.
18. Kerr, M.K.; Churchill, G.A. Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc. Natl. Acad. Sci. USA, 2001, 98, 8961-8966.
19. Dougherty, E.R.; Brun, M. A probabilistic theory of clustering. Pattern Recognit., 2004, 37, 917-925.
20. Brun, M.; Sima, C.; Hua, J.; Lowey, J.; Carroll, B.; Suh, E.; Dougherty, E.R. Model-based evaluation of clustering validation measures. Pattern Recognit., 2006, 40, 807-824.
21. Devroye, L.; Györffi, L.; Lugosi, G. A Probabilistic Theory of Pattern Recognition; Springer-Verlag: New York, 1996.
22. Xing, E.P.; Ng, A.Y.; Jordan, M.I.; Russell, S. Distance metric learning, with application to clustering with side-information. In Adv. Neural. Inf. Process. Syst. 15; Becker, S., Thrun, S., Obermayer, K., Eds.; MIT Press: Cambridge, MA, 2003, pp. 505-512.
23. Bach, F.R.; Jordan, M.I. Learning spectral clustering. In Adv. Neural. Inf. Process. Syst. 16; Thrun, S., Saul, L.K., Scholkopf, B., Eds.; MIT Press: Cambridge, MA, 2004, pp. 305-312.
24. Rosales, R.; Achan, K.; Frey, B. Learning to cluster using local neighborhood structure. In Proc. of the 21st Int. Conf. Machine Learning (ICML '04), 2004.
25. Kamishima, T.; Motoyoshi, F. Learning from cluster examples. Mach. Learn., 2003, 53, 199-233.
26. Cover, T.; Hart, P. Nearest neighbor pattern classification. IEEE Trans. Inf. Theory, 1967, 13, 21-27.
27. Brun, M.; Dougherty, E.R. Clustering algorithms do not learn, but they can be learned. In Proc. SPIE, 2005, 5916, 283-291.
28. Jain, A.K.; Dubes, R.C. Algorithms for Clustering; Prentice-Hall: New Jersey, 1988.
29. Duda, R.O.; Hart, P.E.; Stork, D.G. Pattern Classification and Scene Analysis; John Wiley & Sons: New York, 2002.
30. Gose, E.; Johnsonbaugh, R.; Jost, S. Pattern Recognition and Image Analysis; Prentice Hall: New Jersey, 1996.
31. Theodoridis, S.; Koutroumbas, K. Pattern Recognition; Academic Press: San Diego, 1999.
32. Bottou, L.; Bengio, Y. Convergence properties of the K-means algorithm. In Adv. Neural. Inf. Process. Syst. 7; Tesauro, G., Touretzky, D.S.; Leen, T.K.; Eds.; MIT Press: Cambridge, MA, 1995, pp. 585-592.
33. Fraley, C.; Raftery, A.E. Model-based clustering, discriminant analysis, and density estimation. J. Am. Stat. Assoc., 2002, 97, 611-631.
34. Toronen, P.; Kolehmainen, M.; Wong, G.; Castren, E. Analysis of gene expression data using self-organizing maps. FEBS Lett., 1999, 451, 142-146. (Pubitemid 29231938)
35. Wang, J.; Delabie, J.; Aasheim, H.C.; Smeland, E.; Myklebost, O. Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study. BMC Bioinformatics, 2002, 3, 36. (Pubitemid 38751168)
36. Fisher, L.; Van Ness, J.W. Admissible clustering procedures. Biometrika, 1971, 58, 91-104.
37. Van Ness, J.W. Admissible clustering procedures. Biometrika, 1973, 60, 422-424.
38. Guenter, S.; Bunke, H. Validation indices for graph clustering. In Proc. 3rd IAPR-TC-15 Workshop on Graph-based Representations in Pattern Recognit.; Jolion, J. M.; Kropatsch, W.; Vento, M.; Eds.; 2001, pp. 229-238.
39. Halkidi, M.; Batistakis, Y.; Vazirgiannis, M. On clustering validation techniques. J. Intell. Inf. Syst., 2001, 17, 107-145.
40. Lubovac, Z.; Olsson, B.; Jonsson, P.; Laurio, K.; Anderson, M.L. Biological and statistical evaluation of clusterings of gene expression profiles. In Proc. Math. and Comput. in Biol. and Chem.; D'Attellis, C.E.; Kluev, V.V.; Mastorakis, N.E.; Eds.; 2001, pp. 149-155.
41. Roth, V.; Lange, T.; Braun, M.; Buhmann, J.M. A resampling approach to cluster validation. In Proc. Intl. Conf. Comput. Stat. (COMPSTAT 2002); Härdle, W.; Rönz, B.; Eds.; 2002, pp. 123-128.
42. Azuaje, F. A cluster validity framework for genome expression data. Bioinformatics, 2002, 18, 319-320. (Pubitemid 34183110)
43. Azuaje, F.; Bolshakova, N. Clustering genomic expression data: design and evaluation principles. In A Practical Approach to Microarray Data Analysis; Berrar, D., Dubitzky, W., Granzow, M., Eds.; Kluwer Academic Publishers: Boston/Dordrecht/London, 2002, pp. 230-245.
44. Bolshakova, N.; Azuaje, F. Cluster validation techniques for genome expression data. Signal Processing, 2003, 83, 825-833.
45. Rousseeuw, P.J. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math., 1987, 20, 53-65.
46. Hua, J.; Craig, D.W.; Brun, M.; Webster, J.; Zismann, V.; Tembe, W.; Joshipura, K.; Huentelman, M.J.; Dougherty, E.R.; Stephan, D.A. SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. Bioinformatics, 2007, 23, 57-63.
47. Yeung, K.Y.; Haynor, D.R.; Ruzzo, W.L. Validating clustering for gene expression data. Bioinformatics, 2001, 17, 309-318. (Pubitemid 32421924)
48. Roth, V.; Braun, M.; Lange, T.; Buhmann, J.M. Stability-based model order selection in clustering with applications to gene expression data. In Lecture Notes in Computer Science; Dorronsoro, J.R., Ed.; Springer: Heidelberg, 2002, Vol. 2415, pp. 607-612.
49. Brazma, A.; Vilo, J. Gene expression data analysis. FEBS Lett., 2000, 480, 17-24.
50. Ramoni, M.F.; Sebastiani, P.; Kohane, I.S. Cluster analysis of gene expression dynamics. Proc. Natl. Acad. Sci. USA, 2002, 99, 9121-9126. (Pubitemid 34764577)
51. Johnson, C.D.; Balagurunathan, Y.; Lu, K.P.; Tadesse, M.; Falahatpisheh, M.H.; Carroll, R.J.; Dougherty, E.R.; Afshari, C.A.; Ramos, K.S. Genomic profiles and predictive biological networks in oxidant-induced atherogenesis. Physiol. Genomics, 2003, 13, 263-275.
52. Schliep, A.; Schönhuth, A.; Steinhoff, C. Using hidden markov models to analyze gene expression time course data. Bioinformatics, 2003, 19, 255-263. (Pubitemid 41185629)
53. Bittner, M.L.; Meltzer, P.; Chen, Y.; Jiang, Y.; Seftor, E.; Hendrix, M.; Radmacher, M.; Simon, R.; Yakhini, Z.; Ben-Dor, A.; Sampas, N.; Dougherty, E.R.; Wang, E.; Marincola, F.; Gooden, C.; Lueders, J.; Glatfelter, A.; Pollock, P.; Carpten, J.; Gillanders, E.; Leja, D.; Dietrich, K.; Beaudry, C.; Berens, M.; Alberts, D.; Sondak, V. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature, 2000, 406, 536-540. (Pubitemid 30625740)
54. Alizadeh, A.A.; Eisen, M.B.; Davis, R.E.; Ma, C.; Lossos, I.S.; Rosenwald, A.; Boldrick, J.C.; Sabet, H.; Tran, T.; Yu, X.; Powell, J.I.; Yang, L.; Marti, G.E.; Moore, T.; Hudson, Jr., J.; Lu, L.; Lewis, D.B.; Tibshirani, R.; Sherlock, G.; Chan, W.C.; Greiner, T.C.; Weisenburger, D.D.; Armitage, J.O.; Warnke, R.; Levy, R.; Wilson, W.; Grever, M.R.; Byrd, J.C.; Botstein, D.; Brown, P.O.; Staudt, L.M. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 2000, 403, 503-511. (Pubitemid 30082188)
55. Bullinger, L.; Dohner, K.; Bair, E.; Frohling, S.; Schlenk, R.F.; Tibshirani, R.; Dohner, H.; Pollack, J.R. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N. Engl. J. Med., 2004, 350, 1605-1616.
56. Morrison, C.; Farrar, W.; Kneile, J.; Williams, N.; Liu-Stratton, Y.; Bakaletz, A.; Aldred, M.A.; Eng, C. Molecular classification of parathyroid neoplasia by gene expression profiling. Am. J. Pathol., 2004, 165, 565-576. (Pubitemid 38971386)
57. Zhao, H.; Ljungberg, B.; Grankvist, K.; Rasmuson, T.; Tibshirani, R.; Brooks, J.D. Gene expression profiling predicts survival in conventional renal cell carcinoma. PLoS Med., 2006, 3, 13.