A graph clustering algorithm based on a clustering coefficient for weighted graphs

Journal of the Brazilian Computer Society

Volumn 17, Issue 1, 2011, Pages 19-29

  Nascimento, Mariá C V ^a   Carvalho, André C P L F ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Clustering coefficient; Combinatorial optimization; Graph clustering

Indexed keywords

CLUSTERING COEFFICIENT; COMPLETE GRAPHS; COMPUTATIONAL RESULTS; GRAPH CLUSTERING; GRAPH CLUSTERING ALGORITHMS; NUMBER OF CLUSTERS; RELEVANT INFORMATIONS; WEIGHTED GRAPH;

COMBINATORIAL OPTIMIZATION; COMPUTATIONAL EFFICIENCY;

CLUSTERING ALGORITHMS;

EID: 84867046951     PISSN: 01046500     EISSN: 16784804     Source Type: Journal    
DOI: 10.1007/s13173-010-0027-x     Document Type: Article

References (32)

1. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma sub-classes. Proc Natl Acad Sci USA 98(24): 13790-13795.
2. Boginski V, Butenko S, Pardalos PM (2006) Mining market data: a network approach. Comput Oper Res 33: 3171-3184.
3. Clauset A, Newman MEJ, Moore C (2004) Finding community structure in very large networks. Phys Rev E 70(6): 066111.
4. Dhillon IS, Guan Y, Kulis B (2007) Weighted graph cuts without eigenvectors a multilevel approach. IEEE Trans Pattern Anal Mach Intell 29(11): 1944-1957.
5. Evett IW, Spiehler EJ (1987) Rule induction in forensic science. In: KBS in government, online publications, pp 107-118.
6. Feder T, Hell P, Klein S, Motwani R (1999) Complexity of graph partition problems. In: 31ST ANNUAL ACM STOC. Plenum, New York, pp 464-472.
7. Fisher RA (1936) The use of multiple measurements in taxonomic problems. Ann Eugen 7: 179-188.
8. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439): 531-537.
9. Hoshida Y, Brunet JP, Tamayo P, Golub TR, Mesiro JP (2007) Subclass mapping: identifying common subtypes in independent disease data sets. PLoS ONE 2(11): e1195.
10. Hubert L, Arabie P (1985) Comparing partitions. J Classif 2: 193-218.
11. Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA (2007) Nearest neighbor networks: clustering expression data based on gene neighborhoods. BMC Bioinform 8: 250.
12. Karypis G, Kumar V (1996) Parallel multilevel graph partitioning. In: Proceedings of the international parallel processing symposium.
13. Karypis G, Kumar V (1998) A fast and high quality multilevel scheme for partitioning irregular graphs. SIAM J Sci Comput 20(1): 359-392.
14. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz RR, Golub TR (2005) Microrna expression profiles classify human cancers. Nature 435(7043): 834-838.
15. Maier M, von Luxburg U, Hein M (2009) Influence of graph construction on graph-based clustering measures. In: Koller D, Schuurmans D, Bengio Y, Bottou L (eds) Advances in neural information processing systems, vol 21, pp 1025-1032. Curran, Red Hook.
16. Monti S, Tamayo P, Mesirov J, Golub T (2003) Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Kluwer Academic, Dordrecht. Tech rep, Broad Institute/MIT.
17. Nakai K, Kanehisa M (1991) Expert system for predicting protein localization sites in gram-negative bacteria. Proteins 11: 95-110.
18. Nascimento MCV, Toledo FMB, Carvalho ACPLF (2010) Investigation of a new GRASP-based clustering algorithm applied to biological data. Comput Oper Res 37: 1381-1388.
19. Newman MEJ, Girvan M (2004) Finding and evaluating community structure in networks. Phys Rev E 69: 026113.
20. Onnela JP, Saramäki J, Kertész J, Kaski K (2005) Intensity and coherence of motifs in weighted complex networks. Phys Rev E 71: 065(R), 103(R).
21. Pons P, Latapy M (2005) Computing communities in large networks using random walks. In: Computer and information sciences-ISCIS 2005, pp 284-293.
22. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 98(26): 15, 149-15, 154.
23. Reichardt J, Bornholdt S (2006) Statistical mechanics of community detection. Phys Rev E 74: 016 110.
24. Schaeffer SE (2007) Graph clustering. Comput Sci Rev 1: 27-64.
25. Shi J, Malik J (2000) Normalized cuts and image segmentation. IEEE Trans Pattern Anal Mach Intell 22: 888-905.
26. Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RCT, Gaasenbeek M, Angelo M, Reich M, Pinkus GS, Ray TS, Koval MA, Last KW, Norton A, Lister TA, Mesirov J (2002) Diffuse large b-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med 8: 68-74.
27. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB (2002) Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 99: 4465-4470.
28. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415(6871): 530-536.
29. Venables WN, Smith DM (2010) An introduction to R. R Development Core Team, The R Foundation for Statistical Computing, version 2. 11. 1.
30. Watts D, Strogatz S (1998) Collective dynamics of small-world networks. Nature 393: 440.
31. West M, Blanchette C, Dressman H, Huang E, Ishida S, Spang R, Zuzan H, Olson JA, Marks JR, Nevins JR (2001) Predicting the clinical status of human breast cancer by using gene expression profiles. Proc Natl Acad Sci USA 98(20): 11462-11467.
32. Yeoh EJ, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R, Behm F, Raimondi SC, Relling MV, Patel A, Cheng C, Campana D, Wilkins D, Zhou X, Li J, Liu H, Pui CH, Evans WE, Naeve C, Wong L, Downing J (2002) Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 1: 133-143.