Banded structure in binary matrices

Knowledge and Information Systems

Volumn 28, Issue 1, 2011, Pages 197-226

  Garriga, Gemma C ^a   Junttila, Esa ^b   Mannila, Heikki ^c  

^a UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^b UNIVERSITY OF HELSINKI   (Finland)

^c AALTO UNIVERSITY   (Finland)

Author keywords

Banded matrices; Binary data; Consecutive ones property; Permutation problem

Indexed keywords

INFORMATION SYSTEMS;

ALGORITHMIC PROBLEMS; BANDED MATRICES; BANDED STRUCTURES; BINARY DATA; CONSECUTIVE ONES PROPERTY; FORMAL DEFINITION; OVERLAPPING COMMUNITIES; PERMUTATION PROBLEMS;

MATRIX ALGEBRA;

EID: 79959493655     PISSN: 02191377     EISSN: 02193116     Source Type: Journal    
DOI: 10.1007/s10115-010-0319-7     Document Type: Article

References (35)

1. Agrawal R, Imieliński T, Swami A (1993) Mining association rules between sets of items in large data-bases. In: SIGMOD'93, pp 207-216.
2. Alizadeh F, Karp RM, Newberg LA, Weisser DK (1995) Physical mapping of chromosomes: a combinatorial problem in molecular biology. Algorithmica 13(1/2): 52-76.
3. Atkins J, Boman E, Hendrickson B (1999) A spectral algorithm for seriation and the consecutive ones problem. SIAM J Comput 28(1): 297-310.
4. Aykanat C, Pinar A, Çatalyürek U (2004) Permuting sparse rectangular matrices into block-diagonal form. SIAM J Sci Comput 25(6): 1860-1879.
5. Baeza-Yates R, Ribeiro-Neto B (1999) Modern information retrieval. Addison Wesley, Reading.
6. Banerjee A, Krumpelman C, Ghosh J, Basu S, Mooney R (2005) Model-based overlapping clustering. In: KDD'05, pp 532-537.
7. Bar-Yossef Z, Guy I, Lempel R, Maarek YS, Soroka V (2008) Cluster ranking with an application to mining mailbox networks. Knowl Inf Syst 14(1): 101-139.
8. Bertin J (1999) Graphics and graphic information processing, pp 62-65.
9. Booth KS (1975) PQ-tree algorithms. PhD thesis.
10. Burzyn P, Bonomo F, Durán G (2006) NP-completeness results for edge modification problems. Disc Appl Math 154(13): 1824-1844.
11. Chen K, Liu L (2009) Best k: critical clustering structures in categorical datasets. Knowl Inf Syst 20(1): 1-33.
12. Cormen T, Leiserson C, Rivest R (1990) Introduction to algorithms. MIT Press/McGraw-Hill, Cambridge/New York.
13. Cuthill E, McKee J (1969) Reducing the bandwidth of sparse symmetric matrices. In: Proceedings of the 1969 24th ACM national conference, pp 157-172.
14. Embleton S, Wheeler E (2000) Computerized dialect atlas of Finnish: dealing with ambiguity. J Quant Linguist 7(3): 227-231.
15. Fortelius M (2008) Neogene of the old world database of fossil mammals (NOW). http://www. helsinki. fi/science/now/.
16. Garriga G, Junttila E, Mannila H (2008) Banded structure in binary matrices. In: KDD'08, pp 292-300.
17. Girvan M, Newman M (2002) Community structure in social and biological networks. Proc Natl Acad Sci USA 99(12): 7821-7826.
18. Kirkpatrick S, Gelatt C, Vecchi M (1983) Optimization by simulated annealing. Science 220(4598): 671-680.
19. Knuth D (1993) The Stanford GraphBase: a platform for combinatorial computing. ACM, New York.
20. Lin I-J, West DB (1992) Interval digraphs that are indifference digraphs. In: Graph theory, combinatorics, and algorithms, pp 751-765.
21. Madeira SC, Oliveira AL (2004) Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans Comput Biol Bioinforma 1(1): 24-45.
22. Mäkinen E, Siirtola H (2000) Reordering the reorderable matrix as an algorithmic problem. In: Diagrams '00: proceedings of the first international conference on theory and application of diagrams. Springer, Berlin, pp 453-467.
23. Mannila H, Terz E (2007) Nestedness and segmented nestedness. In: KDD'07, pp 480-489.
24. McConnell RM (2004) A certifying algorithm for the consecutive-ones property. In: SODA'04, pp 768-777.
25. Moise G, Zimek A, Kröger P, Kriegel H, Sander J (2009) Subspace and projected clustering: experimental evaluation and analysis. Knowl Inf Syst 21(3): 299-326.
26. Myllykangas S, Himberg J, Böhling T, Nagy B, Hollmén J, Knuutila S (2006) DNA copy number amplification profiling of human neoplasms. Oncogene 25: 7324-7332.
27. Papadimitriou CH (1976) The NP-completeness of the bandwidth minimization problem. Computing 16: 263-270.
28. Parsons L, Haque E, Liu H (2004) Subspace clustering for high dimensional data: a review. SIGKDD Explor Newsl 6(1): 90-105.
29. Puolamäki K, Fortelius M, Mannila H (2006) Seriation in paleontological data using Markov chain Monte Carlo methods. PLoS Comput Biol 2.
30. Roberts FS (1969) Indifference graphs. In: Proof techniqkues in graph theory, pp 139-146.
31. Rosen R (1968) Matrix bandwidth minimization. In: ACM national conference, pp 585-595.
32. Sen M, Sanyal BK (1994) Indifference digraphs: a generalization of indifference graphs and semiorders. SIAM J Discret Math 7(2): 157-165.
33. Sugiyama K, Tagawa S, Toda M (1981) Methods for visual understanding of hierarchical system structures. IEEE Trans Syst Man Cybern 11(2): 109-125.
34. Tian P, Ma J, Zhang D (1999) Application of the simulated annealing algorithm to the combinatorial optimisation problem with permutation property: An investigation of generation mechanism. Eur J Oper Res 118(1): 81-94.
35. Tucker A (1972) A structure theorem for the consecutive 1's property. J Comb Theory Ser B 12(2): 153-162.