Markov dynamics as a zooming lens for multiscale community detection: Non clique-like communities and the field-of-view limit

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Schaub, Michael T ^a   Delvenne, Jean Charles ^b   Yaliraki, Sophia N ^a   Barahona, Mauricio ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL PARAMETERS; ARTICLE; ARTIFICIAL NEURAL NETWORK; COMMUNITY ASSESSMENT; COMMUNITY DETECTION; COMMUNITY DYNAMICS; COMMUNITY STRUCTURE; CONTROLLED STUDY; FIELD OF VIEW LIMIT; IMAGE ANALYSIS; PROBABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; ALGORITHM; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; DEMOGRAPHY; IMAGE PROCESSING; METHODOLOGY; POWER SUPPLY; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; STATISTICAL MODEL;

ADENYLATE KINASE;

ADENYLATE KINASE; ALGORITHMS; COMPUTATIONAL BIOLOGY; ELECTRIC POWER SUPPLIES; IMAGE PROCESSING, COMPUTER-ASSISTED; MARKOV CHAINS; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RESIDENCE CHARACTERISTICS; SOFTWARE;

EID: 84857539615     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032210     Document Type: Article

References (38)

1. Delvenne JC, Yaliraki SN, Barahona M, (2010) Stability of graph communities across time scales. Proceedings of the National Academy of Sciences 107: 12755-12760 Also at URL http://arxiv. org/abs/0812.1811.
2. Lambiotte R, Delvenne JC, Barahona M, (2008) Laplacian Dynamics and Multiscale Modular Structure in Networks. URL http://arxiv.org/abs/0812.1770. Arxiv preprint.
3. Fortunato S, (2010) Community detection in graphs. Physics Reports 486: 75-174.
4. Castellano C, Fortunato S, Loreto V, (2009) Statistical physics of social dynamics. Rev Mod Phys 81: 591-646.
5. Rives AW, Galitski T, (2003) Modular organization of cellular networks. Proceedings of the National Academy of Sciences of the United States of America 100: 1128-1133.
6. Bullmore E, Sporns O, (2009) Complex brain networks: graph theoretical analysis of structural and functional systems. Nature Reviews Neuroscience 10: 186-198.
7. Newman MEJ, Girvan M, (2004) Finding and evaluating community structure in networks. Phys Rev E 69: 026113.
8. Newman MEJ, (2006) Finding community structure in networks using the eigenvectors of matrices. Phys Rev E 74: 036104.
9. Reichardt J, Bornholdt S, (2004) Detecting Fuzzy Community Structures in Complex Networks with a Potts Model. Phys Rev Lett 93: 218701.
10. Reichardt J, Bornholdt S, (2006) Statistical mechanics of community detection. Phys Rev E 74: 016110.
11. Ronhovde P, Nussinov Z, (2009) Multiresolution community detection for megascale networks by information-based replica correlations. Phys Rev E 80: 016109.
12. Blondel VD, Guillaume JL, Lambiotte R, Lefebvre E, (2008) Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment 2008: P10008.
13. Rosvall M, Bergstrom CT, (2007) An information-theoretic framework for resolving community structure in complex networks. Proceedings of the National Academy of Sciences 104: 7327-7331.
14. Rosvall M, Bergstrom CT, (2008) Maps of random walks on complex networks reveal community structure. Proceedings of the National Academy of Sciences 105: 1118-1123.
15. Danon L, Díaz-Guilera A, Arenas A, (2006) The effect of size heterogeneity on community identification in complex networks. Journal of Statistical Mechanics: Theory and Experiment 2006: P11010.
16. Lancichinetti A, Fortunato S, Radicchi F, (2008) Benchmark graphs for testing community detection algorithms. Phys Rev E 78: 046110.
17. Lancichinetti A, Fortunato S, (2009) Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities. Phys Rev E 80: 016118.
18. Fortunato S, Barthélemy M, (2007) Resolution limit in community detection. Proceedings of the National Academy of Sciences 104: 36-41.
19. Lancichinetti A, Fortunato S, (2009) Community detection algorithms: A comparative analysis. Phys Rev E 80: 056117.
20. Schaub MT, Lambiotte R, Barahona M, (2011) Coding of Markov dynamics for multiscale community detection in complex networks. URL http://arxiv.org/abs/1109.6642. Arxiv preprint.
21. Newman MEJ, (2006) Modularity and community structure in networks. Proceedings of the National Academy of Sciences 103: 8577-8582.
22. Lambiotte R, (2010) Multi-scale modularity in complex networks. In: Modeling and Optimization in Mobile, Ad Hoc and Wireless Networks (WiOpt), 2010 Proceedings of the 8th International Symposium on. IEEE, pp. 546-553. URLhttp://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5520347.
23. Delmotte A, Tate EW, Yaliraki SN, Barahona M, (2011) Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin:myosin light chain interaction. Physical Biology 8: 055010.
24. Meila M, (2007) Comparing clusterings-an information based distance. Journal of Multivariate Analysis 98: 873-895.
25. Karrer B, Newman MEJ, (2011) Stochastic blockmodels and community structure in networks. Phys Rev E 83: 016107.
26. Gupta A, Krauthgamer R, Lee J, (2003) Bounded geometries, fractals, and low-distortion embeddings. Foundations of Computer Science, 2003 pp. 534-543 Proceedings. 44th Annual IEEE Symposium on doi:10.1109/SFCS.2003.1238226.
27. Fraigniaud P, Lebhar E, Viennot L, (2008) The Inframetric Model for the Internet. pp. 1085-1093 In: 27th IEEE International Conference on Computer Communications (INFOCOM). IEEE.
28. Boguna M, Papadopoulos F, Krioukov D, (2010) Sustaining the Internet with Hyperbolic Mapping. Nature Communications 1: 62.
29. Tenenbaum JB, de Silva V, Langford JC, (2000) A Global Geometric Framework for Nonlinear Dimensionality Reduction. Science 290: 2319-2323.
30. Watts DJ, Strogatz SH, (1998) Collective dynamics of 'small-world' networks. Nature 393: 440-442.
31. Taylor A, Higham DJ, (2009) CONTEST: A Controllable Test Matrix Toolbox for MATLAB. ACM Trans Math Softw 35: 26:1-26:17.
32. Barahona M, Pecora LM, (2002) Synchronization in Small-World Systems. Phys Rev Lett 89: 054101.
33. Browet A, Absil P, Van Dooren P, (2011) Community Detection for Hierarchical Image Segmentation. In: Aggarwal J, Barneva R, Brimkov V, Koroutchev K, Korutcheva E, editors. Combinatorial Image Analysis, Springer Berlin/Heidelberg, volume 6636 of Lecture Notes in Computer Science. pp. 358-371. URL http://dx.doi.org/10.1007/978-3-642-21073-0_32.
34. Rosvall M, Bergstrom CT, (2011) Multilevel Compression of Random Walks on Networks Reveals Hierarchical Organization in Large Integrated Systems. PLoS ONE 6: e18209.
35. Rosas-Casals M, Valverde S, Solé RV, (2007) Topological Vulnerability of the European Power Grid under Errors and Attacks. I J Bifurcation and Chaos 17: 2465-2475.
36. Solé RV, Rosas-Casals M, Corominas-Murtra B, Valverde S, (2008) Robustness of the European power grids under intentional attack. Phys Rev E 77: 026102.
37. Traag VA, Van Dooren P, Nesterov Y, (2011) Narrow scope for resolution-limit-free community detection. Phys Rev E 84: 016114.
38. Lancichinetti A, Fortunato S, (2011) Limits of modularity maximization in community detection. Phys Rev E 84: 066122.