Efficiently inferring community structure in bipartite networks

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 90, Issue 1, 2014, Pages

  Larremore, Daniel B ^a   Clauset, Aaron ^b,c,d   Jacobs, Abigail Z ^b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b University of Colorado   (United States)

^c SANTA FE INSTITUTE   (United States)

^d UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PARAMETERIZATION; POPULATION DYNAMICS; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

BIPARTITE NETWORK; COMMUNITY DETECTION; COMMUNITY STRUCTURES; IMPLICIT PARAMETERS; INTERPRETABILITY; PARAMETER CHOICE; STOCHASTIC BLOCK MODELS; TYPE INFORMATION;

COMPUTER NETWORKS;

ALGORITHM; FEMALE; HUMAN; MALARIA; SOCIAL NETWORK; STATISTICS; THEORETICAL MODEL; TRANSMISSION;

ALGORITHMS; FEMALE; HUMANS; MALARIA; MODELS, THEORETICAL; SOCIAL NETWORKING; STOCHASTIC PROCESSES;

EID: 84904189293     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.90.012805     Document Type: Article

References (49)

1. J. Bascompte, Science 312, 431 (2006). SCIEAS 0036-8075 10.1126/science.1123412
2. I. S. Dhillon, in Proceedings of the Seventh ACM SIGKDD (ACM, New York, 2001), p. 269.
3. A. Lancichinetti, arXiv:1402.0422.
4. D. B. Larremore, A. Clauset, and C. O. Buckee, PLoS Comput. Biol. 9, e1003268 (2013). 1553-7358 10.1371/journal.pcbi.1003268
5. T. P. Peixoto, Phys. Rev. Lett. 110, 148701 (2013). PRLTAO 0031-9007 10.1103/PhysRevLett.110.148701
6. T. P. Peixoto, Phys. Rev. X 4, 011047 (2014). 10.1103/PhysRevX.4.011047
7. B. Tjaden and P. Reynolds, http://oracleofbacon.org/.
8. M. Ye, D. Shou, W.-C. Lee, P. Yin, and K. Janowicz, in Proceedings 17th ACM SIGKDD (ACM, New York, 2011), p. 520.
9. M. E. J. Newman, Phys. Rev. E 64, 016131 (2001). 1063-651X 10.1103/PhysRevE.64.016131
10. M. E. J. Newman, Phys. Rev. Lett. 89, 208701 (2002). PRLTAO 0031-9007 10.1103/PhysRevLett.89.208701
11. M. E. J. Newman, Phys. Rev. E 67, 026126 (2003). 1063-651X 10.1103/PhysRevE.67.026126
12. J. W. Grossman, http://www.oakland.edu/enp.
13. T. Zhou, J. Ren, M. Medo, and Y.-C. Zhang, Phys. Rev. E 76, 046115 (2007). PLEEE8 1539-3755 10.1103/PhysRevE.76.046115 (Pubitemid 350023332)
14. M. Girvan and M. E. J. Newman, Proc. Natl. Acad. Sci. USA 99, 7821 (2002). PNASA6 0027-8424 10.1073/pnas.122653799 (Pubitemid 34650963)
15. R. Guimera, M. Sales-Pardo, and Luis A. Nunes Amaral, Phys. Rev. E 76, 036102 (2007). PLEEE8 1539-3755 10.1103/PhysRevE.76.036102 (Pubitemid 47443160)
16. M. J. Barber, Phys. Rev. E 76, 066102 (2007). PLEEE8 1539-3755 10.1103/PhysRevE.76.066102 (Pubitemid 350248354)
17. P. W. Holland, K. B. Laskey, and S. Leinhardt, Social Networks 5, 109 (1983). 0378-8733 10.1016/0378-8733(83)90021-7
18. Y. J. Wang and G. Y. Wong, J. Am. Stat. Assoc. 82, 8 (1987). JSTNAL 0162-1459 10.1080/01621459.1987.10478385
19. K. Nowicki and T. A. B. Snijders, J. Am. Stat. Assoc. 96, 1077 (2001). JSTNAL 0162-1459 10.1198/016214501753208735 (Pubitemid 33333511)
20. B. Karrer and M. E. J. Newman, Phys. Rev. E 83, 016107 (2011). PLEEE8 1539-3755 10.1103/PhysRevE.83.016107
21. A. Decelle, F. Krzakala, C. Moore, and L. Zdeborova, Phys. Rev. Lett. 107, 065701 (2011). PRLTAO 0031-9007 10.1103/PhysRevLett.107.065701
22. H.-W. Shen, X.-Q. Cheng, and J.-F. Guo, Phys. Rev. E 84, 056111 (2011). PLEEE8 1539-3755 10.1103/PhysRevE.84.056111
23. S. Allesina and M. Pascual, Ecol. Lett. 12, 652 (2009). 1461-023X 10.1111/j.1461-0248.2009.01321.x
24. R. Guimera, A. Llorente, E. Moro, and M. Sales-Pardo, PLoS One 7, e44620 (2012). 1932-6203 10.1371/journal.pone.0044620
25. N. Rovira-Asenjo, T. Gumi, M. Sales-Pardo, and R. Guimerà, Sci. Rep. 3, 1999 (2013) 10.1038/srep01999.
26. Given a bipartite network consisting of a single component, one can arbitrarily determine vertex types. This is possible but appropriate only if (Equation presented). For networks of multiple components and unknown types, modified likelihood maximization approaches are conceivable, but we offer none here.
27. A. Coja-Oghlan and A. Lanka, SIAM J. Discrete Math. 23, 1682 (2010). SJDMEC 0895-4801 10.1137/070699354
28. B. W. Kernighan and S. Lin, Bell Syst. Tech. J. 49, 291 (1970). BSTJAN 0005-8580 10.1002/j.1538-7305.1970.tb01770.x
29. An exception to this is made when (Equation presented) or (Equation presented) is equal to 1, in which case some vertices will have no possible moves and are accordingly skipped.
30. B. H. Good, Y.-A. de Montjoye, and A. Clauset, Phys. Rev. E 81, 046106 (2010). PLEEE8 1539-3755 10.1103/PhysRevE.81.046106
31. A. Davis, B. B. Gardner, and M. R. Gardner, Deep South (University of Chicago Press, Chicago, 1941).
32. L. C. Freeman, in Dynamic Social Network Modeling and Analysis: Workshop Summary and Papers, edited by R. Breiger, C. Carley, and P. Pattison (National Academies Press, Washington DC, 2003), pp. 39-97.
33. T. S. Rask, D. A. Hansen, T. G. Theander, A. Gorm Pedersen, and T. Lavstsen, PLoS Comput. Biol. 6, e1000933 (2010). 1553-7358 10.1371/journal.pcbi. 1000933
34. P. C. Bull, Mol. Microbiol. 68, 1519 (2008). MOMIEE 0950-382X 10.1111/j.1365-2958.2008.06248.x (Pubitemid 351725260)
35. L. Danon, A. Díaz-Guilera, J. Duch, and A. Arenas, J. Stat. Mech.: Theory Exp. (2005) P09008. 1742-5468 10.1088/1742-5468/2005/09/P09008
36. L. Danon, A. Díaz-Guilera, and A. Arenas, J. Stat. Mech.: Theory Exp. (2006) P11010. 10.1088/1742-5468/2006/11/P11010
37. M. Rosvall and C. T. Bergstrom, Proc. Natl. Acad. Sci. USA 104, 7327 (2007). PNASA6 0027-8424 10.1073/pnas.0611034104 (Pubitemid 47185904)
38. Not unlike other generative network models, there are restrictions on allowable parameters. In this case, we fix (Equation presented) and let (Equation presented) vary by some multiplicative constant for each community, so that we may plant heterogeneous degrees in (Equation presented) without over- or misspecifying (Equation presented).
39. A. Clauset, M. E. J. Newman, and C. Moore, Phys. Rev. E 70, 066111 (2004). PLEEE8 1539-3755 10.1103/PhysRevE.70.066111 (Pubitemid 40429799)
40. This is accurate, but drastically simplified. For biological details see Refs. [33], [4], and [34].
41. Original data are available at http://www.imdb.com/interfaces. IMDb copyright permits redistribution of IMDb data only in unaltered form.
42. X. Yan, J. Stat. Mech. (2014) P05007. 10.1088/1742-5468/2014/05/P05007
43. L. Peel and A. Clauset, arXiv:1403.0989.
44. E. M. Airoldi, D. M. Blei, S. E. Fienberg, and E. P. Xing, J. Mach. Learning Res. 9, 1981 (2008).
45. B. Ball, B. Karrer, and M. E. J. Newman, Phys. Rev. E 84, 036103 (2011). PLEEE8 1539-3755 10.1103/PhysRevE.84.036103
46. C. Aicher, A. Z. Jacobs, and A. Clauset, arXiv:1305.5782.
47. A. Clauset, C. Moore, and M. E. J. Newman, Nature (London) 453, 98 (2008). NATUAS 0028-0836 10.1038/nature06830 (Pubitemid 351630323)
48. http://danlarremore.com/bipartiteSBM.
49. http://danlarremore.com/bipartiteSBM.