Generating uniformly distributed random networks.

The analysis of real networks taken from the biological, social, and physical sciences often requires a carefully posed statistical null-hypothesis approach. One common method requires comparing real networks to an ensemble of random matrices that satisfy realistic constraints in which each different matrix member is equiprobable. We discuss existing methods for generating uniformly distributed (constrained) random matrices, describe their shortcomings, and present an efficient technique that should have many practical applications.

[1]  M. Newman,et al.  Reply to ``Comment on `Subgraphs in random networks' '' , 2004 .

[2]  Oliver D. King Comment on "Subgraphs in random networks". , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[3]  Sarel J Fleishman,et al.  Comment on "Network Motifs: Simple Building Blocks of Complex Networks" and "Superfamilies of Evolved and Designed Networks" , 2004, Science.

[4]  S. Shen-Orr,et al.  Superfamilies of Evolved and Designed Networks , 2004, Science.

[5]  Arif Zaman,et al.  Random binary matrices in biogeographical ecology—Instituting a good neighbor policy , 2002, Environmental and Ecological Statistics.

[6]  L. Stone,et al.  The checkerboard score and species distributions , 1990, Oecologia.

[7]  Alan Roberts,et al.  Island-sharing by archipelago species , 2004, Oecologia.

[8]  János Podani,et al.  RANDOMIZATION OF PRESENCE–ABSENCE MATRICES: COMMENTS AND NEW ALGORITHMS , 2004 .

[9]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[10]  Sergio de-los-Cobos-Silva,et al.  A reduced formula for the precise number of (0, 1)-matrices in A(R, S) , 2002, Discret. Math..

[11]  Nicholas J. Gotelli,et al.  SPECIES CO‐OCCURRENCE: A META‐ANALYSIS OF J. M. DIAMOND'S ASSEMBLY RULES MODEL , 2002 .

[12]  K. Sneppen,et al.  Specificity and Stability in Topology of Protein Networks , 2002, Science.

[13]  B. Manly,et al.  A NOTE ON NULL MODELS: JUSTIFYING THE METHODOLOGY , 2002 .

[14]  J. Dall,et al.  Faster Monte Carlo simulations at low temperatures. The waiting time method , 2001, cond-mat/0107475.

[15]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[16]  Fuzhen Zhang,et al.  On the precise number of (0, 1)-matrices in U(R, R) , 1998, Discret. Math..

[17]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[18]  D. Gillespie A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[19]  A. B. Bortz,et al.  A new algorithm for Monte Carlo simulation of Ising spin systems , 1975 .

[20]  S. Goldhor Ecology , 1964, The Yale Journal of Biology and Medicine.