A Markov Chain Approach to Randomly Grown Graphs

A Markov chain approach to the study of randomly grown graphs is proposed and applied to some popular models that have found use in biology and elsewhere. For most randomly grown graphs used in biology, it is not known whether the graph or properties of the graph converge (in some sense) as the number of vertices becomes large. Particularly, we study the behaviour of the degree sequence, that is, the number of vertices with degree in large graphs, and apply our results to the partial duplication model. We further illustrate the results by application to real data.

[1]  Mark E. J. Newman,et al.  The Structure and Function of Complex Networks , 2003, SIAM Rev..

[2]  A. Wagner How the global structure of protein interaction networks evolves , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[3]  M. Newman,et al.  Why social networks are different from other types of networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[4]  Carsten Wiuf,et al.  Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum , 2007, PLoS Comput. Biol..

[5]  Sergey N. Dorogovtsev,et al.  Evolution of Networks: From Biological Nets to the Internet and WWW (Physics) , 2003 .

[6]  M. Stumpf,et al.  A likelihood approach to analysis of network data , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Z. Burda,et al.  Statistical ensemble of scale-free random graphs. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[8]  Albert-László Barabási,et al.  Evolution of Networks: From Biological Nets to the Internet and WWW , 2004 .

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

[10]  ALGEBRAIC CHARACTERIZATION OF INFINITE MARKOV CHAINS WHERE MOVEMENT TO THE RIGHT IS LIMITED TO ONE STEP , 1977 .

[11]  M. Vignali,et al.  A protein interaction network of the malaria parasite Plasmodium falciparum , 2005, Nature.

[12]  Béla Bollobás,et al.  Random Graphs , 1985 .

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

[14]  Michael P H Stumpf,et al.  Complex networks and simple models in biology , 2005, Journal of The Royal Society Interface.

[15]  E. Ziv,et al.  Inferring network mechanisms: the Drosophila melanogaster protein interaction network. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[16]  David J. Galas,et al.  A duplication growth model of gene expression networks , 2002, Bioinform..

[17]  V. Romanovsky Note on the Moments of a Binomial (p + q) n about its Mean , 1923 .

[18]  F. Chung,et al.  Complex Graphs and Networks , 2006 .

[19]  S. Shen-Orr,et al.  Networks Network Motifs : Simple Building Blocks of Complex , 2002 .

[20]  Carl M. Harris,et al.  A Note on Feedback Queues with Bulk Service , 1972, JACM.

[21]  R. Tweedie Sufficient conditions for regularity, recurrence and ergodicity of Markov processes , 1975, Mathematical Proceedings of the Cambridge Philosophical Society.

[22]  John F. Padgett,et al.  Robust Action and the Rise of the Medici, 1400-1434 , 1993, American Journal of Sociology.

[23]  Albert-László Barabási,et al.  Statistical mechanics of complex networks , 2001, ArXiv.

[24]  Chris Wiggins,et al.  Discriminative topological features reveal biological network mechanisms , 2004, BMC Bioinformatics.

[25]  Alpan Raval,et al.  Some asymptotic properties of duplication graphs. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[26]  M. Purugganan,et al.  The evolution of molecular genetic pathways and networks , 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

[27]  Fan Chung Graham,et al.  Duplication Models for Biological Networks , 2002, J. Comput. Biol..

[28]  Carsten Wiuf,et al.  Convergence properties of the degree distribution of some growing network models , 2006, Bulletin of mathematical biology.

[29]  M. Stumpf,et al.  Evolution at the system level: the natural history of protein interaction networks. , 2007, Trends in ecology & evolution.

[30]  S. N. Dorogovtsev,et al.  Evolution of networks , 2001, cond-mat/0106144.

[31]  Ricard V. Solé,et al.  A Model of Large-Scale proteome Evolution , 2002, Adv. Complex Syst..