E. M. Airoldi, C. , and K. M. , Sampling algorithms for pure network topologies, ACM KDD Explorations, vol.7, pp.13-22, 2005.

E. M. Airoldi, D. M. Blei, S. E. Fienberg, and E. P. Xing, Mixed membership stochastic blockmodels, J. Mach. Learn. Res, vol.9, pp.1981-2014, 2008.

R. Albert and A. L. Barabási, Statistical mechanics of complex networks, Rev. Modern Phys, vol.74, pp.47-97, 2002.

H. Attias, A variational Bayesian framework for graphical models, Advances in Neural Information Processing Systems, vol.12, pp.209-215, 2000.

A. L. Barabási, A. , and R. , Emergence of scaling in random networks, Science, vol.286, pp.509-512, 1999.

M. J. Beal and Z. Ghahramani, The variational Bayesian EM algorithm for incomplete data: With application to scoring graphical model structures, Bayesian Statistics, p.2003189, 2003.

L. F. Bersier and P. Kehrli, The signature of phylogenetic constraints on food-web structure, Ecol. Complex, vol.5, pp.132-139, 2008.

C. Biernacki, G. Celeux, and G. Govaert, Assessing a mixture model for clustering with the integrated completed likelihood, IEEE Trans. Pattern Anal. Machine Intel, vol.22, pp.719-725, 2000.

S. P. Blomberg and T. J. Garland, Tempo and mode in evolution: Phylogenetic inertia, adaptation and comparative methods, J. Evol. Biol, vol.15, pp.899-910, 2002.

M. Brandle and R. Brandl, Is the composition of phytophagous insects and parasitic fungi among trees predictable, Oikos, vol.113, pp.296-304, 2006.

K. P. Burnham, A. , and R. A. , Model Selection and Inference: A Practical Information-Theoretic Approach, 1998.

M. F. Cattin, L. F. Bersier, C. C. Banasek-richter, R. Baltensperger, and J. P. Gabriel, Phylogenetic constraints and adaptation explain food-web structure, Nature, vol.427, pp.835-839, 2004.

J. Daudin, F. Picard, and S. Robin, A mixture model for random graphs, Statist. Comput, vol.18, pp.173-183, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01197587

A. P. Dempster, N. M. Laird, and D. B. Rubin, Maximum likelihood from incomplete data via the EM algorithm, J. Roy. Statist. Soc. B, vol.39, p.501537, 1977.

P. Erdös and A. Rényi, On random graphs, i, Publ. Math, vol.6, p.120167, 1959.

S. E. Fienberg and S. Wasserman, Categorical data analysis of single sociometric relations, Sociological Methodology, pp.156-192, 1981.

S. E. Fienberg, M. M. Meyer, and S. S. Wasserman, Statistical analysis of multiple sociometric relations, J. Amer. Statist. Assoc, vol.80, pp.51-67, 1985.

L. Getoor and C. P. Diehl, Link mining: A survey, SIGKDD Explor, vol.7, pp.3-12, 2004.

G. S. Gilbert and C. O. Webb, Phylogenetic signal in plant pathogen-host range, Proc. Natl. Acad. Sci. USA, vol.104, pp.4979-4983, 2007.

M. Girvan and M. E. Newman, Community structure in social and biological networks, Proc. Natl. Acad. Sci. USA, vol.99, p.1908073, 2002.

G. Govaert and M. Nadif, An EM algorithm for the block mixture model, IEEE Trans. Pattern Anal. Machine Intel, vol.27, pp.643-647, 2005.

J. M. Hofman and C. H. Wiggins, A Bayesian approach to network modularity, Phys. Rev. Lett, vol.100, p.258701, 2008.

P. Holland and S. Leinhardt, An exponential family of probability distributions for directed graphs, J. Amer. Statist. Assoc, vol.76, pp.33-50, 1981.

A. R. Ives and H. C. Godfray, Phylogenetic analysis of trophic associations, Am. Nat, vol.16, pp.1-14, 2006.

T. Jaakkola, Tutorial on variational approximation methods, Advanced Mean Field Methods: Theory and Practice, 2000.

P. Jaccard, Tude comparative de la distribution florale dans une portion des alpes et des jura, Bullet. Soc. Vaud. Sci. Natur, vol.37, pp.547-579, 1901.

M. I. Jordan, Z. Ghahramani, T. Jaakkola, and L. K. Saul, An introduction to variational methods for graphical models, Mach. Learn, vol.37, pp.183-233, 1999.

C. Kemp, T. H. Griffiths, and J. B. Tenenbaum, Discovering latent classes in relational data, 2004.

M. A. Leisink and H. J. Kappen, A tighter bound for graphical models. Neural Comput, vol.13, pp.2149-2171, 2001.

F. Lorrain and H. C. White, Structural equivalence of individuals in social networks, J. Math. Soc, vol.1, pp.49-80, 1971.

M. Mariadassou, Estimation paramétrique dans le modèle ERMG, 2006.

M. Mariadassou, S. Robin, and C. Vacher, Uncovering latent structure in valued graphs: A variational approach, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01197514

C. A. Mcgrory and D. M. Titterington, Variational approximations in Bayesian model selection for finite mixture distributions, Comput. Statist. Data Anal, vol.51, pp.5352-5367, 2007.

G. Mclahan and D. Peel, Finite Mixture Models, 2000.

M. E. Newman, Fast algorithm for detecting community structure in networks, Phys. Rev. E, vol.69, p.66133, 2004.

M. E. Newman, D. J. Watts, and S. H. Strogatz, Random graph models of social networks, Proc. Natl. Acad. Sci. USA, vol.99, pp.2566-2572, 2002.

K. Nowicki and T. A. Snijders, Estimation and prediction for stochastic blockstructures, J. Amer. Statist. Assoc, vol.96, p.1947255, 2001.

E. Paradis, J. Claude, and K. Strimmer, Ape: Analyses of phylogenetics and evolution in R language, Bioinformatics, vol.20, pp.289-290, 2004.
URL : https://hal.archives-ouvertes.fr/ird-01887318

P. E. Pattison and G. L. Robins, Probabilistic network theory, Handbook of Probability Theory with Applications, 2007.

F. Picard, J. Daudin, V. Miele, M. Mariadassou, and S. Robin, A novel framework for random graph models with heterogeneous connectivity structure, 2007.

R. Poulin, Relative infection levels and taxonomic distances among the host species used by a parasite: Insights into parasite specialization, Parasitology, vol.130, pp.109-115, 2005.

E. L. Rezende, J. E. Lavabre, P. R. Guimaraes, J. R. Jordano, P. Bascompte et al., Non-random coextinctions in phylogenetically structured mutualistic networks, Nature, vol.448, pp.925-928, 2007.

R. E. Ricklefs and G. L. Miller, Community ecology. In Ecology, 2000.

A. G. Rossberg, R. Ishii, T. Amemiya, and K. Itoh, Food webs: Experts consuming families of experts, J. Theoret. Biol, p.2254907, 2006.

J. M. Tykiakanis, T. Tscharntke, and O. T. Lewis, Habitat modification alters the structure of tropical host-parasitoid food webs, Nature, vol.51, pp.202-205, 2007.

C. Vacher, D. Piou, and M. Desprez-loustau, Architecture of an antagonistic tree/fungus network: The asymmetric influence of past evolutionary history, PLoS ONE, vol.3, p.1740, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02669044

U. Von-luxburg, M. Belkin, and O. Bousquet, Consistency of spectral clustering, Ann. Statist, vol.36, p.2396807, 2008.

C. O. Webb and M. J. Donoghue, Phylomatic: Tree assembly for applied phylogenetics, Mol. Ecol. Notes, vol.5, pp.181-183, 2005.

J. Winn, C. M. Bishop, and T. Jaakkola, Variational message passing, J. Mach. Learn. Res, vol.6, p.2249835, 2005.

E. Xing, M. Jordan, and S. Russell, A generalized mean field algorithm for variational inference in exponential families, Proceedings of the 19th Annual Conference on Uncertainty in Artificial Intelligence (UAI-03) 583-591, 2003.

J. S. Yedidia, W. T. Freeman, and Y. Weiss, Constructing free-energy approximations and generalized belief propagation algorithms, IEEE Inform. Theory, vol.15, p.2246363, 2005.