Model criticism based on likelihood-free inference, with an application to protein network evolution

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 26, 2009, Pages 10576-10581

  Ratmann, Oliver ^a   Andrieu, Christophe ^b   Wiuf, Carsten ^c   Richardson, Sylvia ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

^c AARHUS UNIVERSITY   (Denmark)

Author keywords

Approximate Bayesian computation; Bayesian inference; Intractable likelihoods; Markov chain Monte Carlo; Model uncertainty

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; HELICOBACTER PYLORI; HORIZONTAL GENE TRANSFER; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; MONTE CARLO METHOD; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN DATABASE; STATISTICAL MODEL; TREPONEMA PALLIDUM;

ALGORITHMS; BACTERIAL PROTEINS; BAYES THEOREM; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; HELICOBACTER PYLORI; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; MONTE CARLO METHOD; PROTEIN INTERACTION MAPPING; TREPONEMA PALLIDUM;

HELICOBACTER PYLORI; TREPONEMA PALLIDUM;

EID: 67649819681     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0807882106     Document Type: Article

References (33)

1. May RM (2004) Uses and abuses of mathematics in biology. Science 303:790-793. (Pubitemid 38174648)
2. Box GEP (1976) Science and statistics. J Am Stat Assoc 71:791-799.
3. Bernado JM, Smith AFM (1994) Bayesian Theory (Wiley & Sons, Chichester, UK), 1st Ed.
4. Box GEP (1980) Sampling and Bayes' inference in scientific modelling and robustness. J R Soc A (General) 143:383-430.
5. Gelfand AE, Dey DK, Chang H (1992) Bayesian Statistics 4, eds Bernardo JM, Berger JO, Dawid AP, Smith AFM (Oxford Univ Press, Oxford), pp 147-167.
6. Meng XL (1994) Posterior predictive p-values. Ann Stat 22(3):1142-1160.
7. Bayarri MJ, Berger JO (1999) Bayesian Statistics 6, eds Bernardo JM, Berger JO, Dawid AP, Smith AFM (Oxford Univ Press, Oxford), pp 53-82.
8. Liu JS (2001) Monte Carlo Strategies in Scientific Computing (Springer, New York), 343 pp.
9. Gouriéroux C, Monfort A (1996) Simulation-Based Econometric Methods (Oxford Univ Press, Oxford).
10. Marjoram P, Tavaré S (2006) Modern computational approaches for analysing molecular genetic variation data. Nat Rev Genet 7:759-770. (Pubitemid 44413220)
11. Riley S, et al. (2003) Transmission dynamics of the etiological agent of SARS in Hong Kong: Impact of public health interventions. Science 300:1961-1966. (Pubitemid 36734606)
12. Ratmann O, et al. (2007) Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H.pylori and P.falciparum. PLoS Comp Biol 3:e230. (Pubitemid 350241950)
13. Wilkinson RD (2007) Bayesian inference of primate divergence times. PhD thesis (Univ of Cambridge, Cambridge).
14. Fagundes NJR, et al. (2007) Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci USA 104:17614-17619. (Pubitemid 350210884)
15. Toni T, Welch D, Strelkowa N, Ipsen A, Stumpf MPH (2008) Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J R Soc Interf, 10.1098rsif. 2008.0172.
16. Zellner A (1975) Bayesian analysis of regression error terms. J Am Stat Assoc 70:138-144.
17. O'Hagan A (2003) Highly Structured Stochastic Systems, eds Green PJ, Hjort NL, Richardson S (Oxford Univ Press, Oxford), pp 423-453.
18. Rain JC, et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature 409:211-215. (Pubitemid 32144288)
19. Titz B, et al. (2008) The binary protein interactome of Treponema pallidum - The Syphilis spirochete. PLoS ONE 3:e2292.
20. Beltrao P, Serrano L (2007) Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comp Biol 3:e25. (Pubitemid 46318385)
21. Pinney JW, Amoutzias GD, Rattray M, Robertson DL (2007) Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proc Natl Acad Sci USA 104:20449-20453.
22. Hakes L, Pinney JW, Robertson DL, Lovell SC (2008) Protein-protein interaction networks and biology - What's the connection? Nat Biotechnol 26:69-72.
23. Wilkinson RD (2008) Approximate Bayesian Computation (ABC) gives exact results under the assumption of model error. arXiv:0811.3355v1 [stat.CO].
24. Sisson SA, Fan Y, Tanaka MM (2007) Sequential Monte Carlo without likelihoods. Proc Natl Acad Sci USA 104:1760-1765. (Pubitemid 46239852)
25. Gilks WR, Richardson S, Spiegelhalter DJ (1996) Markov Chain Monte Carlo in Practice (Chapman & Hall, London).
26. Marjoram P, Molitor J, Plagnol V, Tavaré S (2003) Markov Chain Monte Carlo without likelihoods. Proc Natl Acad Sci USA 100:15324-15328. (Pubitemid 38020988)
27. Bortot P, Coles S, Sisson S (2007) Inference for stereological extremes. J Am Stat Assoc 102:84-92.
28. Becquet C, Przeworski M (2007) A new approach to estimate parameters of speciation models with application to apes. Genome Res 17:1505-1519. (Pubitemid 47529435)
29. Knudsen M, Wiuf C (2008) A Markov chain approach to randomly grown graphs. J Appl Math, 10.1155/2008/190836.
30. Dagan T, Artzy-Randrup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA 105:10039-10044.
31. Chothia C, Gough J, Vogel C, Teichmann SA (2003) Evolution of the protein repertoire. Science 300:1701-1703. (Pubitemid 36712556)
32. Davidson EH, Erwin DH (2006) Gene regulatory networks and the evolution of animal body plans. Science 311:796-800. (Pubitemid 43228832)
33. Barabási A, Albert R (1999) Emergence of scaling in random networks. Science 286:509-512.