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Inverting Random Functions III: Discrete MLE Revisited

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Abstract

This paper continues our earlier investigations into the inversion of random functions in a general (abstract) setting. In Section 2, we investigate a concept of invertibility and the invertibility of the composition of random functions defined on finite sets. In Section 3, we resolve some questions concerning the number of samples required to ensure the accuracy of maximum likelihood estimation (MLE) in the presence of ‘nuisance’ parameters. A direct application to phylogeny reconstruction is given.

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References

  1. Allman E.S., Ané C., Rhodes J.A.: Identifiability of a Markovian model of molecular evolution with gamma-distributed rates. Adv. in Appl. Probab. 40, 229–249 (2008)

    Article  MATH  MathSciNet  Google Scholar 

  2. Casella G., Berger R.L.: Statistical Inference. Duxbury Press, Belmont (1990)

    MATH  Google Scholar 

  3. Chang J.T.: Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Math. Biosci. 137, 51–73 (1996)

    Article  MATH  MathSciNet  Google Scholar 

  4. Cover T.M., Thomas J.A.: Elements of Information Theory. John Wiley & Sons, Inc., New York (1991)

    Book  MATH  Google Scholar 

  5. Erdös P.L., Steel M.A., Székely L.A., Warnow T.: A few logs suffice to build (almost) all trees (Part 1). Random Structures Algorithms 14, 153–184 (1999)

    Article  MATH  MathSciNet  Google Scholar 

  6. Everitt B.S.: The Cambridge Dictionary of Statistics. Cambridge University Press, Cambridge UK (1998)

    MATH  Google Scholar 

  7. Farris J.S.: Likelihood and inconsistency. Cladistics 15, 199–204 (1999)

    Google Scholar 

  8. Felsenstein J.: Inferring Phylogenies. Sinauer Associates, Inc., Sunderland, MA (2004)

    Google Scholar 

  9. Rogers J.S.: On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences. Syst. Biol. 46, 354–357 (1997)

    Google Scholar 

  10. Rogers J.S.: Maximum likelihood estimation of phylogenetic trees is consistent when substitution rates vary according to the invariable sites plus gamma distribution. Syst. Biol. 50, 713–722 (2001)

    Article  Google Scholar 

  11. Schrijver A.: Theory of Linear and Integer Programming. John Wiley & Sons Ltd., Chichester (1986)

    MATH  Google Scholar 

  12. Semple C., Steel M.: Phylogenetics. Oxford University Press, Oxford (2003)

    MATH  Google Scholar 

  13. Siddall M.E.: Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris zone. Cladistics 14, 209–220 (1998)

    Article  Google Scholar 

  14. Steel M.A., Székely L.A.: Inverting random functions. Ann. Combin. 3, 103–113 (1999)

    Article  MATH  Google Scholar 

  15. Steel M.A., Székely L.A.: Inverting random functions II: explicit bounds for the discrete maximum likelihood estimation, with applications. SIAM J. Discrete Math. 15, 562–575 (2002)

    Article  MATH  MathSciNet  Google Scholar 

  16. Steel M.A., Székely L.A.: Teasing apart two trees. Combin. Probab. Comput. 16, 903–922 (2007)

    Article  MATH  MathSciNet  Google Scholar 

  17. Wald A.: Note on the consistency of the maximum likelihood estimate. Ann. Math. Statist. 20, 595–601 (1949)

    Article  MATH  MathSciNet  Google Scholar 

  18. Yang Z.: Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Syst. Biol. 43, 329–342 (1994)

    Google Scholar 

  19. Yang Z.: Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42, 294–307 (1996)

    Article  Google Scholar 

Download references

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Correspondence to Mike A. Steel.

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We thank the NZIMA Maclaurin Fellowship, the Phylogeny programme at the Isaac Newton Institute of Cambridge University, and Hungarian Bioinformatics MTKD-CT-2006-042794 for supporting this research. The second author was also supported in part by NSF DMS contracts 007 2187, 070 1111, and NIH NIGMS 1 R01 GM078991-01.

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Steel, M.A., Székely, L.A. Inverting Random Functions III: Discrete MLE Revisited. Ann. Comb. 13, 365–382 (2009). https://doi.org/10.1007/s00026-009-0023-z

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  • DOI: https://doi.org/10.1007/s00026-009-0023-z

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