Literature DB >> 15534224

Tropical geometry of statistical models.

Lior Pachter1, Bernd Sturmfels.   

Abstract

This article presents a unified mathematical framework for inference in graphical models, building on the observation that graphical models are algebraic varieties. From this geometric viewpoint, observations generated from a model are coordinates of a point in the variety, and the sum-product algorithm is an efficient tool for evaluating specific coordinates. Here, we address the question of how the solutions to various inference problems depend on the model parameters. The proposed answer is expressed in terms of tropical algebraic geometry. The Newton polytope of a statistical model plays a key role. Our results are applied to the hidden Markov model and the general Markov model on a binary tree.

Mesh:

Year:  2004        PMID: 15534224      PMCID: PMC528960          DOI: 10.1073/pnas.0406010101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  4 in total

1.  A fast algorithm for joint reconstruction of ancestral amino acid sequences.

Authors:  T Pupko; I Pe'er; R Shamir; D Graur
Journal:  Mol Biol Evol       Date:  2000-06       Impact factor: 16.240

2.  Phylogenetic invariants for the general Markov model of sequence mutation.

Authors:  Elizabeth S Allman; John A Rhodes
Journal:  Math Biosci       Date:  2003-12       Impact factor: 2.144

3.  Parametric inference for biological sequence analysis.

Authors:  Lior Pachter; Bernd Sturmfels
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-08       Impact factor: 11.205

4.  Parametric sequence comparisons.

Authors:  M S Waterman; M Eggert; E Lander
Journal:  Proc Natl Acad Sci U S A       Date:  1992-07-01       Impact factor: 11.205

  4 in total
  4 in total

1.  Parametric inference for biological sequence analysis.

Authors:  Lior Pachter; Bernd Sturmfels
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-08       Impact factor: 11.205

2.  The model-specific Markov embedding problem for symmetric group-based models.

Authors:  Muhammad Ardiyansyah; Dimitra Kosta; Kaie Kubjas
Journal:  J Math Biol       Date:  2021-09-09       Impact factor: 2.259

3.  Reduction of dynamical biochemical reactions networks in computational biology.

Authors:  O Radulescu; A N Gorban; A Zinovyev; V Noel
Journal:  Front Genet       Date:  2012-07-19       Impact factor: 4.599

4.  An algebraic topological method for multimodal brain networks comparisons.

Authors:  Tiago Simas; Mario Chavez; Pablo R Rodriguez; Albert Diaz-Guilera
Journal:  Front Psychol       Date:  2015-07-06
  4 in total

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