Parametric Inference for Biological Sequence Analysis

Details Parametric Inference for Biological Sequence Analysis Parametric Inference for Biological Sequence Analysis

2004-01-26

arxiv.org/abs/q-bio/0401033v1

Biology

Quantitative Biology

Genomics

15 pages, 4 figures. See also companion paper "Tropical Geometry of Statistical Models" (q-bio.QM/0311009)

Scientific paper

10.1073/pnas.0406011101

One of the major successes in computational biology has been the unification, using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied towards these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems associated with different statistical models. This paper introduces the \emph{polytope propagation algorithm} for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.

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