Identifiability in phylogenetics using algebraic matroids

DOI10.1016/J.JSC.2020.04.012zbMATH Open1455.92103arXiv1909.13754OpenAlexW3023125334MaRDI QIDQ2229705FDOQ2229705

Seth Sullivant, Benjamin Hollering

Publication date: 18 February 2021

Published in: Journal of Symbolic Computation (Search for Journal in Brave)

Abstract: Identifiability is a crucial property for a statistical model since distributions in the model uniquely determine the parameters that produce them. In phylogenetics, the identifiability of the tree parameter is of particular interest since it means that phylogenetic models can be used to infer evolutionary histories from data. In this paper we introduce a new computational strategy for proving the identifiability of discrete parameters in algebraic statistical models that uses algebraic matroids naturally associated to the models. We then use this algorithm to prove that the tree parameters are generically identifiable for 2-tree CFN and K3P mixtures. We also show that the $k$-cycle phylogenetic network parameter is identifiable under the K2P and K3P models.

Full work available at URL: https://arxiv.org/abs/1909.13754

Recommendations

• Identifiability of large phylogenetic mixture models
• Identifiability of 3-class Jukes-Cantor mixtures
• Estimating trees from filtered data: identifiability of models for morphological phylogenetics
• Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
• scientific article; zbMATH DE number 5247137

zbMATH Keywords

mixture modelsidentifiabilityphylogeneticsalgebraic matroidsgroup-based models

Mathematics Subject Classification ID

Problems related to evolution (92D15) Toric varieties, Newton polyhedra, Okounkov bodies (14M25) Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.) (13P25)

Cites Work

• Phylogeny. Discrete and random processes in evolution
• Title not available (Why is that?)
• Mixed-up trees: the structure of phylogenetic mixtures
• Title not available (Why is that?)
• Invariants of phylogenies in a simple case with discrete states
• Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
• Invariants of some probability models used in phylogenetic inference
• Toric Ideals of Phylogenetic Invariants
• Distinguishing Phylogenetic Networks
• Algebraic Statistics
• Dimensions of group-based phylogenetic mixtures
• Identifiability of 3-class Jukes-Cantor mixtures

Cited In (9)

• Identifiability of species network topologies from genomic sequences using the logDet distance
• Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes
• Classes of explicit phylogenetic networks and their biological and mathematical significance
• Exploring spaces of semi-directed level-1 networks
• Invariants for level-1 phylogenetic networks under the Cavendar-Farris-Neyman model
• Bounding the softwired parsimony score of a phylogenetic network
• Nonlinear algebra and applications
• Identifiability and inference of phylogenetic birth-death models
• Identifiability of homoscedastic linear structural equation models using algebraic matroids

Uses Software

• Macaulay2
• Mathematica
• PhylogeneticTrees

This page was built for publication: Identifiability in phylogenetics using algebraic matroids

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2229705)