Information geometry for phylogenetic trees
From MaRDI portal
Publication:2659042
DOI10.1007/S00285-021-01553-XzbMATH Open1460.92141arXiv2003.13004OpenAlexW3130203632WikidataQ113905593 ScholiaQ113905593MaRDI QIDQ2659042FDOQ2659042
Authors: Maryam K. Garba, Tom M. W. Nye, Jonas Lueg, Stephan F. Huckemann 
Publication date: 25 March 2021
Published in: Journal of Mathematical Biology (Search for Journal in Brave)
Abstract: We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than existing spaces: in wald space, trees are close if they induce similar distributions on genetic sequence data. As a point set, wald space contains the previously developed Billera-Holmes-Vogtmann (BHV) tree space; it also contains disconnected forests, like the edge-product (EP) space but without certain singularities of the EP space. We investigate two related geometries on wald space. The first is the geometry of the Fisher information metric of character distributions induced by the two-state symmetric Markov substitution process on each tree. Infinitesimally, the metric is proportional to the Kullback-Leibler divergence, or equivalently, as we show, any to f -divergence. The second geometry is obtained analogously but using a related continuous-valued Gaussian process on each tree, and it can be viewed as the trace metric of the affine-invariant metric for covariance matrices. We derive a gradient descent algorithm to project from the ambient space of covariance matrices to wald space. For both geometries we derive computational methods to compute geodesics in polynomial time and show numerically that the two information geometries (discrete and continuous) are very similar. In particular geodesics are approximated extrinsically. Comparison with the BHV geometry shows that our canonical and biologically motivated space is substantially different.
Full work available at URL: https://arxiv.org/abs/2003.13004
Recommendations
- Information metrics for phylogenetic trees via distributions of discrete and continuous characters
- Geometry of the space of phylogenetic trees
- On the information content of discrete phylogenetic characters
- Research in Computational Molecular Biology
- Phylogenetic tree reconstruction: geometric approaches
- On geometry of binary symmetric models of phylogenetic trees
- An algebraic metric for phylogenetic trees
- Statistics for phylogenetic trees
- Phylogenetic trees and Euclidean embeddings
- New Gromov-inspired metrics on phylogenetic tree space
Cites Work
- Geometry of the space of phylogenetic trees
- Polyhedral computational geometry for averaging metric phylogenetic trees
- Title not available (Why is that?)
- Subtree transfer operations and their induced metrics on evolutionary trees
- Title not available (Why is that?)
- Title not available (Why is that?)
- The tropical Grassmannian
- A Differential Geometric Approach to the Geometric Mean of Symmetric Positive-Definite Matrices
- Statistics on the manifold of multivariate normal distributions: theory and application to diffusion tensor MRI processing
- Manifolds of nonpositive curvature
- Computing medians and means in Hadamard spaces
- Title not available (Why is that?)
- Principal components analysis in the space of phylogenetic trees
- Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
- Non-Euclidean statistics for covariance matrices, with applications to diffusion tensor imaging
- Tree cumulants and the geometry of binary tree models
- Peeling phylogenetic `oranges'
- Likelihood calculation in molecular phylogenetics
- $f$ -Divergence Inequalities
- A regular decomposition of the edge-product space of phylogenetic trees
- Toric cubes
- Confidence Sets for Phylogenetic Trees
- Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees
- Tropical principal component analysis and its application to phylogenetics
- Tropical Fermat-Weber points
Cited In (14)
- Bures–Wasserstein Minimizing Geodesics between Covariance Matrices of Different Ranks
- Geometry of the space of phylogenetic trees
- Theoretically and Computationally Convenient Geometries on Full-Rank Correlation Matrices
- Foundations of the Wald Space for Phylogenetic Trees
- Tropical logistic regression model on space of phylogenetic trees
- Tropical optimal transport and Wasserstein distances
- Classifying tree topology changes along tropical line segments
- Information metrics for phylogenetic trees via distributions of discrete and continuous characters
- Limiting behaviour of Fréchet means in the space of phylogenetic trees
- Permutation-invariant log-Euclidean geometries on full-rank correlation matrices
- Wald space for phylogenetic trees
- Metric statistics: exploration and inference for random objects with distance profiles
- Tree topologies along a tropical line segment
- Tropical geometric variation of tree shapes
Uses Software
This page was built for publication: Information geometry for phylogenetic trees
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2659042)
