Information geometry for phylogenetic trees
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Publication:2659042
DOI10.1007/S00285-021-01553-XzbMATH Open1460.92141arXiv2003.13004OpenAlexW3130203632WikidataQ113905593 ScholiaQ113905593MaRDI QIDQ2659042FDOQ2659042
Jonas Lueg, Maryam K. Garba, Stephan F. Huckemann, Tom M. W. Nye
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
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Cited In (11)
- Bures–Wasserstein Minimizing Geodesics between Covariance Matrices of Different Ranks
- Theoretically and Computationally Convenient Geometries on Full-Rank Correlation Matrices
- 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
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