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Peer-reviewedCC BYVietnam Journal of Mathematics

Tropical Geometry of Phylogenetic Tree Space: A statistical Perspective

  • Anthea Monod1,2
  • Bo Lin1
  • Ruriko Yoshida3
  • Qiwen Kang4
4 affiliations
  1. 1Department of Mathematics, Imperial College London, London, UK
  2. 2Imperial College London
  3. 3Department of Mathematical Sciences, Aalborg University, Aalborg East, Denmark
  4. 4California Tech Hub, Walmart Global Tech, Sunnyvale, USA
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Abstract

Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry. Although they are important data structures, they face the significant challenge that sets of trees form a non-Euclidean phylogenetic tree space, which means that standard computational and statistical methods cannot be directly applied. In this work, we explore the statistical feasibility of a pure mathematical representation of the set of all phylogenetic trees based on tropical geometry for both descriptive and inferential statistics, and unsupervised and supervised machine learning. Our exploration is both theoretical and practical. We show that the tropical geometric phylogenetic tree space endowed with a generalized Hilbert projective metric exhibits analytic, geometric, and topological properties that are desirable for theoretical studies in probability and statistics and allow for well-defined questions to be posed. We illustrate the statistical feasibility of the tropical geometric perspective for phylogenetic trees with an example of both a descriptive and inferential statistical task. Moreover, this approach exhibits increased computational efficiency and statistical performance over the current state-of-the-art, which we illustrate with a real data example on seasonal influenza. Our results demonstrate the viability of the tropical geometric setting for parametric statistical and probabilistic studies of sets of phylogenetic trees.

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Cite

BibTeXRIS
BibTeX
@article{monod2026tropical,
  title = {{Tropical Geometry of Phylogenetic Tree Space: A statistical Perspective}},
  author = {Anthea Monod and Bo Lin and Ruriko Yoshida and Qiwen Kang},
  journal = {Vietnam Journal of Mathematics},
  year = {2026},
  month = jul,
  doi = {10.1007/s10013-026-00795-w},
  url = {https://doi.org/10.1007/s10013-026-00795-w},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Tropical Geometry of Phylogenetic Tree Space: A statistical Perspective
AU  - Anthea Monod
AU  - Bo Lin
AU  - Ruriko Yoshida
AU  - Qiwen Kang
PY  - 2026
DA  - 2026/07/14
JO  - Vietnam Journal of Mathematics
DO  - 10.1007/s10013-026-00795-w
UR  - https://doi.org/10.1007/s10013-026-00795-w
AB  - Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry. Although they are important data structures, they face the significant challenge that sets of trees form a non-Euclidean phylogenetic tree space, which means that standard computational and statistical methods cannot be directly applied. In this work, we explore the statistical feasibility of a pure mathematical representation of the set of all phylogenetic trees based on tropical geometry for both descriptive and inferential statistics, and unsupervised and supervised machine learning. Our exploration is both theoretical and practical. We show that the tropical geometric phylogenetic tree space endowed with a generalized Hilbert projective metric exhibits analytic, geometric, and topological properties that are desirable for theoretical studies in probability and statistics and allow for well-defined questions to be posed. We illustrate the statistical feasibility of the tropical geometric perspective for phylogenetic trees with an example of both a descriptive and inferential statistical task. Moreover, this approach exhibits increased computational efficiency and statistical performance over the current state-of-the-art, which we illustrate with a real data example on seasonal influenza. Our results demonstrate the viability of the tropical geometric setting for parametric statistical and probabilistic studies of sets of phylogenetic trees.
SN  - 2305-221X
SN  - 2305-2228
ER  -