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A combinatorial method for connecting BHV spaces representing different numbers of taxa

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arxiv 1708.02626 v2 pith:4IFW7IB2 submitted 2017-08-08 q-bio.QM math.COq-bio.PE

classification q-bio.QMmath.COq-bio.PE
keywords treespacetreesdifferentmethodspacescombinatorialcombining
verification ladder T0 review T1 audit T2 compute T3 formal
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The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique to BHV tree space is well known to be computable in polynomial time, which makes it a potentially powerful tool for optimization problems in phylogenetics and phylogenomics. Specifically, there is significant interest in comparing and combining phylogenetic trees. For example, BHV tree space has been shown to be potentially useful in tree summary and consensus methods, which require combining trees with different number of leaves. Yet an open problem is to transition between BHV tree spaces of different maximal dimension, where each maximal dimension corresponds to the complete set of edge-weighted trees with a fixed number of leaves. We show a combinatorial method to transition between copies of BHV tree spaces in which trees with different numbers of taxa can be studied, derived from its topological structure and geometric properties. This method removes obstacles for embedding problems such as supertree and consensus methods in the BHV treespace framework.

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Cited by 2 Pith papers

Reviewed papers in the Pith corpus that reference this work. Sorted by Pith novelty score.

  1. Phylogenetic Tree Inference with Tropical Axial Attention

    q-bio.PE 2026-05 unverdicted novelty 6.0 of 10

    Tropical axial attention learns pairwise distances from alignments and produces matrices closer to BME tree metrics than standard attention baselines by replacing dot-product attention with max-plus operators and addi...

  2. Geometry of the space of phylogenetic trees with non-identical leaves

    q-bio.PE 2025-08 conditional novelty 6.0 of 10

    Towering space is a metric space for comparing phylogenetic trees with non-identical leaf sets, built by gluing BHV spaces along prune-and-regraft moves.

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