PhylaFlow: Hybrid Flow Matching in Billera-Holmes-Vogtmann Tree Space for Phylogenetic Inference
arXiv:2605.21859v1 Announce Type: cross Abstract: Phylogenetic trees are hybrid objects: branch lengths vary continuously, while topologies change discretely through edge contractions and expansions. Billera-Holmes-Vogtmann (BHV) tree space provides a canonical geometry for this structure, representing each resolved topology as a Euclidean orthant and topological changes as motion across shared lower-dimensional boundaries. We introduce PhylaFlow, a hybrid flow-matching model that learns posterior-basin transport in BHV tree space. PhylaFlow is trained on BHV geodesic paths from random startin
The increasing complexity of biological data and advances in AI, particularly flow matching models, are converging to create more sophisticated phylogenetic inference tools.
This development offers a more precise and computationally efficient way to model evolutionary relationships, which is a foundational aspect of synthetic biology and understanding life itself.
Phylogenetic analysis can now incorporate hybrid topological and continuous branch length variations more accurately, potentially leading to better biological insights.
- · Bioinformatics researchers
- · Synthetic biology companies
- · Pharmaceutical R&D
Improved accuracy and speed in constructing phylogenetic trees.
Accelerated discovery of novel biological pathways and proteins through better evolutionary models.
Enhanced design and engineering capabilities in synthetic biology applications, leading to new therapeutics or industrial processes.
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Read at arXiv cs.LG