{"paper":{"title":"PhylaFlow: Hybrid Flow Matching in Billera-Holmes-Vogtmann Tree Space for Phylogenetic Inference","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.LG","q-bio.QM"],"primary_cat":"q-bio.PE","authors_text":"Leo Cui, Marinka Zitnik, Pardis Sabeti, Shrey Jain, Yasha Ektefaie","submitted_at":"2026-05-21T01:13:46Z","abstract_excerpt":"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 starting trees to short-run posterior samples, coupling c"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2605.21859","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2605.21859/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}