Pith Number

pith:BZ2X5GU3

pith:2026:BZ2X5GU3KOSC5CB2M6VATHW6W4

not attested not anchored not stored refs resolved

Phylogenetic Tree Inference with Tropical Axial Attention

Baran Hashemi, Chris Teska, Kurt Pasque, Ruriko Yoshida

Tropical axial attention replaces standard attention with max-plus operators to learn phylogenetic distances aligned with tree geometry.

arxiv:2605.13894 v1 · 2026-05-12 · q-bio.PE · cs.LG

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\usepackage{pith}
\pithnumber{BZ2X5GU3KOSC5CB2M6VATHW6W4}

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Record completeness

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3 Author claim open · sign in to claim

4 Citations open

5 Replications open

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The bundle contains the canonical record plus signed events. A mirror can host it anywhere and recompute the same current state with the deterministic merge algorithm.

Claims

C1strongest claim

tropical attention provides a natural geometric framework for phylogenetic inference. On empirical DS1-DS11 alignments, the tropical model produces distance matrices that are substantially closer to their BME-induced tree metrics than the baseline models.

C2weakest assumption

The piecewise-linear structure induced by max-plus operators and the ultrametric violation penalty will align with actual phylogenetic tree geometry even when true trees are unknown and evaluation relies on BME-induced metrics.

C3one line summary

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 adding ultrametric penalties.

References

36 extracted · 36 resolved · 1 Pith anchors

[1] Capacitated dynamic programming: Faster knap- sack and graph algorithms 2018 · arXiv:1802.06440

[2] J., Duchene, D., and Yoshida, R 2025

[3] Permutations with Restricted Patterns and Dyck Paths 2001 · doi:10.1006/aama.2001

[4] Blassel, L., Sauvage, N., Barrat-Charlaix, P., Boussau, B., Lartillot, N., and Jacob, L. (2025). Likelihood-free inference of phylogenetic tree posterior distributions.arXiv preprint arXiv:2510.12976 2025

[5] Chen, Y., Huang, J., Yang, C., Hsu, K., and Liu, H. (2023). A comprehensive phyloge- netic analysis of sars-cov-2: Utilizing a novel and convenient in-house rt-pcr method for characterization without 2023

Receipt and verification

First computed	2026-05-17T23:39:19.020285Z
Builder	pith-number-builder-2026-05-17-v1
Signature	Pith Ed25519 (`pith-v1-2026-05`) · public key
Schema	pith-number/v1.0

Canonical hash

0e757e9a9b53a42e883a67aa099edeb73d5a1e51d975b37f3456a3039c35af95

Aliases

arxiv: 2605.13894 · arxiv_version: 2605.13894v1 · doi: 10.48550/arxiv.2605.13894 · pith_short_12: BZ2X5GU3KOSC · pith_short_16: BZ2X5GU3KOSC5CB2 · pith_short_8: BZ2X5GU3

Agent API

Resolver JSON Graph JSON Events JSON Schema Signing key

Verify this Pith Number yourself

curl -sH 'Accept: application/ld+json' https://pith.science/pith/BZ2X5GU3KOSC5CB2M6VATHW6W4 \
  | jq -c '.canonical_record' \
  | python3 -c "import sys,json,hashlib; b=json.dumps(json.loads(sys.stdin.read()), sort_keys=True, separators=(',',':'), ensure_ascii=False).encode(); print(hashlib.sha256(b).hexdigest())"
# expect: 0e757e9a9b53a42e883a67aa099edeb73d5a1e51d975b37f3456a3039c35af95

Canonical record JSON

{
  "metadata": {
    "abstract_canon_sha256": "1f2e08ae60e57f2a785a32f24acb133c83a6bbfdfa217ec0a0455bbf3d4ff003",
    "cross_cats_sorted": [
      "cs.LG"
    ],
    "license": "http://creativecommons.org/licenses/by/4.0/",
    "primary_cat": "q-bio.PE",
    "submitted_at": "2026-05-12T10:54:37Z",
    "title_canon_sha256": "5acec2143ef354b38ae4aa90e7a5e80e69ba99f603502d3e7fd8ea3fe706aee2"
  },
  "schema_version": "1.0",
  "source": {
    "id": "2605.13894",
    "kind": "arxiv",
    "version": 1
  }
}