{
  "abstract": "In this work, we introduce a Tropical Axial Attention neural reasoning architecture that replaces vanilla softmax dot-product attention with max-plus operators, inducing a piecewise-linear structure aligned with dynamic programming formulations. From multi-species sequence alignments, our model learns all possible pairwise distances and is trained using a combination of ℓ1 and tropical symmetric distance metric losses with an ultrametric violation penalty. We leverage the well known isomorphic relationship between the space of all phylogenetic trees with n species and tropical Grassmannian to show that tropical attention provides a natural geometric framework for phylogenetic inference. On empirical DS1−DS11 alignments, where true trees are unknown, the tropical model achieves the lowest MAE to its FastME-induced tree metric on every dataset, with a MAE reductions averaging 81.5% relative to Phyloformer and 98.4% relative than Phyloformer 2. These results suggest that tropical attention is a useful geometric inductive bias for neural phylogenetic inference, especially under distribution shift and when tree-metric consistency is important.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Operations Research, Naval Postgraduate School, Monterey, CA, United States",
    "Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Chris Teska"
    },
    {
      "affs": [
        0
      ],
      "name": "Kurt Pasque"
    },
    {
      "affs": [
        0
      ],
      "name": "Ruriko Yoshida"
    },
    {
      "affs": [
        1
      ],
      "name": "Baran Hashemi"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/f113hfy2wfaw7.bib",
  "cited_by": 0,
  "doi": "10.3389/fsysb.2026.1886918",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13696944/",
  "id": "f113hfy2wfaw7",
  "issns": [
    "2674-0702"
  ],
  "landing_url": "https://doi.org/10.3389/fsysb.2026.1886918",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Original Research"
    ],
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7161296277",
  "pdf_url": "https://europepmc.org/articles/PMC13696944?pdf=render",
  "pmcid": "PMC13696944",
  "pmid": "42936321",
  "published": "2026-10-12",
  "publisher": "Frontiers Media SA",
  "ris": "https://research.draconitic.com/paper/f113hfy2wfaw7.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:12Z",
      "native_id": "PMC13696944",
      "source": "pmc",
      "url": "https://doi.org/10.3389/fsysb.2026.1886918"
    },
    {
      "first_seen": "2026-10-30T12:22:24Z",
      "native_id": "MED:42936321",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42936321"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Phylogenetic tree inference with tropical axial attention",
  "title_text": "Phylogenetic tree inference with tropical axial attention",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:34:11Z",
  "url": "https://research.draconitic.com/paper/f113hfy2wfaw7",
  "venue": "Frontiers in Systems Biology",
  "versions": []
}