{
  "abstract": "HER2 status decides who receives HER2-targeted therapy. Pathologists score HER2 protein by immunohistochemistry (IHC); equivocal IHC 2+ tumours, their hardest calls, wait for in situ hybridisation (ISH). We built a HER2 reader for routine H&E slides, owned end to end, as a baseline for pathologists. A 22M-parameter ViT-S/16 tile encoder was trained on public TCGA slides by self-supervision, distillation from H-optimus-0 and two rounds of JEPA refinement; five cross-validated attention-based slide classifiers average their probabilities; and an operating point is fixed on training data. Compared under one paired ten-seed protocol, readers on our encoder rank first of 7 on external validation from TCGA-BRCA to Yale-HER2 (AUC 0.812), level with readers on encoders 4 and 50 times larger. We also rebuilt PathBench's encoder benchmark on public cohorts; our replica reproduces its published order of reference encoders, and under it our encoder ranks first of 7 on TCGA-BRCA (0.689) and sits level with H-optimus-0 and Phikon on Yale-HER2 (0.897). On three external hospitals our deployed reader reaches AUC 0.82 on Yale-HER2 (about 0.81 with training slides balanced for tissue size), 0.75 on HEROHE and 0.63 on BCNB biopsies, and among HEROHE's 85 IHC 2+ cases it ranks ISH-amplified above non-amplified tumours at 0.76, best among our TCGA-trained readers. Per-laboratory score normalisation and a laboratory's own slides improve it further on a new site. Without a GPU our reader needs 5-6 s per slide. It serves as a research-use pre-read in a pathology platform, where it proposes a probability and a call beside IHC and helps prioritise ISH for equivocal cases. Weights, per-slide predictions and the data behind every figure are public at https://huggingface.co/cloudkites/her2-reader.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2610.40662",
  "author_total": 2,
  "authors": [
    {
      "name": "Thang Tran"
    },
    {
      "name": "Lan Dang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/fw0heq0bc926w.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2610.40662",
  "fulltext_url": null,
  "id": "fw0heq0bc926w",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2610.40662",
  "language": null,
  "licence": "LicenseRef-arXiv-nonexclusive-1.0",
  "licence_label": "arXiv licence",
  "licence_source": "article",
  "licence_url": "http://arxiv.org/licenses/nonexclusive-distrib/1.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "cs.CV"
    ],
    [
      "arxiv",
      "cs.LG"
    ],
    [
      "arxiv",
      "cs.SE"
    ],
    [
      "arxiv",
      "q-bio.QM"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://arxiv.org/pdf/2610.40662",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-09",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/fw0heq0bc926w.ris",
  "sources": [
    {
      "first_seen": "2026-11-02T12:21:21Z",
      "native_id": "2610.40662",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2610.40662"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "arxiv:q-bio.QM",
      "subfield": "bioinformatics"
    }
  ],
  "title": "A small HER2 reader for routine H&E slides: real-world deployment",
  "title_text": "A small HER2 reader for routine H&E slides: real-world deployment",
  "type": "preprint",
  "updated_at": "2026-11-04T15:20:53Z",
  "url": "https://research.draconitic.com/paper/fw0heq0bc926w",
  "venue": "arXiv",
  "versions": []
}