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Thesis data, release v4.2 (canonical)

The only data version for the thesis "Agentic Patient Similarity Retrieval". Hosted at https://huggingface.co/datasets/thanminh01/thesis-data and kept as data/ at the repo root (gitignored). Read-only: fixes ship as a new release, never as an edit. What changed from v4.1: CHANGES-v4.2.md. Rules: CONTRACT.md.

Contents

Dataset Bank (confirmed cases) Queries Label space
tcga-nsclc 842 (LUAD 427, LUSC 415) 201 LUAD vs LUSC
bracs 460 (train+val) 87 (test) fine: 7 classes; coarse: 3 classes
ebr-coarse30 2,019 300 30 classes

Vectors: TCGA 1,043, BRACS 547, EBR 2,319 slides. 675 queries in total (588 distinct slides). Exploratory results only: BRACS prompt work sees the test queries.

data/
  <dataset>/                 tcga-nsclc | bracs | ebr-coarse30
    runtime/catalog.sqlite   the ONLY thing the agent may open: label-blind queries, bank labels and bank documents
    runtime/manifest.json    catalog hash and size, release
    bank.sqlite              bank slides with labels and text (owner/builder use)
    scorer/                  query.sqlite, query_labels.csv: SCORER ONLY, never inside the agent
    latents/<slide>.pt       PRISM2 latents, 256x2560 bf16 (used by the morphology tool)
    manifest.json
  bracs/slides.csv           all 547 slides with split (train 395 / val 65 / test 87) and labels
  knowledge/                 knowledge base, sources, gold questions (the runtime copy lives in APS-WSI/knowledge/)
  docs/                      rubric, scorer and build reports
  CONTRACT.md  CHANGES-v4.2.md  SHA256.json

Get it 

hf auth login                      # needs read access if the repo is private
hf download thanminh01/thesis-data --repo-type dataset --local-dir <repo>/data

About 5 GB, mostly latents/. Check integrity: every file's sha256 is in SHA256.json (paths relative to data/).

Use it 

export APS_DATASETS_ROOT=<repo>/data      # or pass --root ../data
cd APS-WSI
python -c "from pathlib import Path; from agent import preflight; from agent.config import Config; \
  print(preflight.run(Config(datasets_root=Path('../data'), dataset='bracs', view='fine', provider='nim', model='m')))"   # [] means clean
python -m agent.run_cli --root ../data --dataset bracs --view fine --model nvidia/nemotron-3-super-120b-a12b --finish-guard --no-llava-texts
python -m agent.scorer_cli baselines --root ../data --dataset bracs --view fine     # scorer only

Rules that keep the benchmark honest:

  • The agent reads <dataset>/runtime/ only. scorer/, latents/, docs/, bank.sqlite and the top-level manifest are denied by agent/runtime_paths.py. Open catalogs read-only (?immutable=1) or on a copy.
  • Queries carry no label and no stored text. Patient id is not used anywhere.
  • WSI-LLaVA bank texts stay off (--no-llava-texts).
  • Source-data documents (EBR clinical_meta, BRACS roi_distribution) can be re-checked against the raw sheets with Documents/plans/2026-10-02-final-run-autofix/verify-source-documents.py ANNOTATION_CSV BRACS_XLSX.
  • Knowledge text is checked against second sources, not clinically validated.

Archived (not here)

Older releases (v4.1, the v4 layout) are in the local archive/old-data-versions/ and on the Thesis drive (Thesis-datasets/releases/).