File size: 3,376 Bytes
16971e4 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | # 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/`).
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