| # 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/`). |
|
|
