Cite every source cohort, note LTS4 supervision
Browse files
DATA.md
CHANGED
|
@@ -369,26 +369,92 @@ StandardScaler + logistic-regression probe as described above.
|
|
| 369 |
weights.
|
| 370 |
- **Hardware timings** are wall-clock measurements on specific GPUs.
|
| 371 |
|
| 372 |
-
##
|
|
|
|
|
|
|
|
|
|
| 373 |
|
| 374 |
-
|
| 375 |
-
|
| 376 |
-
|
| 377 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 378 |
|
| 379 |
```bibtex
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 380 |
@article{nechaev2025spider,
|
| 381 |
-
title
|
| 382 |
-
author
|
| 383 |
-
year
|
| 384 |
-
eprint = {2503.02876},
|
| 385 |
-
archivePrefix = {arXiv}
|
| 386 |
}
|
| 387 |
```
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 388 |
|
| 389 |
`labels/tcga_brca_clinical.tsv` is the open-access GDC clinical export, redistributed under
|
| 390 |
TCGA's open-access terms. The source cohorts keep their own licences, so cite their papers
|
| 391 |
alongside GrapHist.
|
| 392 |
|
| 393 |
-
This work was done by **Mahbod Tajdini** and **Tomás Gadea Alcaide**
|
| 394 |
[LTS4, EPFL](https://www.epfl.ch/labs/lts4/).
|
|
|
|
| 369 |
weights.
|
| 370 |
- **Hardware timings** are wall-clock measurements on specific GPUs.
|
| 371 |
|
| 372 |
+
## Datasets used
|
| 373 |
+
|
| 374 |
+
This release is built from seven public cohorts. If you use it, please cite GrapHist **and**
|
| 375 |
+
the source cohort(s) your work touches.
|
| 376 |
|
| 377 |
+
| Cohort | Used for | Source |
|
| 378 |
+
|---|---|---|
|
| 379 |
+
| **TCGA-BRCA** | pre-training (11.1 M graphs), slide-level evaluation, survival | [GDC Data Portal](https://portal.gdc.cancer.gov/) |
|
| 380 |
+
| **BACH** (ICIAR 2018) | slide-level subtyping, homophily | [Grand Challenge](https://iciar2018-challenge.grand-challenge.org/) |
|
| 381 |
+
| **BRACS** | slide-level subtyping, homophily | [bracs.icar.cnr.it](https://www.bracs.icar.cnr.it/) |
|
| 382 |
+
| **BreakHis** | slide-level subtyping, homophily | [P&D Lab, UFPR](https://web.inf.ufpr.br/vri/databases/breast-cancer-histopathological-database-breakhis/) |
|
| 383 |
+
| **NuCLS** | cell-type identification, homophily | [NuCLS](https://sites.google.com/view/nucls/home) |
|
| 384 |
+
| **PanNuke** | cell-type identification, homophily | [TIA Centre, Warwick](https://warwick.ac.uk/fac/sci/dcs/research/tia/data/pannuke/) |
|
| 385 |
+
| **SPIDER-breast** | patch-level subtyping | [histai/SPIDER-breast](https://huggingface.co/datasets/histai/SPIDER-breast) |
|
| 386 |
+
|
| 387 |
+
<details>
|
| 388 |
+
<summary>BibTeX for the source cohorts</summary>
|
| 389 |
|
| 390 |
```bibtex
|
| 391 |
+
@article{weinstein2013cancer,
|
| 392 |
+
title={The cancer genome atlas pan-cancer analysis project},
|
| 393 |
+
author={Weinstein, John N and Collisson, Eric A and Mills, Gordon B and Shaw, Kenna R and
|
| 394 |
+
Ozenberger, Brad A and Ellrott, Kyle and Shmulevich, Ilya and Sander, Chris and
|
| 395 |
+
Stuart, Joshua M},
|
| 396 |
+
journal={Nature Genetics}, volume={45}, number={10}, pages={1113--1120}, year={2013},
|
| 397 |
+
publisher={Nature Publishing Group}
|
| 398 |
+
}
|
| 399 |
+
|
| 400 |
+
@article{aresta2019bach,
|
| 401 |
+
title={{BACH}: Grand challenge on breast cancer histology images},
|
| 402 |
+
author={Aresta, Guilherme and Ara{\'u}jo, Teresa and Kwok, Scotty and
|
| 403 |
+
Chennamsetty, Sai Saketh and Safwan, Mohammed and Alex, Varghese and others},
|
| 404 |
+
journal={Medical Image Analysis}, volume={56}, pages={122--139}, year={2019},
|
| 405 |
+
publisher={Elsevier}
|
| 406 |
+
}
|
| 407 |
+
|
| 408 |
+
@article{brancati2022bracs,
|
| 409 |
+
title={{BRACS}: A Dataset for BReAst Carcinoma Subtyping in {H\&E} Histology Images},
|
| 410 |
+
author={Brancati, Nadia and Anniciello, Anna Maria and Pati, Pushpak and Riccio, Daniel and
|
| 411 |
+
Scognamiglio, Giosu{\`e} and Jaume, Guillaume and De Pietro, Giuseppe and
|
| 412 |
+
Di Bonito, Maurizio and Foncubierta, Antonio and Botti, Gerardo and others},
|
| 413 |
+
journal={Database}, volume={2022}, pages={baac093}, year={2022},
|
| 414 |
+
publisher={Oxford University Press UK}
|
| 415 |
+
}
|
| 416 |
+
|
| 417 |
+
@article{spanhol2015dataset,
|
| 418 |
+
title={A dataset for breast cancer histopathological image classification},
|
| 419 |
+
author={Spanhol, Fabio A and Oliveira, Luiz S and Petitjean, Caroline and Heutte, Laurent},
|
| 420 |
+
journal={IEEE Transactions on Biomedical Engineering}, volume={63}, number={7},
|
| 421 |
+
pages={1455--1462}, year={2015}, publisher={IEEE}
|
| 422 |
+
}
|
| 423 |
+
|
| 424 |
+
@article{amgad2022nucls,
|
| 425 |
+
title={{NuCLS}: A scalable crowdsourcing approach and dataset for nucleus classification and
|
| 426 |
+
segmentation in breast cancer},
|
| 427 |
+
author={Amgad, Mohamed and Atteya, Lamees A and Hussein, Hagar and Mohammed, Kareem Hosny and
|
| 428 |
+
Hafiz, Ehab and Elsebaie, Maha AT and Alhusseiny, Ahmed M and
|
| 429 |
+
AlMoslemany, Mohamed Atef and Elmatboly, Abdelmagid M and Pappalardo, Philip A and others},
|
| 430 |
+
journal={GigaScience}, volume={11}, pages={giac037}, year={2022},
|
| 431 |
+
publisher={Oxford University Press}
|
| 432 |
+
}
|
| 433 |
+
|
| 434 |
+
@article{gamper2020pannuke,
|
| 435 |
+
title={{PanNuke} dataset extension, insights and baselines},
|
| 436 |
+
author={Gamper, Jevgenij and Koohbanani, Navid Alemi and Benes, Ksenija and Graham, Simon and
|
| 437 |
+
Jahanifar, Mostafa and Khurram, Syed Ali and Azam, Ayesha and Hewitt, Katherine and
|
| 438 |
+
Rajpoot, Nasir},
|
| 439 |
+
journal={arXiv preprint arXiv:2003.10778}, year={2020}
|
| 440 |
+
}
|
| 441 |
+
|
| 442 |
@article{nechaev2025spider,
|
| 443 |
+
title={{SPIDER}: A Comprehensive Multi-Organ Supervised Pathology Dataset and Baseline Models},
|
| 444 |
+
author={Nechaev, Dmitry and Pchelnikov, Alexey and Ivanova, Ekaterina},
|
| 445 |
+
year={2025}, eprint={2503.02876}, archivePrefix={arXiv}, primaryClass={cs.CV}
|
|
|
|
|
|
|
| 446 |
}
|
| 447 |
```
|
| 448 |
+
</details>
|
| 449 |
+
|
| 450 |
+
## Licence
|
| 451 |
+
|
| 452 |
+
Released `cc-by-nc-sa-4.0`. SPIDER-breast is `cc-by-nc-4.0`, research use only, and those
|
| 453 |
+
terms travel with the derived graphs:
|
| 454 |
|
| 455 |
`labels/tcga_brca_clinical.tsv` is the open-access GDC clinical export, redistributed under
|
| 456 |
TCGA's open-access terms. The source cohorts keep their own licences, so cite their papers
|
| 457 |
alongside GrapHist.
|
| 458 |
|
| 459 |
+
This work was done by **Mahbod Tajdini** and **Tomás Gadea Alcaide**, supervised by members of
|
| 460 |
[LTS4, EPFL](https://www.epfl.ch/labs/lts4/).
|