Add bibliography.

README.md

@@ -109,5 +109,107 @@ For any additional questions or comments, contact Alexandre Filiot (`alexandre.f
 
 
 ## Acknowledgements
-We thank [DINOv2](https://github.com/facebookresearch/dinov2) authors for the amazing contribution.
+
+We thank [DINOv2](https://github.com/facebookresearch/dinov2) authors for the amazing contribution [1].
+
+### Computing resources
+
 This work was granted access to the HPC resources of IDRIS under the allocation 2023-A0141012519 made by GENCI.
+
+### Datasets
+
+The results published here are partly based upon data generated by the TCGA Research Network: [https://www.cancer.gov/tcga](https://www.cancer.gov/tcga).
+The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The data used for the analyses described in this manuscript were obtained from the GTEx Portal on 07/01/2023.
+
+
+## Third-party licenses
+
+Vision Transformers architectures were derived from [facebookresearch/dino](https://github.com/facebookresearch/dino) (Apache License 2.0), [huggingface/pytorch-image-models](https://github.com/huggingface/pytorch-image-models/tree/main) (Apache License 2.0).
+This code is built upon [DINOv2](https://github.com/facebookresearch/dinov2) repository (Apache License 2.0).
+
+
+**The following table provides the license associated with each datasets used for pre-training Phikon-v2.**
+
+| Name of the dataset | License           | Dataset home page                                                                                  |
+| ------------------- | ----------------- | -------------------------------------------------------------------------------------------------- |
+| TCGA     | Open Access | [https://portal.gdc.cancer.gov/](https://portal.gdc.cancer.gov/)                             |
+| TCIA [2]     | [TCIA Restricted Licence](https://wiki.cancerimagingarchive.net/download/attachments/4556915/TCIA%20Restricted%20License%2020220519.pdf?version=1&modificationDate=1652965266604&api=v2) | [https://www.cancerimagingarchive.net/](https://www.cancerimagingarchive.net/) 
+| CPTAC [3-14]          | CC-BY 3.0 License   | [https://proteomics.cancer.gov/programs/cptac](https://proteomics.cancer.gov/programs/cptac)       |
+| GTEX    | Open Access   | [https://gtexportal.org/home/downloads/adult-gtex/overview](https://gtexportal.org/home/downloads/adult-gtex/overview) |
+| Biobank-CMB [15 - 19]    | CC BY 4.0 License   | [https://moonshotbiobank.cancer.gov/](https://moonshotbiobank.cancer.gov/) |
+| UPENN-GBM [20]   | CC BY 4.0 License   | [https://www.cancerimagingarchive.net/collection/upenn-gbm/](https://www.cancerimagingarchive.net/collection/upenn-gbm/) |
+| Post-NAT-BRCA [21]   | CC BY 3.0 License   | [https://www.cancerimagingarchive.net/collection/post-nat-brca/](https://www.cancerimagingarchive.net/collection/post-nat-brca/) |
+| Breast Metastases (MSKCC) [22]   | CC BY 3.0 License   | [https://www.cancerimagingarchive.net/collection/sln-breast/](https://www.cancerimagingarchive.net/collection/sln-breast/) |
+| HER2 Tumor ROIs (v3) [23]    | CC BY 4.0 License   | [https://www.cancerimagingarchive.net/collection/her2-tumor-rois/](https://www.cancerimagingarchive.net/collection/her2-tumor-rois/) |
+| TUH DPath Breast    | Free and Without Restriction   | [https://isip.piconepress.com/projects/nedc/html/tuh_dpath/](https://isip.piconepress.com/projects/nedc/html/tuh_dpath/) |
+| Hungarian Colorectal Screening [24]    | CC BY 4.0 License   | [https://www.cancerimagingarchive.net/collection/hungarian-colorectal-screening/](https://www.cancerimagingarchive.net/collection/hungarian-colorectal-screening/) |
+| PennyCuick [25]    | CC BY 4.0 License   | [https://idr.openmicroscopy.org/webclient/?show=project-1251](https://idr.openmicroscopy.org/webclient/?show=project-1251) |
+| NLST-pathology-1225 [26]   | CC BY 4.0 License   | [https://www.cancerimagingarchive.net/collection/nlst/](https://www.cancerimagingarchive.net/collection/nlst/) |
+| Ovarian Bevacizumab Response [27]    | CC BY 4.0 License   | [https://www.cancerimagingarchive.net/collection/ovarian-bevacizumab-response/](https://www.cancerimagingarchive.net/collection/ovarian-bevacizumab-response/) |
+| PTRC-HGSOC [28]   | CC BY 4.0 License   | [https://www.cancerimagingarchive.net/collection/ptrc-hgsoc/](https://www.cancerimagingarchive.net/collection/ptrc-hgsoc/) |
+| Hodis [29]   | CC BY 4.0 License   | [https://idr.openmicroscopy.org/webclient/?show=project-2351](https://idr.openmicroscopy.org/webclient/?show=project-2351) |
+
+
+## References
+
+Here is the uniformized bibliography in APA style:
+
+1. Oquab, M., Darcet, T., Moutakanni, T., Vo, H., Szafraniec, M., Khalidov, V., Fernandez, P., Haziza, D., Massa, F., El-Nouby, A., Assran, M., Ballas, N., Galuba, W., Howes, R., Huang, P.-Y., Li, S.-W., Misra, I., Rabbat, M., Sharma, V., Synnaeve, G., Xu, H., Jegou, H., Mairal, J., Labatut, P., Joulin, A., & Bojanowski, P. (2024). Dinov2: Learning robust visual features without supervision. *arXiv*.
+
+2. Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and operating a public information repository. *Journal of Digital Imaging, 26*(6), 1045–1057. Springer Science and Business Media LLC. https://doi.org/10.1007/s10278-013-9622-7
+
+3. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2019). The Clinical Proteomic Tumor Analysis Consortium Acute Myeloid Leukemia Collection (CPTAC-AML) (Version 4) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.2019.B6FOE619
+
+4. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Glioblastoma Multiforme Collection (CPTAC-GBM) (Version 15) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.3RJE41Q1
+
+5. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2020). The Clinical Proteomic Tumor Analysis Consortium Breast Invasive Carcinoma Collection (CPTAC-BRCA) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.CAEM-YS80
+
+6. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2020). The Clinical Proteomic Tumor Analysis Consortium Colon Adenocarcinoma Collection (CPTAC-COAD) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.YZWQ-ZZ63
+
+7. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection (CPTAC-HNSCC) (Version 16) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.UW45NH81
+
+8. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Clear Cell Renal Cell Carcinoma Collection (CPTAC-CCRCC) (Version 13) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.OBLAMN27
+
+9. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Lung Squamous Cell Carcinoma Collection (CPTAC-LSCC) (Version 15) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.6EMUB5L2
+
+10. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2019). The Clinical Proteomic Tumor Analysis Consortium Sarcomas Collection (CPTAC-SAR) (Version 10) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.2019.9BT23R95
+
+11. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2020). The Clinical Proteomic Tumor Analysis Consortium Ovarian Serous Cystadenocarcinoma Collection (CPTAC-OV) (Version 3) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.ZS4A-JD58
+
+12. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Pancreatic Ductal Adenocarcinoma Collection (CPTAC-PDA) (Version 14) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.SC20FO18
+
+13. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Cutaneous Melanoma Collection (CPTAC-CM) (Version 11) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.ODU24GZE
+
+14. National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2019). The Clinical Proteomic Tumor Analysis Consortium Uterine Corpus Endometrial Carcinoma Collection (CPTAC-UCEC) (Version 12) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.3R3JUISW
+
+15. Cancer Moonshot Biobank. (2022). Cancer Moonshot Biobank – Colorectal Cancer Collection (CMB-CRC) (Version 5) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/DJG7-GZ87
+
+16. Cancer Moonshot Biobank. (2022). Cancer Moonshot Biobank – Melanoma Collection (CMB-MEL) (Version 5) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/GWSP-WH72
+
+17. Cancer Moonshot Biobank. (2022). Cancer Moonshot Biobank – Gastroesophageal Cancer Collection (CMB-GEC) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/E7KH-R486
+
+18. Cancer Moonshot Biobank. (2022). Cancer Moonshot Biobank – Lung Cancer Collection (CMB-LCA) (Version 5) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/3CX3-S132
+
+19. Cancer Moonshot Biobank. (2022). Cancer Moonshot Biobank – Multiple Myeloma Collection (CMB-MML) (Version 4) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/SZKB-SW39
+
+20. Bakas, S., Sako, C., Akbari, H., Bilello, M., Sotiras, A., Shukla, G., Rudie, J. D., Flores Santamaria, N., Fathi Kazerooni, A., Pati, S., Rathore, S., Mamourian, E., Ha, S. M., Parker, W., Doshi, J., Baid, U., Bergman, M., Binder, Z. A., Verma, R., … Davatzikos, C. (2021). Multi-parametric magnetic resonance imaging (mpMRI) scans for de novo Glioblastoma (GBM) patients from the University of Pennsylvania Health System (UPENN-GBM) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.709X-DN49
+
+21. Martel, A. L., Nofech-Mozes, S., Salama, S., Akbar, S., & Peikari, M. (2019). Assessment of residual breast cancer cellularity after neoadjuvant chemotherapy using digital pathology [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.2019.4YIBTJNO
+
+22. Campanella, G., Hanna, M. G., Brogi, E., & Fuchs, T. J. (2019). Breast metastases to axillary lymph nodes [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.2019.3XBN2JCC
+
+23. Farahmand, S., Fernandez, A. I., Ahmed, F. S., Rimm, D. L., Chuang, J. H., Reisenbichler, E., & Zarringhalam, K. (2022). HER2 and trastuzumab treatment response H&E slides with tumor ROI annotations (Version 3) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/E65C-AM96
+
+24. Pataki, B. A., Olar, A., Ribli, D., Pesti, A., Kontsek, E., Gyongyosi, B., Bilecz, A., Kovács,
+
+ T., Kovács, K. A., Kiss, Z., Szócska, M., Pollner, P., & Csabai, I. (2021). Digital pathological slides from Hungarian (Europe) colorectal cancer screening (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.9CJF-0127
+
+25. Pennycuick, A., Teixeira, V. H., AbdulJabbar, K., Raza, S. E. A., Lund, T., Akarca, A. U., Rosenthal, R., Kalinke, L., Chandrasekharan, D. P., Pipinikas, C. P., Lee-Six, H., Hynds, R. E., Gowers, K. H. C., Henry, J. Y., Millar, F. R., Hagos, Y. B., Denais, C., Falzon, M., Moore, D. A., Antoniou, S., Durrenberger, P. F., Furness, A. J., Carroll, B., Marceaux, C., Asselin-Labat, M. L., Larson, W., Betts, C., Coussens, L. M., Thakrar, R. M., George, J., Swanton, C., Thirlwell, C., Campbell, P. J., Marafioti, T., Yuan, Y., Quezada, S. A., McGranahan, N., & Janes, S. M. (2020). Immune surveillance in clinical regression of preinvasive squamous cell lung cancer. *Cancer Discovery, 10*(10), 1489-1499. https://doi.org/10.1158/2159-8290.CD-19-1366
+
+26. National Lung Screening Trial Research Team. (2013). Data from the National Lung Screening Trial (NLST) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.HMQ8-J677
+
+27. Wang, C.-W., Chang, C.-C., Lo, S.-C., Lin, Y.-J., Liou, Y.-A., Hsu, P.-C., Lee, Y.-C., & Chao, T.-K. (2021). A dataset of histopathological whole slide images for classification of treatment effectiveness to ovarian cancer (Ovarian Bevacizumab Response) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.985G-EY35
+
+28. Chowdhury, S., Kennedy, J. J., Ivey, R. G., Murillo, O., Hosseini, N., Song, X., Petralia, F., Calinawan, A., Voytovich, U. J., Savage, S. R., Berry, A., Reva, B., Ozbek, U., Krek, A., Ma, W., da Veiga Leprevost, F., Ji, J., Yoo, S., Lin, C., … Paulovich, A. G. (2023). Proteogenomic analysis of chemo-refractory high grade serous ovarian cancer (PTRC-HGSOC) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/6RDA-P940
+
+29. Hodis, E., Torlai Triglia, E., Kwon, J. Y. H., Biancalani, T., Zakka, L. R., Parkar, S., Hütter, J. C., Buffoni, L., Delorey, T. M., Phillips, D., Dionne, D., Nguyen, L. T., Schapiro, D., Maliga, Z., Jacobson, C. A., Hendel, A., Rozenblatt-Rosen, O., Mihm, M. C. Jr., Garraway, L. A., & Regev, A. (2022). Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment. *Science, 376*(6592), eabi8175. https://doi.org/10.1126/science.abi8175