| --- |
| configs: |
| - config_name: clinical |
| data_files: |
| - split: train |
| path: Clinical Data (gatortron-base)/* |
| - config_name: pathology_report |
| data_files: |
| - split: train |
| path: Pathology Report (gatortron-base)/* |
| - config_name: wsi |
| data_files: |
| - split: train |
| path: Slide Image (UNI)/* |
| - config_name: molecular |
| data_files: |
| - split: train |
| path: Molecular (SeNMo)/* |
| language: |
| - en |
| tags: |
| - medical |
| pretty_name: TCGA |
| --- |
| |
| # Dataset Card for The Cancer Genome Atlas (TCGA) Multimodal Dataset |
| <!-- Provide a quick summary of the dataset. --> |
|
|
| The Cancer Genome Atlas (TCGA) Multimodal Dataset is a comprehensive collection of clinical data, pathology reports, and slide images for cancer patients. |
| This dataset aims to facilitate research in multimodal machine learning for oncology by providing embeddings generated using state-of-the-art models such as GatorTron and UNI. |
|
|
| - **Curated by:** Lab Rasool |
| - **Language(s) (NLP):** English |
|
|
|
|
| ## Uses |
| <!-- Address questions around how the dataset is intended to be used. --> |
|
|
| ```python |
| from datasets import load_dataset |
| |
| clinical_dataset = load_dataset("Lab-Rasool/TCGA", "clinical", split="train") |
| pathology_report_dataset = load_dataset("Lab-Rasool/TCGA", "pathology_report", split="train") |
| wsi_dataset = load_dataset("Lab-Rasool/TCGA", "wsi", split="train") |
| molecular_dataset = load_dataset("Lab-Rasool/TCGA", "molecular", split="train") |
| ``` |
|
|
| ## Dataset Creation |
|
|
| #### Data Collection and Processing |
| The raw data for this dataset was acquired using MINDS, a multimodal data aggregation tool developed by Lab Rasool. |
| The collected data includes clinical information, pathology reports, and whole slide images from The Cancer Genome Atlas (TCGA). |
| The embeddings were generated using the HoneyBee embedding processing tool, which utilizes foundational models such as GatorTron and UNI. |
|
|
| #### Who are the source data producers? |
| The source data for this dataset was originally collected and maintained by The Cancer Genome Atlas (TCGA) program, a landmark cancer genomics project jointly managed by the National Cancer Institute (NCI). |
|
|
|
|
| ## Citation |
| <!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. --> |
|
|
| ``` |
| @article{honeybee, |
| title={HoneyBee: A Scalable Modular Framework for Creating Multimodal Oncology Datasets with Foundational Embedding Models}, |
| author={Aakash Tripathi and Asim Waqas and Yasin Yilmaz and Ghulam Rasool}, |
| year={2024}, |
| eprint={2405.07460}, |
| archivePrefix={arXiv}, |
| primaryClass={cs.LG} |
| } |
| @article{waqas2024senmo, |
| title={SeNMo: A self-normalizing deep learning model for enhanced multi-omics data analysis in oncology}, |
| author={Waqas, Asim and Tripathi, Aakash and Ahmed, Sabeen and Mukund, Ashwin and Farooq, Hamza and Schabath, Matthew B and Stewart, Paul and Naeini, Mia and Rasool, Ghulam}, |
| journal={arXiv preprint arXiv:2405.08226}, |
| year={2024} |
| } |
| ``` |
|
|
| ### For more information about the data acquisition and processing tools used in creating this dataset, please refer to the following resources: |
|
|
| - MINDS paper: https://pubmed.ncbi.nlm.nih.gov/38475170/ |
| - MINDS codebase: https://github.com/lab-rasool/MINDS |
| - HoneyBee repository: https://github.com/lab-rasool/HoneyBee/tree/main |
