Official repo for Foundation Models for Quantitative Biomarker Discovery in Cancer Imaging [INSERT DOI]
Project description
Foundation Models for Quantitative Imaging Biomarker Discovery in Cancer Imaging
Overview
This is the the official repository for the paper Foundation Models for Quantitative Imaging Biomarker Discovery for Cancer Imaging
Suraj Pai, Dennis Bontempi, Vasco Prudente, Ibrahim Hadzic, Mateo Sokač, Tafadzwa L. Chaunzwa, Simon Bernatz, Ahmed Hosny, Raymond H Mak, Nicolai J Birkbak, Hugo JWL Aerts
Repository Structure
├── foundation_image_biomarker/ # Python package for the repository. You don't need to use this unless you want to contribute to the repo
├── data/ # Download and pre-processing scripts for the data
├── experiments/ # Configuration files to reproduce the final experiments of the paper
├── models/ # Notebooks to download and test each of the final models used in the paper
└── tests/
Quick Start
The easiest way to use this repository is by installing it through pip. This will load all the dependencies and allow you to load model weights dynamically.
pip install foundation-image-biomarker
Once you do this, you can look run each of our described pipelines
Data pre-processing
You can find detailed instructions for this here
Using all trained models
You can find detailed instructions for this here
Re-running all the experiments outlined in the paper
You can find detailed instructions for this here
🛡 License
This project is licensed under the terms of the MIT license. See LICENSE for more details.
📃 Citation
@misc{foundation-image-biomarker,
author = {AIM-Harvard},
title = {Official repo for "Foundation Models for Quantitative Biomarker Discovery in Cancer Imaging"},
year = {2023},
publisher = {GitHub},
journal = {GitHub repository},
howpublished = {\url{https://github.com/AIM-Harvard/foundation-cancer-image-biomarker}}
}
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