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FROMAGe

Dataset Info

  • Images and text files are in different folder.
    • The image super folder is: /datasets/mimic/cxr-jpg/physionet.org/files/mimic-cxr-jpg/2.0.0/files
    • The text super folder is: /datasets/mimic/cxr/physionet.org/files/mimic-cxr/2.0.0/files

Setup

  1. Create conda environment: conda env create -f environment.yml

  2. Activate conda environment: conda activate fromage

  3. Install packages via pip: pip install -r requirements.txt

  4. Download MIMIC_JPG_<SPLIT>.tsvfiles and biovil_backbone_2048.pt from Drive

  5. Place MIMIC_JPG_<SPLIT>.tsv files under data/ folder and biovil_backbone_2048.pt under bin/ folder.

  6. Run pip install -e . to install the fromage as an editable package.

Run Experiments

To run experiments, you need to login to Weights & Biases from your terminal (Link, select the command line option).

For this project, we follow YAML-based configuration. You need to change logger/name and logger/version for every run that you create. The model reads configuration from config/train.yaml file.

After logging in to Weights & Biases and setting config, you can run fromage_train.sh script by sbatch fromage_train.sh command.

For any questions, please get in contact with Osman Batur.