CTxAI - Eligibility Criteria

This is the repository for the manuscript "Analysis of Eligibility Criterion Clusters Based on Large Language Models for Clinical Trial Design".

Install Dependencies

You can install the dependencies using Conda (but feel free to use your own ways):

1. Install Miniconda or Anaconda on your system if you haven't already.

2. Create a new Conda environment using the environment/setup_env.sh script:

   ./environment/setup_env.sh
   

3. Activate the new environment:

   conda activate ctxai
   

Running the experiments

Start by downloading the raw dataset by executing:

./download_raw_data.sh

Then, build the eligibility criterion dataset by executing:

python src/parse_data.py  # this step processes around 100k CTs

Then, run all experiments. Ensure each experiment completes before running the next one. Experiment takes some time, consider running them in a screen session. Logs about each tasked experiment will be written in ./logs/

python experiments/experiment_1.py  # this experiment will only plot 50k ECs to avoid GPU memory errors (can be modified in the config.yaml file)
python experiments/experiment_2.py
./experiments/experiment_3.sh

Finally, plot the results.

python experiments/plot_experiment_1.py
python experiments/plot_experiment_2.py
python experiments/plot_experiment_3.py