Code for Pathway-based AEs https://arxiv.org/abs/2306.05813
Please cite our paper if you used this repository in your work.
For the results presented in the paper, including trained PAAE models please see here.
To setup the conda environment, please use the setup_conda_environment.sh script. Then run external-internal.sh to run the experiments. Run viz-brca.ipynb after the internal validation has finished to select the best models. Then you may run viz-brca-external.ipynb to generate the main plots. For the interpretability experiments you may run dists-brca-external.ipynb and dists-brca-external-featureimportance.ipynb, setting the variables accordingly to select specific models to analyse.
Pathway definitions in the data folder or here