added	data_prep/shortest_paths/shortest_paths.py
added	environment.yml
added	img/rare_diseases_pipeline.png
added	img/shepherd_overview.png
added	install_pyg.sh
added	project_config.py
added	project_utils.py
added	shepherd/__init__.py
added	shepherd/dataset.py
added	shepherd/decoders.py
added	shepherd/gene_prioritization_model.py
added	shepherd/hparams.py
added	shepherd/node_embedder_model.py
added	shepherd/patient_nca_model.py
added	shepherd/predict.py
added	shepherd/preprocess.py
added	shepherd/pretrain.py
added	shepherd/run_causal_gene_discovery.sh
added	shepherd/run_disease_characterization.sh
added	shepherd/run_patients_like_me.sh
added	shepherd/run_predict.sh
added	shepherd/run_pretrain.sh
added	shepherd/samplers.py
added	shepherd/task_heads/__init__.py
added	shepherd/task_heads/gp_aligner.py