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run_predict.sh
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run_predict.sh
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# Bash script to run SHEPHERD to generate predictions
# Command to run this bash script:
# bash predict.sh
# IMPORTANT
# - To generate predictions on your own dataset (default), please use --patient_data my_data
# - To generate predictions on simulated test patients, please use --patient_data test_predict
# Command to run the predict script for each task. Comment out tasks you don't want to generate predictions for.
python predict.py \
--run_type causal_gene_discovery \
--patient_data test_predict \
--edgelist KG_edgelist_mask.txt \
--node_map KG_node_map.txt \
--saved_node_embeddings_path checkpoints/pretrain.ckpt \
--best_ckpt checkpoints/causal_gene_discovery.ckpt
python predict.py \
--run_type patients_like_me \
--patient_data my_data \
--edgelist KG_edgelist_mask.txt \
--node_map KG_node_map.txt \
--saved_node_embeddings_path checkpoints/pretrain.ckpt \
--best_ckpt checkpoints/patients_like_me.ckpt
python predict.py \
--run_type disease_characterization \
--patient_data my_data \
--edgelist KG_edgelist_mask.txt \
--node_map KG_node_map.txt \
--saved_node_embeddings_path checkpoints/pretrain.ckpt \
--best_ckpt checkpoints/disease_characterization.ckpt