--- a
+++ b/shepherd/run_predict.sh
@@ -0,0 +1,34 @@
+# 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