--- a
+++ b/shepherd/run_causal_gene_discovery.sh
@@ -0,0 +1,20 @@
+# Bash script to train SHEPHERD for causal gene discovery
+
+# Command to run this bash script:
+# bash run_causal_gene_discovery.sh
+
+# Command to run with the best hyperparameters from the paper
+python train.py \
+        --edgelist KG_edgelist_mask.txt \
+        --node_map KG_node_map.txt \
+        --patient_data disease_simulated \
+        --run_type causal_gene_discovery \
+        --saved_node_embeddings_path checkpoints/pretrain.ckpt \
+        --sparse_sample 100 \
+        --lr 1e-05 \
+        --upsample_cand 2 \
+        --neighbor_sampler_size -1 \
+        --lmbda 0.4 \
+        --alpha 0.5 \
+        --kappa 0.18
+