--- a
+++ b/shepherd/run_disease_characterization.sh
@@ -0,0 +1,18 @@
+# Bash script to train SHEPHERD for novel disease characterization
+
+# Command to run this bash script:
+# bash run_disease_characterization.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 disease_characterization \
+        --saved_node_embeddings_path checkpoints/pretrain.ckpt \
+        --sparse_sample 300 \
+        --lr 1e-05 \
+        --upsample_cand 3 \
+        --neighbor_sampler_size 15 \
+        --lmbda 0.9 \
+        --kappa 0.029999999999999992
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