# 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