first_stage_folder_name=cleaned_chembl
first_refined_stage_folder_name=EGFR
second_refined_stage_folder_name=EGFR_inner_extra_layer_adam_finetuning
molecule_generation encode outputs/$first_refined_stage_folder_name protein_target_data/${first_refined_stage_folder_name}/original/train.smiles outputs/${first_refined_stage_folder_name}/latent_mean_var
mkdir 2_stage_vae/${second_refined_stage_folder_name}_stage2
python train_vae_latent.py --refine_type inner ${second_refined_stage_folder_name}_stage2 --encoder_layer_sizes "1024|1024|1024|1024|1024" --layer_sizes "1024|1024|1024|1024|1024" -e -5 --square -lr 0.00001 --data_file outputs/${first_refined_stage_folder_name}/latent_mean_var --refine 2_stage_vae/${first_stage_folder_name}_stage2/model.9999.pkl -tdv --num_epochs 50000
python train_vae_latent.py --refine_type inner ${second_refined_stage_folder_name}_stage2 --encoder_layer_sizes "1024|1024|1024|1024|1024" --layer_sizes "1024|1024|1024|1024|1024" -e -5 --square --data_file outputs/${first_refined_stage_folder_name}/latent_mean_var --sample model.49999.pkl --encode --output_latent_file stage3_latents.npy
mkdir 2_stage_vae/${second_refined_stage_folder_name}_stage3
python train_vae_latent.py ${second_refined_stage_folder_name}_stage3 --num_epochs 50000 --encoder_layer_sizes "1024|1024|1024|1024|1024" --layer_sizes "1024|1024|1024|1024|1024" -e -5 --square -tdv -lr 0.000001 --data_file 2_stage_vae/${second_refined_stage_folder_name}_stage2/stage3_latents.npy --refine 2_stage_vae/${first_stage_folder_name}_stage3/model.9999.pkl
