first_stage_folder_name=chembl_remove_properties_latent64
molecule_generation encode outputs/$first_stage_folder_name chembl/original/train.smiles outputs/$first_stage_folder_name/latent_mean_var
mkdir 2_stage_vae/${first_stage_folder_name}_stage2
python train_vae_latent.py ${first_stage_folder_name}_stage2 --encoder_layer_sizes "1024|1024|1024|1024|1024" --layer_sizes "1024|1024|1024|1024|1024" -e -5 --square --data_file outputs/${first_stage_folder_name}/latent_mean_var -tdv --num_epochs 3000
python train_vae_latent.py ${first_stage_folder_name}_stage2 --encoder_layer_sizes "1024|1024|1024|1024|1024" --layer_sizes "1024|1024|1024|1024|1024" -e -5 --square --data_file outputs/${first_stage_folder_name}/latent_mean_var --sample model.2999.pkl --encode --output_latent_file stage3_latents.npy
mkdir 2_stage_vae/${first_stage_folder_name}_stage3
python train_vae_latent.py ${first_stage_folder_name}_stage3 --num_epochs 3000 --encoder_layer_sizes "1024|1024|1024|1024|1024" --layer_sizes "1024|1024|1024|1024|1024" -e -5 --square -tdv --data_file 2_stage_vae/${first_stage_folder_name}_stage2/stage3_latents.npy 
