#!/bin/bash source ~/anaconda3/etc/profile.d/conda.sh conda activate pytorch_p38 ########### ## Propedia ########### python train.py --accelerator gpu \ --max_epochs 500 \ --precision 16 \ --num_layers 3 \ --node_h_dim 200 32 \ --edge_h_dim 64 2 \ --dataset_name Propedia \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/Propedia \ --residual \ --num_workers 8 \ --bs 32 \ --lr 1e-3 \ --early_stopping_patience 10 \ --residue_featurizer_name MACCS \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/Propedia_GVP_MACCS python train.py --accelerator gpu \ --devices 4 \ --max_epochs 2 \ --precision 16 \ --dataset_name Propedia \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/Propedia \ --residual \ --num_workers 16 \ --bs 16 \ --lr 1e-3 \ --early_stopping_patience 10 \ --residue_featurizer_name MACCS \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/Propedia_GVP_MACCS python train.py --accelerator gpu \ --devices 4 \ --max_epochs 500 \ --precision 16 \ --dataset_name Propedia \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/Propedia \ --data_suffix small \ --residual \ --num_workers 4 \ --bs 16 \ --lr 1e-3 \ --early_stopping_patience 10 \ --residue_featurizer_name MACCS \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/Propedia_small_GVP_MACCS \ --persistent_workers True # selfdock: refine the positive complexes python train.py --accelerator gpu \ --devices 4 \ --max_epochs 500 \ --precision 16 \ --dataset_name Propedia \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/Propedia \ --data_suffix small_selfdock \ --residual \ --num_workers 4 \ --bs 16 \ --lr 1e-3 \ --early_stopping_patience 10 \ --residue_featurizer_name MACCS \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/Propedia_small_GVP_MACCS \ --persistent_workers True # selfdock + noise python train.py --accelerator gpu \ --devices 4 \ --max_epochs 500 \ --precision 16 \ --dataset_name Propedia \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/Propedia \ --data_suffix small_selfdock \ --residual \ --num_workers 4 \ --bs 16 \ --lr 1e-3 \ --early_stopping_patience 10 \ --residue_featurizer_name MACCS \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/Propedia_small_GVP_MACCS \ --add_noise 0.02 # crystal + noise python train.py --accelerator gpu \ --devices 4 \ --max_epochs 500 \ --precision 16 \ --dataset_name Propedia \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/Propedia \ --data_suffix small \ --residual \ --num_workers 4 \ --bs 16 \ --lr 1e-3 \ --early_stopping_patience 10 \ --residue_featurizer_name MACCS \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/Propedia_small_GVP_MACCS \ --add_noise 0.02 # less persistent workers to save CPU RAM # -> still may run out of CPU RAM python train.py --accelerator gpu \ --devices 4 \ --max_epochs 500 \ --precision 16 \ --num_layers 3 \ --node_h_dim 200 32 \ --edge_h_dim 64 2 \ --dataset_name Propedia \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/Propedia \ --residual \ --num_workers 8 \ --bs 16 \ --lr 1e-3 \ --early_stopping_patience 10 \ --residue_featurizer_name MACCS \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/Propedia_GVP_MACCS \ --persistent_workers True ########### ## PDBBind binary classification ########### python train.py --accelerator gpu \ --devices 1 \ --max_epochs 500 \ --precision 16 \ --num_layers 3 \ --node_h_dim 200 32 \ --edge_h_dim 64 2 \ --dataset_name PDBBind \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/PIGNet/data/pdbbind_v2019_processed/scoring \ --residual \ --num_workers 4 \ --bs 32 \ --lr 1e-4 \ --early_stopping_patience 10 \ --residue_featurizer_name MACCS \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/PDBBind_bin_GVP_MACCS \ --persistent_workers True \ --binary_cutoff 6.7 python train.py --accelerator gpu \ --devices 1 \ --max_epochs 500 \ --precision 16 \ --num_layers 3 \ --node_h_dim 200 32 \ --edge_h_dim 64 2 \ --dataset_name PDBBind \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/PIGNet/data/pdbbind_v2019_processed/scoring \ --residual \ --num_workers 4 \ --bs 32 \ --lr 1e-4 \ --early_stopping_patience 10 \ --residue_featurizer_name MolT5-small \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/PDBBind_bin_GVP_MolT5_small \ --persistent_workers True \ --binary_cutoff 6.7 ########### ## ProtCID ########### python train.py --accelerator gpu \ --devices 1 \ --max_epochs 500 \ --precision 16 \ --dataset_name Propedia \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/ProtCID/JaredJanssen_Benchmark \ --data_suffix small \ --residual \ --num_workers 8 \ --bs 16 \ --lr 1e-3 \ --early_stopping_patience 10 \ --residue_featurizer_name MACCS \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/ProtCID_small_GVP_MACCS \ --persistent_workers True python train.py --accelerator gpu \ --devices 1 \ --max_epochs 500 \ --precision 16 \ --dataset_name Propedia \ --input_type complex \ --data_dir /home/ec2-user/SageMaker/efs/data/ProtCID/JaredJanssen_Benchmark \ --data_suffix small \ --residual \ --num_workers 4 \ --bs 16 \ --lr 1e-3 \ --early_stopping_patience 10 \ --residue_featurizer_name MolT5-small \ --default_root_dir /home/ec2-user/SageMaker/efs/model_logs/zichen/ProtCID_small_GVP_MolT5_small \ --persistent_workers True