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181b6d4 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_charges_eps_4
train_path=../data/charges_eps_4/train.csv
val_path=../data/charges_eps_4/val.csv
test_path=../data/charges_eps_4/test.csv
train_constraints_path=../data/charges_eps_4/train_constraints.csv
val_constraints_path=../data/charges_eps_4/val_constraints.csv
test_constraints_path=../data/charges_eps_4/test_constraints.csv
external_test_path=../data/charges_eps_4/external_test_set.csv
external_test_constraints_path=../data/charges_eps_4/external_test_set_constraints.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py \
--dataset_type regression \
--data_path $train_path \
--separate_val_path $val_path \
--separate_test_path $val_path \
--constraints_path $train_constraints_path \
--separate_val_constraints_path $val_constraints_path \
--separate_test_constraints_path $val_constraints_path \
--num_iters 30 \
--epochs 50 \
--aggregation norm \
--search_parameter_keywords depth ffn_num_layers hidden_size ffn_hidden_size dropout \
--config_save_path $results_dir/config.json \
--hyperopt_checkpoint_dir $results_dir \
--log_dir $results_dir \
--adding_h \
--is_atom_bond_targets \
--no_shared_atom_bond_ffn \
--no_adding_bond_types
#Training with optimized hyperparameters
python $chemprop_dir/train.py \
--dataset_type regression \
--data_path $train_path \
--separate_val_path $val_path \
--separate_test_path $test_path \
--constraints_path $train_constraints_path \
--separate_val_constraints_path $val_constraints_path \
--separate_test_constraints_path $test_constraints_path \
--epochs 50 \
--aggregation norm \
--config_path $results_dir/config.json \
--save_dir $results_dir \
--adding_h \
--is_atom_bond_targets \
--no_shared_atom_bond_ffn \
--no_adding_bond_types \
--ensemble_size 5 \
--save_preds \
--extra_metrics mae
#Predict on external test set
python $chemprop_dir/predict.py \
--test_path $external_test_path \
--constraints_path $external_test_constraints_path \
--preds_path $results_dir/preds_external_test.csv \
--checkpoint_dir $results_dir
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