scripts/multi_molecule.sh

#!/bin/bash

chemprop_dir=../../../chemprop  # location of chemprop directory, CHANGE ME

results_dir=results_multi_molecule
train_path=../data/multi_molecule/train.csv
val_path=../data/multi_molecule/val.csv
test_path=../data/multi_molecule/test.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 \
--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 \
--number_of_molecules 2

#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 \
--epochs 50 \
--aggregation norm \
--config_path $results_dir/config.json \
--save_dir $results_dir \
--number_of_molecules 2 \
--ensemble_size 5 \
--save_preds \
--extra_metrics mae r2