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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 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_uncertainty_mve
train_path=../data/uncertainty/train.csv
val_path=../data/uncertainty/val.csv
test_path=../data/uncertainty/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 \
--loss_function mve
#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 \
--loss_function mve
#Predict, analyze uncertainty
python $chemprop_dir/predict.py \
--test_path $test_path \
--preds_path $results_dir/test_preds_unc_mve.csv \
--checkpoint_dir $results_dir \
--uncertainty_method mve \
--calibration_method zscaling \
--calibration_path $val_path \
--regression_calibrator_metric stdev \
--calibration_interval_percentile 95 \
--evaluation_methods nll spearman ence miscalibration_area \
--evaluation_scores_path $results_dir/unc_eval_scores_mve.csv
cat $results_dir/unc_eval_scores_mve.csv
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