modified create splits and data processing script, and created splits…

.gitignore

@@ -107,3 +107,12 @@ ENV/
 
 
 *.pt
+
+# output files from sigopt engaging hyperparameter optimization
+*.out
+
+# results directories from sigopt engaging hyperparameter optimization
+results/
+
+# file size too large
+models.tar.gz.1

bash_scripts/batch_scripts/predict2.py

@@ -0,0 +1 @@
+../predict2.py

bash_scripts/batch_scripts_hyperparam_opt/abs_all_group_by_smiles.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J abs_all_group_by_smiles
+#SBATCH -o abs_all_group_by_smiles-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name abs_all --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/abs_all_random.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J abs_all_random
+#SBATCH -o abs_all_random-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name abs_all --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/abs_all_scaffold.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J abs_all_scaffold
+#SBATCH -o abs_all_scaffold-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name abs_all --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/both_peaks_group_by_smiles.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J both_peaks_group_by_smiles
+#SBATCH -o both_peaks_group_by_smiles-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name both_peaks --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/both_peaks_random.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J both_peaks_random
+#SBATCH -o both_peaks_random-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name both_peaks --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/both_peaks_scaffold.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J both_peaks_scaffold
+#SBATCH -o both_peaks_scaffold-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name both_peaks --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/chemprop_sigopt_engaging.py

@@ -0,0 +1 @@
+../chemprop_sigopt_engaging.py

bash_scripts/batch_scripts_hyperparam_opt/emi_all_group_by_smiles.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J emi_all_group_by_smiles
+#SBATCH -o emi_all_group_by_smiles-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name emi_all --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/emi_all_random.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J emi_all_random
+#SBATCH -o emi_all_random-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name emi_all --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/emi_all_scaffold.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J emi_all_scaffold
+#SBATCH -o emi_all_scaffold-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name emi_all --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/lambda_max_abs_group_by_smiles.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J lambda_max_abs_group_by_smiles
+#SBATCH -o lambda_max_abs_group_by_smiles-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name lambda_max_abs --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/lambda_max_abs_random.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J lambda_max_abs_random
+#SBATCH -o lambda_max_abs_random-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name lambda_max_abs --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/lambda_max_abs_scaffold.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J lambda_max_abs_scaffold
+#SBATCH -o lambda_max_abs_scaffold-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name lambda_max_abs --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/lambda_max_emi_group_by_smiles.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J lambda_max_emi_group_by_smiles
+#SBATCH -o lambda_max_emi_group_by_smiles-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name lambda_max_emi --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/lambda_max_emi_random.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J lambda_max_emi_random
+#SBATCH -o lambda_max_emi_random-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name lambda_max_emi --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/lambda_max_emi_scaffold.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J lambda_max_emi_scaffold
+#SBATCH -o lambda_max_emi_scaffold-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name lambda_max_emi --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/log_lifetime_group_by_smiles.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J log_lifetime_group_by_smiles
+#SBATCH -o log_lifetime_group_by_smiles-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name log_lifetime --observation_budget 50 --save_dir $(pwd)

bash_scripts/batch_scripts_hyperparam_opt/log_lifetime_random.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -p sched_mit_rafagb,sched_mit_rafagb_amd
+#SBATCH -J log_lifetime_random
+#SBATCH -o log_lifetime_random-%j.out
+#SBATCH -t 3-00:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH --mem=30gb
+#SBATCH --gres=gpu:1
+#SBATCH --mail-type=END,FAIL
+#SBATCH [email protected]
+
+echo "Date              = $(date)"
+echo "Hostname          = $(hostname -s)"
+echo "Working Directory = $(pwd)"
+echo ""
+
+module load anaconda3/2020.11
+source activate chemprop
+
+python chemprop_sigopt_engaging.py --data_path smiles_target_test.csv --separate_val_path smiles_target_val.csv --separate_test_path smiles_target_test.csv --metric rmse --name log_lifetime --observation_budget 50 --save_dir $(pwd)