diff --git a/bluepebble.sh b/bluepebble.sh index 3dcfbb1..a11332b 100644 --- a/bluepebble.sh +++ b/bluepebble.sh @@ -10,7 +10,7 @@ #SBATCH --cpus-per-task=28 #SBATCH --time=2-12:00:00 #SBATCH --mem=100000M -#SBATCH --array=1-8 +#SBATCH --array=1-46 # Load the modules/environment module purge @@ -29,8 +29,7 @@ echo JOB ID: ${SLURM_JOBID} echo PBS ARRAY ID: ${SLURM_ARRAY_TASK_ID} echo Working Directory: $(pwd) -cmds=('ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_1_2_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 1 --n-activity-days 2 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_2_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 2 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_1_4_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 1 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_4_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_1_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 1 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_6_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 6 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_6_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 6 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' ) - +cmds=('ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_1_2_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 1 --n-activity-days 2 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_2_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 2 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_1_3_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 1 --n-activity-days 3 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_3_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 3 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_1_4_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 1 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_4_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_1_5_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 1 --n-activity-days 5 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_5_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 5 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_1_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 1 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_1_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 1 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_2_3_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 2 --n-activity-days 3 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_2_3_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 2 --n-activity-days 3 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_2_4_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 2 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_2_4_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 2 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_2_5_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 2 --n-activity-days 5 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_2_5_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 2 --n-activity-days 5 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_2_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 2 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_2_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 2 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_2_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 2 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_2_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 2 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_3_4_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 3 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_3_4_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 3 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_3_5_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 3 --n-activity-days 5 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_3_5_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 3 --n-activity-days 5 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_3_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 3 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_3_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 3 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_3_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 3 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_3_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 3 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_4_5_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 4 --n-activity-days 5 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_4_5_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 4 --n-activity-days 5 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_4_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 4 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_4_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 4 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_4_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 4 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_4_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 4 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_5_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 5 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_5_6_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 5 --n-activity-days 6 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_5_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 5 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_5_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 5 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_6_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 6 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/rbf/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_6_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 6 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_6_7_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 6 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/linear/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_4_QN_ANSCOMBE_LOG/2To2 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To2 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers linear --enable-regularisation' 'ml.py --no-export-hpc-string --study-id delmas --output-dir output/main_experiment/rbf/delmas_dataset4_mrnn_7day/delmas_dataset4_mrnn_7day_delmas_RepeatedKFold_6_7_QN_ANSCOMBE_LOG/2To1 --dataset-folder datasets/delmas_dataset4_mrnn_7day --n-imputed-days 6 --n-activity-days 7 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To1 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers rbf --enable-regularisation' 'ml.py --no-export-hpc-string --study-id cedara --output-dir output/main_experiment/linear/cedara_datasetmrnn7_23/cedara_datasetmrnn7_23_cedara_RepeatedKFold_1_4_QN_ANSCOMBE_LOG/2To1 --dataset-folder datasets/cedara_datasetmrnn7_23 --n-imputed-days 1 --n-activity-days 4 --syhth-thresh 7 --n-job 1 --cv RepeatedKFold --preprocessing-steps QN --preprocessing-steps ANSCOMBE --preprocessing-steps LOG --class-healthy-label 1To1 --class-unhealthy-label 2To1 --meta-columns label --meta-columns id --meta-columns imputed_days --meta-columns date --meta-columns health --meta-columns target --classifiers linear --enable-regularisation') # Execute code mkdir ${WORK_DIR}/logs echo ${cmds[${SLURM_ARRAY_TASK_ID}]} diff --git a/eval_regularisation.py b/eval_regularisation.py index c338241..2e9ab89 100644 --- a/eval_regularisation.py +++ b/eval_regularisation.py @@ -5,29 +5,30 @@ def plot_heatmap(df, col, out_dir, title=""): - scores = df[col].values - scores = np.array(scores).reshape(len(df["C"].unique()), len(df["gamma"].unique())) - #plt.figure(figsize=(8, 6)) - #plt.subplots_adjust(left=.2, right=0.95, bottom=0.15, top=0.95) - fig, ax = plt.subplots() - im = ax.imshow(scores[::-1, :], interpolation='nearest') - # im = ax.imshow(scores, interpolation='nearest', - # norm=MidpointNormalize(vmin=-.2, midpoint=0.5)) - ax.set_xlabel('gamma') - ax.set_ylabel('C') - fig.colorbar(im) - ax.set_xticks(np.arange(len(df["gamma"].unique())), - [np.format_float_scientific(i, 1) for i in df["gamma"].unique()], rotation=45) - ax.set_yticks(np.arange(len(df["C"].unique()))[::-1], - [np.format_float_scientific(i, ) for i in df["C"].unique()]) - ax.set_title(f'Regularisation AUC\n{title}') - fig.tight_layout() - fig.show() - out_dir.mkdir(parents=True, exist_ok=True) - filename = f"heatmap_{col}_{title}.png".replace(":", "_").replace(" ", "_") - filepath = out_dir / filename - print(filepath) - fig.savefig(filepath) + df = df.fillna("linear") + for g in df["gamma"].unique(): + df_ = df[df["gamma"] == g] + scores = df_[col].values + scores = np.array(scores).reshape(len(df_["C"].unique()), len(df_["gamma"].unique())) + #plt.figure(figsize=(8, 6)) + #plt.subplots_adjust(left=.2, right=0.95, bottom=0.15, top=0.95) + fig, ax = plt.subplots() + im = ax.imshow(scores[::-1, :], interpolation='nearest') + # im = ax.imshow(scores, interpolation='nearest', + # norm=MidpointNormalize(vmin=-.2, midpoint=0.5)) + # ax.set_xlabel('gamma') + ax.set_ylabel('C') + fig.colorbar(im) + ax.set_xticks(np.arange(len(df_["gamma"].unique())), [i for i in df_["gamma"].unique()], rotation=45) + ax.set_yticks(np.arange(len(df_["C"].unique()))[::-1], + [np.format_float_scientific(i, ) for i in df_["C"].unique()]) + ax.set_title(f'Regularisation AUC\n{title}') + fig.tight_layout() + fig.show() + out_dir.mkdir(parents=True, exist_ok=True) + filename = f"heatmap_{g}_{col}_{title}.png".replace(":", "_").replace(" ", "_") + filepath = out_dir / filename + print(filepath) def plot_fig(df, col, out_dir, title=""): diff --git a/main.py b/main.py index 59f307a..186c027 100644 --- a/main.py +++ b/main.py @@ -10,13 +10,13 @@ def main( exp_temporal: bool = False, exp_cross_farm: bool = False, weather_exp: bool = False, - regularisation_exp: bool = False, + regularisation_exp: bool = True, output_dir: Path = Path("output"), delmas_dir_mrnn: Path = Path("datasets/delmas_dataset4_mrnn_7day"), cedara_dir_mrnn: Path = Path("datasets/cedara_datasetmrnn7_23"), n_job: int = 5, - enable_regularisation: bool = False, - export_hpc_string: bool = False, + enable_regularisation: bool = True, + export_hpc_string: bool = True, plot_2d_space: bool = False ): """Thesis script runs all key experiments for data exploration chapter @@ -33,8 +33,8 @@ def main( for steps in steps_list: slug = "_".join(steps) for clf in ["rbf"]: - for i_day in [6]: - for a_day in [7]: + for i_day in [1,2,3,4,5,6]: + for a_day in [1,2,3,4,5,6,7]: if i_day >= a_day: continue for cv in ["RepeatedKFold"]: @@ -63,7 +63,7 @@ def main( ], study_id=farm_id, export_fig_as_pdf=False, - plot_2d_space=True, + plot_2d_space=plot_2d_space, pre_visu=False, export_hpc_string=export_hpc_string, skip=False, diff --git a/model/svm.py b/model/svm.py index b613fdb..5321d3f 100644 --- a/model/svm.py +++ b/model/svm.py @@ -916,9 +916,9 @@ def cross_validate_svm_fast( if kernel in ["linear", "rbf"]: if enable_regularisation: print("Grid search...") - svc = SVC(kernel=kernel, probability=True) - parameters["kernel"] = [kernel] - clf = GridSearchCV(svc, parameters, return_train_score=True, cv=10, scoring='roc_auc', n_jobs=-1) + svc = SVC(probability=True) + # parameters["kernel"] = [kernel] + clf = GridSearchCV(svc, parameters, return_train_score=True, cv=5, scoring='roc_auc', n_jobs=-1) else: if C is not None and gamma is not None: clf = SVC(kernel=kernel, probability=True, C=C, gamma=gamma) diff --git a/var.py b/var.py index 6056fb9..70de089 100644 --- a/var.py +++ b/var.py @@ -42,11 +42,15 @@ # ], # } -parameters = { - "C": [1e-100, 1.7782794100389228e-75, 3.1622776601683795e-50, 5.623413251903491e-25, 10.0], - "gamma": [1e-100, 1e-25, 1e+50, 1e+125, 1e+200] -} +parameters = [ + {'C': [0.000001, 0.00001, 0.0001, 0.001, 0.01, 0.1, 1, 10, 100, 1000], 'kernel': ['linear']}, + {'C': [0.000001, 0.00001, 0.0001, 0.001, 0.01, 0.1, 1, 10, 100, 1000], 'gamma': ['scale'], 'kernel': ['rbf']}, + ] +# parameters = [ +# {'C': [0.0001, 100], 'kernel': ['linear']}, +# {'C': [0.0001, 100], 'gamma': ['scale'], 'kernel': ['rbf']}, +# ] transponders_delmas = [ "40101310316",