Commit 7b6dfeea authored by Patrick Scheibe's avatar Patrick Scheibe
Browse files

Fix for cases. Locally tested.

parent c8d37055
......@@ -112,9 +112,9 @@ def importDstoxTSV(tsvfilename: str) -> pd.DataFrame:
conversion_rules = {
"Sun_etal_dataset.csv": importSmilesCSV,
"dsstox_20160701.tsv": importDstoxTSV,
"S_extended_subset.csv": importSmilesCSV
"S_dataset.csv": importSmilesCSV,
"S_dataset_extended.csv": importSmilesCSV,
"D_dataset.tsv": importDstoxTSV
}
......
......@@ -4,4 +4,4 @@ source /home/patrick/build/local/miniconda3/etc/profile.d/conda.sh
conda activate dfpl_env
conda develop dfpl
bash scripts/run-all-cases.sh
bash scripts/run-all-publication-cases.sh
......@@ -29,4 +29,4 @@ conda activate dfpl_env
conda develop dfpl
# Run the program:
srun scripts/run-all-publication-cases.sh > mpcdf_dfpl_stdout.txt
srun scripts/run-all-publication-cases.sh &> mpcdf_dfpl_run.log
......@@ -34,10 +34,8 @@ function call_predict() {
call_convert "data"
call_train "validation/case_00/train_AC_D.json"
call_train "validation/case_00/train_AC_S.json"
call_train "validation/case_00/train_AC_T.json"
call_train "validation/case_00/train_AC_X.json"
call_train "validation/case_00/train_AC_D.json"
call_train "validation/case_01/train.json"
call_train "validation/case_01/train_0p5.json"
......@@ -79,23 +77,23 @@ call_predict "validation/case_07_Sext/predict_fullAR03.json"
call_predict "validation/case_07_Sext/predict_fullED03.json"
call_predict "validation/case_07_Sext/predict_fullER03.json"
call_predict "validation/case_08_D/predict_bestAR03.json"
call_predict "validation/case_08_D/predict_bestED03.json"
call_predict "validation/case_08_D/predict_bestER03.json"
call_predict "validation/case_08_D/predict_fullAR03.json"
call_predict "validation/case_08_D/predict_fullED03.json"
call_predict "validation/case_08_D/predict_fullER03.json"
call_predict "validation/case_08_S/predict_bestAR03.json"
call_predict "validation/case_08_S/predict_bestED03.json"
call_predict "validation/case_08_S/predict_bestER03.json"
call_predict "validation/case_08_S/predict_fullAR03.json"
call_predict "validation/case_08_S/predict_fullED03.json"
call_predict "validation/case_08_S/predict_fullER03.json"
call_predict "validation/case_08_Sext/predict_bestAR03.json"
call_predict "validation/case_08_Sext/predict_bestED03.json"
call_predict "validation/case_08_Sext/predict_bestER03.json"
call_predict "validation/case_08_Sext/predict_fullAR03.json"
call_predict "validation/case_08_Sext/predict_fullED03.json"
call_predict "validation/case_08_Sext/predict_fullER03.json"
call_predict "validation/case_08_D/predict_bestARext03.json"
call_predict "validation/case_08_D/predict_bestEDext03.json"
call_predict "validation/case_08_D/predict_bestERext03.json"
call_predict "validation/case_08_D/predict_fullARext03.json"
call_predict "validation/case_08_D/predict_fullEDext03.json"
call_predict "validation/case_08_D/predict_fullERext03.json"
call_predict "validation/case_08_S/predict_bestARext03.json"
call_predict "validation/case_08_S/predict_bestEDext03.json"
call_predict "validation/case_08_S/predict_bestERext03.json"
call_predict "validation/case_08_S/predict_fullARext03.json"
call_predict "validation/case_08_S/predict_fullEDext03.json"
call_predict "validation/case_08_S/predict_fullERext03.json"
call_predict "validation/case_08_Sext/predict_bestARext03.json"
call_predict "validation/case_08_Sext/predict_bestEDext03.json"
call_predict "validation/case_08_Sext/predict_bestERext03.json"
call_predict "validation/case_08_Sext/predict_fullARext03.json"
call_predict "validation/case_08_Sext/predict_fullEDext03.json"
call_predict "validation/case_08_Sext/predict_fullERext03.json"
......@@ -38,7 +38,20 @@ call_train "validation/case_00/train_AC_S.json"
call_train "validation/case_00/train_AC_D.json"
call_train "validation/case_01/train.json"
call_train "validation/case_01/train_0p5.json"
call_train "validation/case_01/train_0p6.json"
call_train "validation/case_01/train_0p7.json"
call_train "validation/case_01/train_0p8.json"
call_train "validation/case_01/train_0p9.json"
call_train "validation/case_01/train_1p0.json"
call_train "validation/case_02/train.json"
call_train "validation/case_02/train_0p5.json"
call_train "validation/case_02/train_0p6.json"
call_train "validation/case_02/train_0p7.json"
call_train "validation/case_02/train_0p8.json"
call_train "validation/case_02/train_0p9.json"
call_train "validation/case_02/train_1p0.json"
call_train "validation/case_03_S/train.json"
call_train "validation/case_03_Sext/train.json"
......@@ -64,37 +77,23 @@ call_predict "validation/case_07_Sext/predict_fullAR03.json"
call_predict "validation/case_07_Sext/predict_fullED03.json"
call_predict "validation/case_07_Sext/predict_fullER03.json"
call_predict "validation/case_08_D/predict_bestAR03.json"
call_predict "validation/case_08_D/predict_bestED03.json"
call_predict "validation/case_08_D/predict_bestER03.json"
call_predict "validation/case_08_D/predict_fullAR03.json"
call_predict "validation/case_08_D/predict_fullED03.json"
call_predict "validation/case_08_D/predict_fullER03.json"
call_predict "validation/case_08_S/predict_bestAR03.json"
call_predict "validation/case_08_S/predict_bestED03.json"
call_predict "validation/case_08_S/predict_bestER03.json"
call_predict "validation/case_08_S/predict_fullAR03.json"
call_predict "validation/case_08_S/predict_fullED03.json"
call_predict "validation/case_08_S/predict_fullER03.json"
call_predict "validation/case_08_Sext/predict_bestAR03.json"
call_predict "validation/case_08_Sext/predict_bestED03.json"
call_predict "validation/case_08_Sext/predict_bestER03.json"
call_predict "validation/case_08_Sext/predict_fullAR03.json"
call_predict "validation/case_08_Sext/predict_fullED03.json"
call_predict "validation/case_08_Sext/predict_fullER03.json"
call_train "validation/case_01/train_0p5.json"
call_train "validation/case_01/train_0p6.json"
call_train "validation/case_01/train_0p7.json"
call_train "validation/case_01/train_0p8.json"
call_train "validation/case_01/train_0p9.json"
call_train "validation/case_01/train_1p0.json"
call_train "validation/case_02/train_0p5.json"
call_train "validation/case_02/train_0p6.json"
call_train "validation/case_02/train_0p7.json"
call_train "validation/case_02/train_0p8.json"
call_train "validation/case_02/train_0p9.json"
call_train "validation/case_02/train_1p0.json"
call_predict "validation/case_08_D/predict_bestARext03.json"
call_predict "validation/case_08_D/predict_bestEDext03.json"
call_predict "validation/case_08_D/predict_bestERext03.json"
call_predict "validation/case_08_D/predict_fullARext03.json"
call_predict "validation/case_08_D/predict_fullEDext03.json"
call_predict "validation/case_08_D/predict_fullERext03.json"
call_predict "validation/case_08_S/predict_bestARext03.json"
call_predict "validation/case_08_S/predict_bestEDext03.json"
call_predict "validation/case_08_S/predict_bestERext03.json"
call_predict "validation/case_08_S/predict_fullARext03.json"
call_predict "validation/case_08_S/predict_fullEDext03.json"
call_predict "validation/case_08_S/predict_fullERext03.json"
call_predict "validation/case_08_Sext/predict_bestARext03.json"
call_predict "validation/case_08_Sext/predict_bestEDext03.json"
call_predict "validation/case_08_Sext/predict_bestERext03.json"
call_predict "validation/case_08_Sext/predict_fullARext03.json"
call_predict "validation/case_08_Sext/predict_fullEDext03.json"
call_predict "validation/case_08_Sext/predict_fullERext03.json"
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/dsstox_20160701.pkl",
"inputFile": "data/D_dataset.pkl",
"outputDir": "validation/case_00/results_AC_D/",
"ecWeightsFile": "ac_D.encoder.hdf5",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/S_dataset_extended.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_00/results_AC_S/",
"ecWeightsFile": "ac_S.encoder.hdf5",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/T_tox21ChallengeData_4training.pkl",
"outputDir": "validation/case_00/results_AC_T/",
"ecWeightsFile": "ac_T.encoder.hdf5",
"type": "smiles",
"fpType": "topological",
"epochs": 3000,
"fpSize": 2048,
"encFPSize": 256,
"kFolds": 5,
"testingFraction": 0.2,
"enableMultiLabel": false,
"verbose": 2,
"trainAC": true,
"trainFNN": false,
"compressFeatures": true
}
\ No newline at end of file
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/SunBDBTox21.merged4training.pkl",
"outputDir": "validation/case_00/results_AC_X/",
"ecWeightsFile": "ac_X.encoder.hdf5",
"type": "smiles",
"fpType": "topological",
"epochs": 3000,
"fpSize": 2048,
"encFPSize": 256,
"kFolds": 5,
"testingFraction": 0.2,
"enableMultiLabel": false,
"verbose": 2,
"trainAC": true,
"trainFNN": false,
"compressFeatures": true
}
\ No newline at end of file
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_01/results/",
"ecWeightsFile": "",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_01/results_0p5/",
"ecWeightsFile": "",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_01/results_0p6/",
"ecWeightsFile": "",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_01/results_0p7/",
"ecWeightsFile": "",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_01/results_0p8/",
"ecWeightsFile": "",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_01/results_0p9/",
"ecWeightsFile": "",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_01/results_1p0/",
"ecWeightsFile": "",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_02/results/",
"ecWeightsFile": "validation/case_00/results_AC_S/ac_S.encoder.hdf5",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_02/results_0p5/",
"ecWeightsFile": "validation/case_00/results_AC_S/ac_S.encoder.hdf5",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_02/results_0p6/",
"ecWeightsFile": "validation/case_00/results_AC_S/ac_S.encoder.hdf5",
"type": "smiles",
......
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.pkl",
"inputFile": "data/S_dataset.pkl",
"outputDir": "validation/case_02/results_0p7/",
"ecWeightsFile": "validation/case_00/results_AC_S/ac_S.encoder.hdf5",
"type": "smiles",
......
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