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Commit 7fb00d9f authored by Jana Schor's avatar Jana Schor
Browse files

rearrange cases according to used training data sets

parent 3651b8e3
......@@ -11,6 +11,7 @@ import autoencoder as ac
import feedforwardNN as fNN
import predictions
project_directory = pathlib.Path(__file__).parent.parent.absolute()
test_train_args = options.TrainOptions(
inputFile=f"{project_directory}/data/Sun_etal_dataset.csv",
......
......@@ -110,11 +110,13 @@ def autoencoder_callback(checkpoint_path: str, patience: int) -> list:
# enable early stopping if val_loss is not improving anymore
early_stop = EarlyStopping(patience=patience,
verbose=1,
restore_best_weights=True)
return [checkpoint, early_stop]
def train_full_ac(df: pd.DataFrame, opts: options.TrainOptions) -> Model:
"""
Train an autoencoder on the given feature matrix X. Response matrix is only used to
......
{
"py/object": "dfpl.options.PredictOptions",
"inputFile": "data/07_BindingDB.trainingSet.csv",
"outputDir": "validation/case_01/results",
"acFile": "Sun_etal_dataset.AC.encoder.weights.hdf5",
"model": "AR_compressed-True.full.FNN-.model.hdf5",
"type": "smiles",
"fpType": "topological"
}
\ No newline at end of file
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.csv",
"outputDir": "validation/case_01/results",
"acFile": "Sun_etal_dataset.AC.encoder.weights.hdf5",
"type": "smiles",
"fpType": "topological",
"epochs": 100,
"fpSize": 2048,
"encFPSize": 256,
"kFolds": 5,
"testingFraction": 0.2,
"enableMultiLabel": false,
"verbose": 2,
"trainAC": true,
"trainFNN": true
}
\ No newline at end of file
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/07_BindingDB.trainingSet.csv",
"outputDir": "validation/case_01/results",
"acFile": "BindingDB.AC.encoder.weights.hdf5",
"type": "smiles",
"fpType": "topological",
"epochs": 3000,
"fpSize": 2048,
"encFPSize": 256,
"kFolds": 5,
"testingFraction": 0.2,
"enableMultiLabel": false,
"verbose": 2,
"trainAC": true,
"trainFNN": true
}
\ No newline at end of file
......@@ -2,7 +2,7 @@
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.csv",
"outputDir": "validation/case_03/results/",
"acFile": "",
"acFile": "encoder.checkpoint_path.hdf5",
"type": "smiles",
"fpType": "topological",
"epochs": 3000,
......@@ -14,5 +14,5 @@
"verbose": 2,
"trainAC": false,
"trainFNN": true,
"compressFeatures": false
"compressFeatures": true
}
\ No newline at end of file
{
"py/object": "dfpl.options.TrainOptions",
"inputFile": "data/Sun_etal_dataset.csv",
"inputFile": "data/SunBDBTox21.merged4training.csv",
"outputDir": "validation/case_06/results/",
"acFile": "ACmodel.hdf5",
"acFile": "encoder.checkpoint_path.hdf5",
"type": "smiles",
"fpType": "topological",
"epochs": 3000,
......@@ -12,7 +12,7 @@
"testingFraction": 0.2,
"enableMultiLabel": true,
"verbose": 2,
"trainAC": true,
"trainAC": false,
"trainFNN": true,
"compressFeatures": true
}
\ No newline at end of file
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