updated example, not tested

README.md

@@ -38,7 +38,7 @@ or you can start a shell script (look at [run-all-publication-cases.sh](scripts/
 example)
 
 ```shell script
-singularity run --nv dfpl.sif ". ./scripts/run-all-cases.sh"
+singularity run --nv dfpl.sif ". ./example/run-multiple-cases.sh"
 ```
 
 It's also possible to get an interactive shell into the container

example/models/AR_saved_model/keras_metadata.pb

+
+8root"_tf_keras_sequential*8{"name": "sequential_2", "trainable": true, "expects_training_arg": true, "dtype": "float32", "batch_input_shape": null, "must_restore_from_config": false, "class_name": "Sequential", "config": {"name": "sequential_2", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 256]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "dense_8_input"}}, {"class_name": "Dense", "config": {"name": "dense_8", "trainable": true, "batch_input_shape": {"class_name": "__tuple__", "items": [null, 256]}, "dtype": "float32", "units": 128, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}}, {"class_name": "AlphaDropout", "config": {"name": "alpha_dropout_6", "trainable": true, "dtype": "float32", "rate": 0.02382519002555714}}, {"class_name": "Dense", "config": {"name": "dense_9", "trainable": true, "dtype": "float32", "units": 64, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}}, {"class_name": "AlphaDropout", "config": {"name": "alpha_dropout_7", "trainable": true, "dtype": "float32", "rate": 0.01191259501277857}}, {"class_name": "Dense", "config": {"name": "dense_10", "trainable": true, "dtype": "float32", "units": 32, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}}, {"class_name": "AlphaDropout", "config": {"name": "alpha_dropout_8", "trainable": true, "dtype": "float32", "rate": 0.005956297506389285}}, {"class_name": "Dense", "config": {"name": "dense_11", "trainable": true, "dtype": "float32", "units": 1, "activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "bias_initializer": null, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}}]}, "shared_object_id": 15, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 256}}, "shared_object_id": 16}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 256]}, "is_graph_network": true, "full_save_spec": {"class_name": "__tuple__", "items": [[{"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 256]}, "float32", "dense_8_input"]}], {}]}, "save_spec": {"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 256]}, "float32", "dense_8_input"]}, "keras_version": "2.6.0", "backend": "tensorflow", "model_config": {"class_name": "Sequential", "config": {"name": "sequential_2", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 256]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "dense_8_input"}, "shared_object_id": 0}, {"class_name": "Dense", "config": {"name": "dense_8", "trainable": true, "batch_input_shape": {"class_name": "__tuple__", "items": [null, 256]}, "dtype": "float32", "units": 128, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "shared_object_id": 3}, {"class_name": "AlphaDropout", "config": {"name": "alpha_dropout_6", "trainable": true, "dtype": "float32", "rate": 0.02382519002555714}, "shared_object_id": 4}, {"class_name": "Dense", "config": {"name": "dense_9", "trainable": true, "dtype": "float32", "units": 64, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 5}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 6}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "shared_object_id": 7}, {"class_name": "AlphaDropout", "config": {"name": "alpha_dropout_7", "trainable": true, "dtype": "float32", "rate": 0.01191259501277857}, "shared_object_id": 8}, {"class_name": "Dense", "config": {"name": "dense_10", "trainable": true, "dtype": "float32", "units": 32, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 9}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 10}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "shared_object_id": 11}, {"class_name": "AlphaDropout", "config": {"name": "alpha_dropout_8", "trainable": true, "dtype": "float32", "rate": 0.005956297506389285}, "shared_object_id": 12}, {"class_name": "Dense", "config": {"name": "dense_11", "trainable": true, "dtype": "float32", "units": 1, "activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 13}, "bias_initializer": null, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "shared_object_id": 14}]}}, "training_config": {"loss": {"class_name": "BinaryCrossentropy", "config": {"reduction": "auto", "name": "binary_crossentropy", "from_logits": false, "label_smoothing": 0, "axis": -1}, "shared_object_id": 17}, "metrics": [[{"class_name": "BinaryAccuracy", "config": {"name": "accuracy", "dtype": "float32", "threshold": 0.5}, "shared_object_id": 18}, {"class_name": "AUC", "config": {"name": "auc_2", "dtype": "float32", "num_thresholds": 200, "curve": "ROC", "summation_method": "interpolation", "multi_label": false, "label_weights": null}, "shared_object_id": 19}, {"class_name": "Precision", "config": {"name": "precision_2", "dtype": "float32", "thresholds": null, "top_k": null, "class_id": null}, "shared_object_id": 20}, {"class_name": "Recall", "config": {"name": "recall_2", "dtype": "float32", "thresholds": null, "top_k": null, "class_id": null}, "shared_object_id": 21}]], "weighted_metrics": null, "loss_weights": null, "optimizer_config": {"class_name": "Adam", "config": {"name": "Adam", "learning_rate": 7.83711232114358e-06, "decay": 0.0, "beta_1": 0.9, "beta_2": 0.999, "epsilon": 1e-07, "amsgrad": false}}}}2

+
root.layer_with_weights-0"_tf_keras_layer*{"name": "dense_8", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": {"class_name": "__tuple__", "items": [null, 256]}, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_8", "trainable": true, "batch_input_shape": {"class_name": "__tuple__", "items": [null, 256]}, "dtype": "float32", "units": 128, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "shared_object_id": 3, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 256}}, "shared_object_id": 16}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 256]}}2

+root.layer-1"_tf_keras_layer*{"name": "alpha_dropout_6", "trainable": true, "expects_training_arg": true, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "AlphaDropout", "config": {"name": "alpha_dropout_6", "trainable": true, "dtype": "float32", "rate": 0.02382519002555714}, "shared_object_id": 4}2

+root.layer_with_weights-1"_tf_keras_layer*{"name": "dense_9", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_9", "trainable": true, "dtype": "float32", "units": 64, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 5}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 6}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "shared_object_id": 7, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 128}}, "shared_object_id": 22}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 128]}}2

+root.layer-3"_tf_keras_layer*{"name": "alpha_dropout_7", "trainable": true, "expects_training_arg": true, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "AlphaDropout", "config": {"name": "alpha_dropout_7", "trainable": true, "dtype": "float32", "rate": 0.01191259501277857}, "shared_object_id": 8}2

+root.layer_with_weights-2"_tf_keras_layer*{"name": "dense_10", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_10", "trainable": true, "dtype": "float32", "units": 32, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 9}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 10}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "shared_object_id": 11, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 64}}, "shared_object_id": 23}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 64]}}2

+root.layer-5"_tf_keras_layer*{"name": "alpha_dropout_8", "trainable": true, "expects_training_arg": true, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "AlphaDropout", "config": {"name": "alpha_dropout_8", "trainable": true, "dtype": "float32", "rate": 0.005956297506389285}, "shared_object_id": 12}2

+root.layer_with_weights-3"_tf_keras_layer*{"name": "dense_11", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_11", "trainable": true, "dtype": "float32", "units": 1, "activation": "sigmoid", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 13}, "bias_initializer": null, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "shared_object_id": 14, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 32}}, "shared_object_id": 24}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 32]}}2

+
Zroot.keras_api.metrics.0"_tf_keras_metric*
{"class_name": "Mean", "name": "loss", "dtype": "float32", "config": {"name": "loss", "dtype": "float32"}, "shared_object_id": 25}2

+
[root.keras_api.metrics.1"_tf_keras_metric*
{"class_name": "BinaryAccuracy", "name": "accuracy", "dtype": "float32", "config": {"name": "accuracy", "dtype": "float32", "threshold": 0.5}, "shared_object_id": 18}2

+\root.keras_api.metrics.2"_tf_keras_metric*
{"class_name": "AUC", "name": "auc_2", "dtype": "float32", "config": {"name": "auc_2", "dtype": "float32", "num_thresholds": 200, "curve": "ROC", "summation_method": "interpolation", "multi_label": false, "label_weights": null}, "shared_object_id": 19}2

+]root.keras_api.metrics.3"_tf_keras_metric*
{"class_name": "Precision", "name": "precision_2", "dtype": "float32", "config": {"name": "precision_2", "dtype": "float32", "thresholds": null, "top_k": null, "class_id": null}, "shared_object_id": 20}2

+
^root.keras_api.metrics.4"_tf_keras_metric*
{"class_name": "Recall", "name": "recall_2", "dtype": "float32", "config": {"name": "recall_2", "dtype": "float32", "thresholds": null, "top_k": null, "class_id": null}, "shared_object_id": 21}2

\ No newline at end of file

example/models/generic_encoder/keras_metadata.pb

+
+%root"_tf_keras_network*%{"name": "model_1", "trainable": true, "expects_training_arg": true, "dtype": "float32", "batch_input_shape": null, "must_restore_from_config": false, "class_name": "Functional", "config": {"name": "model_1", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 2048]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_1"}, "name": "input_1", "inbound_nodes": []}, {"class_name": "Dense", "config": {"name": "dense", "trainable": true, "dtype": "float32", "units": 1024, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense", "inbound_nodes": [[["input_1", 0, 0, {}]]]}, {"class_name": "Dense", "config": {"name": "dense_1", "trainable": true, "dtype": "float32", "units": 512, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_1", "inbound_nodes": [[["dense", 0, 0, {}]]]}, {"class_name": "Dense", "config": {"name": "dense_2", "trainable": true, "dtype": "float32", "units": 256, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_2", "inbound_nodes": [[["dense_1", 0, 0, {}]]]}], "input_layers": [["input_1", 0, 0]], "output_layers": [["dense_2", 0, 0]]}, "shared_object_id": 10, "input_spec": [{"class_name": "InputSpec", "config": {"dtype": null, "shape": {"class_name": "__tuple__", "items": [null, 2048]}, "ndim": 2, "max_ndim": null, "min_ndim": null, "axes": {}}}], "build_input_shape": {"class_name": "TensorShape", "items": [null, 2048]}, "is_graph_network": true, "full_save_spec": {"class_name": "__tuple__", "items": [[{"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 2048]}, "float32", "input_1"]}], {}]}, "save_spec": {"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 2048]}, "float32", "input_1"]}, "keras_version": "2.6.0", "backend": "tensorflow", "model_config": {"class_name": "Functional", "config": {"name": "model_1", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 2048]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_1"}, "name": "input_1", "inbound_nodes": [], "shared_object_id": 0}, {"class_name": "Dense", "config": {"name": "dense", "trainable": true, "dtype": "float32", "units": 1024, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense", "inbound_nodes": [[["input_1", 0, 0, {}]]], "shared_object_id": 3}, {"class_name": "Dense", "config": {"name": "dense_1", "trainable": true, "dtype": "float32", "units": 512, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 4}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 5}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_1", "inbound_nodes": [[["dense", 0, 0, {}]]], "shared_object_id": 6}, {"class_name": "Dense", "config": {"name": "dense_2", "trainable": true, "dtype": "float32", "units": 256, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 7}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 8}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_2", "inbound_nodes": [[["dense_1", 0, 0, {}]]], "shared_object_id": 9}], "input_layers": [["input_1", 0, 0]], "output_layers": [["dense_2", 0, 0]]}}}2

+
root.layer-0"_tf_keras_input_layer*{"class_name": "InputLayer", "name": "input_1", "dtype": "float32", "sparse": false, "ragged": false, "batch_input_shape": {"class_name": "__tuple__", "items": [null, 2048]}, "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 2048]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_1"}}2

+root.layer_with_weights-0"_tf_keras_layer*{"name": "dense", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense", "trainable": true, "dtype": "float32", "units": 1024, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["input_1", 0, 0, {}]]], "shared_object_id": 3, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 2048}}, "shared_object_id": 12}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 2048]}}2

+root.layer_with_weights-1"_tf_keras_layer*{"name": "dense_1", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_1", "trainable": true, "dtype": "float32", "units": 512, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 4}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 5}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense", 0, 0, {}]]], "shared_object_id": 6, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 1024}}, "shared_object_id": 13}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 1024]}}2

+root.layer_with_weights-2"_tf_keras_layer*{"name": "dense_2", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_2", "trainable": true, "dtype": "float32", "units": 256, "activation": "selu", "use_bias": true, "kernel_initializer": {"class_name": "LecunNormal", "config": {"seed": null}, "shared_object_id": 7}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 8}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_1", 0, 0, {}]]], "shared_object_id": 9, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 512}}, "shared_object_id": 14}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 512]}}2

\ No newline at end of file

example/predict.json

 {
-  "py/object": "dfpl.options.PredictOptions",
+  "py/object": "dfpl.options.Options",
   "inputFile": "example/data/predict_data.csv",
   "outputDir": "example/results_predict",
-  "ecWeightsFile": "example/models/generic_encoder.hdf5",
-  "model": "example/models/AR.model.hdf5",
-  "type": "smiles",
-  "fpType": "topological"
+  "outputFile": "predict_data_AR.csv",
+  "ecModelDir": "example/models/generic_encoder",
+  "fnnModelDir": "example/models/AR_saved_model",
+  "compressFeatures": true,
+  "trainAC": false,
+  "trainFNN": false
 }

example/run-multiple-cases.sh

+#!/usr/bin/env bash
+
+# This script needs to be run from the deepFPlearn directory.
+# Importantly, the conda environment needs to be set up and activated! For certain machines/HPC,
+# we have a batch-job that does exactly that and then calls this file
+
+function log_error() {
+  echo "$@" 1>&2
+}
+
+function call_convert() {
+  if [ -d "$1" ]; then
+    python -m dfpl convert -f "$1"
+  else
+    log_error "Could not find directory for data conversion $1"
+  fi
+}
+
+function call_train() {
+  if [ -f "$1" ]; then
+    python -m dfpl train -f "$1"
+  else
+    log_error "Could not find training file $1"
+  fi
+}
+
+function call_predict() {
+  if [ -f "$1" ]; then
+    python -m dfpl predict -f "$1"
+  else
+    log_error "Could not find prediction file $1"
+  fi
+}
+
+call_convert "data"
+
+call_train "train.json"
+
+call_predict "predict.json"

example/train.json

 {
-  "py/object": "dfpl.options.TrainOptions",
+  "py/object": "dfpl.options.Options",
   "inputFile": "example/data/train_data.csv",
   "outputDir": "example/results_train/",
-  "ecWeightsFile": "encoder.hdf5",
+  "ecWeightsFile": "example/models/generic_encoder",
   "type": "smiles",
   "fpType": "topological",
-  "epochs": 3000,
   "fpSize": 2048,
   "encFPSize": 256,
-  "kFolds": 5,
-  "testingFraction": 0.2,
   "enableMultiLabel": false,
   "verbose": 2,
-  "trainAC": true,
+  "trainAC": false,
   "trainFNN": true,
-  "compressFeatures": true
+  "compressFeatures": true,
+
+  "kFolds": 1,
+  "testSize": 0.2,
+  "optimizer": "Adam",
+  "lossFunction": "bce",
+  "epochs": 3000,
+  "batchSize": 128,
+  "activationFunction": "selu",
+  "dropout": 0.02382519002555714,
+  "learningRate": 0.00000783711232114358
 }