├── HybridML ├── ModelCreator.py ├── NodeRegistry.py ├── Project.py ├── Visualization.py ├── __init__.py ├── building │ ├── BaseBuilders.py │ ├── DataModel.py │ ├── __init__.py │ └── nodes │ │ ├── ArithmeticExpression.py │ │ ├── BasicFunction.py │ │ ├── ExistingModel.py │ │ ├── GeneralOde.py │ │ ├── LinearOde.py │ │ ├── NeuralNetwork.py │ │ └── __init__.py ├── keras │ ├── Builders.py │ ├── Containers.py │ ├── __init__.py │ └── layers │ │ ├── ArithmeticExpression.py │ │ ├── CasadiLinearOde.py │ │ ├── GeneralOde.py │ │ ├── LinearOde.py │ │ ├── TensorflowLinearOde.py │ │ └── __init__.py ├── parsing │ ├── BaseParsers.py │ ├── DataModel.py │ ├── ParserImplementation.py │ ├── __init__.py │ ├── models_schema.json │ └── nodes │ │ ├── ArithmeticExpression.py │ │ ├── BasicFunction.py │ │ ├── ExistingModel.py │ │ ├── GeneralOde.py │ │ ├── LinearOde.py │ │ ├── NeuralNetwork.py │ │ └── __init__.py ├── templates │ ├── model_template.json │ └── project_template.json └── utils │ ├── DataSource.py │ ├── FileUtil.py │ ├── NetDrawer.py │ ├── TensorBoard.py │ ├── __init__.py │ └── history_plotter.py ├── LICENSE ├── MANIFEST.in ├── README.md ├── create-nodes.md ├── demo ├── __init__.py ├── extrapolation_demo │ ├── extrapolation_demo.py │ ├── extrapolation_search.py │ └── projects │ │ └── extrapolation_demo │ │ ├── blackbox.json │ │ ├── extrapolation_demo.json │ │ ├── hybrid.json │ │ ├── test.csv │ │ ├── train.csv │ │ └── val.csv ├── flux │ ├── __init__.py │ ├── datasource.py │ ├── flux_benchmark.py │ ├── flux_benchmark_data.py │ ├── flux_demo.py │ ├── flux_random_architecture.py │ ├── preprocessing.py │ ├── projects │ │ ├── data │ │ │ ├── Fluvoxamine │ │ │ │ ├── Population based on de Vries 1993_50mgSD_NA_NA-Results.csv │ │ │ │ ├── Population based on de Vries-Population.csv │ │ │ │ ├── covariateToUseTable.xlsx │ │ │ │ ├── psp412397-sup-0002-DataS1.pksim5 │ │ │ │ └── three_bb_covariates.xlsx │ │ │ └── PBPK Models for CYP3A4 and P‐gp DDI Prediction │ │ │ │ ├── psp4.12343.pdf │ │ │ │ ├── psp412397-sup-0001-SupplementS1.pdf │ │ │ │ ├── psp412397-sup-0002-DataS1.pksim5 │ │ │ │ ├── psp412397-sup-0003-DataS2.pksim5 │ │ │ │ ├── psp412397-sup-0004-DataS3.pksim5 │ │ │ │ ├── psp412397-sup-0005-DataS4.pksim5 │ │ │ │ ├── psp412397-sup-0006-DataS5.pksim5 │ │ │ │ └── psp412397-sup-0007-DataS6.pksim5 │ │ ├── flux_demo │ │ │ ├── flux_demo.json │ │ │ └── flux_model.json │ │ └── structured_flux_demo │ │ │ ├── parameter selection.csv │ │ │ ├── structured_flux_demo.json │ │ │ └── structured_flux_model.json │ ├── random_search_analysis.py │ ├── structured_flux_demo.py │ ├── training.py │ └── visualization.py ├── simple_demo.py ├── simple_model.json └── theoph │ ├── plot_animation.py │ ├── projects │ ├── theoph_demo │ │ ├── theoph.csv │ │ ├── theoph_demo.json │ │ ├── theoph_model_2_compartments.json │ │ ├── theoph_model_3_compartments.json │ │ └── theoph_normalized.csv │ ├── theoph_lin_ode │ │ ├── Benchmark loss.png │ │ ├── ODE Benchmark.txt │ │ ├── bb_outp_direct_into_ode.json │ │ ├── bb_outp_normalized_into_ode.json │ │ ├── normalize_theoph.py │ │ ├── plots │ │ │ ├── params_1k.png │ │ │ └── params_final.png │ │ ├── theoph.csv │ │ ├── theoph_lin_ode.json │ │ ├── theoph_model.json │ │ ├── theoph_model_2.json │ │ ├── theoph_model_3.json │ │ └── theoph_normalized.csv │ └── theoph_one_bb │ │ ├── plots │ │ ├── all_3lyr_sigmoid_epochs_100.png │ │ ├── all_andreas_epochs_5.png │ │ ├── all_no_bbs_sebastian_solution.png │ │ ├── all_one_bb_epochs_090.png │ │ ├── single_3lyr_sigmoid_epochs_100.png │ │ ├── single_andreas_epochs_5.png │ │ ├── single_no_bbs_sebastian_solution.png │ │ └── single_one_bb_epochs_090.png │ │ ├── theoph_model_3_compartments.json │ │ ├── theoph_model_3_compartments_one_bb.json │ │ ├── theoph_normalized.csv │ │ └── theoph_one_bb.json │ ├── theoph_demo.py │ ├── theoph_lin_ode.py │ ├── theoph_one_bb.py │ ├── theoph_random_architecture.py │ ├── theoph_train_on.py │ ├── theoph_vis_process.py │ ├── theoph_vis_results.py │ └── theoph_visualize.py ├── dockerfile ├── model-json.md ├── requirements.txt ├── setup.py └── tests ├── .gitignore ├── __init__.py ├── run_tests.py ├── test_arithmetic_expression_layer.py ├── test_arithmetic_expression_node.py ├── test_arithmetic_expression_node.py.json ├── test_casadi_linear_ode_node.py ├── test_casadi_linear_ode_node.py.json ├── test_containers.py ├── test_containers.py.json ├── test_existing_model_layer.py ├── test_existing_model_layer.py.json ├── test_flux_demo.py ├── test_general_ode_layer.py ├── test_general_ode_node.py ├── test_general_ode_node.py.json ├── test_linear_ode_node.py ├── test_linear_ode_node.py.json ├── test_neural_net_node.py ├── test_neural_net_node.py.json ├── test_new_format.py ├── test_new_format.py.json ├── test_simple_demo.py ├── test_theoph_demo.py └── test_utility.py /HybridML/ModelCreator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/ModelCreator.py -------------------------------------------------------------------------------- /HybridML/NodeRegistry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/NodeRegistry.py -------------------------------------------------------------------------------- /HybridML/Project.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/Project.py -------------------------------------------------------------------------------- /HybridML/Visualization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/Visualization.py -------------------------------------------------------------------------------- /HybridML/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /HybridML/building/BaseBuilders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/building/BaseBuilders.py -------------------------------------------------------------------------------- /HybridML/building/DataModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/building/DataModel.py -------------------------------------------------------------------------------- /HybridML/building/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/building/__init__.py -------------------------------------------------------------------------------- /HybridML/building/nodes/ArithmeticExpression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/building/nodes/ArithmeticExpression.py -------------------------------------------------------------------------------- /HybridML/building/nodes/BasicFunction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/building/nodes/BasicFunction.py -------------------------------------------------------------------------------- /HybridML/building/nodes/ExistingModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/building/nodes/ExistingModel.py -------------------------------------------------------------------------------- /HybridML/building/nodes/GeneralOde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/building/nodes/GeneralOde.py -------------------------------------------------------------------------------- /HybridML/building/nodes/LinearOde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/building/nodes/LinearOde.py -------------------------------------------------------------------------------- /HybridML/building/nodes/NeuralNetwork.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/building/nodes/NeuralNetwork.py -------------------------------------------------------------------------------- /HybridML/building/nodes/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /HybridML/keras/Builders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/keras/Builders.py -------------------------------------------------------------------------------- /HybridML/keras/Containers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/keras/Containers.py -------------------------------------------------------------------------------- /HybridML/keras/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/keras/__init__.py -------------------------------------------------------------------------------- /HybridML/keras/layers/ArithmeticExpression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/keras/layers/ArithmeticExpression.py -------------------------------------------------------------------------------- /HybridML/keras/layers/CasadiLinearOde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/keras/layers/CasadiLinearOde.py -------------------------------------------------------------------------------- /HybridML/keras/layers/GeneralOde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/keras/layers/GeneralOde.py -------------------------------------------------------------------------------- /HybridML/keras/layers/LinearOde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/keras/layers/LinearOde.py -------------------------------------------------------------------------------- /HybridML/keras/layers/TensorflowLinearOde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/keras/layers/TensorflowLinearOde.py -------------------------------------------------------------------------------- /HybridML/keras/layers/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /HybridML/parsing/BaseParsers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/BaseParsers.py -------------------------------------------------------------------------------- /HybridML/parsing/DataModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/DataModel.py -------------------------------------------------------------------------------- /HybridML/parsing/ParserImplementation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/ParserImplementation.py -------------------------------------------------------------------------------- /HybridML/parsing/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/__init__.py -------------------------------------------------------------------------------- /HybridML/parsing/models_schema.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/models_schema.json -------------------------------------------------------------------------------- /HybridML/parsing/nodes/ArithmeticExpression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/nodes/ArithmeticExpression.py -------------------------------------------------------------------------------- /HybridML/parsing/nodes/BasicFunction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/nodes/BasicFunction.py -------------------------------------------------------------------------------- /HybridML/parsing/nodes/ExistingModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/nodes/ExistingModel.py -------------------------------------------------------------------------------- /HybridML/parsing/nodes/GeneralOde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/nodes/GeneralOde.py -------------------------------------------------------------------------------- /HybridML/parsing/nodes/LinearOde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/nodes/LinearOde.py -------------------------------------------------------------------------------- /HybridML/parsing/nodes/NeuralNetwork.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/parsing/nodes/NeuralNetwork.py -------------------------------------------------------------------------------- /HybridML/parsing/nodes/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /HybridML/templates/model_template.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/templates/model_template.json -------------------------------------------------------------------------------- /HybridML/templates/project_template.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/templates/project_template.json -------------------------------------------------------------------------------- /HybridML/utils/DataSource.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/utils/DataSource.py -------------------------------------------------------------------------------- /HybridML/utils/FileUtil.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/utils/FileUtil.py -------------------------------------------------------------------------------- /HybridML/utils/NetDrawer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/utils/NetDrawer.py -------------------------------------------------------------------------------- /HybridML/utils/TensorBoard.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/utils/TensorBoard.py -------------------------------------------------------------------------------- /HybridML/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /HybridML/utils/history_plotter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/HybridML/utils/history_plotter.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/README.md -------------------------------------------------------------------------------- /create-nodes.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/create-nodes.md -------------------------------------------------------------------------------- /demo/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /demo/extrapolation_demo/extrapolation_demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/extrapolation_demo/extrapolation_demo.py -------------------------------------------------------------------------------- /demo/extrapolation_demo/extrapolation_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/extrapolation_demo/extrapolation_search.py -------------------------------------------------------------------------------- /demo/extrapolation_demo/projects/extrapolation_demo/blackbox.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/extrapolation_demo/projects/extrapolation_demo/blackbox.json -------------------------------------------------------------------------------- /demo/extrapolation_demo/projects/extrapolation_demo/extrapolation_demo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/extrapolation_demo/projects/extrapolation_demo/extrapolation_demo.json -------------------------------------------------------------------------------- /demo/extrapolation_demo/projects/extrapolation_demo/hybrid.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/extrapolation_demo/projects/extrapolation_demo/hybrid.json -------------------------------------------------------------------------------- /demo/extrapolation_demo/projects/extrapolation_demo/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/extrapolation_demo/projects/extrapolation_demo/test.csv -------------------------------------------------------------------------------- /demo/extrapolation_demo/projects/extrapolation_demo/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/extrapolation_demo/projects/extrapolation_demo/train.csv -------------------------------------------------------------------------------- /demo/extrapolation_demo/projects/extrapolation_demo/val.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/extrapolation_demo/projects/extrapolation_demo/val.csv -------------------------------------------------------------------------------- /demo/flux/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /demo/flux/datasource.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/datasource.py -------------------------------------------------------------------------------- /demo/flux/flux_benchmark.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/flux_benchmark.py -------------------------------------------------------------------------------- /demo/flux/flux_benchmark_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/flux_benchmark_data.py -------------------------------------------------------------------------------- /demo/flux/flux_demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/flux_demo.py -------------------------------------------------------------------------------- /demo/flux/flux_random_architecture.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/flux_random_architecture.py -------------------------------------------------------------------------------- /demo/flux/preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/preprocessing.py -------------------------------------------------------------------------------- /demo/flux/projects/data/Fluvoxamine/Population based on de Vries 1993_50mgSD_NA_NA-Results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/Fluvoxamine/Population based on de Vries 1993_50mgSD_NA_NA-Results.csv -------------------------------------------------------------------------------- /demo/flux/projects/data/Fluvoxamine/Population based on de Vries-Population.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/Fluvoxamine/Population based on de Vries-Population.csv -------------------------------------------------------------------------------- /demo/flux/projects/data/Fluvoxamine/covariateToUseTable.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/Fluvoxamine/covariateToUseTable.xlsx -------------------------------------------------------------------------------- /demo/flux/projects/data/Fluvoxamine/psp412397-sup-0002-DataS1.pksim5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/Fluvoxamine/psp412397-sup-0002-DataS1.pksim5 -------------------------------------------------------------------------------- /demo/flux/projects/data/Fluvoxamine/three_bb_covariates.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/Fluvoxamine/three_bb_covariates.xlsx -------------------------------------------------------------------------------- /demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp4.12343.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp4.12343.pdf -------------------------------------------------------------------------------- /demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0001-SupplementS1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0001-SupplementS1.pdf -------------------------------------------------------------------------------- /demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0002-DataS1.pksim5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0002-DataS1.pksim5 -------------------------------------------------------------------------------- /demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0003-DataS2.pksim5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0003-DataS2.pksim5 -------------------------------------------------------------------------------- /demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0004-DataS3.pksim5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0004-DataS3.pksim5 -------------------------------------------------------------------------------- /demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0005-DataS4.pksim5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0005-DataS4.pksim5 -------------------------------------------------------------------------------- /demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0006-DataS5.pksim5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0006-DataS5.pksim5 -------------------------------------------------------------------------------- /demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0007-DataS6.pksim5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/data/PBPK Models for CYP3A4 and P‐gp DDI Prediction/psp412397-sup-0007-DataS6.pksim5 -------------------------------------------------------------------------------- /demo/flux/projects/flux_demo/flux_demo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/flux_demo/flux_demo.json -------------------------------------------------------------------------------- /demo/flux/projects/flux_demo/flux_model.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/flux_demo/flux_model.json -------------------------------------------------------------------------------- /demo/flux/projects/structured_flux_demo/parameter selection.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/structured_flux_demo/parameter selection.csv -------------------------------------------------------------------------------- /demo/flux/projects/structured_flux_demo/structured_flux_demo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/structured_flux_demo/structured_flux_demo.json -------------------------------------------------------------------------------- /demo/flux/projects/structured_flux_demo/structured_flux_model.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/projects/structured_flux_demo/structured_flux_model.json -------------------------------------------------------------------------------- /demo/flux/random_search_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/random_search_analysis.py -------------------------------------------------------------------------------- /demo/flux/structured_flux_demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/structured_flux_demo.py -------------------------------------------------------------------------------- /demo/flux/training.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/training.py -------------------------------------------------------------------------------- /demo/flux/visualization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/flux/visualization.py -------------------------------------------------------------------------------- /demo/simple_demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/simple_demo.py -------------------------------------------------------------------------------- /demo/simple_model.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/simple_model.json -------------------------------------------------------------------------------- /demo/theoph/plot_animation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/plot_animation.py -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_demo/theoph.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_demo/theoph.csv -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_demo/theoph_demo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_demo/theoph_demo.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_demo/theoph_model_2_compartments.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_demo/theoph_model_2_compartments.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_demo/theoph_model_3_compartments.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_demo/theoph_model_3_compartments.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_demo/theoph_normalized.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_demo/theoph_normalized.csv -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/Benchmark loss.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/Benchmark loss.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/ODE Benchmark.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/ODE Benchmark.txt -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/bb_outp_direct_into_ode.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/bb_outp_direct_into_ode.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/bb_outp_normalized_into_ode.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/bb_outp_normalized_into_ode.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/normalize_theoph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/normalize_theoph.py -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/plots/params_1k.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/plots/params_1k.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/plots/params_final.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/plots/params_final.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/theoph.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/theoph.csv -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/theoph_lin_ode.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/theoph_lin_ode.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/theoph_model.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/theoph_model.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/theoph_model_2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/theoph_model_2.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/theoph_model_3.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/theoph_model_3.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_lin_ode/theoph_normalized.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_lin_ode/theoph_normalized.csv -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/plots/all_3lyr_sigmoid_epochs_100.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/plots/all_3lyr_sigmoid_epochs_100.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/plots/all_andreas_epochs_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/plots/all_andreas_epochs_5.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/plots/all_no_bbs_sebastian_solution.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/plots/all_no_bbs_sebastian_solution.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/plots/all_one_bb_epochs_090.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/plots/all_one_bb_epochs_090.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/plots/single_3lyr_sigmoid_epochs_100.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/plots/single_3lyr_sigmoid_epochs_100.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/plots/single_andreas_epochs_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/plots/single_andreas_epochs_5.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/plots/single_no_bbs_sebastian_solution.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/plots/single_no_bbs_sebastian_solution.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/plots/single_one_bb_epochs_090.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/plots/single_one_bb_epochs_090.png -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/theoph_model_3_compartments.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/theoph_model_3_compartments.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/theoph_model_3_compartments_one_bb.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/theoph_model_3_compartments_one_bb.json -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/theoph_normalized.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/theoph_normalized.csv -------------------------------------------------------------------------------- /demo/theoph/projects/theoph_one_bb/theoph_one_bb.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/projects/theoph_one_bb/theoph_one_bb.json -------------------------------------------------------------------------------- /demo/theoph/theoph_demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/theoph_demo.py -------------------------------------------------------------------------------- /demo/theoph/theoph_lin_ode.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/theoph_lin_ode.py -------------------------------------------------------------------------------- /demo/theoph/theoph_one_bb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/theoph_one_bb.py -------------------------------------------------------------------------------- /demo/theoph/theoph_random_architecture.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/theoph_random_architecture.py -------------------------------------------------------------------------------- /demo/theoph/theoph_train_on.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/theoph_train_on.py -------------------------------------------------------------------------------- /demo/theoph/theoph_vis_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/theoph_vis_process.py -------------------------------------------------------------------------------- /demo/theoph/theoph_vis_results.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/theoph_vis_results.py -------------------------------------------------------------------------------- /demo/theoph/theoph_visualize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/demo/theoph/theoph_visualize.py -------------------------------------------------------------------------------- /dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/dockerfile -------------------------------------------------------------------------------- /model-json.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/model-json.md -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/setup.py -------------------------------------------------------------------------------- /tests/.gitignore: -------------------------------------------------------------------------------- 1 | test_new_format_project 2 | -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/run_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/run_tests.py -------------------------------------------------------------------------------- /tests/test_arithmetic_expression_layer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_arithmetic_expression_layer.py -------------------------------------------------------------------------------- /tests/test_arithmetic_expression_node.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_arithmetic_expression_node.py -------------------------------------------------------------------------------- /tests/test_arithmetic_expression_node.py.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_arithmetic_expression_node.py.json -------------------------------------------------------------------------------- /tests/test_casadi_linear_ode_node.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_casadi_linear_ode_node.py -------------------------------------------------------------------------------- /tests/test_casadi_linear_ode_node.py.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_casadi_linear_ode_node.py.json -------------------------------------------------------------------------------- /tests/test_containers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_containers.py -------------------------------------------------------------------------------- /tests/test_containers.py.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_containers.py.json -------------------------------------------------------------------------------- /tests/test_existing_model_layer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_existing_model_layer.py -------------------------------------------------------------------------------- /tests/test_existing_model_layer.py.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_existing_model_layer.py.json -------------------------------------------------------------------------------- /tests/test_flux_demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_flux_demo.py -------------------------------------------------------------------------------- /tests/test_general_ode_layer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_general_ode_layer.py -------------------------------------------------------------------------------- /tests/test_general_ode_node.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_general_ode_node.py -------------------------------------------------------------------------------- /tests/test_general_ode_node.py.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_general_ode_node.py.json -------------------------------------------------------------------------------- /tests/test_linear_ode_node.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_linear_ode_node.py -------------------------------------------------------------------------------- /tests/test_linear_ode_node.py.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_linear_ode_node.py.json -------------------------------------------------------------------------------- /tests/test_neural_net_node.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_neural_net_node.py -------------------------------------------------------------------------------- /tests/test_neural_net_node.py.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_neural_net_node.py.json -------------------------------------------------------------------------------- /tests/test_new_format.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_new_format.py -------------------------------------------------------------------------------- /tests/test_new_format.py.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_new_format.py.json -------------------------------------------------------------------------------- /tests/test_simple_demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_simple_demo.py -------------------------------------------------------------------------------- /tests/test_theoph_demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_theoph_demo.py -------------------------------------------------------------------------------- /tests/test_utility.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JRC-COMBINE/HybridML/HEAD/tests/test_utility.py --------------------------------------------------------------------------------