├── .gitignore ├── Configs ├── Benchmark │ └── GIN_grid.yaml ├── WandB_Grids │ └── example_grid.yaml └── config.yaml ├── Data └── Splits │ ├── CSL │ ├── test.index │ ├── train.index │ └── val.index │ └── QM9 │ ├── test.index │ ├── train.index │ └── val.index ├── Exp ├── __init__.py ├── parser.py ├── preparation.py ├── run_experiment.py ├── run_model.py └── training_loop_functions.py ├── LICENSE ├── Misc ├── __init__.py ├── add_zero_edge_attr.py ├── config.py ├── cosine_scheduler.py ├── drop_features.py ├── pad_node_attr.py ├── select_only_one_target.py ├── tracking.py ├── utils.py └── weighted_cross_entropy_loss.py ├── Models ├── ESAN │ ├── __init__.py │ ├── models.py │ └── preprocessing.py ├── __init__.py ├── encoder.py ├── mlp.py ├── mpnn.py └── utils.py ├── README.md ├── Results └── .gitignore ├── Scripts ├── clean_datasets_dir.py ├── investigate_qm9.py └── split_dataset.py ├── Tests ├── __init__.py ├── run_exp_test_config.yaml ├── test_models.py └── test_run_exp.py └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/.gitignore -------------------------------------------------------------------------------- /Configs/Benchmark/GIN_grid.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Configs/Benchmark/GIN_grid.yaml -------------------------------------------------------------------------------- /Configs/WandB_Grids/example_grid.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Configs/WandB_Grids/example_grid.yaml -------------------------------------------------------------------------------- /Configs/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Configs/config.yaml -------------------------------------------------------------------------------- /Data/Splits/CSL/test.index: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Data/Splits/CSL/test.index -------------------------------------------------------------------------------- /Data/Splits/CSL/train.index: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Data/Splits/CSL/train.index -------------------------------------------------------------------------------- /Data/Splits/CSL/val.index: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Data/Splits/CSL/val.index -------------------------------------------------------------------------------- /Data/Splits/QM9/test.index: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Data/Splits/QM9/test.index -------------------------------------------------------------------------------- /Data/Splits/QM9/train.index: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Data/Splits/QM9/train.index -------------------------------------------------------------------------------- /Data/Splits/QM9/val.index: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Data/Splits/QM9/val.index -------------------------------------------------------------------------------- /Exp/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Exp/parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Exp/parser.py -------------------------------------------------------------------------------- /Exp/preparation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Exp/preparation.py -------------------------------------------------------------------------------- /Exp/run_experiment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Exp/run_experiment.py -------------------------------------------------------------------------------- /Exp/run_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Exp/run_model.py -------------------------------------------------------------------------------- /Exp/training_loop_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Exp/training_loop_functions.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/LICENSE -------------------------------------------------------------------------------- /Misc/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Misc/add_zero_edge_attr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Misc/add_zero_edge_attr.py -------------------------------------------------------------------------------- /Misc/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Misc/config.py -------------------------------------------------------------------------------- /Misc/cosine_scheduler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Misc/cosine_scheduler.py -------------------------------------------------------------------------------- /Misc/drop_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Misc/drop_features.py -------------------------------------------------------------------------------- /Misc/pad_node_attr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Misc/pad_node_attr.py -------------------------------------------------------------------------------- /Misc/select_only_one_target.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Misc/select_only_one_target.py -------------------------------------------------------------------------------- /Misc/tracking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Misc/tracking.py -------------------------------------------------------------------------------- /Misc/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Misc/utils.py -------------------------------------------------------------------------------- /Misc/weighted_cross_entropy_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Misc/weighted_cross_entropy_loss.py -------------------------------------------------------------------------------- /Models/ESAN/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Models/ESAN/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Models/ESAN/models.py -------------------------------------------------------------------------------- /Models/ESAN/preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Models/ESAN/preprocessing.py -------------------------------------------------------------------------------- /Models/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Models/encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Models/encoder.py -------------------------------------------------------------------------------- /Models/mlp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Models/mlp.py -------------------------------------------------------------------------------- /Models/mpnn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Models/mpnn.py -------------------------------------------------------------------------------- /Models/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Models/utils.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/README.md -------------------------------------------------------------------------------- /Results/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Results/.gitignore -------------------------------------------------------------------------------- /Scripts/clean_datasets_dir.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Scripts/clean_datasets_dir.py -------------------------------------------------------------------------------- /Scripts/investigate_qm9.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Scripts/investigate_qm9.py -------------------------------------------------------------------------------- /Scripts/split_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Scripts/split_dataset.py -------------------------------------------------------------------------------- /Tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Tests/run_exp_test_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Tests/run_exp_test_config.yaml -------------------------------------------------------------------------------- /Tests/test_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Tests/test_models.py -------------------------------------------------------------------------------- /Tests/test_run_exp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ocatias/BasicGNNProject/HEAD/Tests/test_run_exp.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | matplotlib 2 | ogb 3 | wandb 4 | networkx 5 | torchmetrics 6 | --------------------------------------------------------------------------------