├── .gitignore ├── LICENSE ├── README.md ├── __init__.py ├── configs ├── __init__.py ├── config.yaml ├── dataset │ ├── comm20.yaml │ ├── ego.yaml │ ├── guacamol.yaml │ ├── moses.yaml │ ├── planar.yaml │ ├── protein.yaml │ ├── qm9.yaml │ └── sbm.yaml ├── experiment │ ├── comm20.yaml │ ├── debug.yaml │ ├── ego.yaml │ ├── final_test.yaml │ ├── guacamol.yaml │ ├── moses.yaml │ ├── nx_graphs.yaml │ ├── planar.yaml │ ├── protein.yaml │ ├── qm9_no_h.yaml │ ├── qm9_with_h.yaml │ ├── sbm.yaml │ └── test.yaml ├── general │ └── general_default.yaml ├── model │ └── discrete.yaml └── train │ └── train_default.yaml ├── requirements.txt ├── setup.py └── sparse_diffusion ├── __init__.py ├── analysis ├── __init__.py ├── dist_helper.py ├── orca │ ├── orca.cpp │ └── orca.h └── visualization.py ├── datasets ├── __init__.py ├── abstract_dataset.py ├── dataset_utils.py ├── guacamol_dataset.py ├── moses_dataset.py ├── protein_dataset.py ├── qm9_dataset.py └── spectre_dataset_pyg.py ├── diffusion ├── __init__.py ├── diffusion_utils.py ├── distributions.py ├── extra_features.py ├── extra_features_molecular.py ├── noise_schedule.py ├── sample_edges.py └── sample_edges_utils.py ├── diffusion_model_sparse.py ├── main.py ├── metrics ├── __init__.py ├── abstract_metrics.py ├── fcd │ ├── ChemNet_v0.13_pretrained.pt │ ├── __init__.py │ ├── fcd.py │ ├── torch_layers.py │ └── utils.py ├── metrics_utils.py ├── molecular_metrics.py ├── neural_metrics.py ├── sampling_metrics.py ├── spectre_utils.py └── train_metrics.py ├── models ├── __init__.py ├── conv_transformer_model.py ├── layers.py ├── sign_pos_encoder.py ├── transconv_layer.py └── transformer_model.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qym7/SparseDiff/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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