├── .gitattributes ├── .github └── workflows │ └── basic_ci.yml ├── .gitignore ├── LICENCE ├── Procfile ├── README.md ├── assets ├── MassSpecGym_abstract.png ├── MassSpecGym_abstract.svg ├── MassSpecGym_infrastructure.svg ├── MassSpecGym_poster_neurips2024.pdf ├── table1.png └── table1_SI.png ├── config └── simulation │ ├── demo.yml │ ├── fp_formula.yml │ ├── fp_mass.yml │ ├── fp_noret.yml │ ├── gnn_formula.yml │ ├── gnn_mass.yml │ ├── gnn_noret.yml │ ├── preconly_formula.yml │ ├── preconly_mass.yml │ ├── preconly_noret.yml │ └── template.yml ├── data ├── debug │ ├── example_5_spectra.mgf │ ├── example_5_spectra_candidates.json │ └── example_5_spectra_split.tsv └── misc │ └── random_de_novo_element_stats_from_trn_with_hydrogens.pkl ├── massspecgym ├── __init__.py ├── data │ ├── __init__.py │ ├── data_module.py │ ├── datasets.py │ └── transforms.py ├── definitions.py ├── feat_utils.py ├── models │ ├── __init__.py │ ├── base.py │ ├── de_novo │ │ ├── __init__.py │ │ ├── base.py │ │ ├── dummy.py │ │ ├── random.py │ │ └── smiles_tranformer.py │ ├── layers.py │ ├── retrieval │ │ ├── __init__.py │ │ ├── base.py │ │ ├── deepsets.py │ │ ├── fingerprint_ffn.py │ │ ├── from_dict.py │ │ └── random.py │ ├── simulation │ │ ├── __init__.py │ │ ├── base.py │ │ ├── fp.py │ │ ├── gnn.py │ │ └── prec_only.py │ └── tokenizers.py ├── simulation_utils │ ├── __init__.py │ ├── feat_utils.py │ ├── formula_embedder.py │ ├── misc_utils.py │ ├── model_utils.py │ ├── nn_utils.py │ ├── run_utils.py │ └── spec_utils.py └── utils.py ├── notebooks ├── dataset_analysis │ ├── analyze_leakage.ipynb │ ├── dataset_statistics.ipynb │ ├── dataset_statistics_main.ipynb │ └── examples.ipynb ├── dataset_construction │ ├── 1_Load_data_from_repositories.ipynb │ ├── 2_clean_library.ipynb │ ├── 3_remove_duplicates_and_profiled_spectra.ipynb │ ├── 4_standardization_and_cleaning.ipynb │ ├── 5_split.ipynb │ ├── 6_final_postprocessing.ipynb │ └── 7_format_conversions.ipynb ├── demo.ipynb ├── evaluation.ipynb ├── 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