├── .gitignore ├── LICENSE ├── README.md ├── analysis ├── .gitkeep └── evaluate_pred.py ├── configs ├── _public_fast_filter.yaml ├── _public_mist_cf.yaml ├── fast_filter.yaml ├── ffn_canopus.yaml ├── ffn_canopus_nist.yaml ├── mist_cf_canopus.yaml ├── mist_cf_canopus_nist.yaml ├── mist_cf_canopus_nist_max_subpeak.yaml ├── ms1_canopus.yaml ├── ms1_canopus_nist.yaml ├── xformer_canopus.yaml └── xformer_canopus_nist.yaml ├── data └── demo_specs.mgf ├── environment.yml ├── launcher_scripts ├── generic_slurm.sh ├── launch_tensorboard.sh └── run_from_config.py ├── mist_cf_graphic.png ├── notebooks ├── .gitkeep ├── demo_mist_cf.ipynb ├── mist_cf_fig_benchmark.ipynb ├── mist_cf_fig_casmi22.ipynb ├── mist_cf_fig_data.ipynb ├── mist_cf_fig_fast_filter.ipynb ├── mist_cf_fig_max_subpeak.ipynb ├── mist_cf_fig_sirius_compare.ipynb └── mist_cf_si_timing.ipynb ├── preprocessing ├── 01_create_split_file.py ├── 02_create_decoy_label.py ├── 03_create_pred_label.py ├── 04_create_subformulae_assignment.py ├── 05_sirius_to_mgf.py ├── biomols_scripts │ ├── 01_filter_smiles.py │ ├── 02_extract_formulae.py │ ├── 03_create_formulae_decoys.py │ ├── 04_create_formulae_split.py │ └── run_all.sh ├── casmi │ └── casmi_preprocess.ipynb ├── run_all.sh └── xx_remove_nist_data.py ├── quickstart ├── download_model.sh └── run_model.sh ├── requirements.txt ├── run_scripts ├── benchmarking │ ├── eval_models.py │ ├── train_ffn.sh │ ├── train_mist_cf.sh │ ├── train_ms1.sh │ └── train_xformer.sh ├── casmi22_eval │ ├── eval_models.py │ ├── run_mist_cf.sh │ ├── run_mist_cf_more_peaks.sh │ ├── run_sirius.sh │ ├── wrangle_sirius.py │ └── wrangle_sirius_submission.py ├── fast_filter │ ├── launch_fast_pred.py │ └── launch_fast_train.sh ├── hyperparams │ ├── find_fast_params.sh │ ├── find_ffn_params.sh │ ├── find_mist_cf_params.sh │ └── find_xformer_params.sh ├── max_subpeak │ ├── eval_models.py │ └── train_mist_cf_subpeak.sh ├── public_data_train │ ├── train_fast_filter.sh │ └── train_mist_cf.sh ├── sirius_compare │ ├── eval_models.py │ ├── mist_cf_1_predict.sh │ ├── sirius_1_run.py │ └── sirius_2_wrangle.py └── timing_experiments.py ├── setup.cfg ├── setup.py └── src └── mist_cf ├── .gitkeep ├── common ├── __init__.py ├── chem_utils.py ├── misc_utils.py ├── parallel_utils.py ├── parse_utils.py ├── plot_utils.py ├── splitter.py └── tune_utils.py ├── decomp ├── __init__.py └── sirius_decomp.py ├── fast_form_score ├── fast_form_data.py ├── fast_form_hyperopt.py ├── fast_form_model.py ├── predict.py └── train.py ├── ffn_score ├── ffn_data.py ├── ffn_hyperopt.py ├── ffn_model.py ├── predict.py └── train.py ├── mist_cf_score ├── mist_cf_data.py ├── mist_cf_hyperopt.py ├── mist_cf_model.py ├── predict.py ├── predict_mgf.py └── train.py ├── nn_utils ├── .gitkeep ├── __init__.py ├── base_hyperopt.py ├── form_embedder.py ├── nn_utils.py └── transformer_layers.py └── xformer_score ├── predict.py ├── train.py ├── xformer_data.py ├── xformer_hyperopt.py └── xformer_model.py /.gitignore: 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