├── .github └── workflows │ ├── ci.yaml │ ├── ci_workflow.yaml │ ├── test_pkg_on_colab.yaml │ └── workflow_website.yaml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE.md ├── README.md ├── docs ├── Figures │ ├── Molecular_structures_of_the_21_proteinogenic_amino_acids.svg │ ├── amino_acids_iupac_iub_1983.png │ ├── fig_proteomics_pipeline.png │ └── schema_orbitrap_instrument.jpg ├── Makefile ├── README.md ├── conf.py ├── docutils.conf ├── environment.yml ├── index.rst ├── logos │ ├── logo.png │ └── logo_thumbnail.png ├── make.bat ├── other │ ├── project_readme.rst │ └── tutorial.rst ├── proteomics_intro.md └── venv_setup.md ├── environment.yml ├── pimmslearn ├── README.md ├── __init__.py ├── analyzers │ ├── __init__.py │ ├── analyzers.py │ ├── compare_predictions.py │ └── diff_analysis.py ├── cmd_interface │ ├── __init__.py │ ├── setup_diff_analysis_website.py │ └── setup_imp_cp_website.py ├── data_handling.py ├── databases │ ├── __init__.py │ └── diseases.py ├── filter.py ├── imputation.py ├── io │ ├── __init__.py │ ├── dataloaders.py │ ├── datasets.py │ ├── datasplits.py │ ├── format.py │ ├── load.py │ └── types.py ├── logging.py ├── model.py ├── models │ ├── __init__.py │ ├── ae.py │ ├── analysis.py │ ├── collab.py │ ├── collect_dumps.py │ └── vae.py ├── nb.py ├── normalization.py ├── pandas │ ├── __init__.py │ ├── calc_errors.py │ └── missing_data.py ├── plotting │ ├── __init__.py │ ├── data.py │ ├── defaults.py │ ├── errors.py │ └── plotly.py ├── sampling.py ├── sklearn │ ├── __init__.py │ ├── ae_transformer.py │ └── cf_transformer.py ├── stats │ └── __init__.py ├── transform.py └── utils.py ├── project ├── 00_5_training_data_exploration.py ├── 00_6_0_permute_data.ipynb ├── 00_6_0_permute_data.py ├── 00_8_add_random_missing_values.py ├── 01_0_install_R_packages.R ├── 01_0_install_R_packages.ipynb ├── 01_0_split_data.ipynb ├── 01_0_split_data.py ├── 01_0_transform_data_to_wide_format.ipynb ├── 01_0_transform_data_to_wide_format.py ├── 01_1_train_CF.ipynb ├── 01_1_train_CF.py ├── 01_1_train_DAE.ipynb ├── 01_1_train_DAE.py ├── 01_1_train_KNN.ipynb ├── 01_1_train_KNN.py ├── 01_1_train_KNN_unique_samples.py ├── 01_1_train_Median.ipynb ├── 01_1_train_Median.py ├── 01_1_train_NAGuideR_methods.R ├── 01_1_train_NAGuideR_methods.ipynb ├── 01_1_train_RSN.ipynb ├── 01_1_train_RSN.py ├── 01_1_train_VAE.ipynb ├── 01_1_train_VAE.py ├── 01_1_transfer_NAGuideR_pred.ipynb ├── 01_1_transfer_NAGuideR_pred.py ├── 01_2_performance_plots.ipynb ├── 01_2_performance_plots.py ├── 01_3_revision3.py ├── 02_1_aggregate_metrics.py.ipynb ├── 02_1_aggregate_metrics.py.py ├── 02_1_join_metrics.py.ipynb ├── 02_1_join_metrics.py.py ├── 02_2_aggregate_configs.py.ipynb ├── 02_2_aggregate_configs.py.py ├── 02_2_join_configs.py.ipynb ├── 02_2_join_configs.py.py ├── 02_3_grid_search_analysis.ipynb ├── 02_3_grid_search_analysis.py ├── 02_4_best_models_over_all_data.ipynb ├── 02_4_best_models_over_all_data.py ├── 03_1_best_models_comparison.ipynb ├── 03_1_best_models_comparison.py ├── 03_2_best_models_comparison_fig2.ipynb ├── 03_2_best_models_comparison_fig2.py ├── 03_3_combine_experiment_result_tables.ipynb ├── 03_3_combine_experiment_result_tables.py ├── 03_4_join_tables.py ├── 03_5_join_benchmarks.py ├── 03_6_setup_comparison_rev3.py ├── 04_1_train_pimms_models.ipynb ├── 04_1_train_pimms_models.py ├── 10_0_ald_data.ipynb ├── 10_0_ald_data.py ├── 10_0_ald_data_3v3.py ├── 10_1_ald_diff_analysis.ipynb ├── 10_1_ald_diff_analysis.py ├── 10_2_ald_compare_methods.ipynb ├── 10_2_ald_compare_methods.py ├── 10_3_ald_ml_new_feat.ipynb ├── 10_3_ald_ml_new_feat.py ├── 10_4_ald_compare_single_pg.ipynb ├── 10_4_ald_compare_single_pg.py ├── 10_5_comp_diff_analysis_repetitions.ipynb ├── 10_5_comp_diff_analysis_repetitions.py ├── 10_6_interpret_repeated_ald_da.py ├── 10_7_ald_reduced_dataset_plots.ipynb ├── 10_7_ald_reduced_dataset_plots.py ├── README.md ├── bin │ ├── README.md │ ├── create_qsub_commands.py │ ├── run_snakemake.sh │ └── run_snakemake_cluster.sh ├── config │ ├── README.md │ ├── across_datasets │ │ ├── collab.yaml │ │ ├── config.yaml │ │ ├── dae.yaml │ │ ├── shared_splits.yaml │ │ └── vae.yaml │ ├── ald_data.yaml │ ├── alzheimer_study │ │ ├── README.md │ │ ├── comparison.yaml │ │ └── config.yaml │ ├── appl_ald_data │ │ └── plasma │ │ │ ├── aggPeptides │ │ │ ├── config.yaml │ │ │ ├── split.yaml │ │ │ └── train.yaml │ │ │ ├── grid_search │ │ │ └── config_grid.yaml │ │ │ ├── proteinGroups │ │ │ ├── comparison.yaml │ │ │ ├── config.yaml │ │ │ ├── config_reps.yaml │ │ │ ├── inspect_data.yaml │ │ │ ├── split.yaml │ │ │ ├── train_CF.yaml │ │ │ ├── train_DAE.yaml │ │ │ ├── train_KNN.yaml │ │ │ ├── train_Median.yaml │ │ │ ├── train_RSN.yaml │ │ │ └── train_VAE.yaml │ │ │ └── proteinGroups_80perc_dataset │ │ │ ├── comparison.yaml │ │ │ ├── config.yaml │ │ │ └── split.yaml │ ├── erda_dumps.py │ ├── grid_search_large_data │ │ ├── config_grid.yaml │ │ ├── config_grid_small.yaml │ │ ├── evidence_split.yaml │ │ ├── peptides_split.yaml │ │ └── proteinGroups_split.yaml │ ├── grid_search_small_data │ │ ├── config_grid.yaml │ │ ├── evidence_split.yaml │ │ ├── peptides_split.yaml │ │ └── proteinGroups_split.yaml │ ├── knn_comparison │ │ ├── ald_pgs_all │ │ │ ├── README.md │ │ │ └── config.yaml │ │ └── hela_pgs_large │ │ │ ├── README.md │ │ │ ├── config.yaml │ │ │ ├── inspect_data.yaml │ │ │ └── split.yaml │ ├── permuted_dataset │ │ ├── config.yaml │ │ └── split.yaml │ ├── repeat_best │ │ ├── split.yaml │ │ └── train.yaml │ └── single_dev_dataset │ │ ├── evidence │ │ ├── config.yaml │ │ ├── split.yaml │ │ ├── train_CF.yaml │ │ ├── train_DAE.yaml │ │ ├── train_KNN.yaml │ │ ├── train_Median.yaml │ │ └── train_VAE.yaml │ │ ├── evidence_N50 │ │ ├── config.yaml │ │ ├── split.yaml │ │ ├── train_CF.yaml │ │ ├── train_DAE.yaml │ │ ├── train_KNN.yaml │ │ ├── train_Median.yaml │ │ └── train_VAE.yaml │ │ ├── example │ │ ├── config.yaml │ │ ├── split.yaml │ │ ├── train_CF.yaml │ │ ├── train_DAE.yaml │ │ ├── train_KNN.yaml │ │ ├── train_Median.yaml │ │ ├── train_RSN.yaml │ │ └── train_VAE.yaml │ │ ├── mnar_mcar │ │ ├── evi_l.yaml │ │ ├── evi_m.yaml │ │ ├── pep_l.yaml │ │ ├── pep_m.yaml │ │ ├── pg_l.yaml │ │ └── pg_m.yaml │ │ ├── peptides │ │ ├── config.yaml │ │ ├── split.yaml │ │ ├── train_CF.yaml │ │ ├── train_DAE.yaml │ │ ├── train_KNN.yaml │ │ ├── train_Median.yaml │ │ └── train_VAE.yaml │ │ ├── peptides_N50 │ │ ├── config.yaml │ │ ├── split.yaml │ │ ├── train_CF.yaml │ │ ├── train_DAE.yaml │ │ ├── train_KNN.yaml │ │ ├── train_Median.yaml │ │ └── train_VAE.yaml │ │ ├── proteinGroups │ │ ├── config.yaml │ │ ├── inspect_data.yaml │ │ ├── split.yaml │ │ ├── train_CF.yaml │ │ ├── train_DAE.yaml │ │ ├── train_KNN.yaml │ │ ├── train_Median.yaml │ │ └── train_VAE.yaml │ │ └── proteinGroups_N50 │ │ ├── README.md │ │ ├── config.yaml │ │ ├── config_v2.yaml │ │ ├── split.yaml │ │ ├── train_CF.yaml │ │ ├── train_DAE.yaml │ │ ├── train_KNN.yaml │ │ ├── train_Median.yaml │ │ └── train_VAE.yaml ├── data │ ├── ALD_study │ │ └── README.md │ ├── Alzheimer_study │ │ └── README.md │ ├── README.md │ ├── dev_datasets │ │ └── HeLa_6070 │ │ │ ├── README.md │ │ │ ├── files_selected_metadata_N50.csv │ │ │ ├── protein_groups_wide_N50.csv │ │ │ ├── protein_groups_wide_N50_M227.csv │ │ │ └── protein_groups_wide_N50_M454.csv │ ├── download_dev_dataset.py │ └── mqpar_example.xml ├── jupytext.toml ├── misc_embeddings.ipynb ├── misc_embeddings.py ├── misc_illustrations.ipynb ├── misc_illustrations.py ├── misc_json_formats.ipynb ├── misc_json_formats.py ├── misc_pytorch_fastai_dataloaders.ipynb ├── misc_pytorch_fastai_dataloaders.py ├── misc_pytorch_fastai_dataset.ipynb ├── misc_pytorch_fastai_dataset.py ├── misc_sampling_in_pandas.ipynb ├── misc_sampling_in_pandas.py ├── src │ └── R_NAGuideR │ │ ├── GMSimpute_0.0.1.1.tar.gz │ │ ├── GSimp.R │ │ ├── Imput_funcs.r │ │ └── SeqKnn_1.0.1.tar.gz ├── tutorials │ ├── pandas_categorical.ipynb │ └── pandas_multiindex.ipynb └── workflow │ ├── README.md │ ├── Snakefile │ ├── Snakefile_ald_comparison.smk │ ├── Snakefile_ald_comparison_repeated.smk │ ├── Snakefile_best_across_datasets.smk │ ├── Snakefile_best_repeated_split.smk │ ├── Snakefile_best_repeated_train.smk │ ├── Snakefile_grid.smk │ ├── Snakefile_small_N.smk │ ├── Snakefile_v2.smk │ ├── TestNotebooks.smk │ ├── bin │ ├── README.md │ ├── qsub-status.py │ └── qsub-status_v2.py │ ├── envs │ ├── pimms.yaml │ └── trainRmodels.yaml │ ├── notebooks │ ├── best_repeated_split_collect_metrics.ipynb │ ├── best_repeated_split_collect_metrics.py │ ├── best_repeated_train_collect_metrics.ipynb │ └── best_repeated_train_collect_metrics.py │ ├── rulegraphs │ ├── default.png │ ├── rulegraph_ald_comparison.png │ └── rulegraph_gridsearch.png │ └── scripts │ └── copy_clinical_data.py ├── pyproject.toml ├── setup.cfg ├── setup.py ├── snakemake_env.yml └── tests ├── io ├── test_data_objects.py ├── test_dataloaders.py ├── test_dataset.py └── test_datasplits.py ├── pandas └── test_calc_errors.py ├── 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