├── .gitignore ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── MAINTAINERS.md ├── README.md ├── datasets ├── README.md └── amia-ic-2024 │ ├── Readme.md │ └── binary_sdoh_clinical_relations.json ├── docs ├── building-kgs-hspo.md ├── classes.md ├── img │ ├── hspo-logo.png │ ├── hspo-sam-example-disease.png │ └── hspo-sam-main-example.png ├── index.md └── ontology-specification │ ├── 406.html │ ├── index.html │ ├── ontology.jsonld │ ├── ontology.nt │ ├── ontology.rdf │ ├── ontology.ttl │ ├── resources │ ├── extra.css │ ├── jquery.js │ ├── marked.min.js │ ├── owl.css │ ├── primer.css │ └── rec.css │ └── webvowl │ ├── css │ ├── webvowl.app.css │ └── webvowl.css │ ├── data │ └── ontology.json │ ├── favicon.ico │ ├── index.html │ ├── js │ ├── d3.min.js │ ├── webvowl.app.js │ └── webvowl.js │ └── license.txt ├── hspo-kg-builder ├── data-lifting │ └── mimic │ │ ├── 1_data_selection.py │ │ ├── 2_1_data_wrangling.py │ │ ├── 2_2_data_wrangling_grouped_icd9.py │ │ ├── 3_1_data_mapping_dictionaries.py │ │ ├── 3_2_data_mapping_dictionaries_grouped_icd9.py │ │ ├── 4_data_sampling.py │ │ ├── 5_notes_info_integration.py │ │ ├── 6_1_data_analysis_overall.py │ │ ├── 6_2_data_analysis_per_group.py │ │ ├── 6_3_data_analysis_specific_use_case.py │ │ ├── README.md │ │ ├── data │ │ ├── dictionaries │ │ │ ├── black_list_textual_description_diagnoses.json │ │ │ ├── codes_diag_updated.json │ │ │ └── codes_proc_updated.json │ │ ├── example_ethnicity_mappings.json │ │ ├── example_mapping_umls_employment.csv │ │ ├── example_mapping_umls_household.csv │ │ ├── example_mapping_umls_housing.csv │ │ ├── example_marital_status_mappings.json │ │ ├── example_religion_mappings.json │ │ ├── initial_data │ │ │ └── .gitkeep │ │ ├── processed_data │ │ │ └── .gitkeep │ │ └── selected_data │ │ │ └── .gitkeep │ │ ├── extract_explore_use_cases.py │ │ ├── notes_cui_extraction │ │ ├── MetaMap │ │ │ └── extract_umls_codes.py │ │ ├── __pycache__ │ │ │ └── utils_.cpython-310.pyc │ │ ├── find_remaining_files_create_note_buckets.py │ │ ├── map_extracted_umls_files.py │ │ └── utils_.py │ │ └── utils_.py └── kg-generation │ └── mimic │ ├── README.md │ ├── example_ethnicity_ontology_mapping.json │ ├── example_gender_ontology_mapping.json │ ├── example_marital_status_ontology_mapping.json │ ├── example_religion_ontology_mapping.json │ ├── graph_creation_ontology_mapping.py │ └── utils_.py ├── kg-embedding ├── gnn-models │ └── mimic │ │ ├── 0_data_split.py │ │ ├── README.md │ │ ├── datasets.py │ │ ├── helper.py │ │ ├── main.py │ │ ├── models.py │ │ ├── run_experiments.sh │ │ └── utils │ │ ├── check_result_completence.ipynb │ │ ├── explore_results.py │ │ └── find_best_results.ipynb └── transformation │ └── mimic │ ├── 1_graph_transformation.py │ ├── 2_find_graphs_with_missing_info_v4.py │ ├── 3_vocabulary.py │ ├── 4_embedding_initialization.py │ ├── 5_graph_preprocessing.py │ ├── README.md │ ├── helper.py │ └── run_graph_processing.sh ├── mkdocs.yml ├── ontology └── hspo.ttl 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