├── .gitignore ├── LICENSE ├── README.md ├── data ├── datasets.md ├── mimic-iii-0 │ └── .gitkeep ├── sepsis │ └── .gitkeep └── tadpole │ └── .gitkeep ├── data_preprocessing ├── __init__.py ├── dataset_graph_split_sepsis.py ├── graph_subsampling_mimic.py ├── mimic_data_analysis.py ├── sepsis_analysis.py └── transform_data.py ├── exps └── .gitkeep ├── graphormer ├── EHR_dataset.py ├── algos.pyx ├── collator.py ├── data.py ├── entry.py ├── lr.py ├── model.py ├── utils │ ├── col_lists.py │ ├── evaluators.py │ ├── flag.py │ ├── mask_utils.py │ └── utils.py └── wrapper.py ├── overview.jpg └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- 1 | /.idea/ 2 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/README.md -------------------------------------------------------------------------------- /data/datasets.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/data/datasets.md -------------------------------------------------------------------------------- /data/mimic-iii-0/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/sepsis/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/tadpole/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data_preprocessing/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data_preprocessing/dataset_graph_split_sepsis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/data_preprocessing/dataset_graph_split_sepsis.py -------------------------------------------------------------------------------- /data_preprocessing/graph_subsampling_mimic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/data_preprocessing/graph_subsampling_mimic.py -------------------------------------------------------------------------------- /data_preprocessing/mimic_data_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/data_preprocessing/mimic_data_analysis.py -------------------------------------------------------------------------------- /data_preprocessing/sepsis_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/data_preprocessing/sepsis_analysis.py -------------------------------------------------------------------------------- /data_preprocessing/transform_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/data_preprocessing/transform_data.py -------------------------------------------------------------------------------- /exps/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /graphormer/EHR_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/EHR_dataset.py -------------------------------------------------------------------------------- /graphormer/algos.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/algos.pyx -------------------------------------------------------------------------------- /graphormer/collator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/collator.py -------------------------------------------------------------------------------- /graphormer/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/data.py -------------------------------------------------------------------------------- /graphormer/entry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/entry.py -------------------------------------------------------------------------------- /graphormer/lr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/lr.py -------------------------------------------------------------------------------- /graphormer/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/model.py -------------------------------------------------------------------------------- /graphormer/utils/col_lists.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/utils/col_lists.py -------------------------------------------------------------------------------- /graphormer/utils/evaluators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/utils/evaluators.py -------------------------------------------------------------------------------- /graphormer/utils/flag.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/utils/flag.py -------------------------------------------------------------------------------- /graphormer/utils/mask_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/utils/mask_utils.py -------------------------------------------------------------------------------- /graphormer/utils/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/utils/utils.py -------------------------------------------------------------------------------- /graphormer/wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/graphormer/wrapper.py -------------------------------------------------------------------------------- /overview.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/overview.jpg -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChantalMP/Unsupervised_pre-training_of_graph_transformers_on_patient_population_graphs/HEAD/requirements.txt --------------------------------------------------------------------------------