├── LICENCE ├── README.md ├── conda_linux_x86_environment.yml ├── data ├── cgl_mimic3_disease_codes.txt ├── cgl_patient_splits.pkl ├── disease_codes_all.txt └── med_codes_all.txt ├── dev ├── examples │ ├── diagnosis_training_example.sh │ ├── heart_failure_training_example.sh │ └── medication_training_example.sh ├── run_training_concepts.py ├── text_concept_extraction.py └── umls_graph_extraction.py ├── images ├── architecture_wide.png └── logo.png └── kg ├── README.md ├── kg ├── __init__.py ├── data │ ├── __init__.py │ ├── analysis.py │ ├── cached_datasets.py │ ├── contants.py │ ├── datasets.py │ ├── eicu.py │ ├── graph.py │ ├── processing.py │ ├── quickumls.py │ ├── umls.py │ └── vocabulary.py ├── model │ ├── __init__.py │ ├── cgl_modules.py │ ├── contractions.py │ ├── embedding_modules.py │ ├── gbert_modules.py │ ├── graph_modules.py │ ├── lightning_modules.py │ ├── pretraining_modules.py │ ├── umls_modules.py │ └── utility_modules.py ├── training │ ├── __init__.py │ ├── cgl.py │ ├── dataloader.py │ ├── gbert.py │ └── loss.py └── utils │ ├── __init__.py │ ├── constants.py │ ├── metrics.py │ ├── monitoring.py │ ├── tensors.py │ └── training.py ├── pyproject.toml └── setup.py /LICENCE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/LICENCE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/README.md -------------------------------------------------------------------------------- /conda_linux_x86_environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/conda_linux_x86_environment.yml -------------------------------------------------------------------------------- /data/cgl_mimic3_disease_codes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/data/cgl_mimic3_disease_codes.txt -------------------------------------------------------------------------------- /data/cgl_patient_splits.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/data/cgl_patient_splits.pkl -------------------------------------------------------------------------------- /data/disease_codes_all.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/data/disease_codes_all.txt -------------------------------------------------------------------------------- /data/med_codes_all.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/data/med_codes_all.txt -------------------------------------------------------------------------------- /dev/examples/diagnosis_training_example.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/dev/examples/diagnosis_training_example.sh -------------------------------------------------------------------------------- /dev/examples/heart_failure_training_example.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/dev/examples/heart_failure_training_example.sh -------------------------------------------------------------------------------- /dev/examples/medication_training_example.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/dev/examples/medication_training_example.sh -------------------------------------------------------------------------------- /dev/run_training_concepts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/dev/run_training_concepts.py -------------------------------------------------------------------------------- /dev/text_concept_extraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/dev/text_concept_extraction.py -------------------------------------------------------------------------------- /dev/umls_graph_extraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/dev/umls_graph_extraction.py -------------------------------------------------------------------------------- /images/architecture_wide.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/images/architecture_wide.png -------------------------------------------------------------------------------- /images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/images/logo.png -------------------------------------------------------------------------------- /kg/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/README.md -------------------------------------------------------------------------------- /kg/kg/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/__init__.py -------------------------------------------------------------------------------- /kg/kg/data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /kg/kg/data/analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/analysis.py -------------------------------------------------------------------------------- /kg/kg/data/cached_datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/cached_datasets.py -------------------------------------------------------------------------------- /kg/kg/data/contants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/contants.py -------------------------------------------------------------------------------- /kg/kg/data/datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/datasets.py -------------------------------------------------------------------------------- /kg/kg/data/eicu.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/eicu.py -------------------------------------------------------------------------------- /kg/kg/data/graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/graph.py -------------------------------------------------------------------------------- /kg/kg/data/processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/processing.py -------------------------------------------------------------------------------- /kg/kg/data/quickumls.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/quickumls.py -------------------------------------------------------------------------------- /kg/kg/data/umls.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/umls.py -------------------------------------------------------------------------------- /kg/kg/data/vocabulary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/data/vocabulary.py -------------------------------------------------------------------------------- /kg/kg/model/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /kg/kg/model/cgl_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/model/cgl_modules.py -------------------------------------------------------------------------------- /kg/kg/model/contractions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/model/contractions.py -------------------------------------------------------------------------------- /kg/kg/model/embedding_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/model/embedding_modules.py -------------------------------------------------------------------------------- /kg/kg/model/gbert_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/model/gbert_modules.py -------------------------------------------------------------------------------- /kg/kg/model/graph_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/model/graph_modules.py -------------------------------------------------------------------------------- /kg/kg/model/lightning_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/model/lightning_modules.py -------------------------------------------------------------------------------- /kg/kg/model/pretraining_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/model/pretraining_modules.py -------------------------------------------------------------------------------- /kg/kg/model/umls_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/model/umls_modules.py -------------------------------------------------------------------------------- /kg/kg/model/utility_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/model/utility_modules.py -------------------------------------------------------------------------------- /kg/kg/training/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /kg/kg/training/cgl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/training/cgl.py -------------------------------------------------------------------------------- /kg/kg/training/dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/training/dataloader.py -------------------------------------------------------------------------------- /kg/kg/training/gbert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/training/gbert.py -------------------------------------------------------------------------------- /kg/kg/training/loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/training/loss.py -------------------------------------------------------------------------------- /kg/kg/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /kg/kg/utils/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/utils/constants.py -------------------------------------------------------------------------------- /kg/kg/utils/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/utils/metrics.py -------------------------------------------------------------------------------- /kg/kg/utils/monitoring.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/utils/monitoring.py -------------------------------------------------------------------------------- /kg/kg/utils/tensors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/utils/tensors.py -------------------------------------------------------------------------------- /kg/kg/utils/training.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/kg/utils/training.py -------------------------------------------------------------------------------- /kg/pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/pyproject.toml -------------------------------------------------------------------------------- /kg/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/mmugl/HEAD/kg/setup.py --------------------------------------------------------------------------------