MIMIC-IV MEDS Extraction ETL

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This pipeline extracts the MIMIC-IV dataset (from physionet) into the MEDS format.

Usage:

pip install MIMIC_IV_MEDS
MEDS_extract-MIMIC_IV raw_input_dir=$RAW_INPUT pre_MEDS_dir=$PRE_MEDS MEDS_cohort_dir=$COHORT

Examples and More Info:

You can run MEDS_extract-MIMIC_IV --help for more information on the arguments and options. You can also run

MEDS_extract-MIMIC_IV raw_input_dir=$RAW_INPUT pre_MEDS_dir=$PRE_MEDS MEDS_cohort_dir=$COHORT do_demo=True

to run the entire pipeline over the publicly available, fully open MIMIC-IV demo dataset.

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  • Released:
Newer release available (0.2.0)

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Credits

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Author: Matthew McDermott

License

MIT License

Requires

Python >=3.11

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