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defaults: | ||
- _extract | ||
- _self_ | ||
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description: |- | ||
This pipeline extracts the MIMIC-IV dataset in longitudinal, sparse form from an input dataset meeting | ||
select criteria and converts them to the flattened, MEDS format. You can control the key arguments to this | ||
pipeline by setting environment variables: | ||
```bash | ||
export EVENT_CONVERSION_CONFIG_FP=# Path to your event conversion config | ||
export MIMICIV_PRE_MEDS_DIR=# Path to the output dir of the pre-MEDS step | ||
export MIMICIV_MEDS_COHORT_DIR=# Path to where you want the dataset to live | ||
``` | ||
# The event conversion configuration file is used throughout the pipeline to define the events to extract. | ||
event_conversion_config_fp: ${oc.env:EVENT_CONVERSION_CONFIG_FP} | ||
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input_dir: ${oc.env:MIMICIV_PRE_MEDS_DIR} | ||
cohort_dir: ${oc.env:MIMICIV_MEDS_COHORT_DIR} | ||
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etl_metadata: | ||
dataset_name: MIMIC-IV | ||
dataset_version: 2.2 | ||
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stage_configs: | ||
shard_events: | ||
infer_schema_length: 999999999 | ||
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stages: | ||
- shard_events | ||
- split_and_shard_subjects | ||
- convert_to_sharded_events | ||
- merge_to_MEDS_cohort | ||
- extract_code_metadata | ||
- finalize_MEDS_metadata | ||
- finalize_MEDS_data |
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raw_cohort_dir: ??? | ||
output_dir: ??? | ||
input_dir: ${oc.env:MIMICIV_RAW_DIR} | ||
cohort_dir: ${oc.env:MIMICIV_PRE_MEDS_DIR} | ||
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do_overwrite: false | ||
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log_dir: ${cohort_dir}/.logs | ||
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# Hydra | ||
hydra: | ||
job: | ||
name: pre_MEDS_${now:%Y-%m-%d_%H-%M-%S} | ||
run: | ||
dir: ${output_dir}/.logs/${hydra.job.name} | ||
dir: ${log_dir} | ||
sweep: | ||
dir: ${output_dir}/.logs/${hydra.job.name} | ||
dir: ${log_dir} |
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