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Add YAIB benchmark tasks for MIMIC-IV #1338

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Add YAIB benchmark tasks for MIMIC-IV
Logiquo Oct 27, 2026
ec0004f
Use built-in generics and ClassVar schemas in the YAIB tasks
Logiquo Oct 27, 2026
a83b8f8
Add deathtime to the MIMIC-IV admissions test fixture
Logiquo Oct 27, 2026
98fdc0d
Require transfers for the YAIB mortality task and document pre-ICU on…
Logiquo Oct 27, 2026
6ac17e7
Document the unknown last ward rule and test the SOFA vasopressor, ve…
Logiquo Oct 28, 2026
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82 changes: 82 additions & 0 deletions pyhealth/datasets/configs/mimic4_ehr.yaml
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Expand Up @@ -25,6 +25,7 @@ tables:
- "race"
- "discharge_location"
- "dischtime"
- "deathtime"
- "hospital_expire_flag"

icustays:
Expand Down Expand Up @@ -117,3 +118,84 @@ tables:
- "hcpcs_cd"
- "seq_num"
- "short_description"

transfers:

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[medium] New MIMIC-IV tables are not exercised by any dataset-level test

The six tables added here (transfers, microbiologyevents, chartevents, outputevents, inputevents, procedureevents) are only read through hand-built Patient objects in tests/core/test_yaib_mimic4.py. No test loads them through MIMIC4EHRDataset, runs YAIB's pre_filter through set_task, or checks the config column names against a real table layout. The demo fixture in test-resources/core/mimic4demo has none of these tables, while existing MIMIC-IV task tests (tests/core/test_mimic4_los.py, tests/core/test_mimic4_dka.py) run set_task on that fixture. Fix: add minimal CSV fixtures for these tables (or extend the demo fixture) and one set_task test per task family, including the missing-table ValueError path through the real loader.

file_path: "hosp/transfers.csv.gz"
patient_id: "subject_id"
timestamp: "intime"
attributes:
- "hadm_id"
- "transfer_id"
- "eventtype"
- "careunit"
- "outtime"

microbiologyevents:
file_path: "hosp/microbiologyevents.csv.gz"
patient_id: "subject_id"
timestamp: "chartdate"
attributes:
- "hadm_id"
- "micro_specimen_id"
- "charttime"
- "spec_itemid"
- "spec_type_desc"
- "test_itemid"
- "test_name"
- "org_itemid"
- "org_name"

chartevents:
file_path: "icu/chartevents.csv.gz"
patient_id: "subject_id"
timestamp: "charttime"
attributes:
- "hadm_id"
- "stay_id"
- "itemid"
- "value"
- "valuenum"
- "valueuom"

outputevents:
file_path: "icu/outputevents.csv.gz"
patient_id: "subject_id"
timestamp: "charttime"
attributes:
- "hadm_id"
- "stay_id"
- "itemid"
- "value"
- "valueuom"

inputevents:
file_path: "icu/inputevents.csv.gz"
patient_id: "subject_id"
timestamp: "starttime"
attributes:
- "hadm_id"
- "stay_id"
- "itemid"
- "endtime"
- "amount"
- "amountuom"
- "rate"
- "rateuom"
- "patientweight"
- "orderid"
- "linkorderid"
- "ordercategoryname"
- "statusdescription"

procedureevents:
file_path: "icu/procedureevents.csv.gz"
patient_id: "subject_id"
timestamp: "starttime"
attributes:
- "hadm_id"
- "stay_id"
- "itemid"
- "endtime"
- "value"
- "valueuom"
- "statusdescription"
7 changes: 7 additions & 0 deletions pyhealth/tasks/__init__.py
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Expand Up @@ -87,6 +87,13 @@
VariantClassificationClinVar,
)
from .patient_linkage_mimic3 import PatientLinkageMIMIC3Task
from .yaib_mimic4 import (

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[low] New public tasks have no API docs entry

Five public task classes are exported here, but no docs/api/tasks/*.rst file or docs/api/tasks.rst toctree entry is added, unlike other task modules such as InHospitalMortalityMIMIC4. Add an autoclass page per task (or one for the module) so the new tasks appear in the API reference.

YAIBAKIMIMIC4 as YAIBAKIMIMIC4,
YAIBKidneyFunctionMIMIC4 as YAIBKidneyFunctionMIMIC4,
YAIBLengthOfStayMIMIC4 as YAIBLengthOfStayMIMIC4,
YAIBMortalityMIMIC4 as YAIBMortalityMIMIC4,
YAIBSepsisMIMIC4 as YAIBSepsisMIMIC4,
)


def __getattr__(name: str):
Expand Down
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