Add sepsis prediction task for MIMIC-IV (SepsisPredictionMIMIC4) - #1188
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Add sepsis prediction task for MIMIC-IV (SepsisPredictionMIMIC4)#1188AnishGupta551 wants to merge 2 commits into
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Labels each admission for sepsis onset using a qSOFA-based Sepsis-3 approximation (Seymour et al., JAMA 2016): antibiotic order as the suspected-infection signal, qSOFA >= 2 (respiratory rate, systolic BP, GCS-derived mental status) as the organ-dysfunction signal. Features are censored strictly before onset to avoid label leakage. Adds a chartevents (vitals) table to the MIMIC-IV config, since PyHealth had no vitals source configured for any existing task. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
check_pr_rules.py flagged the SepsisPredictionMIMIC4 import as unused; switch to the redundant-alias re-export pattern used by other entries in this file. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Contributor: Anish Gupta (anishg8@illinois.edu)
Contribution Type: New Task
Description: Added SepsisPredictionMIMIC4, a sepsis-onset prediction task for MIMIC-IV. Labels each hospital admission using a qSOFA-based approximation of the Sepsis-3 clinical criteria (Seymour et al., JAMA 2016) -- an antibiotic order as the suspected-infection signal, qSOFA >= 2 (respiratory rate, systolic BP, GCS-derived mental status) as the organ-dysfunction signal. Features are censored strictly before onset to prevent label leakage. Also adds a chartevents (vitals) table to PyHealth's MIMIC-IV config, since no existing task had wired in vitals.
Files to Review:
pyhealth/tasks/sepsis_prediction_mimic4.py- Main task implementationpyhealth/datasets/configs/mimic4_ehr.yaml- New chartevents tabletests/core/test_sepsis_prediction_mimic4.py- 10 test cases (synthetic data)examples/sepsis_prediction_mimic4_demo.py- End-to-end usage example