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pyhealth

k-dense-ai/scie…t-skills

Builds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes. Use for PyHealth dataset loading, MIMIC-III/IV, eICU or OMOP prediction tasks, patient-level evaluation, mortality/readmission/length-of-stay modeling, medication recommendation, sleep staging, Trainer checkpoints, and ICD/ATC/NDC/RxNorm mapping.

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安装命令

npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill pyhealth

SKILL.md

PyHealth

Targets PyHealth 2.0.2, verified against its released wheel, current official documentation, and CPU execution on Python 3.12/Torch 2.7.1. PyHealth's pipeline is Dataset -> Task -> Model -> Trainer -> Metrics; its 1.x and 2.x interfaces differ. Do not combine legacy Visit examples with the 2.x event/processor API.

When to use

Use for clinical prediction with PyHealth, including EHR sequences, physiological signals, imaging tasks, or medical-code lookup. Establish the cohort, prediction time, observation window, outcome horizon, and unit of evaluation before modeling. For general tabular learning without a PyHealth dataset/task, this skill is optional.

Install and smoke-test

uv run --no-project --isolated --python 3.12 --with pyhealth==2.0.2 python assets/starter_pipeline.py --demo --epochs 1

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