pyhealth

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Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD coding, EEG events), instantiating models (Transformer, RETAIN, GAMENet, SafeDrug, MICRON, StageNet, AdaCare, CNN/RNN/MLP), training with the PyHealth Trainer, computing clinical metrics, and using medical code utilities (ICD/ATC/NDC/RxNorm lookup and cross-mapping). Use this skill whenever the user mentions PyHealth, MIMIC, eICU, OMOP, EHR modeling, clinical prediction, drug recommendation, sleep staging, medical code mapping, ICD/ATC codes, or any healthcare ML pipeline that fits the dataset → task → model → trainer → metrics pattern, even if "PyHealth" isn't named explicitly.

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Sourcecrazymsn/academic-skills

Added on2026-06-02

NPX Install

npx skill4agent add crazymsn/academic-skills pyhealth

SKILL.md Content

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PyHealth

PyHealth (https://pyhealth.dev/) is a Python toolkit for clinical deep learning. It provides a unified, modular pipeline across electronic health records (EHR), physiological signals, and medical imaging.

The library is built around a 5-stage pipeline —

Dataset → Task → Model → Trainer → Metrics

— where each stage is replaceable and the interfaces between stages are stable. Code that follows this pipeline shape composes well; code that bypasses it usually fights the library.

When to use this skill

Use this skill whenever the user is doing clinical/healthcare ML and any of the following are true:

They mention PyHealth, MIMIC-III/IV, eICU, OMOP-CDM, EHRShot, SleepEDF, SHHS, ISRUC, COVID19-CXR, ChestX-ray14, TUEV/TUAB.
They want to predict mortality, readmission, length of stay, drug recommendations, sleep stages, ICD codes, EEG events, or de-identification.
They need to look up or cross-map medical codes (ICD-9-CM, ICD-10-CM, ATC, NDC, RxNorm, CCS).
They have EHR-shaped data and want to train a clinical model without writing the plumbing themselves.

PyHealth is the right tool when the workflow fits its 5 stages. If the user just wants generic PyTorch on tabular data, this skill is not necessary.

Installation (uv)

PyHealth 2.0 requires Python ≥ 3.12, < 3.14. Use

uv

for environment management — it's faster and reproducible.

bash

# Create a project with the right Python
uv init my-pyhealth-project
cd my-pyhealth-project
uv python pin 3.12

# Add PyHealth (this also pulls in PyTorch and friends)
uv add pyhealth

# Run scripts inside the env
uv run python train.py

For a one-off script without a project, use

uv run --with pyhealth python script.py

. For the legacy 1.x line (Python 3.9+),

uv add pyhealth==1.16

. Detailed install notes, MIMIC access, and GPU/CPU device tips are in

references/installation.md

.

The 5-stage pipeline

A complete pipeline is typically <20 lines. This is the canonical shape — start here and modify pieces:

python

from pyhealth.datasets import MIMIC3Dataset, split_by_patient, get_dataloader
from pyhealth.tasks import MortalityPredictionMIMIC3
from pyhealth.models import Transformer
from pyhealth.trainer import Trainer
from pyhealth.metrics.binary import binary_metrics_fn

# 1. Dataset — raw patient registry
base = MIMIC3Dataset(
    root="https://storage.googleapis.com/pyhealth/Synthetic_MIMIC-III/",
    tables=["DIAGNOSES_ICD", "PROCEDURES_ICD", "PRESCRIPTIONS"],
)

# 2. Task — converts patients into supervised samples
samples = base.set_task(MortalityPredictionMIMIC3())

# 3. Split + DataLoaders (split by patient to avoid leakage)
train_ds, val_ds, test_ds = split_by_patient(samples, [0.8, 0.1, 0.1])
train_loader = get_dataloader(train_ds, batch_size=32, shuffle=True)
val_loader   = get_dataloader(val_ds,   batch_size=32, shuffle=False)
test_loader  = get_dataloader(test_ds,  batch_size=32, shuffle=False)

# 4. Model — must be passed the SampleDataset, not the BaseDataset
model = Transformer(dataset=samples)

# 5. Train + evaluate
trainer = Trainer(model=model)
trainer.train(
    train_dataloader=train_loader,
    val_dataloader=val_loader,
    epochs=50,
    monitor="pr_auc",
)

y_true, y_prob, _ = trainer.inference(test_loader)
print(binary_metrics_fn(y_true, y_prob, metrics=["pr_auc", "roc_auc"]))

A copy-pasteable starter is in

assets/starter_pipeline.py

.

Critical things to get right

These are the mistakes that PyHealth code most commonly trips on. Internalize them before writing pipelines:

Models take a
SampleDataset
, not a
BaseDataset
.
```
MIMIC3Dataset(...)
```
returns a
```
BaseDataset
```
(a queryable patient registry). Only after
```
.set_task(task)
```
do you get a
```
SampleDataset
```
, which is what models, splitters, and DataLoaders expect. If you pass
```
base
```
to a model, it will fail or behave wrong.
Always split by patient (or visit), not by sample. Random sample-level splits leak information across train/test because the same patient can appear in both. Use
```
split_by_patient
```
for patient-level prediction,
```
split_by_visit
```
only when visits are independent.
Match the task to the dataset. Tasks are dataset-specific:
```
MortalityPredictionMIMIC3
```
won't work on MIMIC-IV — use
```
MortalityPredictionMIMIC4
```
or
```
InHospitalMortalityMIMIC4
```
. The full mapping is in
```
references/tasks.md
```
.
Pick
monitor
to match the task type. For binary classification use
```
"pr_auc"
```
or
```
"roc_auc"
```
. For multilabel (drug rec) use
```
"pr_auc_samples"
```
or
```
"jaccard_samples"
```
. For multiclass use
```
"accuracy"
```
or
```
"f1_macro"
```
. Wrong monitor → checkpoint selection saves the wrong epoch.
MIMIC-IV uses
ehr_root=
, not
root=
. This is the one inconsistency in the dataset constructors.
For reproducible work, point
cache_dir=
somewhere persistent. PyHealth caches the parsed dataset; without
```
cache_dir
```
, you re-parse every run.

How to use this skill

PyHealth has a large API surface — there's no point loading it all at once. Read the reference file that matches the user's task:

If the user is asking about…	Read
Installing, env setup, MIMIC access, GPU	`references/installation.md`
Which dataset class to use, loading patterns, splitting	`references/datasets.md`
What prediction task to choose (mortality, readmission, drug rec, sleep…)	`references/tasks.md`
Picking a model architecture, model-specific arguments	`references/models.md`
Looking up or cross-mapping ICD/ATC/NDC/RxNorm/CCS codes, tokenizers	`references/medcode.md`
End-to-end recipes for common scenarios	`references/examples.md`

For multi-step tasks (e.g., "build a drug recommendation pipeline on MIMIC-IV"), read

tasks.md

+

models.md

+

examples.md

together — they cross-reference each other.

A note on style

Write minimal, idiomatic PyHealth. The library is opinionated; lean into its abstractions instead of reimplementing them in raw PyTorch. If you find yourself writing a custom training loop, ask whether

Trainer

would do the job — it almost always will, and it handles checkpointing, logging, and best-model selection for free.

When the user has private MIMIC access, point them at the local CSV root; for demos and learning, the synthetic MIMIC-III bucket (

https://storage.googleapis.com/pyhealth/Synthetic_MIMIC-III/

) is fine and works without credentialing.