Quickstart¶

This quickstart uses the bundled TJH COVID-19 ICU example. It walks through the core pipeline steps: preprocess, train, test, analyze, and plot.

For more detailed tutorials with Jupyter notebooks, see Tutorials.

0. Convert The Source Data (once)¶

uv run python examples/tjh/convert.py

This reads the raw Excel file and produces inside examples/tjh/:

• dynamic.csv, static.csv -- shared across all tasks
• label_mortality.csv -- patient-level binary mortality
• label_los.csv -- time-level remaining LOS (regression)
• label_mortality_time.csv -- time-level binary mortality

Example Configs¶

The TJH example ships three experiment configs:

1. Preprocess¶

uv run oneehr preprocess --config examples/tjh/mortality_patient.toml

This creates runs/tjh/preprocess/, writes manifest.json, the split contract, and materializes binned feature views.

2. Train¶

uv run oneehr train --config examples/tjh/mortality_patient.toml

Trains all models configured in [[models]] and writes checkpoints under runs/tjh/train/.

3. Test¶

uv run oneehr test --config examples/tjh/mortality_patient.toml

Evaluates all trained models on the held-out test split. Writes runs/tjh/test/predictions.parquet and metrics.json.

4. Analyze¶

uv run oneehr analyze --config examples/tjh/mortality_patient.toml

Writes structured analysis outputs under runs/tjh/analyze/, including cross-system comparison, feature importance, fairness metrics, and statistical tests.

5. Plot (Optional)¶

oneehr plot --config examples/tjh/mortality_patient.toml --style nature

Renders publication-quality figures (ROC, PR, calibration, forest plot, etc.) under runs/tjh/figures/.

Using Standard Datasets¶

Convert MIMIC-III, MIMIC-IV, or eICU data before running the pipeline:

oneehr convert --dataset mimic3 --raw-dir ~/data/mimic-iii/ --output-dir data/mimic3/ --task mortality

Then update your TOML config to point to the converted files. See Dataset Converters for details.

Try Other Tasks¶

Run the time-level mortality task:

uv run oneehr preprocess --config examples/tjh/mortality_time.toml
uv run oneehr train      --config examples/tjh/mortality_time.toml
uv run oneehr test       --config examples/tjh/mortality_time.toml
uv run oneehr analyze    --config examples/tjh/mortality_time.toml

Run the time-level remaining-LOS regression task:

uv run oneehr preprocess --config examples/tjh/los_time.toml
uv run oneehr train      --config examples/tjh/los_time.toml
uv run oneehr test       --config examples/tjh/los_time.toml
uv run oneehr analyze    --config examples/tjh/los_time.toml