CLI Reference¶
OneEHR exposes six top-level commands:
| Command | Purpose |
|---|---|
preprocess |
Bin event data, build features, create labels, and save the split contract |
train |
Train configured ML/DL models |
test |
Evaluate trained models and configured systems on the held-out test split |
analyze |
Write structured analysis outputs from test/predictions.parquet |
plot |
Render figures from saved run artifacts |
convert |
Convert supported raw datasets into OneEHR CSV tables |
View the live interface:
oneehr --helponeehr preprocess¶
oneehr preprocess --config <toml>Reads the dataset tables, bins dynamic events, creates labels, saves the patient split, and writes the run manifest.
| Flag | Required | Description |
|---|---|---|
--config |
Yes | Path to TOML experiment config |
Outputs are written to {output.root}/{output.run_name}/preprocess/.
oneehr train¶
oneehr train --config <toml> [--force]Trains all models defined in [[models]] and writes checkpoints under {run_dir}/train/{model_name}/.
| Flag | Required | Description |
|---|---|---|
--config |
Yes | Path to TOML experiment config |
--force |
No | Overwrite an existing train directory |
oneehr test¶
oneehr test --config <toml> [--force]Runs trained models and configured [[systems]] on the held-out test split. Writes predictions.parquet and metrics.json under {run_dir}/test/.
| Flag | Required | Description |
|---|---|---|
--config |
Yes | Path to TOML experiment config |
--force |
No | Overwrite an existing test directory |
oneehr analyze¶
oneehr analyze --config <toml> [--module NAME]Reads test/predictions.parquet and writes JSON outputs under {run_dir}/analyze/.
| Flag | Required | Description |
|---|---|---|
--config |
Yes | Path to TOML experiment config |
--module |
No | Run one analysis module instead of all modules |
Available modules:
| Module | Output |
|---|---|
comparison |
Metrics by system with bootstrap confidence intervals where supported |
feature_importance |
Native importance, SHAP, permutation importance, or integrated gradients depending on model type |
fairness |
Demographic parity, equalized odds, predictive parity, and SMD summaries for binary tasks |
calibration |
Calibration metrics and calibrated predictions for binary tasks |
statistical_tests |
Pairwise statistical tests and multiple-testing correction |
missing_data |
Missingness summaries from preprocessed features |
oneehr plot¶
oneehr plot --config <toml> [--figure NAME ...] [--style STYLE] [--output DIR]Renders figures whose required artifacts exist in the run directory.
| Flag | Required | Description |
|---|---|---|
--config |
Yes | Path to TOML experiment config |
--figure |
No | Figure names to render; defaults to all currently available figures |
--style |
No | Style preset: default, nature, lancet, or wide |
--output |
No | Output directory for figures; defaults to {run_dir}/figures/ |
Registered figure names:
| Figure | Required Artifact |
|---|---|
roc |
test/predictions.parquet |
pr |
test/predictions.parquet |
forest |
analyze/comparison.json |
calibration |
test/predictions.parquet |
feature_importance |
analyze/feature_importance.json |
confusion |
test/predictions.parquet |
training_curves |
train/ |
fairness |
analyze/fairness.json |
missing_data |
preprocess/binned.parquet |
decision_curve |
test/predictions.parquet |
significance |
analyze/statistical_tests.json |
cohort_flow |
preprocess/split.json |
oneehr convert¶
oneehr convert --dataset <name> --raw-dir <path> --output-dir <path> [--task TASK]Converts a supported raw clinical dataset into OneEHR CSV tables.
| Flag | Required | Description |
|---|---|---|
--dataset |
Yes | Source dataset: mimic3, mimic4, or eicu |
--raw-dir |
Yes | Path to raw dataset directory |
--output-dir |
Yes | Output directory for converted CSVs |
--task |
No | Label task to export; defaults to all available tasks |
Supported datasets and tasks:
| Dataset | Expected Layout | Available Tasks |
|---|---|---|
mimic3 |
Flat directory with ADMISSIONS.csv, PATIENTS.csv, LABEVENTS.csv, and related MIMIC-III files |
mortality, readmission, los_3day, los_7day |
mimic4 |
hosp/ and icu/ subdirectories, with flat-directory fallback |
mortality, readmission, los_3day, los_7day |
eicu |
Flat directory with patient.csv, lab.csv, and related eICU files |
mortality, los_3day, los_7day |
Examples:
oneehr convert --dataset mimic3 --raw-dir ~/data/mimic-iii --output-dir data/mimic3 --task mortality
oneehr convert --dataset mimic4 --raw-dir ~/data/mimic-iv --output-dir data/mimic4