oneehr 0.1.1

Unified platform for longitudinal EHR experiments across ML, DL, and LLM agents

OneEHR

OneEHR is a unified Python platform for longitudinal EHR experiments across ML, DL, and LLM agents. It provides shared infrastructure for preprocessing, modeling, testing, and analysis on one shared run contract — the first toolkit bridging classical machine learning, deep learning, and agentic AI for clinical prediction.

Key Features

• 38 model architectures — tabular ML, recurrent/non-recurrent DL, irregular-time, KG-enhanced, and survival models
• Unified ML/DL/LLM comparison — all predictions in one predictions.parquet with bootstrap CI and statistical tests
• Dataset converters — built-in support for MIMIC-III, MIMIC-IV, and eICU
• Medical code ontologies — ICD-9/10 mapping, CCS grouping, ATC drug hierarchy
• Survival analysis — DeepSurv, DeepHit, concordance index, Kaplan-Meier visualization
• Fairness & interpretability — demographic parity, equalized odds, SHAP, LIME, integrated gradients, attention visualization
• Publication-quality figures — ROC, PR, calibration, DCA, forest plots, KM curves with Nature/Lancet style presets
• Reproducibility by design — single TOML config = complete experiment specification

Workflow At A Glance

oneehr preprocess --config experiment.toml   # Bin features, split patients
oneehr train      --config experiment.toml   # Train ML/DL models
oneehr test       --config experiment.toml   # Evaluate on test set
oneehr analyze    --config experiment.toml   # Cross-system comparison
oneehr plot       --config experiment.toml   # Publication figures

All commands operate on the same run directory under {output.root}/{output.run_name}/.

Install

OneEHR requires Python 3.12+.

pip install oneehr

# Or from source:
uv venv .venv --python 3.12
uv pip install -e .
oneehr --help

Quickstart

Use the bundled TJH COVID-19 ICU example:

# Convert source data (only needed once)
python examples/tjh/convert.py

# Run the full pipeline
oneehr preprocess --config examples/tjh/mortality_patient.toml
oneehr train      --config examples/tjh/mortality_patient.toml
oneehr test       --config examples/tjh/mortality_patient.toml
oneehr analyze    --config examples/tjh/mortality_patient.toml

Or use the Python API:

import oneehr

config = oneehr.load_config("examples/tjh/mortality_patient.toml")
oneehr.preprocess(config)
oneehr.train(config)
oneehr.test(config)
oneehr.analyze(config)

Dataset Converters

Convert standard clinical datasets into OneEHR's three-table format:

# MIMIC-III
oneehr convert --dataset mimic3 --raw-dir /path/to/mimic3 --output-dir data/mimic3/ --task mortality

# MIMIC-IV
oneehr convert --dataset mimic4 --raw-dir /path/to/mimic4 --output-dir data/mimic4/ --task mortality

# eICU
oneehr convert --dataset eicu --raw-dir /path/to/eicu --output-dir data/eicu/ --task mortality

Each converter produces labels for mortality, readmission, and length-of-stay tasks.

Models

OneEHR ships 38 model architectures:

Category	Models
Tabular ML	XGBoost, CatBoost, Random Forest, Decision Tree, GBDT, Logistic Regression
Recurrent	GRU, LSTM, RNN, GRU-D, Dipole, HiTANet, M3Care, PAI
Non-recurrent	CNN, TCN, Transformer, SAnD, MLP, Deepr, EHR-Mamba, Jamba, LSAN
Irregular-time	mTAND, Raindrop, ContiFormer, TECO
EHR-specialised	AdaCare, StageNet, RETAIN, ConCare, GRASP, MCGRU, DrAgent, PRISM, SAFARI
KG-enhanced	GraphCare, KerPrint, ProtoEHR
Survival	DeepSurv, DeepHit

Models with static branches (ConCare, GRASP, MCGRU, DrAgent, PRISM, SAFARI, TECO) automatically use patient-level static features when static.csv is provided.

Task Types

Task	Config	Description
Binary classification	kind = "binary"	Mortality, readmission, etc.
Multiclass	kind = "multiclass"	Phenotyping, diagnosis groups
Regression	kind = "regression"	Length of stay, lab value prediction
Survival	kind = "survival"	Time-to-event with censoring
Multi-label	kind = "multilabel"	ICD coding, multi-diagnosis

Medical Code Ontologies

from oneehr.medcode import ICD9, ICD10, CodeMapper, CCSGrouper, ATCHierarchy

# ICD code utilities
ICD9.chapter("401.9")    # → "Circulatory system"
ICD10.category("I10.0")  # → "I10"

# Aggregate codes by ontology for dimensionality reduction
mapper = CodeMapper()
mapper.add_icd_chapter_mapping(version=9)
mapped_events = mapper.apply(events_df)

Configuration

OneEHR uses TOML as the experiment contract:

• [dataset] — input table paths (dynamic, static, label)
• [preprocess] — binning, feature engineering, preprocessing pipeline
• [task] — task kind and prediction mode (patient or time)
• [split] — patient-level train/val/test splitting
• [[models]] — model selection with per-model params
• [trainer] — DL training config (mixed precision, LR schedulers, early stopping)
• [[systems]] — LLM/agent system definitions
• [output] — run root and run name

Tutorials

Tutorial	Description
01 Quickstart	End-to-end TJH mortality prediction
02 Custom Dataset	Bring your own data + medical code mapping
03 Model Comparison	ML vs DL with bootstrap CI and statistical tests
04 Fairness & Explainability	Bias detection + feature importance
05 Survival Analysis	DeepSurv, C-index, Kaplan-Meier curves

Documentation

Full documentation: medx-pku.github.io/OneEHR/

• Installation
• Quickstart
• Data Model
• Core Workflows
• CLI Reference
• Configuration
• Models
• Artifacts
• Dataset Converters
• Medical Codes

Build docs locally:

uvx --from "mkdocs @ git+https://github.com/encode/mkdocs.git" mkdocs serve

Contributing

See CONTRIBUTING.md for development setup and guidelines.

Validation

pytest tests/ -v                                                    # 150 tests
oneehr preprocess --config examples/tjh/mortality_patient.toml      # End-to-end