Clinical Data Python Packages

pyhealth

A Deep Learning Python Toolkit for Healthcare Applications.

omophub

Python SDK for OMOP/OHDSI vocabularies - query 10M+ medical concepts across SNOMED, ICD-10, RxNorm, LOINC & 90+ terminologies via simple API

medpython

Medial Research Libs Infrastructure

pycyclops

A toolkit for evaluating and monitoring AI models in clinical settings

cleandat

Python functions to facilitate the pre-processing of data for ML tasks in a clinical context.

medpython-etl

Medial EarlySign ETL Library

prevmed

Une plateforme minimaliste permettant aux utilisateurs non techniques de créer des questionnaires cliniques sans stocker de données personnelles. | A minimalist platform enabling non-technical users to create clinical questionnaires without storing personal data.

medkit-learn

The Medkit-Learn(ing) Environment: Medical Decision Modelling through Simulation (NeurIPS 2021) by Alex J. Chan, Ioana Bica, Alihan Huyuk, Daniel Jarrett, and Mihaela van der Schaar.

yaib

🧪Yet Another ICU Benchmark: a holistic framework for the standardization of clinical prediction model experiments. Provide custom datasets, cohorts, prediction tasks, endpoints, preprocessing, and models. Paper: https://arxiv.org/abs/2306.05109

mosaic-harmonize

MOSAIC: Multi-site Optimal-transport Shift Alignment with Interval Calibration for clinical data harmonization