Ehr Python Packages

meds-reader

A high-performance database and Python reader interface for MEDS datasets

medpython

Medial Research Libs Infrastructure

ehrdata

A datastructure for EHR data

ehrapy

Electronic Health Record Analysis with Python.

healthchain

Python SDK for healthcare AI: connect models to live EHR systems, skip the integration tax 💫 🏥

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

faker-healthcare-provider

🏥 Faker provider for generating healthcare fake data - diseases, ICD-10, drugs, procedures

cycquery

A tool to query EHR databases

pat2vec

A comprehensive Python package for healthcare data engineering, designed to extract, transform, and feature engineer patient data from CogStack-based electronic health record (EHR) datalakes. It provides tools for cohort building, batch data processing, clinical note analysis, and creating machine learning-ready datasets.

fhirpack

FHIR Python Analysis Client and Kit (FHIRPACK) is a general purpose FHIR client that simplifies the access, analysis and representation of FHIR and EHR data using PANDAS, an ETL philosophy and a functional syntax. It was initially developed at the IKIM and HDDBS in Germany. Read more at https://zenodo.org/record/8006589

medpython-etl

Medial Research Tools for Machine learning in medical data, EMR

oneehr

Python package for longitudinal EHR experiments across ML, DL, and LLM or agent systems

ehrax

EHRs io+processing for JAX+equinox compatible tasks, e.g. mainly ML.

cleandat

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

chartfold

Collect and consolidate personal health data from multiple EHR systems into a single queryable database

lemonpie

A deep learning library for Electronic Health Record (EHR) data

openemr-agent

Healthcare AI agent sidecar for OpenEMR — clinical decision support with drug interaction checking, patient data retrieval, and safety verification

mai-dx

An open source implementation of the paper: "Sequential Diagnosis with Language Models" From Microsoft Built with Swarms Framework