Clinical Python Packages

medpython

Medial Research Libs Infrastructure

fedbiomed

A collaborative learning framework for empowering biomedical research

imednet

A Unofficial Python SDK that makes it "easy" to work with the iMednet REST API from your code or the command line. Manage studies, subjects, records, and more with a "friendly" interface. No need to worry about the low-level details.

preclinical

Preclinical is an open-source healthcare AI safety testing platform. It simulates realistic adversarial patient interactions against your agent, stores transcripts, and grades outcomes against safety rubrics.

medpython-etl

Medial Research Tools for Machine learning in medical data, EMR

zensols-mimicsid

MIMIC-III corpus parsing and section prediction with MedSecId (COLING paper)

torchmimic

PyTorch library for MIMIC III Benchmark experiments

charger

Characterization of Germline variants

eyetrace

Open-source toolkit for ocular metrics and fatigue detection

sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

zensols-clinicamr

Clincial Domain Abstract Meaning Representation Graphs

microsalt

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.

zensols-dsprov

Provenience of discharge summaries Pythonic access (BioNLP paper)