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.

zensols-mimicsid

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

charger

Characterization of Germline variants

medpython-etl

Medial Research Tools for Machine learning in medical data, EMR

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.

clinicalguard

Constitutional AI governance for clinical decision support

torchmimic

PyTorch library for MIMIC III Benchmark experiments

sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

eyetrace

An open-source toolkit extracting physiological and behavioral metrics from facial videos to assess fatigue, drowsiness, and cognitive load.

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)