Repositories list

• medhelm

  Public
  Python

  •0•0•0•3•Updated Aug 13, 2025Aug 13, 2025

• femr

  Public
  FEMR (Framework for Electronic Medical Records) provides tooling for large-scale, self-supervised learning using electronic health records

  healthcareelectronic-health-recordsself-supervised-learning+ 1foundation-models

  Python

  •

  Apache License 2.0

  •27•155•3•3•Updated Aug 11, 2025Aug 11, 2025

• medalign-website

  Public
  Landing page and website for the MedAlign project

  HTML

  •

  MIT License

  •2•0•0•2•Updated Aug 11, 2025Aug 11, 2025

• factehr

  Public
  Fact Verification for Clinical Notes with LLMs

  benchmarkingehrclinical-notes+ 3clinical-nlpfact-verificationllms

  Python

  •0•30•0•0•Updated Aug 8, 2025Aug 8, 2025

• factehr-website

  Public
  Website for FactEHR: A Dataset for Evaluating Factuality in Clinical Notes Using LLMs

  HTML

  •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• hf_ehr

  Public
  Training HuggingFace models on EHR data

  machine-learninghealthcareelectronic-health-records+ 1foundation-models

  Jupyter Notebook

  •

  Apache License 2.0

  •7•28•4•0•Updated Jul 21, 2025Jul 21, 2025

• mimic_tutorial

  Public
  Python

  •0•3•0•0•Updated Jul 7, 2025Jul 7, 2025

• inspect-website

  Public
  SCSS

  •

  MIT License

  •0•0•0•0•Updated Jul 4, 2025Jul 4, 2025

• meds_reader

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

  healthcareehrelectronic-health-record+ 2medsfoundation-models

  C++

  •

  Apache License 2.0

  •0•19•1•0•Updated Jun 29, 2025Jun 29, 2025

• med-nota

  Public
  Python

  •3•12•0•0•Updated Jun 11, 2025Jun 11, 2025

• opt-paradox

  Public
  Python

  •1•8•0•0•Updated Jun 10, 2025Jun 10, 2025

• TIMER

  Public
  Python

  •0•1•0•0•Updated Jun 9, 2025Jun 9, 2025

• ehrshot-benchmark

  Public
  A benchmark for few-shot evaluation of foundation models for electronic health records (EHRs)

  Jupyter Notebook

  •

  Apache License 2.0

  •23•185•0•0•Updated Jun 6, 2025Jun 6, 2025

• INSPECT_public

  Public
  INSPECT dataset/benchmark paper, accepted by NeurIPS 2023

  Python

  •

  Apache License 2.0

  •3•38•9•0•Updated May 20, 2025May 20, 2025

• medalign

  Public
  MedAlign is a clinician-generated dataset for instruction following with electronic medical records.

  benchmarkinghealthcareehr+ 4electronic-health-recordsinstruction-followingfoundation-modelsllms

  MIT License

  •9•95•0•0•Updated May 17, 2025May 17, 2025

• tte-pretraining

  Public
  Code for the paper "Time-to-event pretraining for 3D medical imaging"

  Python

  •0•6•0•0•Updated May 8, 2025May 8, 2025

• aplusml

  Public
  APLUS ML = A Python Library for Usefulness Simulations of Machine Learning models

  Jupyter Notebook

  •

  Apache License 2.0

  •5•24•4•0•Updated May 7, 2025May 7, 2025

• med-s1

  Public
  s1: Simple test-time scaling

  Jupyter Notebook

  •

  Apache License 2.0

  •759•2•0•0•Updated Apr 11, 2025Apr 11, 2025

• ehrshot-website

  Public
  Public website for EHRSHOT

  SCSS

  •

  MIT License

  •1•1•0•0•Updated Mar 18, 2025Mar 18, 2025

• clinical_trial_patient_matching

  Public
  Zero-shot clinical trial matching with LLMs

  Python

  •4•12•0•0•Updated Mar 1, 2025Mar 1, 2025

• motor_tutorial

  Public
  Tutorial repository for the official MOTOR release

  Jupyter Notebook

  •

  Apache License 2.0

  •0•14•0•0•Updated Feb 22, 2025Feb 22, 2025

• clinical_trial_patient_matching-website

  Public
  Public facing website for zero-shot CT patient matching paper

  JavaScript

  •0•4•0•0•Updated Feb 19, 2025Feb 19, 2025

• shahlab-blog

  Public
  Shah Lab Jekyll website

  HTML

  •

  MIT License

  •1•1•0•0•Updated Dec 11, 2024Dec 11, 2024

• meds_reader_paper_code

  Public
  C++

  •0•0•0•0•Updated Nov 9, 2024Nov 9, 2024

• torch_hawk

  Public
  C++

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 2, 2024Nov 2, 2024

• Clinfo.AI

  Public
  This is Clinfo.AI Demo Instruction

  Jupyter Notebook

  •

  MIT License

  •8•36•1•0•Updated Aug 20, 2024Aug 20, 2024

• slurmtool

  Public
  SLURM helper

  Python

  •0•1•0•0•Updated Aug 5, 2024Aug 5, 2024

• gpt4usmle

  Public
  Tools for automated evaluation and generation of USMLE-style questions

  Jupyter Notebook

  •

  MIT License

  •1•1•0•0•Updated Aug 1, 2024Aug 1, 2024

• RATE-experiments

  Public
  Code for reproducing the analyses that appear in "Evaluating Treatment Prioritization Rules via Rank-Weighted Average Treatment Effects"

  HTML

  •0•3•0•0•Updated Jul 4, 2024Jul 4, 2024

• data-align

  Public
  Clinical text summarization by adapting large language models

  Python

  •31•0•0•0•Updated Jun 19, 2024Jun 19, 2024