Repositories list

• 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

  •15•119•3•2•Updated Jan 6, 2025Jan 6, 2025

• long_context_clues

  Public
  Taking off-the-shelf HF models and training them on EHR data

  Jupyter Notebook

  •0•8•0•0•Updated Jan 3, 2025Jan 3, 2025

• meds_reader

  Public
  C++

  •

  Apache License 2.0

  •0•15•0•0•Updated Dec 18, 2024Dec 18, 2024

• shahlab-blog

  Public
  Shah Lab Jekyll website

  HTML

  •

  MIT License

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

• factehr

  Public
  Python

  •0•3•0•0•Updated Dec 9, 2024Dec 9, 2024

• ehrshot-benchmark

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

  Jupyter Notebook

  •

  Apache License 2.0

  •10•145•3•0•Updated Nov 21, 2024Nov 21, 2024

• meds_reader_paper_code

  Public
  C++

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

• mimic_tutorial

  Public
  Python

  •0•3•0•0•Updated Oct 9, 2024Oct 9, 2024

• medalign-website

  Public
  Landing page and website for the MedAlign project

  HTML

  •

  MIT License

  •2•0•0•2•Updated Oct 7, 2024Oct 7, 2024

• INSPECT_public

  Public
  INSPECT dataset/benchmark paper, accepted by NeurIPS 2023

  Python

  •

  Apache License 2.0

  •2•25•1•0•Updated Aug 27, 2024Aug 27, 2024

• Clinfo.AI

  Public
  This is Clinfo.AI Demo Instruction

  Jupyter Notebook

  •

  MIT License

  •8•29•1•0•Updated Aug 20, 2024Aug 20, 2024

• aplusml

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

  Jupyter Notebook

  •

  Apache License 2.0

  •3•20•4•0•Updated Aug 14, 2024Aug 14, 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

  •0•0•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•2•0•0•Updated Jul 4, 2024Jul 4, 2024

• inspect-website

  Public
  SCSS

  •

  MIT License

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

• clinical_trial_patient_matching

  Public
  Zero-shot clinical trial matching with LLMs

  Python

  •0•7•0•0•Updated Jun 22, 2024Jun 22, 2024

• data-align

  Public
  Clinical text summarization by adapting large language models

  Python

  •26•0•0•0•Updated Jun 19, 2024Jun 19, 2024

• ehrshot-website

  Public
  Public website for EHRSHOT

  SCSS

  •

  MIT License

  •1•1•0•0•Updated Jun 18, 2024Jun 18, 2024

• motor_tutorial

  Public
  Tutorial repository for the official MOTOR release

  Jupyter Notebook

  •

  Apache License 2.0

  •0•8•0•0•Updated May 6, 2024May 6, 2024

• motor_code_release

  Public
  Python

  •0•3•0•0•Updated Mar 27, 2024Mar 27, 2024

• temp_ds_shift_robustness

  Public
  Jupyter Notebook

  •

  MIT License

  •0•6•0•1•Updated Mar 5, 2024Mar 5, 2024

• clinical_trial_patient_matching-website

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

  JavaScript

  •0•4•0•0•Updated Feb 16, 2024Feb 16, 2024

• pancreatic_cancer_tutorial

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Nov 4, 2023Nov 4, 2023

• medalign

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

  MIT License

  •9•90•1•0•Updated Oct 19, 2023Oct 19, 2023

• pad

  Public
  A repository for building and testing a simple PAD model

  Python

  •0•0•0•0•Updated Aug 25, 2023Aug 25, 2023

• survlearners

  Public
  Metalearners for Survival Data

  survival-analysiscausal-inference

  R

  •1•13•4•0•Updated Jul 31, 2023Jul 31, 2023

• manifest

  Public
  Prompt programming with FMs.

  Python

  •

  Apache License 2.0

  •46•1•0•0•Updated Jul 31, 2023Jul 31, 2023

• TrialProbe

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •0•6•0•0•Updated Jul 7, 2023Jul 7, 2023

• CLMBR-contrastive-learning

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 5, 2023May 5, 2023