ehr-data

A Claude Skill for connecting to and analyzing personal health records via SMART on FHIR

CEHR-BERT: Incorporating temporal information from structured EHR data to improve prediction tasks

[ICML'25] MedTok: Multimodal Medical Code Tokenizer

[arXiv 2025] Pre-training script for Clinical ModernBERT

Code to generate realistic synthetic healthcare data with diffusion models

[Cell Patterns 2024] A comprehensive benchmark for COVID-19 predictive modeling using electronic health records in intensive care

An open workbench for leakage-aware, calibrated, explainable risk modeling on longitudinal EHR-style data — built for students, labs, and health-informatics research.

KDD2020 paper; Identifying Sepsis Subphenotypes via Time-Aware Multi-Modal Auto-Encoder

[npj Digital Medicine 2025] Multiple Embedding Model for EHR (MEME) used for strong prediction on Emergency Department tasks

LLM graph-RAG SQL generator for large databases with poor documentation

R package for cleaning anthropometric (height and weight) data from electronic health record systems.

Built a regression model that predicts the expected days of hospitalization time and an uncertainty range estimation.

Pipeline of Data Extraction, Preprocessing, Representation, and Training for MIMIC-III

attribute-based access control implementation for EHRs

Official implementation of TACCO (Task-guided Co-clustering).

omopcept : an R package to access OMOP conCEPTs (no cons!) and flexible tidyverse compatible R functions for querying and visualising.

This is a set of useful tools for using, creating, validating and generally working with Codelists in Health Research. The tools are in Rust with Python and R bindings so they can be used in any of the 3 languages.

HACSurv: A Hierarchical Copula-based Approach for Survival Analysis with Dependent Competing Risks

Nature Medicine paper. A Multidimensional Precision Medicine Approach for Autism Subtype Identification.

CLEF: Controllable Sequence Editing for Biological and Clinical Trajectories