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

COVID-19 EHR data analysis pipeline

Code to generate realistic synthetic healthcare data with diffusion models

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

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

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

attribute-based access control implementation for EHRs

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

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

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

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

A software toolkit for the interconversion of standard data models for phenotypic data

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

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

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

Pipeline for building Machine Learning Classifiers for the diagnosis of EHR text-data. We used this pipeline for our study, published here: https://doi.org/10.2196/23930.

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.

IPEHR-gateway is a solution to provide benefits of decentralized architecture to common HMS apps using standard APIs. IPEHR gateway is used to encrypt and decrypt passing data, support AQL queries of encrypted data and manage user’s cryptographic keys.