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

COVID-19 EHR data analysis pipeline

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

Code to generate realistic synthetic healthcare data with diffusion models

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

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

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

[arXiv 2025] Pre-training script for Clinical ModernBERT

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

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

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

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

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.

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

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

Missing data imputation for longitudinal multi-variable EHR data. Paper in JAMIA.

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.

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.