JosephSBoyle
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[EMNLP 2020] Multi-label Few/Zero-shot Learning with Knowledge Aggregated from Multiple Label Graphs
An MCP-powered demo for natural-language epidemiology, patient cohort generation, and SQL queries over synthetic OMOP and non-OMOP healthcare data.
This repository provides the official implementation of the paper “JointCoder: Exploring Automated ICD Coding on Real-World Chinese EHRs with a Multi-Agent Framework”, including a real-world Chines…
The "Minds Meet Machines" Challenge. A concept set development study by the OHDSI Phenotype development and evaluation workgroup
R package for manipulating problem and diagnosis lists
Machine-readable version of electronic health record phenotypes for Kuan V. and Denaxas S. et al.
[In Development] An application to parse freetext inclusion criteria and produce a structured cohort definition that can be executed against OMOP CDM
Test-Driven Development for OHDSI Cohort Definitions
Demo project showing test-driven development for OHDSI cohort definitions
The lean application framework for Python. Build sophisticated user interfaces with a simple Python API. Run your apps in the terminal and a web browser.
HDR UK National Phenotype Library
Python SDK for the OHDSI Athena Concepts API
Model Context Protocol (MCP) server for mapping clinical terminology to Observational Medical Outcomes Partnership (OMOP) concepts using Large Language Models
DoWhy is a Python library for causal inference that supports explicit modeling and testing of causal assumptions. DoWhy is based on a unified language for causal inference, combining causal graphic…
"Context engineering is the delicate art and science of filling the context window with just the right information for the next step." — Andrej Karpathy. A frontier, first-principles handbook inspi…
OpenCodelists is an open platform for creating and sharing codelists of clinical terms and drugs.
A Dataset for Evaluating Contextualized Representation of Biomedical Concepts in Language Models
A full spaCy pipeline and models for scientific/biomedical documents.
Julep — durable, composable AI agents. Flows that crash and resume, retry safely, and explain every step.
Towards Scalable Language-Image Pre-training for 3D Medical Imaging [TMLR 2026]
An async Python micro framework for building web applications.
A package supporting the conversion from Synthea CSV to OMOP CDM
Definition and DDLs for the OMOP Common Data Model (CDM)