matchminer-ai

Overview

matchminer-ai is a Python package for running the clinical trial matching inference workflow described in Altreuter et al., MatchMiner-AI: An Open-Source Solution for Cancer Clinical Trial Matching. The package provides modular functions for the core MatchMiner-AI workflow: summarizing trials and patient histories, generating embeddings of each, retrieving candidate matches, scoring match quality, and assessing exclusion criteria.

For detailed instructions, please see the documentation website.

Compute requirements

A GPU is recommended for the clinical trial matching inference workflow. Please see the requirements documentation for more information on compute expectations and GPU recommendations.

Installation

This package requires Python 3.12+.

The package has been tested in Linux environments.

We recommend using uv to create the Python environment and install the package:

uv venv --python 3.12
source .venv/bin/activate
uv pip install matchminer-ai

Quickstart

See the example notebook for a full walkthrough using sample input data: example notebook

Citation

If you use matchminer-ai, please cite:

Altreuter J, Trukhanov P, Paul MA, Hassett MJ, Riaz IB, Afzal MU, Mohammed AA, Sammons S, Lindsay J, Mallaber E, Klein HR, Gungor G, Galvin M, Deletto M, Van Nostrand SC, Provencher J, Yu J, Tahir N, Wischhusen J, Kozyreva O, Ortiz T, Tuncer H, Masri JE, Malcolm A, Mazor T, Cerami E, Kehl KL. MatchMiner-AI: An Open-Source Solution for Cancer Clinical Trial Matching. arXiv. 2026. doi: 10.48550/arXiv.2412.17228

Contributing

Contributions are welcome! Please follow our contribution instructions if you are interested in contributing to this project.