cz-benchmarks Documentation
What is cz-benchmarks?
cz-benchmarks is a package for standardized evaluation and comparison of machine learning models for biological applications (first, in the single-cell transcriptomics domain, with future plans to expand to additional domains). The package provides a toolkit for running containerized models, executing biologically-relevant tasks, and computing performance metrics. We see this tool as a step towards ensuring that large-scale ML Models can be harnessed to deliver genuine biological insights – by building trust, accelerating development, and bridging the gap between ML and biology communities.
Why benchmarking? Why now?
Last year, CZI hosted a workshop focused on benchmarking and evaluation of ML Models in biology, and the insights gained have reinforced our commitment to supporting the development of a robust benchmarking infrastructure, which we see as critical to achieving our Virtual Cell vision.
💬 Community Feedback & Contributions
CZI welcome your feedback and contributions as we continue to improve the package. If you encounter any issues or have suggestions, please open an issue on GitHub or reach out to us at virtualcellmodels@chanzuckerberg.com.
You can find cz-benchmarks on: