README.md

---
license: apache-2.0
task_categories:
- other
tags:
- biology
- single-cell
- benchmark
- bioinformatics
size_categories:
- n<1K
---

# scBench Canonical Data Files

This dataset contains the .h5ad data files for the scBench canonical subset (30 evaluations across 5 platforms).

## About scBench

scBench is a benchmark for agentic single-cell RNA-seq analysis. It evaluates whether AI agents can solve practical bioinformatics tasks with deterministic grading.

- **Paper**: https://arxiv.org/abs/2602.09063
- **GitHub**: https://github.com/latchbio/scbench
- **Inspect Evals**: https://github.com/UKGovernmentBEIS/inspect_evals

## Files

This dataset includes 18 .h5ad files corresponding to the canonical subset:

- **Platforms**: Chromium, CSGenetics, Illumina, MissionBio, ParseBio
- **Task categories**: QC, normalization, dimensionality reduction, clustering, cell typing, differential expression, trajectory analysis

## Usage

These files are used with the scBench evaluation in inspect_evals:

```bash
pip install inspect-evals
uv run inspect eval inspect_evals/scbench --model anthropic/claude-haiku-4-5-20251001
```

## License

Apache 2.0 (following the scBench upstream license)

## Citation

If you use this dataset, please cite the scBench paper:

```bibtex
@misc{scbench2025,
  title={scBench: A Benchmark for Agentic Single Cell Data Analysis},
  author={LatchBio},
  year={2025},
  eprint={2602.09063},
  archivePrefix={arXiv}
}
```