tomyuanyucheng/spmind

SP-Mind / SP-Bench

This dataset repository supports SP-Mind: An Autonomous Reasoning Agent for Spatial Proteomics Analysis, accepted to ICML 2026.

• Paper: https://arxiv.org/abs/2606.24235
• Code: https://github.com/tomtommyyuan/spmind
• Project page: https://tomtommyyuan.github.io/spmind/

Dataset Summary

SP-Mind is an autonomous AI agent for end-to-end spatial proteomics analysis. It converts natural-language user requests into executable workflows for multiplexed tissue imaging, including illumination correction, registration/stitching, background subtraction, tissue dearraying, probability mapping, cell segmentation, quantification, clustering, phenotyping, and cell-type annotation.

This repository hosts data assets used by SP-Mind and SP-Bench, a benchmark for evaluating agentic spatial proteomics workflows.

SP-Bench contains:

• 102 natural-language spatial proteomics tasks
• 18 task categories
• 8 pipeline stages
• 4 difficulty tiers
• workflows involving realistic multiplexed imaging analysis objectives

Intended Uses

Use this dataset to:

• reproduce SP-Mind experiments;
• evaluate AI agents on spatial proteomics workflow execution;
• test tool-use, planning, and recovery behavior in biomedical agents;
• build or compare agents for multiplexed tissue imaging analysis.

Download

huggingface-cli download tomyuanyucheng/spmind --repo-type dataset --local-dir data

Related Software

Install SP-Mind from GitHub:

git clone https://github.com/tomtommyyuan/spmind.git
cd spmind
pip install -e .

Run an example task:

spmind -p "Perform cell probability mapping and segmentation on 1.ome.tif, save the result to ./output" \
  --path ./data \
  --dangerously-skip-permissions

Citation

If you use SP-Mind, SP-Bench, or this dataset repository, please cite:

@misc{yuan2026spmindautonomousreasoningagent,
  title={SP-Mind: An Autonomous Reasoning Agent for Spatial Proteomics Analysis},
  author={Yucheng Yuan and Yuanfeng Ji and Zhongxiao Li and Ruijiang Li},
  year={2026},
  eprint={2606.24235},
  archivePrefix={arXiv},
  primaryClass={cs.AI},
  url={https://arxiv.org/abs/2606.24235}
}

License

This repository is released under Apache-2.0 unless otherwise noted. Some underlying third-party imaging datasets, tools, or container images may carry separate licenses or usage terms. Please review the original sources before commercial use.

Contact

For questions, issues, benchmark submissions, or reproducibility reports, please open an issue at:

https://github.com/tomtommyyuan/spmind/issues