Biology-driven insights into the power of single-cell foundation models
This benchmark introduces novel evaluation perspectives, identifying the strengths and limitations of current scFMs, and paves the way for their effective application in biological and clinical research, including cell atlas construction, tumor microenvironment studies, and treatment decision-making.
Authors
- Tingjun Hou (ORCID: https://orcid.org/0000-0001-7227-2580)
- Yilin Wang (ORCID: https://orcid.org/0000-0003-1005-8508)
- Yiheng Zhu (ORCID: https://orcid.org/0000-0002-3857-1533)
- Mingze Yin
- Renling Hu (ORCID: https://orcid.org/0009-0004-8773-0635)
- Tianyue Wang (ORCID: https://orcid.org/0000-0002-1037-1935)
- Qing Ye (ORCID: https://orcid.org/0000-0002-6756-0630)
- Jialu Wu
- Jike Wang (ORCID: https://orcid.org/0000-0002-8118-8572)
- Chang-Yu Hsieh (ORCID: https://orcid.org/0000-0002-6242-4218)
Institutions
- Zhejiang Lab (CN)
- First Affiliated Hospital Zhejiang University (CN)
- Nano Carbon (Poland) (PL)
- Zhejiang University (CN)
Publication Details
- Journal
- Genome biology
- Published
- 2025-10-03
- DOI
- https://doi.org/10.1186/s13059-025-03781-6
- Citations
- 5
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 4.03
Funders
- National Natural Science Foundation of China