scGPT

Generative single-cell multi-omics foundation model pretrained on over 33 million cells, from the Wang lab (University Health Network / University of Toronto).

Unsigned

Overview

scGPT is a generative foundation model for single-cell multi-omics, pretrained on a corpus of over 33 million human cells, developed by the Wang lab (University Health Network and University of Toronto). It is peer-reviewed in Nature Methods (Cui, Wang, Maan et al., "scGPT: toward building a foundation model for single-cell multi-omics using generative AI", Nature Methods, 2024, doi:10.1038/s41592-024-02201-0; the repository's own citation still points to the earlier 2023 bioRxiv preprint, which this description notes rather than overriding). scGPT ships a model zoo of pretrained checkpoints (whole-human, brain, blood, heart, lung, kidney, pan-cancer) and is used for cell-type annotation, perturbation prediction, and multi-omic integration, standard single-cell genomics research workflows also listed on the Chan Zuckerberg Initiative's Virtual Cells Platform. It is a general single-cell representation model rather than a variant-effect predictor, similar in kind to this registry's existing Geneformer entry.

**Licence note**: MIT, confirmed directly against the repository's own raw `LICENSE` file (not GitHub's derived badge alone).

**Registry note on `model_card_uri`**: this points to a Hugging Face mirror of the pretrained checkpoint (`tdc/scGPT`), which carries a standard Hugging Face model card, rather than a GA4GH Genomic AI Model Card v0.6.0-formatted document. No model has yet published a card in the GA4GH v0.6.0 format, since it is a newly drafted specification. The primary source repository remains `github.com/bowang-lab/scGPT`.

Details

Licence: MIT
Version: whole-human (recommended checkpoint)
Category: Genomic foundation model
Homepage: https://github.com/bowang-lab/scGPT
Repository: https://github.com/bowang-lab/scGPT
Maintainers: Susheel Varma (@susheel, GA4GH AI Workstream / Sage Bionetworks)
Keywords: single-cellmulti-omicstranscriptomicsgenomicsfoundation-modelcell-type-annotation

Safety classification

No safety classification has been submitted for this entry.

Model Card

View the full GA4GH Genomic AI Model Card ↗

Hosting: github
Access: https://github.com/bowang-lab/scGPT

Mirrored data last synced from the Model Card at 2026-09-08T00:00:00.000Z. See the linked card for the authoritative, live version.

Provenance

Created: 2026-09-08T00:00:00.000Z
Updated: 2026-09-08T00:00:00.000Z
Last verified: 2026-09-08T00:00:00.000Z