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scGPT Whole-human ​

scGPT is a single-cell foundation model built for single-cell and multi-omics data. Liatir currently exposes the Whole-human checkpoint for local cell embeddings.

What it does ​

scGPT learns representations of cells and genes from large single-cell datasets. Those representations can support tasks such as cell embedding, reference mapping, batch correction, and perturbation hypotheses.

Current status in Liatir ​

scGPT is published as signed Runtime Boxes for macOS arm64 Metal, Linux x86_64 CPU and Linux x86_64 CUDA 12.9. Windows x86_64 runs both Linux boxes through WSL2. Liatir installs the complete target-specific environment and records the exact box release in Results provenance.

Expected inputs ​

  • AnnData .h5ad file.
  • Expression matrix and gene metadata.
  • Optional batch or cell metadata for integration workflows.

Expected outputs ​

  • Embedded AnnData with cell embeddings in obsm["X_scgpt"].
  • A bounded CSV preview for visualization.
  • JSON summary, warnings and Runtime Box provenance.

Hardware and installation ​

Use only the exact published target compatible with the host. The CUDA target is CUDA 12.9, on Linux or on Windows through WSL2; support for it does not imply other CUDA or driver combinations. The model and its dependencies live inside the Runtime Box and are never added to the base app or system Python.

Official source ​