scgpt

scGPT — Single-Cell Foundation Model

Prerequisites

How to run

Loading the vocabulary and checkpoint

scGPT checkpoints are raw directories (args.json, best_model.pt, vocab.json) — not Hugging Face hub repos. Point at the directory, not an HF repo id.

from scgpt.tokenizer.gene_tokenizer import GeneVocab
gv = GeneVocab.from_file("/path/to/scgpt-human/vocab.json")
print(len(gv))   # 60697 for the released human checkpoint

Embedding an AnnData

import anndata as ad
from scgpt.tasks import embed_data

adata = ad.read_h5ad("dataset.h5ad")        # var must contain a gene-name column
emb = embed_data(
    adata,
    model_dir="/path/to/scgpt-human",
    gene_col="feature_name",
    use_fast_transformer=False,             # see Gotchas
)
# emb is an AnnData with .obsm["X_scGPT"]

Output format

embed_data returns an AnnData whose .obsm["X_scGPT"] is the per-cell embedding (n_cells × emb_dim, 512 by default). Downstream: feed to scanpy.pp.neighbors / scanpy.tl.umap.

Remote compute

Needs ≥24 GB VRAM and the released human checkpoint (~200 MB: args.json, best_model.pt, vocab.json). Use a selected and probed ssh:<alias> context and load remote-compute-ssh. Confirm the environment and checkpoint with bounded read-only discovery, then write a self-contained runs/scgpt_embed.py and submit it with run_in_context:

{
  "context_id": "ssh:gpu-box",
  "title": "scGPT embedding for 50k cells",
  "command": "source ~/miniforge3/etc/profile.d/conda.sh && conda activate scgpt && python scgpt_embed.py --input dataset.h5ad --model-dir /srv/models/scgpt-human --output /home/me/wisp-results/scgpt/embedded.h5ad",
  "timeout_secs": 1800,
  "input_paths": ["runs/scgpt_embed.py", "data/dataset.h5ad"],
  "output_specs": [
    {
      "glob": "ssh://gpu-box/home/me/wisp-results/scgpt/embedded.h5ad",
      "kind": "h5ad",
      "residency": "remote"
    }
  ]
}

Replace every context and remote path with discovered values. For large data already on the server, use an absolute remote path instead of staging it. Call monitor_run once to wait, get_run once for a snapshot, or cancel_run to stop. If flash-attn is unavailable in that environment, set use_fast_transformer=False.

Gotchas

• use_fast_transformer default is True but resolves to a FlashAttention path that may not import in every env. Pass use_fast_transformer=False unless you've confirmed flash_attn loads cleanly.
• The package historically depended on torchtext.vocab.Vocab; in environments without torchtext a pure-Python shim provides Vocab — functionally identical for GeneVocab, but if you hit AttributeError: 'Vocab' object has no attribute …, you're on a stale shim.
• Gene names must match the vocab; unmatched genes are dropped. Set gene_col to the column in adata.var that holds symbols.

Troubleshooting

Next: cluster/annotate the embedding with the scanpy library (sc.pp.neighbors → sc.tl.leiden / sc.tl.umap), or compare to an scvi-tools latent space on the same data.