State Embedding model checkpoints are meant to be used with the Arc State repository.
State is distributed via uv.
Running from pypi
uv tool install arc-state
To generate embeddings given an AnnData:
state emb --model-folder <SE-600M_MODEL_PATH> --input <INPUT_ANNDATA>.h5ad --output <OUTPUT_PATH>.h5ad
Running from source
# Clone repo
git clone github.com:arcinstitute/state
cd state
# Initialize venv
uv venv
# Install
uv tool install -e .
To generate embeddings given an AnnData:
state emb --model-folder <SE-600M_MODEL_PATH> --input <INPUT_ANNDATA>.h5ad --output <OUTPUT_PATH>.h5ad
For model licenses please see MODEL_ACCEPTABLE_USE_POLICY.md, MODEL_LICENSE.md, and LICENSE.md.