How to use ctheodoris/Geneformer with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("fill-mask", model="ctheodoris/Geneformer")
# pip install -U transformers accelerate # Load model directly from transformers import AutoTokenizer, AutoModelForMaskedLM tokenizer = AutoTokenizer.from_pretrained("ctheodoris/Geneformer") model = AutoModelForMaskedLM.from_pretrained("ctheodoris/Geneformer", device_map="auto")
https://huggingface.co/ctheodoris/Geneformer/resolve/caec2855ca523f772b903115267a9d5468349da4/examples/extract_and_plot_cell_embeddings.ipynb
hf download hf://ctheodoris/Geneformer@caec2855ca523f772b903115267a9d5468349da4/examples/extract_and_plot_cell_embeddings.ipynb
curl -L -o extract_and_plot_cell_embeddings.ipynb https://huggingface.co/ctheodoris/Geneformer/resolve/caec2855ca523f772b903115267a9d5468349da4/examples/extract_and_plot_cell_embeddings.ipynb
