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/9f0fa5d773efa20d201f2d548baff6edca7d08d5/examples/in_silico_perturbation.ipynb
hf download hf://ctheodoris/Geneformer@9f0fa5d773efa20d201f2d548baff6edca7d08d5/examples/in_silico_perturbation.ipynb
curl -L -o in_silico_perturbation.ipynb https://huggingface.co/ctheodoris/Geneformer/resolve/9f0fa5d773efa20d201f2d548baff6edca7d08d5/examples/in_silico_perturbation.ipynb
