Instructions to use ctheodoris/Geneformer with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
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")# Load model directly from transformers import AutoTokenizer, AutoModelForMaskedLM tokenizer = AutoTokenizer.from_pretrained("ctheodoris/Geneformer") model = AutoModelForMaskedLM.from_pretrained("ctheodoris/Geneformer") - Inference
- Notebooks
- Google Colab
- Kaggle
EmbExtractor type error
Dear team,
thank you for the great tool. I have been trying to implement the perturbation workflow on my dataset and I face the following error when I extract the embeddings with get_state_embs() function
RuntimeError: Expected tensor for argument #1 'indices' to have one of the following scalar types: Long, Int; but got torch.cuda.FloatTensor instead (while checking arguments for embedding)
I have only 2 states, start and goal.
Thank you for the question - could you please send the full error trace for context?
Thank you for including the full error trace! We would suggest checking your tokenized dataset to ensure that each label is of the same type within that label and that your input_ids are all integer token IDs as expected.

