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")# 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") - Inference
- Notebooks
- Google Colab
- Kaggle
Commit History
update instructions to include reminder about token dictionary cb1b0d5 verified
anndata_tokenizer (#170) 4302f48
Add instructions to convert gene annotations w/ Ensembl Biomart 77eb432
Christina Theodoris commited on
Add further explanation regarding input file format for transcriptome tokenizer c34ead6
Christina Theodoris commited on
Update instructions in tokenizing example to clarify requirement for Ensembl ID d468697
Christina Theodoris commited on
Update instructions in tokenizing example to clarify requirement for Ensembl ID e606e1c
Christina Theodoris commited on
Add further explanation to tokenizer example script and updated tokenizer to match loompy raised error 78dd83b
Christina Theodoris commited on
Add example for tokenizing .loom dataset f89f796
Christina Theodoris commited on