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ctheodoris
/
Geneformer

Fill-Mask
Transformers
Safetensors
bert
single-cell
genomics
Model card Files Files and versions
xet
Community
585

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
Geneformer / examples
Ctrl+K
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  • 20 contributors
History: 21 commits
Christina Theodoris
Add instructions to convert gene annotations w/ Ensembl Biomart
77eb432 almost 3 years ago
  • pretraining_new_model
    Update links including unsorted example lengths file almost 3 years ago
  • cell_classification.ipynb
    95.5 kB
    Remove unused evalset variable from cell classification example almost 3 years ago
  • gene_classification.ipynb
    167 kB
    Add uniform max len for padding for predictions almost 3 years ago
  • hyperparam_optimiz_for_disease_classifier.py
    6.77 kB
    Add example for hyperparameter optimization for disease classifier about 3 years ago
  • in_silico_perturbation.ipynb
    3.37 kB
    Add in silico perturbation example notebook. almost 3 years ago
  • tokenizing_scRNAseq_data.ipynb
    3.25 kB
    Add instructions to convert gene annotations w/ Ensembl Biomart almost 3 years ago