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ctheodoris
/
Geneformer

Fill-Mask
Transformers
Safetensors
bert
single-cell
genomics
Model card Files Files and versions
xet
Community
594

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", device_map="auto")
  • Inference
  • Notebooks
  • Google Colab
  • Kaggle
Geneformer / geneformer
3.06 MB
Ctrl+K
Ctrl+K
  • 21 contributors
History: 59 commits
Christina Theodoris
change doc formatting
17f036a over 2 years ago
  • __init__.py
    558 Bytes
    Add function to extract and plot cell embeddings about 3 years ago
  • collator_for_classification.py
    29.8 kB
    Subclass collator for cell classification over 3 years ago
  • emb_extractor.py
    29.4 kB
    change doc formatting over 2 years ago
  • gene_median_dictionary.pkl

    Detected Pickle imports (2)

    • "numpy.dtype",
    • "numpy.core.multiarray.scalar"

    How to fix it?

    941 kB
    Add Geneformer tokenizer and updated model card about 4 years ago
  • gene_name_id_dict.pkl

    Pickle imports

    • No problematic imports detected

    What is a pickle import?

    1.12 MB
    xet
    Upload gene_name_id_dict.pkl (#14) over 3 years ago
  • in_silico_perturber.py
    38.7 kB
    change doc formatting over 2 years ago
  • in_silico_perturber_stats.py
    43 kB
    change doc formatting over 2 years ago
  • perturber_utils.py
    24.7 kB
    update dependencies, reinstate compatibility with python<3.9 with typing for List over 2 years ago
  • pretrainer.py
    37 kB
    fix: incorrect condition control flow (#261) almost 3 years ago
  • token_dictionary.pkl

    Detected Pickle imports (2)

    • "numpy.core.multiarray.scalar",
    • "numpy.dtype"

    How to fix it?

    788 kB
    Update token_dictionary.pkl over 3 years ago
  • tokenizer.py
    15.4 kB
    change doc formatting over 2 years ago