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ctheodoris
/
Geneformer

Fill-Mask
Transformers
Safetensors
bert
single-cell
genomics
Model card Files Files and versions
xet
Community
589

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
2.99 MB
Ctrl+K
Ctrl+K
  • 20 contributors
History: 27 commits
Christina Theodoris
Modify tokenizer to allow renaming attr names btwn loom and .dataset
e78c44d about 3 years ago
  • __init__.py
    518 Bytes
    Subclass collator for cell classification about 3 years ago
  • collator_for_classification.py
    29.8 kB
    Subclass collator for cell classification about 3 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 almost 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) about 3 years ago
  • in_silico_perturber.py
    40.3 kB
    Modify quant_layers to convert layer nums to integers before calculating max about 3 years ago
  • in_silico_perturber_stats.py
    24.7 kB
    Modify documentation for modeling only 2 cell states about 3 years ago
  • pretrainer.py
    37 kB
    Update pretrainer for transformers==4.28.0 about 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
    8.54 kB
    Modify tokenizer to allow renaming attr names btwn loom and .dataset about 3 years ago