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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
1.88 MB
Ctrl+K
Ctrl+K
  • 20 contributors
History: 13 commits
David Wen
fix in silico perturber
f404882 about 3 years ago
  • __init__.py
    580 Bytes
    add in silico perturbation module about 3 years ago
  • collator_for_cell_classification.py
    28.8 kB
    Add data collator for cell classification and example for cell classification almost 4 years ago
  • collator_for_gene_classification.py
    28.1 kB
    Add data collator for gene classification and example for gene classification almost 4 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
  • in_silico_perturber.py
    38.2 kB
    add in silico perturbation module about 3 years ago
  • in_silico_perturber_stats.py
    15 kB
    fix in silico perturber about 3 years ago
  • pretrainer.py
    36.8 kB
    add in silico perturbation module 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
    7.89 kB
    Fix bug with metadata when processing multiple .loom files (#3) over 3 years ago