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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
3.14 MB
Ctrl+K
Ctrl+K
  • 20 contributors
History: 74 commits
davidjwen's picture
davidjwen
Upload in_silico_perturber_stats.py
bde1f23 verified over 2 years ago
  • __init__.py
    646 Bytes
    Prevent ruff/isort on init over 2 years ago
  • classifier.py
    50.7 kB
    update examples for predict_eval and handle roc for 2 cell classes over 2 years ago
  • classifier_utils.py
    14.8 kB
    Add classifier module and examples over 2 years ago
  • collator_for_classification.py
    29.8 kB
    Subclass collator for cell classification about 3 years ago
  • emb_extractor.py
    29.3 kB
    Add classifier module and examples over 2 years ago
  • evaluation_utils.py
    9.76 kB
    update examples for predict_eval and handle roc for 2 cell classes over 2 years ago
  • gene_median_dictionary.pkl
    941 kB
    Add Geneformer tokenizer and updated model card almost 4 years ago
  • gene_name_id_dict.pkl
    1.12 MB
    xet
    Upload gene_name_id_dict.pkl (#14) about 3 years ago
  • in_silico_perturber.py
    38.7 kB
    add load model for train and fix validate anchor gene error over 2 years ago
  • in_silico_perturber_stats.py
    43.5 kB
    Upload in_silico_perturber_stats.py over 2 years ago
  • perturber_utils.py
    24.9 kB
    add load model for train and fix validate anchor gene error over 2 years ago
  • pretrainer.py
    37 kB
    fix: incorrect condition control flow (#261) almost 3 years ago
  • token_dictionary.pkl
    788 kB
    Update token_dictionary.pkl over 3 years ago
  • tokenizer.py
    16.5 kB
    correct typo over 2 years ago