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
Add function to get number of model embeddings
Browse files
geneformer/perturber_utils.py
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@@ -156,6 +156,10 @@ def quant_layers(model):
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return int(max(layer_nums)) + 1
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def get_model_input_size(model):
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return int(re.split("\(|,", str(model.bert.embeddings.position_embeddings))[1])
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return int(max(layer_nums)) + 1
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def get_model_embedding_dimensions(model):
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return int(re.split("\(|,", str(model.bert.embeddings.position_embeddings))[2].strip().replace(")", ""))
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def get_model_input_size(model):
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return int(re.split("\(|,", str(model.bert.embeddings.position_embeddings))[1])
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