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
Christina Theodoris commited on
Commit ·
86fe0dd
1
Parent(s): 94095d1
refer to token dictionary in self
Browse files- geneformer/classifier.py +1 -1
geneformer/classifier.py
CHANGED
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@@ -233,7 +233,7 @@ class Classifier:
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# load token dictionary (Ensembl IDs:token)
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if self.token_dictionary_file is None:
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self.token_dictionary_file = TOKEN_DICTIONARY_FILE
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with open(token_dictionary_file, "rb") as f:
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self.gene_token_dict = pickle.load(f)
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self.token_gene_dict = {v: k for k, v in self.gene_token_dict.items()}
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# load token dictionary (Ensembl IDs:token)
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if self.token_dictionary_file is None:
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self.token_dictionary_file = TOKEN_DICTIONARY_FILE
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+
with open(self.token_dictionary_file, "rb") as f:
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self.gene_token_dict = pickle.load(f)
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self.token_gene_dict = {v: k for k, v in self.gene_token_dict.items()}
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