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")# pip install -U transformers accelerate # 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
Commit ·
57f02a4
1
Parent(s): 25dd1da
clone embs_i to resolve memory leak in cls embs
Browse files
geneformer/emb_extractor.py
CHANGED
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@@ -148,7 +148,7 @@ def get_embs(
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del embs_h
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del dict_h
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elif emb_mode == "cls":
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-
cls_embs = embs_i[:,0,:] # CLS token layer
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embs_list.append(cls_embs)
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del cls_embs
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del embs_h
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del dict_h
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elif emb_mode == "cls":
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+
cls_embs = embs_i[:,0,:].clone().detach() # CLS token layer
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embs_list.append(cls_embs)
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del cls_embs
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