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
Fix bug with metadata when processing multiple .loom files
#3
by davidjwen - opened
- geneformer/tokenizer.py +2 -1
geneformer/tokenizer.py
CHANGED
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@@ -108,7 +108,8 @@ class TranscriptomeTokenizer:
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loom_file_path
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)
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tokenized_cells += file_tokenized_cells
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-
cell_metadata.
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return tokenized_cells, cell_metadata
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loom_file_path
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)
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tokenized_cells += file_tokenized_cells
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+
for k in cell_metadata.keys():
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+
cell_metadata[k] += file_cell_metadata[k]
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return tokenized_cells, cell_metadata
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