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
Update geneformer/emb_extractor.py
#303
by hchen725 - opened
geneformer/emb_extractor.py
CHANGED
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@@ -565,7 +565,7 @@ class EmbExtractor:
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filtered_input_data, cell_state, self.nproc
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)
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downsampled_data = pu.downsample_and_sort(filtered_input_data, self.max_ncells)
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-
model = pu.load_model(self.model_type, self.num_classes, model_directory)
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layer_to_quant = pu.quant_layers(model) + self.emb_layer
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embs = get_embs(
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model,
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filtered_input_data, cell_state, self.nproc
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)
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downsampled_data = pu.downsample_and_sort(filtered_input_data, self.max_ncells)
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+
model = pu.load_model(self.model_type, self.num_classes, model_directory, mode = "eval")
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layer_to_quant = pu.quant_layers(model) + self.emb_layer
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embs = get_embs(
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model,
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