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Geneformer

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Geneformer / geneformer

15 contributors

History: 89 commits

ctheodoris's picture

extract emb_dims and input_size from config

89fc737 verified 5 months ago

__init__.py

656 Bytes

fix cell state gene embeddings bug (#345) 6 months ago
classifier.py

60.7 kB

patch datasets save_to_disk 7 months ago
classifier_utils.py

16.7 kB

Update for gene classification (#330) 8 months ago
collator_for_classification.py

29.8 kB

Subclass collator for cell classification over 1 year ago
emb_extractor.py

31.7 kB

clone embs_i to resolve memory leak in cls embs 5 months ago
evaluation_utils.py

9.76 kB

update examples for predict_eval and handle roc for 2 cell classes 9 months ago
gene_median_dictionary.pkl
Detected Pickle imports (2)
- "numpy.dtype",
- "numpy.core.multiarray.scalar"
How to fix it?
941 kB

Add Geneformer tokenizer and updated model card about 2 years ago
gene_name_id_dict.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
1.12 MB
LFS

Upload gene_name_id_dict.pkl (#14) over 1 year ago
in_silico_perturber.py

38.9 kB

fix cell state gene embeddings bug (#345) 6 months ago
in_silico_perturber_stats.py

44.2 kB

update perturber stats to reflect cos sim and emb_extractor to suppress warnings for non-cls 5 months ago
perturber_utils.py

26.9 kB

extract emb_dims and input_size from config 5 months ago
pretrainer.py

37.1 kB

update kwargs for pretrainer 8 months ago
token_dictionary.pkl
Detected Pickle imports (2)
- "numpy.dtype",
- "numpy.core.multiarray.scalar"
How to fix it?
788 kB

Update token_dictionary.pkl over 1 year ago
tokenizer.py

16.5 kB

update tokenizer to include eos token 6 months ago