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Geneformer

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Geneformer / geneformer

15 contributors

History: 46 commits

davidjwen's picture

Update geneformer/in_silico_perturber.py

9151b3e over 1 year ago

__init__.py

558 Bytes

Add function to extract and plot cell embeddings over 1 year ago
collator_for_classification.py

29.8 kB

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

17.6 kB

Fixed error with perturbing individual genes and updated ways to specify cell_states_to_model (#146) over 1 year 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

65.6 kB

Update geneformer/in_silico_perturber.py over 1 year ago
in_silico_perturber_stats.py

34.8 kB

Re-update stats to handle case of empty alt_states over 1 year ago
pretrainer.py

37 kB

Update pretrainer for transformers==4.28.0 over 1 year 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

9.32 kB

Add error for no files found and suppress loompy import warning over 1 year ago