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Geneformer

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Geneformer / geneformer

14 contributors

History: 65 commits

ctheodoris's picture

Add option for variable input_size and to add CLS/SEP Tokens (#299)

aa25cd2 verified 8 months 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

29.4 kB

edit docstring codeblock highlighting 10 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

38.7 kB

add load model for train and fix validate anchor gene error 8 months ago
in_silico_perturber_stats.py

43 kB

Handle case of single gene del for isp modeling of gene embs 9 months ago
perturber_utils.py

24.9 kB

add load model for train and fix validate anchor gene error 8 months ago
pretrainer.py

37 kB

fix: incorrect condition control flow (#261) about 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

16.3 kB

Add option for variable input_size and to add CLS/SEP Tokens (#299) 8 months ago