Geneformer / geneformer

15 contributors

History: 136 commits

ctheodoris

Prepare data cell level pass cell state dict instead of genes (#483)

69e6887 verified 10 days ago

gene_dictionaries_30m
Update geneformer/tokenizer.py (#415) 5 months ago
mtl
Fix how mappings and train and val data are returned (#473) 19 days ago
__init__.py

1.22 kB

precommit formatting 6 months ago
classifier.py

65 kB

Prepare data cell level pass cell state dict instead of genes (#483) 10 days ago
classifier_utils.py

23.5 kB

ensure gene class dict only inverted when using gene classifier 10 days ago
collator_for_classification.py

31.2 kB

Refactor: Convert mask_token_id, pad_token_id, and all_special_ids to properties (#395) 6 months ago
emb_extractor.py

32.3 kB

Update geneformer/emb_extractor.py (#453) 3 months ago
ensembl_mapping_dict_gc95M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
3.96 MB
LFS

Add function for summing of Ensembl IDs (#377) 6 months ago
evaluation_utils.py

9.99 kB

make plot roc compatible with eval-only metrics 14 days ago
gene_median_dictionary_gc95M.pkl
Detected Pickle imports (2)
- "numpy.core.multiarray.scalar",
- "numpy.dtype"
How to fix it?
1.51 MB
LFS

Add function for summing of Ensembl IDs (#377) 6 months ago
gene_name_id_dict_gc95M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
1.66 MB
LFS

Upload gene_name_id_dict_gc95M.pkl (#470) about 1 month ago
in_silico_perturber.py

66.4 kB

Upload in_silico_perturber.py (#432) 2 months ago
in_silico_perturber_stats.py

45.1 kB

update function for N_Detections for mixture_model without anchor_token 4 months ago
mtl_classifier.py

13.7 kB

edit docs formatting 6 months ago
perturber_utils.py

32.4 kB

CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling (#416) 5 months ago
pretrainer.py

29.5 kB

remove unused imports while no longer using distributed sampler 2 months ago
token_dictionary_gc95M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
426 kB
LFS

update with 12L and 20L i4096 gc95M models, multitask and quantiz code 6 months ago
tokenizer.py

29.5 kB

Add checks for custom attributes and n_counts prior to sum ensembl id (#461) 2 months ago

Pickle imports

Detected Pickle imports (2)

Pickle imports

Pickle imports