Geneformer / geneformer

15 contributors

History: 122 commits

ctheodoris

update pretrainer to not use distributed sampler (Trainer uses accelerate)

8140c51 verified 27 days ago

gene_dictionaries_30m
Update geneformer/tokenizer.py (#415) 3 months ago
mtl
dictionaries from parent dir (#405) 3 months ago
__init__.py

1.22 kB

precommit formatting 4 months ago
classifier.py

64.7 kB

Update trainer output dir (#427) 2 months ago
classifier_utils.py

23.3 kB

precommit formatting 4 months ago
collator_for_classification.py

31.2 kB

Refactor: Convert mask_token_id, pad_token_id, and all_special_ids to properties (#395) 3 months ago
emb_extractor.py

32 kB

add check to ensure emb_label is None for getting state embs dict about 1 month 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) 4 months ago
evaluation_utils.py

9.76 kB

move dict loading to function in eval utils 3 months 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) 4 months ago
gene_name_id_dict_gc95M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
2.04 MB
LFS

rename for consistency 4 months ago
in_silico_perturber.py

65.5 kB

allow model_type valid options to take params model_type : {"Pretrained", "GeneClassifier", "CellClassifier", "MTLCellClassifier", "MTLCellClassifier-Quantized"} (#390) 3 months ago
in_silico_perturber_stats.py

45.1 kB

update function for N_Detections for mixture_model without anchor_token about 1 month ago
mtl_classifier.py

13.7 kB

edit docs formatting 3 months ago
perturber_utils.py

32.4 kB

CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling (#416) 3 months ago
pretrainer.py

29.6 kB

update pretrainer to not use distributed sampler (Trainer uses accelerate) 27 days 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 4 months ago
tokenizer.py

28 kB

Update geneformer/tokenizer.py (#415) 3 months ago

Pickle imports

Detected Pickle imports (2)

Pickle imports

Pickle imports