Geneformer / geneformer

11.2 MB

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20 contributors

History: 116 commits

madhavanvenkatesh

CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling

2d782dd verified over 1 year ago

gene_dictionaries_30m
update with 12L and 20L i4096 gc95M models, multitask and quantiz code over 1 year ago
mtl
dictionaries from parent dir (#405) over 1 year ago
__init__.py

1.22 kB
precommit formatting over 1 year ago
classifier.py

64.7 kB
sync token_dictionary variable name w/ classifier over 1 year ago
classifier_utils.py

23.3 kB
precommit formatting over 1 year ago
collator_for_classification.py

31.2 kB
Refactor: Convert mask_token_id, pad_token_id, and all_special_ids to properties (#395) over 1 year ago
emb_extractor.py

31.8 kB
precommit formatting over 1 year ago
ensembl_mapping_dict_gc95M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
3.96 MB
xet

Add function for summing of Ensembl IDs (#377) over 1 year ago
evaluation_utils.py

9.76 kB
move dict loading to function in eval utils over 1 year ago
gene_median_dictionary_gc95M.pkl
Detected Pickle imports (2)
- "numpy.dtype",
- "numpy.core.multiarray.scalar"
How to fix it?
1.51 MB
xet

Add function for summing of Ensembl IDs (#377) over 1 year ago
gene_name_id_dict_gc95M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
2.04 MB
xet

rename for consistency over 1 year 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) over 1 year ago
in_silico_perturber_stats.py

44.9 kB
precommit formatting over 1 year ago
mtl_classifier.py

13.7 kB
edit docs formatting over 1 year ago
perturber_utils.py

32.4 kB
CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling over 1 year ago
pretrainer.py

36.6 kB
update with 12L and 20L i4096 gc95M models, multitask and quantiz code over 1 year ago
token_dictionary_gc95M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
426 kB
xet

update with 12L and 20L i4096 gc95M models, multitask and quantiz code over 1 year ago
tokenizer.py

27.4 kB
edit docs formatting over 1 year ago

Pickle imports

Detected Pickle imports (2)

Pickle imports

Pickle imports