13 contributors

History: 116 commits

Christina Theodoris

Handle case of single gene del for isp modeling of gene embs

316d817 8 months ago

docs
add readthedocs link to model card 8 months ago
examples
Add functions for extracting gene embeddings, move state_embs_dict outside isp, fix bugs in isp 10 months ago
fine_tuned_models
Add fine-tuned CellClassifier for cardiomyopathy about 1 year ago
geneformer-12L-30M
Upload 12 layer Geneformer model about 1 year ago
geneformer
Handle case of single gene del for isp modeling of gene embs 8 months ago
.gitattributes

1.3 kB

Adding `safetensors` variant of this model (#209) about 1 year ago
.gitignore

3.08 kB

Add gitignore file over 1 year ago
.pre-commit-config.yaml

737 Bytes

Add pre-commit config 10 months ago
.readthedocs.yaml

396 Bytes

update readthedocs.yaml 8 months ago
MANIFEST.in

127 Bytes

Fixes to stats and adding gene dict attempt number 2 (#13) over 1 year ago
README.md

6.87 kB

add readthedocs link to model card 8 months ago
config.json

565 Bytes

upload Geneformer 6L-30M config over 2 years ago
model.safetensors

41.2 MB
LFS

Adding `safetensors` variant of this model (#209) about 1 year ago
pytorch_model.bin
Detected Pickle imports (4)
- "torch._utils._rebuild_tensor_v2",
- "torch.LongStorage",
- "collections.OrderedDict",
- "torch.FloatStorage"
What is a pickle import?
41.2 MB
LFS

upload Geneformer 6L-30M over 2 years ago
requirements.txt

281 Bytes

update dependencies, reinstate compatibility with python<3.9 with typing for List 8 months ago
setup.py

972 Bytes

update dependencies, reinstate compatibility with python<3.9 with typing for List 8 months ago
training_args.bin
Detected Pickle imports (4)
- "transformers.trainer_utils.IntervalStrategy",
- "transformers.training_args.TrainingArguments",
- "transformers.trainer_utils.SchedulerType",
- "torch.device"
How to fix it?
2.61 kB
LFS

upload training args for Geneformer 6L-30M over 2 years ago

Detected Pickle imports (4)

Detected Pickle imports (4)