14 contributors

History: 108 commits

Christina Theodoris

add readthedocs yaml and req

142fe6f 10 months ago

docs
add readthedocs yaml and req 10 months ago
examples
Add functions for extracting gene embeddings, move state_embs_dict outside isp, fix bugs in isp 12 months ago
fine_tuned_models
Add fine-tuned CellClassifier for cardiomyopathy over 1 year ago
geneformer-12L-30M
Upload 12 layer Geneformer model over 1 year ago
geneformer
add sphinx docs 10 months ago
.gitattributes

1.3 kB

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

3.08 kB

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

737 Bytes

Add pre-commit config 12 months ago
.readthedocs.yaml

397 Bytes

add readthedocs yaml and req 10 months ago
MANIFEST.in

127 Bytes

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

6.78 kB

add sphinx docs 10 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) over 1 year ago
pytorch_model.bin
Detected Pickle imports (4)
- "torch._utils._rebuild_tensor_v2",
- "torch.FloatStorage",
- "torch.LongStorage",
- "collections.OrderedDict"
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 10 months ago
setup.py

972 Bytes

update dependencies, reinstate compatibility with python<3.9 with typing for List 10 months ago
training_args.bin
Detected Pickle imports (4)
- "transformers.trainer_utils.IntervalStrategy",
- "transformers.trainer_utils.SchedulerType",
- "transformers.training_args.TrainingArguments",
- "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)