Commit History
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Adding tags to the model
Verified signatureHi, your HuggingFace page is awesome. Adding both tags will help users to find these models and hopefully we get more models available on Huggingface in the single-cell field. Can (Lead developer of scvi-tools)be2d226
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update transformers version to match pretrainer using accelerate
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update pretrainer to not use distributed sampler (Trainer uses accelerate)
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update function for N_Detections for mixture_model without anchor_token
Christina Theodorisdf297bc
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add check to ensure emb_label is None for getting state embs dict
Christina Theodoris39b4444
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change default emb to cls
Verified signature9ee140a
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include install time in model card
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Update trainer output dir (#427)
Verified signature- Update trainer output dir (414cf94616fe848b0d773ec954db7fd83723e2e2) Co-authored-by: Han Chen <hchen725@users.noreply.huggingface.co>dc23c5f
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Update geneformer/tokenizer.py (#415)
Verified signature- Update geneformer/tokenizer.py (be7ceb5f505d41eb4d0eaf019096b63992f19909) - Update geneformer/tokenizer.py (6cfc5c452a15390d0364b5e8ca16fb4266bbaa58) - Upload ensembl_mapping_dict_gc30M.pkl (4cdb505ba17393dbb90a47b3cbce06dc891d6b0e) - Update geneformer/tokenizer.py (704ef0ded88e4ce7a82c298ff893bba8400f5ed7) - Update geneformer/tokenizer.py (cf2a3b5acc1f8cb6e1ca634c42fad7b8df31e60e) Co-authored-by: Han Chen <hchen725@users.noreply.huggingface.co>63275a8 -
Create multi-task_cell_classification.ipynb (#418)
Verified signature- Create multi-task_cell_classification.ipynb (a2d284f77702bc62fc4c226e2d5cf282ef7fea9f) - replace notebook format (abafc19e2ba4e6c9b9c53faf0268eea387d936a7) - update mtl cell classification notebook format (dc90822f2c1770b370adb49111d5f49d30850ce7) - delete notebook with problematic formatting (ae4e0e0ea1c565821928284a74e0648bff051d33) - Delete prior nb (40624e87b838652e60022e79eadfa72997315446) - Rename mtl example nb (628247599bf5f5aa2de011b9fd982e137059ef52) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>b138ba5
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CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling (#416)
Verified signature- CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling (2d782dddfb391028edb514df03ffcaa4eea61f86) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>b6d28c3
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Add find_packages to automatically include mtl and subpackages in setup.py (#410)
Verified signature- Add find_packages to automatically include mtl and subpackages in setup.py (72823c2a24c15c49f1021b85f6462aca5c405aa0) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>3b78204 -
adding tensorboard to setup.py (#409)
Verified signature- adding tensorboard to setup.py (056061996712aa9a0c4f1ab136b72a696735ccf8) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>94d98d1 -
tensorboard add to reqs (#407)
Verified signature- tensorboard add to reqs (662af56a0682675766496148db3a5f48bf113c3b) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>e8fa43a
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dictionaries from parent dir (#405)
Verified signature- dictionaries form parent dir (713240f3833d3547237ba53fe2c7e09bfc04e5f0) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>85f295e -
remove token dictionary and unpickling from init (#403)
Verified signature- nested import for dictionaries from parent (3b4533faff40ad00e85ec014cae258b31cdd2647) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>7eca269
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move dict loading to function in eval utils
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edit doc formatting
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edit docs formatting
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add mtl_classifier to docs
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add input size tip to instructions
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update tokenizer to defaults for 95M models for special token and input size
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update instructions to include reminder about token dictionary
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pointing dictionaries from the mtl module's init (#397)
Verified signature- pointing dictionaries from the mtl module's init (5539d14469f84e2f0b13a7cb3f6054b2b0cbf1f3) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>7470753 -
Refactored token dictionary loading and encapsulated dictionary (#398)
Verified signature- Refactored token dictionary loading and encapsulated dictionary (fad91b8ccc1ad2931ed53fcb30902a04f6f30f90) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>beb62a4 -
Refactor: Convert mask_token_id, pad_token_id, and all_special_ids to properties (#395)
Verified signature- Refactor: Convert mask_token_id, pad_token_id, and all_special_ids to properties (02febb8c9cc71177ab74ab03ab83e597b7ec1df7) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>2e06f1a
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sync token_dictionary variable name w/ classifier
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update setup with req and manifest with updated filenames
a34fbc2
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fix imports mtl/eval_utils
eab1878
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allow model_type valid options to take params model_type : {"Pretrained", "GeneClassifier", "CellClassifier", "MTLCellClassifier", "MTLCellClassifier-Quantized"} (#390)
Verified signature- allow model_type valid options to take params model_type : {"Pretrained", "GeneClassifier", "CellClassifier", "MTLCellClassifier", "MTLCellClassifier-Quantized"} (f8687d834ba074caf734cf29424902e42a8a8b18) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>47e0ef8 -
peft>=0.11.1 (#387)
Verified signature- peft>=0.11.1 (ddcaee0389760fa3dd12e6003dc1664b59a4eadc) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>4c9dda5 -
"save_model_without_heads" is redundant (#385)
Verified signature- "save_model_without_heads" is redundant (e384cc651481232513ac8ebd1fd2169f184e6a19) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>de10ab0 -
comment out "def save_model_without_heads(original_model_save_directory)"; redundant for ISP/Emb extractor (#382)
Verified signature- comment out "def save_model_without_heads(original_model_save_directory)"; redundant for ISP/Emb extractor (0a4e8a4ba076513934876cf83b1d3e727c26d46e) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>22bf20f -
fixed bug related to dynamic ranges in dictionary with 'min' and 'max' value mismatch in optuna suggest fn (#380)
Verified signature- fixed bug related to dynamic ranges in dictionary with 'min' and 'max' value mismatch in optuna suggest fn (76101b4cbc824eb4b61f8c3985f9652ba413d516) Co-authored-by: Madhavan Venkatesh <madhavanvenkatesh@users.noreply.huggingface.co>fe1640b
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Update README.md
Verified signature11bcee7
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precommit formatting
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update with 12L and 20L i4096 gc95M models, multitask and quantiz code
933ca80
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rename for consistency
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delete old gene name dict
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update to only have gene names as keys in gene_name_id_dict
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Add function for summing of Ensembl IDs (#377)
Verified signature- Add function for summing of Ensembl IDs (fb901a02a4aea5582603c2c3bf21d992b8a4f3b5) - Add init for ensembl mapping dict (43b42906ba1e5b16d2a71deb6881c4779007a24d) - Upload ensembl_mapping_dict_gc95M.pickle (47341ab1ee7a6d195a1a2527af51a0dc3abd0090) - Update geneformer/tokenizer.py (5197a60707457a72cf3c6f663e3eae65fc276831) - Filter gene mapping dict for items that exist in gene_token_dict (1e8d481b099f532afa8b9edf1f544d838edfea2f) - Update geneformer/tokenizer.py (b8b87fd14eec11e8e21105d30098c50496ae2ba5) - Upload ensembl_mapping_dict.pkl (e86dc76200df4aa1b02149d4d64254b92a0816d1) - Update geneformer/__init__.py (ad4b8e0c046cf6f51cb71573b04efa851923e4b6) - Upload 2 files (c9ba1f736b47384d602d714d49c1bdee21ae8bac) - Delete ensembl_mapping_dict.pkl (c5cea51562669bba7b068a12ca13510b865e7aff) - Upload 4 files (05bffd62fd51f24efcbb7d8db5eacabb976d7c95) - Delete geneformer/ensembl_mapping_dict_gc95M.pickle (004f5b40c72722df27d77991b6078510b15a0bd1) - Update .gitattributes (e91adac093c1667d6…1e18102
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save pval
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add typing list import
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move dicts to init
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add random state to umap
eb2a04b
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update get_embs with token_gene_dict arg
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update refs to get_model_emb_dims
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embs_df with all model embeddings (#363)
Verified signature- embs_df with all model embeddings (9026cc190f358b9be7181ddb2d1368904e3393e1) - incorporate prior changes (8e35e450dafc6f1b57fd1f0fb73f99e127c1e088) Co-authored-by: Han Chen <hchen725@users.noreply.huggingface.co>2e64874 -
Add function to get number of model embeddings (#364)
Verified signature- Add function to get number of model embeddings (01313fd5b2416d697ae4d21db9f1ec80c91ab8bc) - extract emb_dims and input_size from config (89fc737b00596ae9b4f226da087e872022bf5a26) Co-authored-by: Han Chen <hchen725@users.noreply.huggingface.co>c90d791
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clone embs_i to resolve memory leak in cls embs
57f02a4