Commit History
Update geneformer/tokenizer.py (#450)
664f71e
verified
update isp default mode to cls
0c99403
verified
ctheodoris
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Adding tags to the model (#448)
3a68669
verified
update transformers version to match pretrainer using accelerate
3d62bb9
verified
ctheodoris
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update pretrainer to not use distributed sampler (Trainer uses accelerate)
8140c51
verified
ctheodoris
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update function for N_Detections for mixture_model without anchor_token
df297bc
Christina Theodoris
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add check to ensure emb_label is None for getting state embs dict
39b4444
Christina Theodoris
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change default emb to cls
9ee140a
verified
ctheodoris
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include install time in model card
21d36cd
verified
ctheodoris
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Update trainer output dir (#427)
dc23c5f
verified
Update geneformer/tokenizer.py (#415)
63275a8
verified
Create multi-task_cell_classification.ipynb (#418)
b138ba5
verified
CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling (#416)
b6d28c3
verified
Add find_packages to automatically include mtl and subpackages in setup.py (#410)
3b78204
verified
adding tensorboard to setup.py (#409)
94d98d1
verified
tensorboard add to reqs (#407)
e8fa43a
verified
dictionaries from parent dir (#405)
85f295e
verified
remove token dictionary and unpickling from init (#403)
7eca269
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move dict loading to function in eval utils
57bc17e
ctheodoris
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edit doc formatting
fce3f6e
ctheodoris
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edit docs formatting
ef094b2
ctheodoris
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add mtl_classifier to docs
bedb3b7
ctheodoris
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add input size tip to instructions
2732369
verified
ctheodoris
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update tokenizer to defaults for 95M models for special token and input size
da8cf3d
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ctheodoris
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update instructions to include reminder about token dictionary
cb1b0d5
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ctheodoris
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pointing dictionaries from the mtl module's init (#397)
7470753
verified
Refactored token dictionary loading and encapsulated dictionary (#398)
beb62a4
verified
Refactor: Convert mask_token_id, pad_token_id, and all_special_ids to properties (#395)
2e06f1a
verified
sync token_dictionary variable name w/ classifier
a021deb
verified
ctheodoris
commited on
update setup with req and manifest with updated filenames
a34fbc2
ctheodoris
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fix imports mtl/eval_utils
eab1878
ctheodoris
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allow model_type valid options to take params model_type : {"Pretrained", "GeneClassifier", "CellClassifier", "MTLCellClassifier", "MTLCellClassifier-Quantized"} (#390)
47e0ef8
verified
peft>=0.11.1 (#387)
4c9dda5
verified
"save_model_without_heads" is redundant (#385)
de10ab0
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comment out "def save_model_without_heads(original_model_save_directory)"; redundant for ISP/Emb extractor (#382)
22bf20f
verified
fixed bug related to dynamic ranges in dictionary with 'min' and 'max' value mismatch in optuna suggest fn (#380)
fe1640b
verified
Update README.md
11bcee7
verified
ctheodoris
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precommit formatting
f07bfd7
ctheodoris
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update with 12L and 20L i4096 gc95M models, multitask and quantiz code
933ca80
ctheodoris
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rename for consistency
ec19834
verified
ctheodoris
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delete old gene name dict
817eca2
verified
ctheodoris
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update to only have gene names as keys in gene_name_id_dict
e61485e
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ctheodoris
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Add function for summing of Ensembl IDs (#377)
1e18102
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save pval
b07f4b1
ctheodoris
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add typing list import
42053dc
ctheodoris
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move dicts to init
ea428cb
ctheodoris
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add random state to umap
eb2a04b
ctheodoris
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update get_embs with token_gene_dict arg
ace12e9
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ctheodoris
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update refs to get_model_emb_dims
3fe35ba
verified
ctheodoris
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