Prepare data cell level pass cell state dict instead of genes (#483)

ensure gene class dict only inverted when using gene classifier

make plot roc compatible with eval-only metrics

Merge remote-tracking branch 'origin/main'

fix gene class dict labeling

Fix how mappings and train and val data are returned (#473)

Upload gene_name_id_dict_gc95M.pkl (#470)

Add checks for custom attributes and n_counts prior to sum ensembl id (#461)

further emphasize different token dictionaries in examples

remove unused imports while no longer using distributed sampler

Raise error for train and validation mismatch (#459)

Upload in_silico_perturber.py (#432)

Update geneformer/emb_extractor.py (#453)

Update geneformer/tokenizer.py (#450)

update isp default mode to cls

Adding tags to the model (#448)

update transformers version to match pretrainer using accelerate

update pretrainer to not use distributed sampler (Trainer uses accelerate)

update function for N_Detections for mixture_model without anchor_token

add check to ensure emb_label is None for getting state embs dict

change default emb to cls

include install time in model card

Update trainer output dir (#427)

Update geneformer/tokenizer.py (#415)

Create multi-task_cell_classification.ipynb (#418)

CUDA kernels incompatible with standard PyTorch device movement with 4bit/8bit, necessitating device-specific handling (#416)

Add find_packages to automatically include mtl and subpackages in setup.py (#410)

adding tensorboard to setup.py (#409)

tensorboard add to reqs (#407)

dictionaries from parent dir (#405)

remove token dictionary and unpickling from init (#403)

move dict loading to function in eval utils

edit doc formatting

edit docs formatting

add mtl_classifier to docs

add input size tip to instructions

update tokenizer to defaults for 95M models for special token and input size

update instructions to include reminder about token dictionary

pointing dictionaries from the mtl module's init (#397)

Refactored token dictionary loading and encapsulated dictionary (#398)

Refactor: Convert mask_token_id, pad_token_id, and all_special_ids to properties (#395)

sync token_dictionary variable name w/ classifier

update setup with req and manifest with updated filenames

fix imports mtl/eval_utils

allow model_type valid options to take params model_type : {"Pretrained", "GeneClassifier", "CellClassifier", "MTLCellClassifier", "MTLCellClassifier-Quantized"} (#390)

peft>=0.11.1 (#387)

"save_model_without_heads" is redundant (#385)

comment out "def save_model_without_heads(original_model_save_directory)"; redundant for ISP/Emb extractor (#382)

fixed bug related to dynamic ranges in dictionary with 'min' and 'max' value mismatch in optuna suggest fn (#380)

Update README.md