plot umap for all labels in same view

silence tensor copy warning

clone rather than wrap tensors

update collator with dummy save fn for transformers compatibility

fix to properly move model after checking device

move model to device after checking

update V1 token dict usage to self attr

move V1 autoformatting to after validate_options

add option for relabeling data from prior label class dict, update dict paths in manifest

add V2 models

update with V2 models

fix TypeError: TrainingArguments.__init__() got an unexpected keyword argument 'evaluation_strategy' (#539)

add fallback task_type for LoraConfig to support different PEFT versions (#538)

update eval_strategy for new transformers version

move import wandb to conditional

fully qualified imports to resolve name-space conflicts (#532)

ddp_mtl_nccl_support (#524)

edit imports in perturber_utils

fix exact_mean subselection to be for index rather than col name

fix exact_mean and exact_median to subselect dataframe emb cols, not cell rows

add quantization for pretrained model

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)

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

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

Update trainer output dir (#427)

Update geneformer/tokenizer.py (#415)

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

dictionaries from parent dir (#405)

remove token dictionary and unpickling from init (#403)

move dict loading to function in eval utils

edit docs formatting

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

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)