ctheodoris/Geneformer

Use dynamic CUDA check instead of hardcoded device in perturber_utils.py (#594)

Update README.md

Update geneformer/mtl/model.py (#585)

update readme citations

Update geneformer/mtl/train.py (#582)

default id_class_dict to None for gene classifiers

track metadata in predictions

add emb extractor option for saving all gene embs

add pickle suffix option to isp stats

Fix TypeError in make_perturbation_batch_special (#567)

add empty tokenized_counts for loom to pass until keep_counts implemented

subsample heatmap with max_ncells_to_plot when max_ncells is None

tokenizer zarr integration (#561)

Update geneformer/perturber_utils.py to be compatible with different versions of the datasets package. (#553)

Update geneformer/evaluation_utils.py to be compatible with different versions of the datasets package. (#552)

add input_identifier to tokenize specific matched files

plot umap for all labels in same view

Update README.md

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

delete first version of dist multitask example

update dist multitask example name

Add example notebook for distributed multi-task cell classification (#543)

specify bitsandbites version

add V2 models

update with V2 models

edit docs to remove backend isp functions

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)