ctheodoris/Geneformer · Discussions

#582 opened 7 months ago by

MajorasMeow

Fix TypeError in make_perturbation_batch_special

#567 opened 10 months ago by

so298

Add fix for new datasets version to make_perturbation_batch_special

#562 opened about 1 year ago by

tusharagashe

tokenizer zarr integration

#561 opened about 1 year ago by

jo-mengr

add support for zarr files in tokenizer

#560 opened about 1 year ago by

jo-mengr

pull_geneformer

#557 opened about 1 year ago by

spartanzhao

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

#553 opened about 1 year ago by

IchigoJiken

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

#552 opened about 1 year ago by

IchigoJiken

Add example notebook for distributed multi-task cell classification

#543 opened about 1 year ago by

fix AssertionError: First token is not <cls> token value in extract_and_plot_cell_embeddings.ipynb

2

#541 opened about 1 year ago by

jackkuo

fix TypeError: TrainingArguments.init() got an unexpected keyword argument 'evaluation_strategy'

👍 2

#539 opened about 1 year ago by

jackkuo

add fallback task_type for LoraConfig to support different PEFT versions

#538 opened about 1 year ago by

add fallback task_type for LoraConfig to support different PEFT versions

#537 opened about 1 year ago by

fully qualified imports to resolve name-space conflicts

#532 opened over 1 year ago by

ddp_mtl_nccl_support

#524 opened over 1 year ago by

ddp_mtl_nccl

#523 opened over 1 year ago by

fix quantize logic (and lora adapter weights loading)

4

#522 opened over 1 year ago by

yuz299

fix: pin transformers to v4.49.0 to fix ImportError: cannot import name 'AdamW' from 'transformers'

#516 opened over 1 year ago by

valenzuelaomar

Prepare data cell level pass cell state dict instead of genes

#483 opened over 1 year ago by

Fix how mappings and train and val data are returned

#473 opened over 1 year ago by

Upload gene_name_id_dict_gc95M.pkl

#470 opened over 1 year ago by

Add checks for custom attributes and n_counts prior to sum ensembl id

#461 opened almost 2 years ago by

Raise error for train and validation mismatch

#459 opened almost 2 years ago by

raise error for train and validation mismatch

#458 opened almost 2 years ago by

mvenk

Update geneformer/emb_extractor.py

#453 opened almost 2 years ago by

Update geneformer/tokenizer.py

#450 opened almost 2 years ago by

Adding tags to the model

#448 opened almost 2 years ago by

canergen

Upload in_silico_perturber.py

#432 opened almost 2 years ago by

davidjwen

GenePooler

#429 opened almost 2 years ago by

jamieb-nvs

Update trainer output dir

#427 opened almost 2 years ago by

test pr for notebook rendering

#419 opened almost 2 years ago by

Create multi-task_cell_classification.ipynb

#418 opened almost 2 years ago by

Upload Multi-Task_cell_classification.ipynb

#417 opened almost 2 years ago by

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

#416 opened almost 2 years ago by

Update geneformer/tokenizer.py

#415 opened almost 2 years ago by

Add find_packages to automatically include mtl and subpackages in setup.py

#410 opened about 2 years ago by

adding tensorboard to setup.py

#409 opened about 2 years ago by

tensorboard add to reqs

#407 opened about 2 years ago by

dictionaries from parent dir

#405 opened about 2 years ago by

parent directory for dictionary

#404 opened about 2 years ago by

remove token dictionary and unpickling from init

#403 opened about 2 years ago by

Refactored token dictionary loading and encapsulated dictionary

#398 opened about 2 years ago by

pointing dictionaries from the mtl module's init

#397 opened about 2 years ago by

inheritance issues

#396 opened about 2 years ago by

Refactor: Convert mask_token_id, pad_token_id, and all_special_ids to properties

#395 opened about 2 years ago by

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

#390 opened about 2 years ago by

Add "gc" to pkl file names

#388 opened about 2 years ago by

lhl1bit

peft>=0.11.1

#387 opened about 2 years ago by

add peft==0.11.1 to req

#386 opened about 2 years ago by