├── LICENSE ├── README.md ├── geneformer_peft ├── Pretrain_ckpts │ └── README.md ├── README.md ├── chage.py ├── convert.py ├── geneformer │ ├── __init__.py │ ├── collator_for_classification.py │ ├── emb_extractor.py │ ├── emb_extractor_h5ad.py │ ├── gene_median_dictionary.pkl │ ├── in_silico_perturbation.py │ ├── in_silico_perturber.py │ ├── in_silico_perturber_stats.py │ ├── pretrainer.py │ ├── token_dictionary.pkl │ ├── tokenizer.py │ ├── tokenizer_new.py │ └── tokenizer_new_top2000.py ├── transformerslocal │ └── transformerslocal.zip └── utils │ ├── convert_gene_symbol.py │ └── read_pkl.py ├── img └── overview.jpg ├── pipeline_scBERT ├── Benckmark_utils.py ├── Mapping_scBERT.py ├── README.md ├── performer_pytorch │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── performer_pytorch_prompt.cpython-38.pyc │ │ └── reversible.cpython-38.pyc │ ├── performer_pytorch_finetune.py │ ├── performer_pytorch_prompt.py │ └── reversible.py └── utils.py ├── reproduction └── README.md ├── requirements.yaml ├── scfoundation ├── annotation │ ├── OS_scRNA_gene_index.19264.tsv │ ├── README.md │ ├── load.py │ ├── models │ │ └── download.txt │ └── pretrainmodels │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── activation_for_LoRA.cpython-310.pyc │ │ ├── functional_local.cpython-310.pyc │ │ ├── mae_autobin.cpython-310.pyc │ │ ├── performer.cpython-310.pyc │ │ ├── reversible.cpython-310.pyc │ │ ├── select_model.cpython-310.pyc │ │ ├── transformer.cpython-310.pyc │ │ └── transformer_layer.cpython-310.pyc │ │ ├── activation_for_LoRA.py │ │ ├── functional_local.py │ │ ├── mae_autobin.py │ │ ├── performer.py │ │ ├── pytorchTransformer.py │ │ ├── reversible.py │ │ ├── select_model.py │ │ ├── transformer.py │ │ └── transformer_layer.py └── perturbation │ ├── gears │ ├── __init__.py │ ├── data_utils.py │ ├── gears.py │ ├── genes_with_hi_mean.npy │ ├── inference.py │ ├── model.py │ ├── pertdata.py │ ├── utils.py │ └── version.py │ └── modules │ ├── __init__.py │ ├── activation_for_LoRA.py │ ├── attention.py │ ├── encoders.py │ ├── functional_local.py │ ├── mae_autobin.py │ ├── performer_module.py │ ├── reversible.py │ ├── transformer.py │ └── transformer_layer.py ├── scgpt ├── __init__.py ├── data_collator.py ├── data_sampler.py ├── loss.py ├── model │ ├── MultiheadAttentionLoRA.py │ ├── __init__.py │ ├── dsbn.py │ ├── generation_model.py │ ├── grad_reverse.py │ ├── model.py │ └── multiomic_model.py ├── preprocess.py ├── tasks │ ├── __init__.py │ ├── cell_emb.py │ └── grn.py ├── tokenizer │ ├── __init__.py │ ├── default_census_vocab.json │ ├── default_gene_vocab.json │ └── gene_tokenizer.py ├── trainer.py └── utils │ ├── __init__.py │ └── util.py └── tutorial_peft ├── Tutorial_BatchCorrection.ipynb ├── Tutorial_CellPopulationDiscovery.ipynb ├── Tutorial_CrossSpecies.ipynb ├── Tutorial_HomologeneMapping.ipynb ├── Tutorial_Identification.ipynb ├── Tutorial_MarkerGeneDetection.ipynb ├── Tutorial_Perturbation.ipynb ├── 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