├── .ipynb_checkpoints ├── 1node_train-checkpoint.sh ├── attention-checkpoint.py ├── data_process-checkpoint.py ├── earlystop-checkpoint.py ├── lora-checkpoint.py ├── loss_function-checkpoint.py ├── metrics-checkpoint.py ├── model-checkpoint.py ├── readme-checkpoint.md ├── retention-checkpoint.py ├── scheduler_sc100m-checkpoint.sh ├── train-checkpoint.py ├── utils-checkpoint.py └── worker_sc100m-checkpoint.sh ├── 1node_train.sh ├── LICENSE-cc-by-nc-nd-4.0 ├── __pycache__ ├── attention.cpython-39.pyc ├── config.cpython-39.pyc ├── data_process.cpython-39.pyc ├── lora.cpython-39.pyc ├── loss_function.cpython-39.pyc ├── metrics.cpython-39.pyc ├── model.cpython-39.pyc ├── retention.cpython-39.pyc └── utils.cpython-39.pyc ├── attention.py ├── config.py ├── csv ├── .ipynb_checkpoints │ ├── dump-checkpoint.json │ ├── gene_info-checkpoint.csv │ ├── genemap-checkpoint.csv │ └── updated_hgcn-checkpoint.tsv ├── dump.json ├── expand_gene_info.csv ├── gene_info.csv ├── genemap.csv └── updated_hgcn.tsv ├── data_process.py ├── earlystop.py ├── figures └── model.png ├── get_gene_emb.py ├── lora.py ├── loss_function.py ├── metrics.py ├── model.py ├── readme.md ├── retention.py ├── scheduler_sc100m.sh ├── train.py ├── tutorials ├── BatchIntegration │ ├── BatchIntegration.ipynb │ └── finetune_intergration_model.py ├── BinaryclassGeneFunction.ipynb ├── CellAnnotation │ ├── CellAnnotation_finetune.ipynb │ ├── CellAnnotation_zeroshot.ipynb │ └── annotation_model.py ├── ChemicalPerturbation │ ├── cellot_model │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── transport.cpython-39.pyc │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── cell.cpython-39.pyc │ │ │ │ └── utils.cpython-39.pyc │ │ │ ├── cell.py │ │ │ └── utils.py │ │ ├── losses │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ └── mmd.cpython-39.pyc │ │ │ └── mmd.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── ae.cpython-39.pyc │ │ │ │ ├── cellfm.cpython-39.pyc │ │ │ │ └── cellot.cpython-39.pyc │ │ │ ├── ae.py │ │ │ ├── cellfm.py │ │ │ └── cellot.py │ │ ├── networks │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── icnns.cpython-39.pyc │ │ │ │ ├── retention.cpython-39.pyc │ │ │ │ └── scret.cpython-39.pyc │ │ │ ├── icnns.py │ │ │ ├── retention.py │ │ │ └── scret.py │ │ ├── preprocess.py │ │ ├── train │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── experiment.cpython-39.pyc │ │ │ │ ├── summary.cpython-39.pyc │ │ │ │ └── train.cpython-39.pyc │ │ │ ├── experiment.py │ │ │ ├── summary.py │ │ │ ├── train.py │ │ │ └── utils.py │ │ ├── transport.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── evaluate.cpython-39.pyc │ │ │ ├── helpers.cpython-39.pyc │ │ │ └── loaders.cpython-39.pyc │ │ │ ├── evaluate.py │ │ │ ├── flags.py │ │ │ ├── helpers.py │ │ │ ├── loaders.py │ │ │ └── viz.py │ ├── configs │ │ ├── models │ │ │ ├── cae-4i.yaml │ │ │ ├── cae.yaml │ │ │ ├── cellot.yaml │ │ │ ├── cellot_cellfm.yaml │ │ │ ├── identity.yaml │ │ │ ├── random.yaml │ │ │ ├── scgen-4i.yaml │ │ │ └── scgen.yaml │ │ └── tasks │ │ │ ├── 4i.yaml │ │ │ ├── crossspecies-ood.yaml │ │ │ ├── crossspecies.yaml │ │ │ ├── gbm-ood.yaml │ │ │ ├── gbm.yaml │ │ │ ├── lupuspatients-ood.yaml │ │ │ ├── lupuspatients.yaml │ │ │ ├── sciplex3-ood.yaml │ │ │ ├── sciplex3-top1k.yaml │ │ │ ├── sciplex3.yaml │ │ │ ├── statefate-in_vitro-ood.yaml │ │ │ └── statefate.yaml │ ├── evaluate.py │ ├── finetune_sciplex.py │ ├── readme.md │ ├── requirements.txt │ ├── setup.py │ └── train.py ├── IdentifyingCelltypelncRNAs.ipynb ├── MulticlassGeneFunction.ipynb ├── Perturbation │ ├── GenePerturbation.ipynb │ ├── gears │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── data_utils.cpython-39.pyc │ │ │ ├── gears.cpython-39.pyc │ │ │ ├── inference.cpython-39.pyc │ │ │ ├── model.cpython-39.pyc │ │ │ ├── pertdata.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ ├── data_utils.py │ │ ├── gears.py │ │ ├── genes_with_hi_mean.npy │ │ ├── inference.py │ │ ├── model.py │ │ ├── pertdata.py │ │ ├── utils.py │ │ └── version.py │ └── modules │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── encoders.cpython-310.pyc │ │ ├── encoders.cpython-39.pyc │ │ ├── mae_autobin.cpython-39.pyc │ │ ├── performer_module.cpython-310.pyc │ │ ├── performer_module.cpython-39.pyc │ │ ├── reversible.cpython-39.pyc │ │ └── transformer.cpython-39.pyc │ │ ├── attention.py │ │ ├── encoders.py │ │ ├── mae_autobin.py │ │ ├── performer_module.py │ │ ├── reversible.py │ │ └── transformer.py └── process.ipynb ├── utils.py └── worker_sc100m.sh /.ipynb_checkpoints/1node_train-checkpoint.sh: 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