├── .github ├── CODEOWNERS └── workflows │ └── release.yml ├── .gitignore ├── .gitmodules ├── .python-version ├── LICENSE ├── MODEL_ACCEPTABLE_USE_POLICY.md ├── MODEL_LICENSE.md ├── README.md ├── assets └── generalization_task.png ├── examples ├── fewshot.toml ├── mixed.toml ├── random.h5ad └── zeroshot.toml ├── pyproject.toml ├── ruff.toml ├── scripts └── state_embed_anndata.py ├── singularity.def ├── src └── state │ ├── __init__.py │ ├── __main__.py │ ├── _cli │ ├── __init__.py │ ├── _emb │ │ ├── __init__.py │ │ ├── _eval.py │ │ ├── _fit.py │ │ ├── _preprocess.py │ │ ├── _query.py │ │ └── _transform.py │ └── _tx │ │ ├── __init__.py │ │ ├── _infer.py │ │ ├── _predict.py │ │ ├── _preprocess_infer.py │ │ ├── _preprocess_train.py │ │ └── _train.py │ ├── configs │ ├── __init__.py │ ├── config.yaml │ ├── data │ │ ├── default.yaml │ │ └── perturbation.yaml │ ├── model │ │ ├── celltypemean.yaml │ │ ├── context_mean.yaml │ │ ├── cpa.yaml │ │ ├── decoder_only.yaml │ │ ├── embedsum.yaml │ │ ├── globalsimplesum.yaml │ │ ├── old_neuralot.yaml │ │ ├── pertsets.yaml │ │ ├── perturb_mean.yaml │ │ ├── scgpt-chemical.yaml │ │ ├── scgpt-genetic.yaml │ │ ├── scvi.yaml │ │ ├── state.yaml │ │ ├── state_lg.yaml │ │ ├── state_sm.yaml │ │ ├── tahoe_best.yaml │ │ ├── tahoe_llama_212693232.yaml │ │ └── tahoe_llama_62089464.yaml │ ├── state-defaults.yaml │ ├── training │ │ ├── cpa.yaml │ │ ├── default.yaml │ │ ├── scgpt.yaml │ │ └── scvi.yaml │ └── wandb │ │ └── default.yaml │ ├── emb │ ├── __init__.py │ ├── data │ │ ├── __init__.py │ │ └── loader.py │ ├── eval │ │ ├── __init__.py │ │ └── emb.py │ ├── finetune_decoder.py │ ├── inference.py │ ├── nn │ │ ├── __init__.py │ │ ├── eval_utils.py │ │ ├── flash_transformer.py │ │ ├── loss.py │ │ └── model.py │ ├── tools │ │ ├── __init__.py │ │ └── slurm.py │ ├── train │ │ ├── __init__.py │ │ ├── __main__.py │ │ ├── callbacks.py │ │ └── trainer.py │ ├── utils.py │ └── vectordb.py │ ├── py.typed │ └── tx │ ├── __init__.py │ ├── callbacks │ ├── __init__.py │ ├── batch_speed_monitor.py │ ├── cumulative_flops.py │ └── model_flops_utilization.py │ ├── data │ └── dataset │ │ ├── __init__.py │ │ └── scgpt_perturbation_dataset.py │ ├── models │ ├── __init__.py │ ├── base.py │ ├── context_mean.py │ ├── cpa │ │ ├── __init__.py │ │ ├── _base_modules.py │ │ ├── _callbacks.py │ │ ├── _dists.py │ │ ├── _model.py │ │ ├── _module.py │ │ └── _task.py │ ├── decoder_only.py │ ├── decoders.py │ ├── decoders_nb.py │ ├── embed_sum.py │ ├── old_neural_ot.py │ ├── perturb_mean.py │ ├── pseudobulk.py │ ├── scgpt │ │ ├── __init__.py │ │ ├── dsbn.py │ │ ├── gene_tokenizer.py │ │ ├── generation_model.py │ │ ├── grad_reverse.py │ │ ├── lightning_model.py │ │ ├── loss.py │ │ ├── model.py │ │ └── utils.py │ ├── scvi │ │ ├── __init__.py │ │ ├── _base_modules.py │ │ ├── _callbacks.py │ │ ├── _dists.py │ │ ├── _model.py │ │ ├── _module.py │ │ └── _task.py │ ├── state_transition.py │ └── utils.py │ └── utils │ ├── __init__.py │ └── singleton.py └── tests ├── 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