├── .github └── workflows │ └── code-quality.yaml ├── .gitignore ├── LICENSE.txt ├── README.md ├── notebooks ├── demos │ ├── data_splitter_demo.ipynb │ ├── evaluator_demo.ipynb │ └── generate_prediction_dataframe.ipynb └── neurips2025 │ ├── build_data_scaling_splits.ipynb │ ├── build_imbalance_splits.ipynb │ ├── build_jiang24_frangieh21_splits.ipynb │ ├── compile_results.ipynb │ ├── cpa_verification │ ├── cpa_theis_fork_hparams.yaml │ ├── cpa_verification_norman19.ipynb │ ├── cpa_verification_sciplex3.ipynb │ ├── curate_cpa_norman19.ipynb │ └── train_public_cpa_norman19.ipynb │ ├── data_curation │ ├── curate_Frangieh21.ipynb │ ├── curate_Jiang24_step1.R │ ├── curate_Jiang24_step2.ipynb │ ├── curate_McFalineFigueroa23_step1.R │ ├── curate_McFalineFigueroa23_step2.ipynb │ ├── curate_Norman19.ipynb │ ├── curate_Norman19_cpa_version.ipynb │ ├── curate_Srivatsan20.ipynb │ ├── curate_op3.ipynb │ └── readme.txt │ ├── gears │ ├── final_evaluation.ipynb │ ├── gears_helpers.py │ └── preprocess_norman19_gears.ipynb │ ├── generate_croissant_files.ipynb │ └── generate_scgpt_embeddings.ipynb ├── pyproject.toml ├── setup.py └── src └── perturbench ├── analysis ├── __init__.py ├── benchmarks │ ├── __init__.py │ ├── _rank_genes_helpers.py │ ├── aggregation.py │ ├── differential_expression.py │ ├── evaluation.py │ ├── evaluator.py │ └── metrics.py ├── embed_cells.py ├── plotting.py ├── preprocess.py └── utils.py ├── configs ├── __init__.py ├── callbacks │ ├── default.yaml │ ├── early_stopping.yaml │ ├── lr_monitor.yaml │ ├── model_checkpoint.yaml │ ├── model_summary.yaml │ ├── none.yaml │ └── rich_progress_bar.yaml ├── data │ ├── devel.yaml │ ├── evaluation │ │ ├── avg_metrics.yaml │ │ ├── avg_metrics_final_test.yaml │ │ ├── default.yaml │ │ └── final_test.yaml │ ├── frangieh21.yaml │ ├── jiang24.yaml │ ├── mcfaline23.yaml │ ├── norman19.yaml │ ├── norman19_cpa.yaml │ ├── op3.yaml │ ├── op3_no_controls.yaml │ ├── sciplex3.yaml │ ├── splitter │ │ ├── cell_type_transfer_task.yaml │ │ ├── cell_type_treatment_transfer_task.yaml │ │ ├── combination_prediction_task.yaml │ │ ├── mcfaline23_split.yaml │ │ └── saved_split.yaml │ └── transform │ │ └── linear_model_pipeline.yaml ├── experiment │ └── neurips2025 │ │ ├── cpa_norman19_verification.yaml │ │ ├── cpa_sciplex3_verification.yaml │ │ ├── frangieh21 │ │ ├── biolord_best_params_frangieh21.yaml │ │ ├── cpa_best_params_frangieh21.yaml │ │ ├── cpa_no_adv_best_params_frangieh21.yaml │ │ ├── cpa_scgpt_best_params_frangieh21.yaml │ │ ├── decoder_best_params_frangieh21.yaml │ │ ├── decoder_cov_best_params_frangieh21.yaml │ │ ├── latent_best_params_frangieh21.yaml │ │ ├── latent_scgpt_best_params_frangieh21.yaml │ │ ├── linear_best_params_frangieh21.yaml │ │ ├── sams_best_params_frangieh21.yaml │ │ └── sams_modified_best_params_frangieh21.yaml │ │ ├── jiang24 │ │ ├── cpa_best_params_jiang24.yaml │ │ ├── cpa_no_adv_best_params_jiang24.yaml │ │ ├── decoder_best_params_jiang24.yaml │ │ ├── latent_best_params_jiang24.yaml │ │ ├── linear_best_params_jiang24.yaml │ │ ├── sams_best_params_jiang24.yaml │ │ └── sams_modified_best_params_jiang24.yaml │ │ ├── mcfaline23 │ │ ├── cpa_best_params_mcfaline23_full.yaml │ │ ├── cpa_best_params_mcfaline23_medium.yaml │ │ ├── cpa_best_params_mcfaline23_small.yaml │ │ ├── cpa_no_adv_best_params_mcfaline23_full.yaml │ │ ├── cpa_no_adv_best_params_mcfaline23_medium.yaml │ │ ├── cpa_no_adv_best_params_mcfaline23_small.yaml │ │ ├── decoder_only_best_params_mcfaline23_full.yaml │ │ ├── decoder_only_best_params_mcfaline23_medium.yaml │ │ ├── decoder_only_best_params_mcfaline23_small.yaml │ │ ├── latent_additive_best_params_mcfaline23_full.yaml │ │ ├── latent_additive_best_params_mcfaline23_medium.yaml │ │ ├── latent_additive_best_params_mcfaline23_small.yaml │ │ ├── linear_additive_best_params_mcfaline23_full.yaml │ │ ├── linear_additive_best_params_mcfaline23_medium.yaml │ │ ├── linear_additive_best_params_mcfaline23_small.yaml │ │ ├── sams_best_params_mcfaline23_full.yaml │ │ ├── sams_best_params_mcfaline23_medium.yaml │ │ ├── sams_best_params_mcfaline23_small.yaml │ │ ├── sams_modified_best_params_mcfaline23_full.yaml │ │ ├── sams_modified_best_params_mcfaline23_medium.yaml │ │ └── sams_modified_best_params_mcfaline23_small.yaml │ │ ├── norman19 │ │ ├── biolord_best_params_norman19.yaml │ │ ├── cpa_best_params_norman19.yaml │ │ ├── cpa_no_adv_best_params_norman19.yaml │ │ ├── cpa_scgpt_best_params_norman19.yaml │ │ ├── decoder_best_params_norman19.yaml │ │ ├── latent_best_params_norman19.yaml │ │ ├── latent_scgpt_best_params_norman19.yaml │ │ ├── linear_best_params_norman19.yaml │ │ ├── sams_best_params_norman19.yaml │ │ └── sams_modified_best_params_norman19.yaml │ │ ├── op3 │ │ ├── cpa_best_params_sciplex3.yaml │ │ ├── cpa_no_adv_best_params_sciplex3.yaml │ │ ├── decoder_best_params_sciplex3.yaml │ │ ├── latent_best_params_sciplex3.yaml │ │ ├── linear_best_params_sciplex3.yaml │ │ ├── sams_best_params_sciplex3.yaml │ │ └── sams_modified_best_params_sciplex3.yaml │ │ └── sciplex3 │ │ ├── biolord_best_params_sciplex3.yaml │ │ ├── cpa_best_params_sciplex3.yaml │ │ ├── cpa_no_adv_best_params_sciplex3.yaml │ │ ├── cpa_scgpt_best_params_sciplex3.yaml │ │ ├── decoder_best_params_sciplex3.yaml │ │ ├── decoder_cov_best_params_sciplex3.yaml │ │ ├── latent_best_params_sciplex3.yaml │ │ ├── latent_scgpt_best_params_sciplex3.yaml │ │ ├── linear_best_params_sciplex3.yaml │ │ ├── sams_best_params_sciplex3.yaml │ │ └── sams_modified_best_params_sciplex3.yaml ├── hpo │ ├── biolord_hpo.yaml │ ├── cpa_hpo.yaml │ ├── decoder_only_hpo.yaml │ ├── latent_additive_hpo.yaml │ ├── linear_additive_hpo.yaml │ ├── local.yaml │ └── sams_vae_hpo.yaml ├── hydra │ └── default.yaml ├── logger │ ├── csv.yaml │ ├── default.yaml │ └── tensorboard.yaml ├── model │ ├── biolord.yaml │ ├── cpa.yaml │ ├── decoder_only.yaml │ ├── latent_additive.yaml │ ├── linear_additive.yaml │ └── sams_vae.yaml ├── paths │ └── default.yaml ├── predict.yaml ├── train.yaml └── trainer │ ├── cpu.yaml │ ├── default.yaml │ └── gpu.yaml ├── data ├── __init__.py ├── accessors │ ├── base.py │ ├── download_all_datasets.py │ ├── frangieh21.py │ ├── jiang24.py │ ├── mcfaline23.py │ ├── norman19.py │ ├── op3.py │ └── srivatsan20.py ├── collate.py ├── datasets │ ├── __init__.py │ ├── population.py │ └── singlecell.py ├── datasplitter.py ├── modules.py ├── resources │ ├── __init__.py │ └── devel.h5ad ├── transforms │ ├── __init__.py │ ├── base.py │ ├── encoders.py │ ├── ops.py │ └── pipelines.py ├── types.py └── utils.py └── modelcore ├── __init__.py ├── models ├── __init__.py ├── average.py ├── base.py ├── biolord.py ├── cpa.py ├── decoder_only.py ├── embeddings.py ├── latent_additive.py ├── linear_additive.py └── sams_vae.py ├── nn ├── __init__.py ├── decoders.py ├── mlp.py ├── utils.py └── vae.py ├── predict.py ├── train.py └── utils.py /.github/workflows/code-quality.yaml: 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