├── .env.example ├── .gitattributes ├── .github ├── PULL_REQUEST_TEMPLATE.md ├── codecov.yml ├── dependabot.yml ├── release-drafter.yml └── workflows │ ├── code-quality-main.yaml │ ├── code-quality-pr.yaml │ ├── release-drafter.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .project-root ├── LICENSE ├── Makefile ├── README.md ├── configs ├── __init__.py ├── callbacks │ ├── default.yaml │ ├── early_stopping.yaml │ ├── model_checkpoint.yaml │ ├── model_summary.yaml │ ├── none.yaml │ └── rich_progress_bar.yaml ├── data │ ├── gears.yaml │ └── perturb.yaml ├── debug │ ├── default.yaml │ ├── fdr.yaml │ ├── limit.yaml │ ├── overfit.yaml │ └── profiler.yaml ├── eval.yaml ├── experiment │ ├── mlp_norman_inference.yaml │ ├── mlp_norman_train.yaml │ ├── mlp_replogle_k562_inference.yaml │ └── mlp_replogle_k562_train.yaml ├── extras │ └── default.yaml ├── hparams_search │ ├── optuna_architecture.yaml │ └── optuna_lr.yaml ├── hydra │ ├── default.yaml │ ├── spectra_data_sweep_1.yaml │ ├── spectra_data_sweep_2.yaml │ └── spectra_data_sweep_3.yaml ├── local │ └── .gitkeep ├── logger │ ├── aim.yaml │ ├── comet.yaml │ ├── csv.yaml │ ├── many_loggers.yaml │ ├── mlflow.yaml │ ├── neptune.yaml │ ├── tensorboard.yaml │ └── wandb.yaml ├── model │ ├── gears.yaml │ ├── mean.yaml │ └── mlp.yaml ├── paths │ └── default.yaml ├── train.yaml └── trainer │ ├── cpu.yaml │ ├── ddp.yaml │ ├── ddp_sim.yaml │ ├── default.yaml │ ├── gpu.yaml │ └── mps.yaml ├── data └── .gitkeep ├── environment.yaml ├── figures └── PertEval-scFM.png ├── logs └── .gitkeep ├── notebooks ├── .gitkeep ├── embedding_generation │ └── gf_generate_embs.ipynb ├── plots │ ├── aggregated_perturbation_results.ipynb │ ├── contextual_alignment.ipynb │ ├── edistance_vs_mse_analysis.ipynb │ ├── expression_analysis_top20_vs_tail_genes.ipynb │ ├── gene_level_deg_boxplot.ipynb │ ├── individual_perturbation_results.ipynb │ ├── supp_plot_experiment2.ipynb │ ├── visualize_sparsity.ipynb │ └── visualize_spectra_norman_1.ipynb └── preprocessing │ ├── diff_exp_refactored.ipynb │ ├── generate_deg_scripts.ipynb │ └── significant_perts_edist.ipynb ├── pyproject.toml ├── requirements.txt ├── scripts └── schedule.sh ├── setup.py ├── src ├── __init__.py ├── data │ ├── __init__.py │ ├── components │ │ ├── __init__.py │ │ └── embeddings.py │ ├── perturb_datamodule.py │ ├── perturb_dataset.py │ └── reproduction │ │ ├── __init__.py │ │ └── gears │ │ ├── __init__.py │ │ └── gears_datamodule.py ├── eval.py ├── models │ ├── __init__.py │ ├── components │ │ ├── __init__.py │ │ ├── losses.py │ │ └── predictors.py │ ├── gears_module.py │ ├── prediction_module.py │ ├── pretrained_ckpts │ │ └── __init__.py │ └── reproduction │ │ ├── __init__.py │ │ ├── gears │ │ ├── __init__.py │ │ └── gears.py │ │ └── gears_spectra │ │ ├── gears_environment.yml │ │ ├── gears_with_spectra_singlegene.py │ │ └── gears_with_spectra_twogene.py ├── train.py └── utils │ ├── __init__.py │ ├── instantiators.py │ ├── logging_utils.py │ ├── pylogger.py │ ├── rich_utils.py │ ├── spectra │ ├── __init__.py │ ├── dataset.py │ ├── get_splits.py │ ├── independent_set_algo.py │ ├── perturb.py │ ├── spectra.py │ └── utils.py │ └── utils.py └── tests ├── __init__.py ├── conftest.py ├── helpers ├── __init__.py ├── package_available.py ├── run_if.py └── run_sh_command.py ├── test_configs.py ├── test_datamodules.py ├── test_eval.py ├── test_sweeps.py └── test_train.py /.env.example: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronwtr/PertEval/HEAD/.env.example -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aaronwtr/PertEval/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: 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