├── LICENSE ├── README.md ├── analysis ├── kexin │ ├── README.md │ ├── __init__.py │ ├── analysis_on_norman_adamson.ipynb │ ├── analyze_fold_change.ipynb │ ├── construct train coexpresssion.ipynb │ ├── data.py │ ├── data_analysis_more.ipynb │ ├── data_splits.ipynb │ ├── error_analysis.ipynb │ ├── error_analysis_upreg.ipynb │ ├── evaluate_demo.ipynb │ ├── evaluate_saved_model-More_Metrics.ipynb │ ├── evaluate_saved_model.ipynb │ ├── examine_io.ipynb │ ├── gene-level-variation_analysis.ipynb │ ├── get_more_de.ipynb │ ├── get_signature.ipynb │ ├── gnn_generalization_test-new_model.ipynb │ ├── gnn_generalization_test.ipynb │ ├── go_graph-adamson.ipynb │ ├── go_graph-norman.ipynb │ ├── go_graph-norman_adamson.ipynb │ ├── helper.py │ ├── hyperopt_train.py │ ├── inference.py │ ├── make_CPA_data.ipynb │ ├── mlp mixer.ipynb │ ├── model.py │ ├── playground.ipynb │ ├── simulation_single_data_split_on_new_dataset.ipynb │ ├── split pert order.ipynb │ ├── train.ipynb │ ├── train.py │ ├── train_1.ipynb │ ├── train_2.ipynb │ ├── train_3.ipynb │ ├── train_4.ipynb │ ├── train_5.ipynb │ ├── train_large.ipynb │ ├── uncertainty-reg10.ipynb │ ├── uncertainty.ipynb │ ├── understand_split.ipynb │ └── utils.py └── plot_functions.py ├── data └── preprocessing │ ├── Adamson2016.ipynb │ ├── Norman19.ipynb │ └── Replogle_2022_preprocess.ipynb ├── gears ├── __init__.py ├── data_utils.py ├── gears.py ├── inference.py ├── make_GO.py ├── model.py ├── pertdata.py ├── utils.py └── version.py ├── legacy ├── GI_accuracy.py ├── __init__.py ├── data.py ├── evaluate.py ├── flow.py ├── genes_with_hi_mean.npy ├── inference.py ├── learn_weights.py ├── linear_pert_model.py ├── model.py ├── pertnet.py ├── plot_functions.py ├── train.py └── utils.py └── paper ├── CPA_reproduce ├── README.md ├── __init__.py ├── api.py ├── collect_results.py ├── cpa.sh ├── cpa_to_wandb.py ├── data.py ├── helper.py ├── model.py ├── plotting.py └── train.py ├── CellOracle ├── CellOracle.ipynb └── CellOracle_evaluation_wandb.ipynb ├── Ext_Fig_2.ipynb ├── Ext_Fig_3.ipynb ├── Ext_Fig_5.ipynb ├── Ext_Fig_6a.ipynb ├── Ext_Fig_6a_GI_genes_compute.ipynb ├── Ext_Fig_7.ipynb ├── Fig2b-Adamson2016.ipynb ├── Fig2b-Dixit2016.ipynb ├── Fig2b-gearsonly.ipynb ├── Fig2b-gearsonly_Adamson.ipynb ├── Fig2b-gearsonly_Dixit.ipynb ├── Fig2b-replogle-k562.ipynb ├── Fig2b-replogle-rpe1.ipynb ├── Fig2cd.ipynb ├── Fig2f-gearsonly_Norman.ipynb ├── Fig2f.ipynb ├── Fig2f_mean.ipynb ├── Fig2g.ipynb ├── Fig2h.ipynb ├── Fig3c+Ext_Fig_6.ipynb ├── Fig3c.ipynb ├── Fig3d.ipynb ├── Fig4.ipynb ├── Fig4_UMAP_predict.py ├── Fig4_UMAP_train.py ├── Fig5b.ipynb ├── GRN ├── GRN_model.py ├── README.md ├── SCENIC_norman.ipynb ├── graph_filtering.ipynb ├── learn_weights.py └── run_GRN_baseline.py ├── README.md ├── Random_heatmap.ipynb ├── SI_Fig_15.ipynb ├── SI_Fig_17.ipynb ├── SI_Fig_17_Horlbeck_Jurkat.ipynb ├── archive ├── fig2cd.ipynb ├── fig2f.ipynb └── fig2g.ipynb ├── data ├── GI_data.pkl └── TF_names_v_1.01.txt ├── 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