├── .gitignore ├── .idea ├── .gitignore ├── inspectionProfiles │ └── profiles_settings.xml ├── misc.xml ├── modules.xml ├── other.xml ├── scNODE.iml └── vcs.xml ├── LICENSE ├── README.md ├── baseline ├── MIOFlow_model_revised │ ├── LICENSE │ ├── MIOFlow │ │ ├── (REFERENCE)train.py │ │ ├── __init__.py │ │ ├── _modidx.py │ │ ├── _nbdev.py │ │ ├── constants.py │ │ ├── datasets.py │ │ ├── eval.py │ │ ├── exp.py │ │ ├── geo.py │ │ ├── losses.py │ │ ├── models.py │ │ ├── ode.py │ │ ├── plots.py │ │ ├── train.py │ │ └── utils.py │ ├── __init__.py │ ├── nbs │ │ ├── 00_ode.ipynb │ │ ├── 01_losses.ipynb │ │ ├── 02_utils.ipynb │ │ ├── 03_models.ipynb │ │ ├── 04_plots.ipynb │ │ ├── 05_train.ipynb │ │ ├── 06_constants.ipynb │ │ ├── 07_datasets.ipynb │ │ ├── 08_exp.ipynb │ │ ├── 09_geo.ipynb │ │ ├── 10_eval.ipynb │ │ ├── _quarto.yml │ │ ├── index.ipynb │ │ ├── nbdev.yml │ │ ├── sidebar.yml │ │ └── styles.css │ ├── notebooks │ │ ├── 1NN_Metric.ipynb │ │ ├── EB-fig-5-table-1.ipynb │ │ ├── Interpolation_baseline.ipynb │ │ ├── SDE_New.ipynb │ │ ├── SDE_test.ipynb │ │ ├── [TEMP]Clean_Simple_Variables_Dyngen_good.ipynb │ │ ├── [TEMP]Clean_Variables_Dyngen_good.ipynb │ │ ├── [Tutorial] Dyngen.ipynb │ │ ├── [Tutorial] EB-Hold-out.ipynb │ │ ├── [Tutorial] Hold-out.ipynb │ │ ├── [Tutorial] Load Datasets.ipynb │ │ ├── [Tutorial] Petal.ipynb │ │ ├── [Tutorial] Run TrajectoryNet.ipynb │ │ ├── aml_pca.ipynb │ │ └── petal_good.ipynb │ ├── running.py │ └── scripts │ │ ├── __init__.py │ │ └── run.py ├── README.md ├── __init__.py └── prescient_model │ ├── __init__.py │ ├── prescient │ ├── .gitkeep │ ├── LICENSE │ ├── __init__.py │ ├── __main__.py │ ├── commands │ │ ├── __init__.py │ │ ├── perturbation_analysis.py │ │ ├── process_data.py │ │ ├── simulate_trajectories.py │ │ └── train_model.py │ ├── perturb │ │ ├── __init__.py │ │ └── pert.py │ ├── simulate │ │ ├── __init__.py │ │ └── sim.py │ ├── train │ │ ├── __init__.py │ │ ├── model.py │ │ ├── run.py │ │ ├── run_with_timer.py │ │ └── util.py │ └── utils.py │ ├── process_data.py │ └── running.py ├── benchmark ├── 1_SingleCell_scNODE.py ├── 2_SingleCell_PRESCIENT.py ├── 3_SingleCell_MIOFlow.py ├── BenchmarkUtils.py ├── README.md └── __init__.py ├── data ├── DrosophilaData_Processing.R ├── README.md ├── WOTData_Processing_Reduced.py ├── ZebrafishData_Processing.R └── __init__.py ├── downstream_analysis ├── 1_Perturbation_Analysis.py ├── 2_Recover_Trajectory_MIOFlow.py ├── 2_Recover_Trajectory_PRESCIENT.py ├── 2_Recover_Trajectory_scNODE.py ├── Compute_Aux_Data.py ├── README.md └── __init__.py ├── environment.yml ├── installation ├── model ├── README.md ├── __init__.py ├── diff_solver.py ├── dynamic_model.py └── layer.py ├── model_illustration.jpg ├── model_validation ├── README.md ├── __init__.py ├── distribution_shift │ ├── Evaluate_Data_Distribution_Shift.py │ ├── Plot_Res.py │ └── __init__.py ├── extrapolation │ ├── 1_SingleCell_MIOFlow.py │ ├── 1_SingleCell_PRESCIENT.py │ ├── 1_SingleCell_scNODE.py │ ├── __init__.py │ └── utils.py ├── latent_size │ ├── 1_Run_scNODE_LatentSize.py │ └── __init__.py ├── pretraining │ ├── Run_Diff_PreTrain_TP.py │ ├── Run_Diff_PreTrain_TP_FixLatent.py │ ├── __init__.py │ ├── running.py │ └── utils.py └── tune_reg_coeff │ ├── 1_Run_scNODE_Tune_RegCoeff.py │ ├── Compare_Res.py │ ├── __init__.py │ └── running.py ├── optim ├── README.md ├── __init__.py ├── evaluation.py ├── loss_func.py └── running.py ├── paper_figs ├── Fig2_UMAP.py ├── Fig3_Distribution_Shift_Avg.py ├── Fig4_Trajectory_Inference.py ├── Fig5_Perturbation.py ├── SuppFigS4_Extrapolate_Multiple.py ├── SuppFigS5_Model_Latent.py ├── SuppFigS6_Pretraining_Metric.py ├── SuppFigS7_Latent_Adjustment.py └── __init__.py ├── plotting ├── Compare_Parameter_Setting.py ├── Compare_SingleCell_Predictions.py ├── PlottingUtils.py ├── README.md ├── __init__.py └── visualization.py └── res └── README.md /.gitignore: -------------------------------------------------------------------------------- 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