├── Data ├── cell_density_profiles.npy ├── fisher_KPP_data.npy └── porous_fisher_KPP_data.npy ├── Figures ├── discrepancy_model_Dmlp_Gmlp_IC1e1_rerun_best_eval.pdf ├── discrepancy_model_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval.pdf ├── discrepancy_parameters_Dmlp_Gmlp_IC1e1_rerun_best_eval.pdf ├── discrepancy_parameters_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval.pdf ├── mechanistic_DPFKPP_IC1e1_rerun_best_eval.pdf ├── mechanistic_FKPP_IC1e1_rerun_best_eval.pdf ├── mechanistic_PFKPP_IC1e1_rerun_best_eval.pdf ├── model_Dmlp_Gmlp_IC1e1_rerun_best_eval.pdf ├── model_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval.pdf ├── parameters_RDBINN_and_DRDBINN_IC1e1_rerun_best_eval.pdf ├── parameters_delay-reaction-diffusion-binn_IC1e1_rerun_best_eval.pdf ├── residuals.pdf ├── residuals_Dmlp_Gmlp_IC1e1_rerun_best_eval.pdf ├── residuals_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval.pdf ├── schematic.png ├── scratch_assay_experiment.pdf ├── simulated_model_fits.pdf └── simulated_parameter_fits.pdf ├── Modules ├── Activations │ └── SoftplusReLU.py ├── Loaders │ └── DataFormatter.py ├── Models │ ├── BuildBINNs.py │ └── BuildMLP.py └── Utils │ ├── GetLowestGPU.py │ ├── Gradient.py │ ├── Imports.py │ ├── ModelWrapper.py │ ├── PDESolver.py │ └── TimeRemaining.py ├── Notebooks ├── BINNsEvaluation.ipynb ├── BINNsTraining.ipynb ├── MechanisticModeling.ipynb └── SimulationCaseStudy.ipynb ├── README.md └── Weights ├── cell_density_profiles_10000_Dmlp_Gmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_10000_Dmlp_Gmlp_noconstraints_best_val_model ├── cell_density_profiles_10000_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_10000_TmlpDmlp_TmlpGmlp_noconstraints_best_val_model ├── cell_density_profiles_10000_gamma_0p0_best_val_model ├── cell_density_profiles_10000_gamma_0p2_best_val_model ├── cell_density_profiles_10000_gamma_0p4_best_val_model ├── cell_density_profiles_10000_gamma_0p6_best_val_model ├── cell_density_profiles_12000_Dmlp_Gmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_12000_Dmlp_Gmlp_noconstraints_best_val_model ├── cell_density_profiles_12000_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_12000_TmlpDmlp_TmlpGmlp_noconstraints_best_val_model ├── cell_density_profiles_12000_gamma_0p0_best_val_model ├── cell_density_profiles_12000_gamma_0p2_best_val_model ├── cell_density_profiles_12000_gamma_0p4_best_val_model ├── cell_density_profiles_12000_gamma_0p6_best_val_model ├── cell_density_profiles_14000_Dmlp_Gmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_14000_Dmlp_Gmlp_noconstraints_best_val_model ├── cell_density_profiles_14000_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_14000_TmlpDmlp_TmlpGmlp_noconstraints_best_val_model ├── cell_density_profiles_14000_gamma_0p0_best_val_model ├── cell_density_profiles_14000_gamma_0p2_best_val_model ├── cell_density_profiles_14000_gamma_0p4_best_val_model ├── cell_density_profiles_14000_gamma_0p6_best_val_model ├── cell_density_profiles_16000_Dmlp_Gmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_16000_Dmlp_Gmlp_noconstraints_best_val_model ├── cell_density_profiles_16000_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_16000_TmlpDmlp_TmlpGmlp_noconstraints_best_val_model ├── cell_density_profiles_16000_gamma_0p0_best_val_model ├── cell_density_profiles_16000_gamma_0p2_best_val_model ├── cell_density_profiles_16000_gamma_0p4_best_val_model ├── cell_density_profiles_16000_gamma_0p6_best_val_model ├── cell_density_profiles_18000_Dmlp_Gmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_18000_Dmlp_Gmlp_noconstraints_best_val_model ├── cell_density_profiles_18000_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_18000_TmlpDmlp_TmlpGmlp_noconstraints_best_val_model ├── cell_density_profiles_18000_gamma_0p0_best_val_model ├── cell_density_profiles_18000_gamma_0p2_best_val_model ├── cell_density_profiles_18000_gamma_0p4_best_val_model ├── cell_density_profiles_18000_gamma_0p6_best_val_model ├── cell_density_profiles_20000_Dmlp_Gmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_20000_Dmlp_Gmlp_noconstraints_best_val_model ├── cell_density_profiles_20000_TmlpDmlp_TmlpGmlp_IC1e1_rerun_best_eval_model ├── cell_density_profiles_20000_TmlpDmlp_TmlpGmlp_noconstraints_best_val_model ├── cell_density_profiles_20000_gamma_0p0_best_val_model ├── cell_density_profiles_20000_gamma_0p2_best_val_model ├── cell_density_profiles_20000_gamma_0p4_best_val_model ├── cell_density_profiles_20000_gamma_0p6_best_val_model ├── fisher_KPP_data_simulated_Dmlp_Gmlp_IC1e1_best_eval_model ├── mechanistic_model_parameters.npy └── porous_fisher_KPP_data_simulated_Dmlp_Gmlp_IC1e1_best_eval_model /Data/cell_density_profiles.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jlager/BINNs/HEAD/Data/cell_density_profiles.npy 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