├── .gitignore ├── LICENSE ├── README.md ├── alde.yml ├── analysis ├── ParPgb │ ├── figs │ │ ├── recombination.jpg │ │ └── singles_fitness.svg │ ├── initial │ │ ├── ParPgb_minION2.csv │ │ ├── RL-7-49_Integrations.xlsx │ │ ├── RL-7-50+98_56X.xls │ │ ├── RL-7-50+98_57X.xls │ │ ├── RL-7-50+98_59X.xls │ │ ├── RL-7-50+98_60X.xls │ │ ├── RL-7-50+98_89X.xls │ │ ├── RL-7-99_Data_recombination.xls │ │ ├── original_singles │ │ │ ├── RL-7-50_SSM_AllData_56X-60X+89X.xlsx │ │ │ └── RL-7-55_recombination.xls │ │ └── processed_withZS.csv │ ├── round1 │ │ ├── RL-7-65_Elegen1_Integrations.csv │ │ └── RL-7-66_validation.csv │ ├── round2 │ │ ├── RL-7-77_Elegen2_Trip1_Data.xls │ │ ├── RL-7-77_Elegen2_Trip2_Data.xls │ │ └── RL-7-77_Elegen2_Trip3_Data.xls │ └── trajectory_visualization.ipynb ├── ParPgb_fitness_all.csv ├── all_results.csv ├── all_results_baseline.csv ├── final_processing.ipynb ├── tabulate_results.ipynb └── visualization.ipynb ├── data └── ParPgb │ ├── all_combos.csv │ └── fitness_round1_training.csv ├── execute_production.py ├── execute_simulation.py ├── figs └── ALDE_workflow.png ├── generate_domain.py ├── output2variants.ipynb ├── results └── ParPgb_production │ └── round1 │ └── DNN_ENSEMBLE-DO-0-RBF-TS-[30, 1]_1indices.pt └── src ├── acquisition.py ├── encoding_utils.py ├── models.py ├── networks.py ├── objectives.py ├── optimize.py ├── rndseed.txt └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsunn-y/ALDE/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsunn-y/ALDE/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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