├── .gitignore ├── __init__.py ├── compute_run_overlap.py ├── constants.py ├── control_run_expt_gen.py ├── data ├── L1I-L2I SMU +NH4 aero 2.csv ├── L1I-L2I SMU +NH4 aero.csv ├── L1I-L2I growth data.csv ├── L1IO-L2IO-L3O All Rands SMU UA159 Processed-Aerobic.csv ├── L1L2IO-Rand-Tempest-SMU │ ├── L1IO-L2IO-L3O-All Rands SMU UA159 Processed-aerobic.csv │ ├── L1IO-L2IO-L3O-All Rands SMU UA159 Processed-anaerobic.csv │ ├── L1IO-L2IO-Rand SMU UA159 (2)_data_clean.csv │ ├── MappedData │ │ ├── L1IO-L2IO-Rand SMU UA159 (3)_mapped.csv │ │ ├── L3O-Rand SMU UA159 aerobic_mapped.csv │ │ ├── Randoms SMU UA159 aerobic (1) mapped.csv │ │ ├── Randoms SMU UA159 aerobic (2) mapped .csv │ │ ├── Randoms SMU UA159 aerobic (3) mapped .csv │ │ ├── Randoms SMU UA159 aerobic (4) mapped .csv │ │ ├── Randoms SMU UA159 aerobic (5) mapped .csv │ │ ├── Randoms SMU UA159 aerobic (6) mapped .csv │ │ └── Randoms SMU UA159 aerobic (7) mapped (removed plate 1).csv │ ├── SMU.png │ ├── SMU_L1IO-L2IO-Rand_compare.png │ ├── experiments_sparcity_10.csv │ ├── experiments_sparcity_10_results_no_first_train_500.csv │ ├── l1ins.csv │ ├── no_training │ │ ├── model.h5 │ │ ├── model_params.pkl │ │ └── weights.npz │ └── plot SMU Data.py ├── iSMU-extrapolated │ └── initial_data │ │ ├── train_set_both.csv │ │ ├── train_set_in.csv │ │ └── train_set_out.csv ├── leave_out_datasets │ ├── CDM_leave_out_test.csv │ ├── CDM_leave_out_test_01.csv │ └── CDM_leave_out_validation_01.csv └── no_growth.csv ├── files ├── 96_to_384_Mapping_8plate.csv ├── BacterAI algorithm chart.drawio ├── CDM_reagents_2x_NH4_tempest_optimized.csv ├── CDM_reagents_2x_base+NH4.csv ├── CDM_reagents_2x_base.csv ├── CDM_reagents_4x_base+NH4.csv ├── amino_acid_features.csv ├── commands.txt ├── fractional_design_k10n128.csv ├── hyperparameters.csv ├── hyperparameters_regularization.csv ├── name_mappings_aa.csv ├── name_mappings_aa_alt.csv ├── name_mappings_both.csv ├── name_mappings_tempest_aa.csv ├── tf_test_data_template_batch_meta.csv └── tf_test_data_template_mapped_data.csv ├── gpr_lib.R ├── gpr_lib.Rproj ├── installR.md ├── main.Rmd ├── main.nb.html ├── make_figure_growth_front.py ├── make_figure_stacked_bar.py ├── model.py ├── models.py ├── models ├── iSMUv01.mat ├── iSMUv01.xml ├── iSMUv01_CDM_LOO.xlsx ├── iSMUv01_CDM_LOO.xml └── iSMUv01_CDM_LOO_v2.xml ├── net.py ├── old_agent ├── BacterAI algorithm chart.drawio ├── Pipfile ├── Pipfile.lock ├── SPSA_vs_FDSA_expt.py ├── SPSA_vs_FDSA_simulation.py ├── agent.py ├── agent_progress_graph.py ├── agent_tabular.py ├── analyze_cycle.py ├── bench.py ├── dnf.py ├── mcts.py ├── model.py ├── neural.py ├── protocols │ ├── CDM.py │ └── CDM_NH4_rescale.py ├── spsa.py └── utils.py ├── plot.py ├── published_data ├── SGO aerobic (TL) │ ├── experiment_data.csv │ ├── final_models │ │ ├── bag_model_0.pkl │ │ ├── bag_model_1.pkl │ │ ├── bag_model_10.pkl │ │ ├── bag_model_11.pkl │ │ ├── bag_model_12.pkl │ │ ├── bag_model_13.pkl │ │ ├── bag_model_14.pkl │ │ ├── bag_model_15.pkl │ │ ├── bag_model_16.pkl │ │ ├── bag_model_17.pkl │ │ ├── bag_model_18.pkl │ │ ├── bag_model_19.pkl │ │ ├── bag_model_2.pkl │ │ ├── bag_model_20.pkl │ │ ├── bag_model_21.pkl │ │ ├── bag_model_22.pkl │ │ ├── bag_model_23.pkl │ │ ├── bag_model_24.pkl │ │ ├── bag_model_3.pkl │ │ ├── bag_model_4.pkl │ │ ├── bag_model_5.pkl │ │ ├── bag_model_6.pkl │ │ ├── bag_model_7.pkl │ │ ├── bag_model_8.pkl │ │ └── bag_model_9.pkl │ └── transfer_models_SSA_aerobic │ │ ├── bag_model_0.pkl │ │ ├── bag_model_1.pkl │ │ ├── bag_model_10.pkl │ │ ├── bag_model_11.pkl │ │ ├── bag_model_12.pkl │ │ ├── bag_model_13.pkl │ │ ├── bag_model_14.pkl │ │ ├── bag_model_15.pkl │ │ ├── bag_model_16.pkl │ │ ├── bag_model_17.pkl │ │ ├── bag_model_18.pkl │ │ ├── bag_model_19.pkl │ │ ├── bag_model_2.pkl │ │ ├── bag_model_20.pkl │ │ ├── bag_model_21.pkl │ │ ├── bag_model_22.pkl │ │ ├── bag_model_23.pkl │ │ ├── bag_model_24.pkl │ │ ├── bag_model_3.pkl │ │ ├── bag_model_4.pkl │ │ ├── bag_model_5.pkl │ │ ├── bag_model_6.pkl │ │ ├── bag_model_7.pkl │ │ ├── bag_model_8.pkl │ │ └── bag_model_9.pkl ├── SGO aerobic │ ├── experiment_data.csv │ └── final_models │ │ ├── bag_model_0.pkl │ │ ├── bag_model_1.pkl │ │ ├── bag_model_10.pkl │ │ ├── bag_model_11.pkl │ │ ├── bag_model_12.pkl │ │ ├── bag_model_13.pkl │ │ ├── bag_model_14.pkl │ │ ├── bag_model_15.pkl │ │ ├── bag_model_16.pkl │ │ ├── bag_model_17.pkl │ │ ├── bag_model_18.pkl │ │ ├── bag_model_19.pkl │ │ ├── bag_model_2.pkl │ │ ├── bag_model_20.pkl │ │ ├── bag_model_21.pkl │ │ ├── bag_model_22.pkl │ │ ├── bag_model_23.pkl │ │ ├── bag_model_24.pkl │ │ ├── bag_model_3.pkl │ │ ├── bag_model_4.pkl │ │ ├── bag_model_5.pkl │ │ ├── bag_model_6.pkl │ │ ├── bag_model_7.pkl │ │ ├── bag_model_8.pkl │ │ └── bag_model_9.pkl ├── SGO random │ └── experiment_data.csv ├── SSA aerobic full CDM (TL) │ ├── experiment_data.csv │ ├── final_models │ │ ├── bag_model_0.pkl │ │ ├── bag_model_1.pkl │ │ ├── bag_model_10.pkl │ │ ├── bag_model_11.pkl │ │ ├── bag_model_12.pkl │ │ ├── bag_model_13.pkl │ │ ├── bag_model_14.pkl │ │ ├── bag_model_15.pkl │ │ ├── bag_model_16.pkl │ │ ├── bag_model_17.pkl │ │ ├── bag_model_18.pkl │ │ ├── bag_model_19.pkl │ │ ├── bag_model_2.pkl │ │ ├── bag_model_20.pkl │ │ ├── bag_model_21.pkl │ │ ├── bag_model_22.pkl │ │ ├── bag_model_23.pkl │ │ ├── bag_model_24.pkl │ │ ├── bag_model_3.pkl │ │ ├── bag_model_4.pkl │ │ ├── bag_model_5.pkl │ │ ├── bag_model_6.pkl │ │ ├── bag_model_7.pkl │ │ ├── bag_model_8.pkl │ │ └── bag_model_9.pkl │ └── transfer_data_SSA_aerobic.csv ├── SSA aerobic │ ├── experiment_data.csv │ └── final_models │ │ ├── bag_model_0.pkl │ │ ├── bag_model_1.pkl │ │ ├── bag_model_10.pkl │ │ ├── bag_model_11.pkl │ │ ├── bag_model_12.pkl │ │ ├── bag_model_13.pkl │ │ ├── bag_model_14.pkl │ │ ├── bag_model_15.pkl │ │ ├── bag_model_16.pkl │ │ ├── bag_model_17.pkl │ │ ├── bag_model_18.pkl │ │ ├── bag_model_19.pkl │ │ ├── bag_model_2.pkl │ │ ├── bag_model_20.pkl │ │ ├── bag_model_21.pkl │ │ ├── bag_model_22.pkl │ │ ├── bag_model_23.pkl │ │ ├── bag_model_24.pkl │ │ ├── bag_model_3.pkl │ │ ├── bag_model_4.pkl │ │ ├── bag_model_5.pkl │ │ ├── bag_model_6.pkl │ │ ├── bag_model_7.pkl │ │ ├── bag_model_8.pkl │ │ └── bag_model_9.pkl ├── SSA anaerobic (TL) │ ├── experiment_data.csv │ ├── final_models │ │ ├── bag_model_0.pkl │ │ ├── bag_model_1.pkl │ │ ├── bag_model_10.pkl │ │ ├── bag_model_11.pkl │ │ ├── bag_model_12.pkl │ │ ├── bag_model_13.pkl │ │ ├── bag_model_14.pkl │ │ ├── bag_model_15.pkl │ │ ├── bag_model_16.pkl │ │ ├── bag_model_17.pkl │ │ ├── bag_model_18.pkl │ │ ├── bag_model_19.pkl │ │ ├── bag_model_2.pkl │ │ ├── bag_model_20.pkl │ │ ├── bag_model_21.pkl │ │ ├── bag_model_22.pkl │ │ ├── bag_model_23.pkl │ │ ├── bag_model_24.pkl │ │ ├── bag_model_3.pkl │ │ ├── bag_model_4.pkl │ │ ├── bag_model_5.pkl │ │ ├── bag_model_6.pkl │ │ ├── bag_model_7.pkl │ │ ├── bag_model_8.pkl │ │ └── bag_model_9.pkl │ └── transfer_models_SSA_aerobic │ │ ├── bag_model_0.pkl │ │ ├── bag_model_1.pkl │ │ ├── bag_model_10.pkl │ │ ├── bag_model_11.pkl │ │ ├── bag_model_12.pkl │ │ ├── bag_model_13.pkl │ │ ├── bag_model_14.pkl │ │ ├── bag_model_15.pkl │ │ ├── bag_model_16.pkl │ │ ├── bag_model_17.pkl │ │ ├── bag_model_18.pkl │ │ ├── bag_model_19.pkl │ │ ├── bag_model_2.pkl │ │ ├── bag_model_20.pkl │ │ ├── bag_model_21.pkl │ │ ├── bag_model_22.pkl │ │ ├── bag_model_23.pkl │ │ ├── bag_model_24.pkl │ │ ├── bag_model_3.pkl │ │ ├── bag_model_4.pkl │ │ ├── bag_model_5.pkl │ │ ├── bag_model_6.pkl │ │ ├── bag_model_7.pkl │ │ ├── bag_model_8.pkl │ │ └── bag_model_9.pkl └── readme.md ├── readme.md ├── requirements-dev.txt ├── requirements.in ├── requirements.txt ├── rule_solver_genetic.py ├── rule_validator.py ├── run.py ├── scripts ├── __init__.py ├── aggregate_round_data.py ├── assess_dataset_convexity.py ├── collect_39_final_data.py ├── compare_nn_to_rule.py ├── compare_replicates.py ├── fractional_factorial_regression.py ├── generate_nonaa_tf_test_data.py ├── linear_regression.py ├── nn_dist_gen.py ├── plot_net.py 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