rename_config_files for pathway A

Author: PHvanLent

.gitignore

@@ -0,0 +1,3 @@
+results/
+data/
+figures/

data/config_files_yml/best_sampling/pathwayA/dummy_exp/extra_layer/pathwayA_cycles5_stratified_sampling_beta10_Pstrength2_S100X4N50F10P6_5.yml

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+identifier: 2025-07-31_batch_model_pathwayA_product_A_run5
+optimization_settings:
+  model_filepath: models/bioprocess_models/batch_model_pathwayA.xml
+  target: product_A
+  n_cycles: 5
+  noise_percentage: 0.1
+  noise_type: homoscedastic
+  t_start: 0
+  t_end: 50
+  timepoints: 200
+  parameters_perturbation_values:
+    enzyme_13: &id001
+    - 0.5
+    - 1
+    - 1.5
+    - 2
+    enzyme_17: *id001
+    enzyme_4: *id001
+    enzyme_5: *id001
+    enzyme_12: *id001
+    enzyme_14: *id001
+    enzyme_2: *id001
+    enzyme_16: *id001
+    enzyme_15: *id001
+    enzyme_7: *id001
+cycles:
+  cycle_0:
+    design_build_test:
+      cycle_status: 0
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: library_transform
+      design_method_hyperparams:
+        n_screened_strains: 100
+        sequencing_selection_method: best_sampling
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_1:
+    design_build_test:
+      cycle_status: 1
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: &id002
+        n_screened_strains: 100
+        ml_method: xgboost
+        beta: 10
+        data_strategy: all
+        sequencing_selection_method: best_sampling
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_2:
+    design_build_test:
+      cycle_status: 2
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_3:
+    design_build_test:
+      cycle_status: 3
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_4:
+    design_build_test:
+      cycle_status: 4
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null

data/config_files_yml/best_sampling/pathwayA/dummy_exp/extra_layer/pathwayA_cycles5_stratified_sampling_beta10_Pstrength3_S100X4N50F10P6_5.yml

@@ -0,0 +1,93 @@
+identifier: 2025-07-31_batch_model_pathwayA_product_A_run5
+optimization_settings:
+  model_filepath: models/bioprocess_models/batch_model_pathwayA.xml
+  target: product_A
+  n_cycles: 5
+  noise_percentage: 0.1
+  noise_type: homoscedastic
+  t_start: 0
+  t_end: 50
+  timepoints: 200
+  parameters_perturbation_values:
+    enzyme_13: &id001
+    - 1
+    - 1.5
+    - 2
+    - 3
+    enzyme_17: *id001
+    enzyme_4: *id001
+    enzyme_5: *id001
+    enzyme_12: *id001
+    enzyme_14: *id001
+    enzyme_2: *id001
+    enzyme_16: *id001
+    enzyme_15: *id001
+    enzyme_7: *id001
+cycles:
+  cycle_0:
+    design_build_test:
+      cycle_status: 0
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: library_transform
+      design_method_hyperparams:
+        n_screened_strains: 100
+        sequencing_selection_method: best_sampling
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_1:
+    design_build_test:
+      cycle_status: 1
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: &id002
+        n_screened_strains: 100
+        ml_method: xgboost
+        beta: 10
+        data_strategy: all
+        sequencing_selection_method: best_sampling
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_2:
+    design_build_test:
+      cycle_status: 2
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_3:
+    design_build_test:
+      cycle_status: 3
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_4:
+    design_build_test:
+      cycle_status: 4
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null

data/config_files_yml/best_sampling/pathwayA/dummy_exp/extra_layer/pathwayA_cycles5_stratified_sampling_beta10_Pstrength4_S100X4N50F10P6_5.yml

@@ -0,0 +1,93 @@
+identifier: 2025-07-31_batch_model_pathwayA_product_A_run5
+optimization_settings:
+  model_filepath: models/bioprocess_models/batch_model_pathwayA.xml
+  target: product_A
+  n_cycles: 5
+  noise_percentage: 0.1
+  noise_type: homoscedastic
+  t_start: 0
+  t_end: 50
+  timepoints: 200
+  parameters_perturbation_values:
+    enzyme_13: &id001
+    - 1
+    - 2
+    - 3
+    - 4
+    enzyme_17: *id001
+    enzyme_4: *id001
+    enzyme_5: *id001
+    enzyme_12: *id001
+    enzyme_14: *id001
+    enzyme_2: *id001
+    enzyme_16: *id001
+    enzyme_15: *id001
+    enzyme_7: *id001
+cycles:
+  cycle_0:
+    design_build_test:
+      cycle_status: 0
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: library_transform
+      design_method_hyperparams:
+        n_screened_strains: 100
+        sequencing_selection_method: best_sampling
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_1:
+    design_build_test:
+      cycle_status: 1
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: &id002
+        n_screened_strains: 100
+        ml_method: xgboost
+        beta: 10
+        data_strategy: all
+        sequencing_selection_method: best_sampling
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_2:
+    design_build_test:
+      cycle_status: 2
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_3:
+    design_build_test:
+      cycle_status: 3
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_4:
+    design_build_test:
+      cycle_status: 4
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null

data/config_files_yml/best_sampling/pathwayA/dummy_exp/pathwayA_cycles5_stratified_sampling_beta10_Pstrength2_S100X4N50F10P6_5.yml

@@ -0,0 +1,93 @@
+identifier: 2025-07-31_batch_model_pathwayA_product_A_run5
+optimization_settings:
+  model_filepath: models/bioprocess_models/batch_model_pathwayA.xml
+  target: product_A
+  n_cycles: 5
+  noise_percentage: 0.1
+  noise_type: homoscedastic
+  t_start: 0
+  t_end: 50
+  timepoints: 200
+  parameters_perturbation_values:
+    enzyme_13: &id001
+    - 0.5
+    - 1
+    - 1.5
+    - 2
+    enzyme_17: *id001
+    enzyme_4: *id001
+    enzyme_5: *id001
+    enzyme_12: *id001
+    enzyme_14: *id001
+    enzyme_2: *id001
+    enzyme_16: *id001
+    enzyme_15: *id001
+    enzyme_7: *id001
+cycles:
+  cycle_0:
+    design_build_test:
+      cycle_status: 0
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: library_transform
+      design_method_hyperparams:
+        n_screened_strains: 100
+        sequencing_selection_method: best_sampling
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_1:
+    design_build_test:
+      cycle_status: 1
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: &id002
+        n_screened_strains: 100
+        ml_method: xgboost
+        beta: 10
+        data_strategy: all
+        sequencing_selection_method: best_sampling
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_2:
+    design_build_test:
+      cycle_status: 2
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_3:
+    design_build_test:
+      cycle_status: 3
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null
+  cycle_4:
+    design_build_test:
+      cycle_status: 4
+      n_strains: 50
+      n_engineered_positions: 6
+      design_method: ml_assisted_library_transform
+      design_method_hyperparams: *id002
+      noise_percentage: 0.1
+      noise_type: homoscedastic
+    learn_recommend:
+      recommender_method: greedy
+      recommender_method_hyperparams: null