ml_assisted_library_transform implementation (work in progress)

Author: PHvanLent

data/config.yml data/config_files/config.ymldata/config.yml renamed to data/config_files/config.yml

@@ -0,0 +1,95 @@
+identifier: 2025-04-10_batch_model_v2_product_run1
+optimization_settings:
+  model_filepath: models/bioprocess_models/batch_model_v2.xml
+  target: product
+  n_cycles: 5
+  noise_percentage: 0.1
+  noise_type: heteroscedastic
+  t_start: 0
+  t_end: 50
+  num_tpoints: 200
+  parameters_perturbation_values:
+    vmax_v6:
+    - 1
+    - 2
+    vmax_v7:
+    - 1
+    - 2
+    vmax_v4:
+    - 1
+    - 2
+    vmax_v3:
+    - 1
+    - 2
+    vmax_v10:
+    - 1
+    - 2
+    vmax_v11:
+    - 1
+    - 2
+    vmax_v12:
+    - 1
+    - 2
+cycles:
+  cycle_0:
+    design_build_test:
+      cycle_status: 0
+      n_strains: 10
+      n_engineered_positions: 4
+      design_method: library_transform
+      design_method_hyperparams: &id001
+        n_screened_strains: 60
+        sequencing_selection_method: best_sampling
+      noise_percentage: 0.1
+      noise_type: heteroscedastic
+    learn_recommend:
+      recommender_method: greedy_baseline
+      recommender_method_hyperparams: null
+  cycle_1:
+    design_build_test:
+      cycle_status: 1
+      n_strains: 10
+      n_engineered_positions: 4
+      design_method: library_transform
+      design_method_hyperparams: *id001
+      noise_percentage: 0.1
+      noise_type: heteroscedastic
+    learn_recommend:
+      recommender_method: greedy_baseline
+      recommender_method_hyperparams: null
+  cycle_2:
+    design_build_test:
+      cycle_status: 2
+      n_strains: 10
+      n_engineered_positions: 4
+      design_method: library_transform
+      design_method_hyperparams: *id001
+      noise_percentage: 0.1
+      noise_type: heteroscedastic
+    learn_recommend:
+      recommender_method: greedy_baseline
+      recommender_method_hyperparams: null
+  cycle_3:
+    design_build_test:
+      cycle_status: 3
+      n_strains: 10
+      n_engineered_positions: 4
+      design_method: library_transform
+      design_method_hyperparams: *id001
+      noise_percentage: 0.1
+      noise_type: heteroscedastic
+    learn_recommend:
+      recommender_method: greedy_baseline
+      recommender_method_hyperparams: null
+  cycle_4:
+    design_build_test:
+      cycle_status: 4
+      n_strains: 10
+      n_engineered_positions: 4
+      design_method: library_transform
+      design_method_hyperparams: *id001
+      noise_percentage: 0.1
+      noise_type: heteroscedastic
+    learn_recommend:
+      recommender_method: greedy_baseline
+      recommender_method_hyperparams: null

data/config_files/config_batch_model_v2.yml

@@ -44,7 +44,7 @@ cycles:
       cycle_status: 1
       n_strains: 10
       n_engineered_positions: 2
-      design_method: library_transform
+      design_method: ml_assisted_library_transform
       design_method_hyperparams: *id001
       noise_percentage: 0.1
       noise_type: heteroscedastic

data/config_best_sampling.yml …ta/config_files/config_best_sampling.ymldata/config_best_sampling.yml renamed to data/config_files/config_best_sampling.yml data/config_best_sampling.yml renamed to data/config_files/config_best_sampling.yml

@@ -188,13 +188,13 @@
       </reaction>
       <reaction id="v_maintenance" reversible="false">
         <listOfReactants>
-          <speciesReference species="c_A" stoichiometry="0.166666666666667"/>
           <speciesReference species="c_atp" stoichiometry="1"/>
         </listOfReactants>
         <listOfProducts>
           <speciesReference species="co2" stoichiometry="1"/>
         </listOfProducts>
         <listOfModifiers>
+          <modifierSpeciesReference species="c_A"/>
           <modifierSpeciesReference species="c_biomass"/>
         </listOfModifiers>
         <kineticLaw>