-
@@ -978,7 +979,10 @@ while loop
-
<generator object <genexpr> at 0x0000026C130C34C0>
+<generator object <genexpr> at 0x0000018ABCA73140>
while loop
-Experiments to perform: ['Bubble column', 'Fluid bed', 'Crystalization', 'Ion exchange', 'Solid-liquid extraction']
+Experiments to perform:
+
+
+ ['Bubble column', 'Fluid bed', 'Crystalization', 'Ion exchange', 'Solid-liquid extraction']
Experiments to perform: ['Bubble column', 'Fluid bed', 'Crystalization', 'Ion exchange']
Experiments to perform: ['Bubble column', 'Fluid bed', 'Crystalization']
Only 2 experiments left: ['Bubble column', 'Fluid bed']
diff --git a/WS1/module_1/3_control_flow.html b/WS1/module_1/3_control_flow.html
index 0ee391b..67a81d1 100755
--- a/WS1/module_1/3_control_flow.html
+++ b/WS1/module_1/3_control_flow.html
@@ -256,6 +256,7 @@
Module 2
@@ -673,18 +674,15 @@ Repetition
-Row
-
-
- [0.68736936 0.20126193 0.04658199]
-Element 0.6873693596050051
-Element 0.20126193070467935
-Element 0.04658198840012395
-
-Row [0.57064357 0.57116666 0.75163354]
-Element 0.5706435668382651
-Element 0.5711666629778096
-Element 0.7516335434567888
+Row [0.60350024 0.68351939 0.36690524]
+Element 0.6035002432325545
+Element 0.6835193895418288
+Element 0.3669052446170007
+
+Row [0.94784367 0.65507302 0.35171263]
+Element 0.9478436720918891
+Element 0.6550730171977208
+Element 0.35171262777790113
diff --git a/WS1/module_1/4_exercise_1.html b/WS1/module_1/4_exercise_1.html
index 181773a..6b25133 100755
--- a/WS1/module_1/4_exercise_1.html
+++ b/WS1/module_1/4_exercise_1.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_1/5_exercise_2.html b/WS1/module_1/5_exercise_2.html
index e95efff..f67433d 100755
--- a/WS1/module_1/5_exercise_2.html
+++ b/WS1/module_1/5_exercise_2.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_2/0_intro_module_2.html b/WS1/module_2/0_intro_module_2.html
index 812eba9..f47f76e 100755
--- a/WS1/module_2/0_intro_module_2.html
+++ b/WS1/module_2/0_intro_module_2.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_2/1_dictionaries_and_sets.html b/WS1/module_2/1_dictionaries_and_sets.html
index d50b09e..227debe 100755
--- a/WS1/module_2/1_dictionaries_and_sets.html
+++ b/WS1/module_2/1_dictionaries_and_sets.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_2/2_dataframes.html b/WS1/module_2/2_dataframes.html
index 59fa10c..f196b96 100755
--- a/WS1/module_2/2_dataframes.html
+++ b/WS1/module_2/2_dataframes.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_2/3_numpy_arrays.html b/WS1/module_2/3_numpy_arrays.html
index f2f5668..6856a69 100755
--- a/WS1/module_2/3_numpy_arrays.html
+++ b/WS1/module_2/3_numpy_arrays.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_2/4_data_visualizations.html b/WS1/module_2/4_data_visualizations.html
index bad9b88..d4fe0af 100755
--- a/WS1/module_2/4_data_visualizations.html
+++ b/WS1/module_2/4_data_visualizations.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_2/5_exercise_1.html b/WS1/module_2/5_exercise_1.html
index 35dd7d0..5e8db3f 100755
--- a/WS1/module_2/5_exercise_1.html
+++ b/WS1/module_2/5_exercise_1.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_3/0_intro_module_3.html b/WS1/module_3/0_intro_module_3.html
index 8e1cc97..9aab2de 100755
--- a/WS1/module_3/0_intro_module_3.html
+++ b/WS1/module_3/0_intro_module_3.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/1_operations.html b/WS1/module_3/1_operations.html
index f1e8043..52908e1 100755
--- a/WS1/module_3/1_operations.html
+++ b/WS1/module_3/1_operations.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/2_linear_regression.html b/WS1/module_3/2_linear_regression.html
index 9c30aee..64d3d1d 100755
--- a/WS1/module_3/2_linear_regression.html
+++ b/WS1/module_3/2_linear_regression.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/3_stoichiometry.html b/WS1/module_3/3_stoichiometry.html
index e3018a8..f74aa7a 100755
--- a/WS1/module_3/3_stoichiometry.html
+++ b/WS1/module_3/3_stoichiometry.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/4_stoichiometry_solution.html b/WS1/module_3/4_stoichiometry_solution.html
index 15a3f1c..63d913f 100755
--- a/WS1/module_3/4_stoichiometry_solution.html
+++ b/WS1/module_3/4_stoichiometry_solution.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/5_stoichiometry_pt2.html b/WS1/module_3/5_stoichiometry_pt2.html
index e76d687..673700d 100755
--- a/WS1/module_3/5_stoichiometry_pt2.html
+++ b/WS1/module_3/5_stoichiometry_pt2.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/6_exercise_1.html b/WS1/module_3/6_exercise_1.html
index 5abe523..8773459 100755
--- a/WS1/module_3/6_exercise_1.html
+++ b/WS1/module_3/6_exercise_1.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_4/0_intro_module_4.html b/WS1/module_4/0_intro_module_4.html
index 9b99796..b6dde16 100755
--- a/WS1/module_4/0_intro_module_4.html
+++ b/WS1/module_4/0_intro_module_4.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_4/1_reactors_in_python.html b/WS1/module_4/1_reactors_in_python.html
index 36a5dd9..bc98f49 100755
--- a/WS1/module_4/1_reactors_in_python.html
+++ b/WS1/module_4/1_reactors_in_python.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_4/2_combining_balances.html b/WS1/module_4/2_combining_balances.html
index 31788b1..8292c3f 100755
--- a/WS1/module_4/2_combining_balances.html
+++ b/WS1/module_4/2_combining_balances.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_4/3_combining_balances_solution.html b/WS1/module_4/3_combining_balances_solution.html
index 83392de..5afe7e3 100755
--- a/WS1/module_4/3_combining_balances_solution.html
+++ b/WS1/module_4/3_combining_balances_solution.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_4/4_exercise_1.html b/WS1/module_4/4_exercise_1.html
index aa9f001..b03a301 100755
--- a/WS1/module_4/4_exercise_1.html
+++ b/WS1/module_4/4_exercise_1.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_4/5_exercise_1_solution.html b/WS1/module_4/5_exercise_1_solution.html
index c9d7f2c..3a52acd 100755
--- a/WS1/module_4/5_exercise_1_solution.html
+++ b/WS1/module_4/5_exercise_1_solution.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_4/6_exercise_2.html b/WS1/module_4/6_exercise_2.html
index aa48a0e..e44db91 100755
--- a/WS1/module_4/6_exercise_2.html
+++ b/WS1/module_4/6_exercise_2.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_4/7_exercise_2_solution.html b/WS1/module_4/7_exercise_2_solution.html
index 7c47708..472e73b 100755
--- a/WS1/module_4/7_exercise_2_solution.html
+++ b/WS1/module_4/7_exercise_2_solution.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_5/0_FedBatch_Ecoli_simulation.html b/WS1/module_5/0_FedBatch_Ecoli_simulation.html
index 1600ddd..722e94d 100755
--- a/WS1/module_5/0_FedBatch_Ecoli_simulation.html
+++ b/WS1/module_5/0_FedBatch_Ecoli_simulation.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_6/0_intro_module_6.html b/WS1/module_6/0_intro_module_6.html
index deea236..093dd8a 100755
--- a/WS1/module_6/0_intro_module_6.html
+++ b/WS1/module_6/0_intro_module_6.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_6/1_Mass_Transfer.html b/WS1/module_6/1_Mass_Transfer.html
index 65109ec..f8e35c7 100755
--- a/WS1/module_6/1_Mass_Transfer.html
+++ b/WS1/module_6/1_Mass_Transfer.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_6/2_Diafiltration.html b/WS1/module_6/2_Diafiltration.html
index 8242ba2..85ec14a 100755
--- a/WS1/module_6/2_Diafiltration.html
+++ b/WS1/module_6/2_Diafiltration.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_6/3_Cell_lysis.html b/WS1/module_6/3_Cell_lysis.html
index bc6f838..6484762 100755
--- a/WS1/module_6/3_Cell_lysis.html
+++ b/WS1/module_6/3_Cell_lysis.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/intro_to_ws2.html b/WS2/intro_to_ws2.html
index 3aeb504..3145046 100755
--- a/WS2/intro_to_ws2.html
+++ b/WS2/intro_to_ws2.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_1/0_intro_module_1.html b/WS2/module_1/0_intro_module_1.html
index 2493018..b87cef1 100755
--- a/WS2/module_1/0_intro_module_1.html
+++ b/WS2/module_1/0_intro_module_1.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS2/module_1/1_Fermentation_Scerevisiae_Lignocellulosic_Batch.html b/WS2/module_1/1_Fermentation_Scerevisiae_Lignocellulosic_Batch.html
index 0371931..93364c3 100755
--- a/WS2/module_1/1_Fermentation_Scerevisiae_Lignocellulosic_Batch.html
+++ b/WS2/module_1/1_Fermentation_Scerevisiae_Lignocellulosic_Batch.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_1/2_Fermentation_Scerevisiae_Glucose_Aerobic_CSTR.html b/WS2/module_1/2_Fermentation_Scerevisiae_Glucose_Aerobic_CSTR.html
index 3ebd6cc..04e7d7f 100755
--- a/WS2/module_1/2_Fermentation_Scerevisiae_Glucose_Aerobic_CSTR.html
+++ b/WS2/module_1/2_Fermentation_Scerevisiae_Glucose_Aerobic_CSTR.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_1/3_Fermentation_MonodHerbert_aerobic.html b/WS2/module_1/3_Fermentation_MonodHerbert_aerobic.html
index 7706ae4..0987e78 100755
--- a/WS2/module_1/3_Fermentation_MonodHerbert_aerobic.html
+++ b/WS2/module_1/3_Fermentation_MonodHerbert_aerobic.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_1/4_FedBatch_Ecoli_simulation_proteinproduction.html b/WS2/module_1/4_FedBatch_Ecoli_simulation_proteinproduction.html
index 8ae07e4..d8c9a07 100755
--- a/WS2/module_1/4_FedBatch_Ecoli_simulation_proteinproduction.html
+++ b/WS2/module_1/4_FedBatch_Ecoli_simulation_proteinproduction.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_2/0_intro_module_2.html b/WS2/module_2/0_intro_module_2.html
index 6c102a5..f78cc75 100755
--- a/WS2/module_2/0_intro_module_2.html
+++ b/WS2/module_2/0_intro_module_2.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS2/module_2/1_dd_classification.html b/WS2/module_2/1_dd_classification.html
index 3fd68dd..4abbcae 100755
--- a/WS2/module_2/1_dd_classification.html
+++ b/WS2/module_2/1_dd_classification.html
@@ -60,7 +60,7 @@
-
+
@@ -256,6 +256,7 @@
Module 2
@@ -804,11 +805,11 @@ Notice:#
diff --git a/WS2/module_2/2_dd_regression copy.html b/WS2/module_2/2_dd_regression copy.html
index a64e503..2601ec1 100755
--- a/WS2/module_2/2_dd_regression copy.html
+++ b/WS2/module_2/2_dd_regression copy.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS2/module_2/2_pytorch_tutorial.html b/WS2/module_2/2_pytorch_tutorial.html
index adabf45..59f1f7c 100755
--- a/WS2/module_2/2_pytorch_tutorial.html
+++ b/WS2/module_2/2_pytorch_tutorial.html
@@ -60,6 +60,8 @@
+
+
@@ -122,8 +124,6 @@
-
-
@@ -226,7 +226,7 @@
Model-based Techniques (WS2)
-
+
- Introduction to workshop 2
- Module 1
-- Module 2
+- Module 2
@@ -771,22 +772,25 @@ 7. Model Training
-Epoch 0: Train Loss = 48.6153, Val Loss = 41.8169
-Epoch 10: Train Loss = 0.2252, Val Loss = 0.4560
-Epoch 20: Train Loss = 0.1035, Val Loss = 0.1433
-Epoch 30: Train Loss = 0.0848, Val Loss = 0.1144
+Epoch 0: Train Loss = 48.7267, Val Loss = 45.3895
+Epoch 10: Train Loss = 0.2846, Val Loss = 0.1482
+Epoch 20: Train Loss = 0.0872, Val Loss = 0.1037
-Epoch 40: Train Loss = 0.0653, Val Loss = 0.0906
-Epoch 50: Train Loss = 0.0516, Val Loss = 0.0735
-Epoch 60: Train Loss = 0.0482, Val Loss = 0.0600
+Epoch 30: Train Loss = 0.0676, Val Loss = 0.0645
+Epoch 40: Train Loss = 0.0530, Val Loss = 0.0498
+Epoch 50: Train Loss = 0.0488, Val Loss = 0.0478
-Epoch 70: Train Loss = 0.0398, Val Loss = 0.0514
-Epoch 80: Train Loss = 0.0376, Val Loss = 0.0505
-Epoch 90: Train Loss = 0.0369, Val Loss = 0.0478
+Epoch 60: Train Loss = 0.0423, Val Loss = 0.0437
+Epoch 70: Train Loss = 0.0420, Val Loss = 0.0418
+Epoch 80: Train Loss = 0.0384, Val Loss = 0.0397
+
+
+Epoch 90: Train Loss = 0.0428, Val Loss = 0.0392
+Early stopping triggered at epoch 94
-Test Loss: 0.0503
+Test Loss: 0.0354
@@ -842,7 +846,7 @@ 9. Visualization
-
+
@@ -890,6 +894,24 @@ Next Steps
diff --git a/WS2/module_2/3_dd_regression.html b/WS2/module_2/3_dd_regression.html
index f83a85a..a501e6d 100755
--- a/WS2/module_2/3_dd_regression.html
+++ b/WS2/module_2/3_dd_regression.html
@@ -63,7 +63,7 @@
-
+
@@ -258,6 +258,7 @@
- Module 2
@@ -771,12 +772,12 @@ Process Optimization
- Module 2
diff --git a/WS2/module_3/1_hyb_regression.html b/WS2/module_3/1_hyb_regression.html
index 51abdfa..94dde0e 100755
--- a/WS2/module_3/1_hyb_regression.html
+++ b/WS2/module_3/1_hyb_regression.html
@@ -257,6 +257,7 @@
- Module 2
diff --git a/_images/243ad88cb94fc7d0533cf77f0f420d371812b30388ad52e235868da5d5bd03de.png b/_images/243ad88cb94fc7d0533cf77f0f420d371812b30388ad52e235868da5d5bd03de.png
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diff --git a/_sources/markdown-notebooks.ipynb b/_sources/markdown-notebooks.ipynb
index 726f83f..bb5f780 100755
--- a/_sources/markdown-notebooks.ipynb
+++ b/_sources/markdown-notebooks.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
- "id": "11d864b2",
+ "id": "8eb9d217",
"metadata": {},
"source": [
"# Notebooks with MyST Markdown\n",
@@ -23,7 +23,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "5bbaec37",
+ "id": "2032f76c",
"metadata": {},
"outputs": [
{
@@ -40,7 +40,7 @@
},
{
"cell_type": "markdown",
- "id": "29ab55df",
+ "id": "8b047a20",
"metadata": {},
"source": [
"When your book is built, the contents of any `{code-cell}` blocks will be\n",
diff --git a/genindex.html b/genindex.html
index ae3540c..a4ba30c 100755
--- a/genindex.html
+++ b/genindex.html
@@ -255,6 +255,7 @@
- Module 2
diff --git a/index.html b/index.html
index 4a4cabf..00a8f96 100755
--- a/index.html
+++ b/index.html
@@ -259,6 +259,7 @@
- Module 2
diff --git a/markdown-notebooks.html b/markdown-notebooks.html
index 320801c..e254b01 100755
--- a/markdown-notebooks.html
+++ b/markdown-notebooks.html
@@ -256,6 +256,7 @@
- Module 2
diff --git a/mymarkdownfile.html b/mymarkdownfile.html
index 7c5520b..88be591 100755
--- a/mymarkdownfile.html
+++ b/mymarkdownfile.html
@@ -256,6 +256,7 @@
- Module 2
diff --git a/notebooks.html b/notebooks.html
index 2d4a0a7..cad334e 100755
--- a/notebooks.html
+++ b/notebooks.html
@@ -258,6 +258,7 @@
- Module 2
diff --git a/search.html b/search.html
index ba50b1e..5395cdb 100755
--- a/search.html
+++ b/search.html
@@ -257,6 +257,7 @@
- Module 2
diff --git a/searchindex.js b/searchindex.js
index 59c1600..3a33286 100755
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1. Data Generation": [[42, "data-generation"]], "1. Gaussian Process Regression (GPR)": [[39, "gaussian-process-regression-gpr"]], "1. Introduction to Mechanistic Modeling": [[34, "introduction-to-mechanistic-modeling"]], "1. Introduction to Python": [[1, null]], "1. Loading and inspecting data": [[9, "loading-and-inspecting-data"]], "1. Simple statement": [[3, "simple-statement"]], "1. Statements": [[5, "statements"]], "2. Assignment statement": [[3, "assignment-statement"]], "2. Assignments": [[5, "assignments"]], "2. Dataset Creation": [[42, "dataset-creation"]], "2. Hello, World!": [[2, null]], "2. Indexing": [[9, "indexing"]], "2. Key Concepts in Mechanistic Modeling": [[34, "key-concepts-in-mechanistic-modeling"]], "2. Support Vector Regression (SVR)": [[39, "support-vector-regression-svr"]], "3. Example: Modeling a Simple Chemical Reaction": [[34, "example-modeling-a-simple-chemical-reaction"]], "3. Lists and generators": [[3, "lists-and-generators"], [5, "lists-and-generators"]], "3. Model Definition": [[42, "model-definition"]], "3. Random Forests (RF)": [[39, "random-forests-rf"]], "3. Replacing missing values": [[9, "replacing-missing-values"]], "3. Statements and Packaging": [[3, null]], "4. Compound statement": [[3, "compound-statement"]], "4. Compound statements": [[5, "compound-statements"]], "4. Conditionality and Repetition": [[4, null]], "4. Creating DataFrames from lists and dictionaries": [[9, "creating-dataframes-from-lists-and-dictionaries"]], "4. Early Stopping Implementation": [[42, "early-stopping-implementation"]], "4. Python example: solving reaction kinetics": [[34, "python-example-solving-reaction-kinetics"]], "4. XGBoost": [[39, "xgboost"]], "5. Deep Neural Networks (DNN)": [[39, "deep-neural-networks-dnn"]], "5. Groupby": [[9, "groupby"]], "5. Mechanistic Modeling in Biochemical Engineering": [[34, "mechanistic-modeling-in-biochemical-engineering"]], "5. 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\ No newline at end of file
Experiments to perform: ['Bubble column', 'Fluid bed', 'Crystalization', 'Ion exchange', 'Solid-liquid extraction']
+Experiments to perform:
+
+
+ ['Bubble column', 'Fluid bed', 'Crystalization', 'Ion exchange', 'Solid-liquid extraction']
Experiments to perform: ['Bubble column', 'Fluid bed', 'Crystalization', 'Ion exchange']
Experiments to perform: ['Bubble column', 'Fluid bed', 'Crystalization']
Only 2 experiments left: ['Bubble column', 'Fluid bed']
diff --git a/WS1/module_1/3_control_flow.html b/WS1/module_1/3_control_flow.html
index 0ee391b..67a81d1 100755
--- a/WS1/module_1/3_control_flow.html
+++ b/WS1/module_1/3_control_flow.html
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diff --git a/WS1/module_1/4_exercise_1.html b/WS1/module_1/4_exercise_1.html
index 181773a..6b25133 100755
--- a/WS1/module_1/4_exercise_1.html
+++ b/WS1/module_1/4_exercise_1.html
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Module 2
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index e95efff..f67433d 100755
--- a/WS1/module_1/5_exercise_2.html
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Module 2
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index 812eba9..f47f76e 100755
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Module 2
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index d50b09e..227debe 100755
--- a/WS1/module_2/1_dictionaries_and_sets.html
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Module 2
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index 59fa10c..f196b96 100755
--- a/WS1/module_2/2_dataframes.html
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Module 2
diff --git a/WS1/module_2/3_numpy_arrays.html b/WS1/module_2/3_numpy_arrays.html
index f2f5668..6856a69 100755
--- a/WS1/module_2/3_numpy_arrays.html
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Module 2
diff --git a/WS1/module_2/4_data_visualizations.html b/WS1/module_2/4_data_visualizations.html
index bad9b88..d4fe0af 100755
--- a/WS1/module_2/4_data_visualizations.html
+++ b/WS1/module_2/4_data_visualizations.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_2/5_exercise_1.html b/WS1/module_2/5_exercise_1.html
index 35dd7d0..5e8db3f 100755
--- a/WS1/module_2/5_exercise_1.html
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Module 2
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index 8e1cc97..9aab2de 100755
--- a/WS1/module_3/0_intro_module_3.html
+++ b/WS1/module_3/0_intro_module_3.html
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Module 2
diff --git a/WS1/module_3/1_operations.html b/WS1/module_3/1_operations.html
index f1e8043..52908e1 100755
--- a/WS1/module_3/1_operations.html
+++ b/WS1/module_3/1_operations.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/2_linear_regression.html b/WS1/module_3/2_linear_regression.html
index 9c30aee..64d3d1d 100755
--- a/WS1/module_3/2_linear_regression.html
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Module 2
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index e3018a8..f74aa7a 100755
--- a/WS1/module_3/3_stoichiometry.html
+++ b/WS1/module_3/3_stoichiometry.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/4_stoichiometry_solution.html b/WS1/module_3/4_stoichiometry_solution.html
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--- a/WS1/module_3/4_stoichiometry_solution.html
+++ b/WS1/module_3/4_stoichiometry_solution.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/5_stoichiometry_pt2.html b/WS1/module_3/5_stoichiometry_pt2.html
index e76d687..673700d 100755
--- a/WS1/module_3/5_stoichiometry_pt2.html
+++ b/WS1/module_3/5_stoichiometry_pt2.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_3/6_exercise_1.html b/WS1/module_3/6_exercise_1.html
index 5abe523..8773459 100755
--- a/WS1/module_3/6_exercise_1.html
+++ b/WS1/module_3/6_exercise_1.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_4/0_intro_module_4.html b/WS1/module_4/0_intro_module_4.html
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--- a/WS1/module_4/0_intro_module_4.html
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Module 2
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--- a/WS1/module_4/1_reactors_in_python.html
+++ b/WS1/module_4/1_reactors_in_python.html
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Module 2
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Module 2
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Module 2
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Module 2
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Module 2
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--- a/WS1/module_4/6_exercise_2.html
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Module 2
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Module 2
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Module 2
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@@ -258,6 +258,7 @@
Module 2
diff --git a/WS1/module_6/2_Diafiltration.html b/WS1/module_6/2_Diafiltration.html
index 8242ba2..85ec14a 100755
--- a/WS1/module_6/2_Diafiltration.html
+++ b/WS1/module_6/2_Diafiltration.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS1/module_6/3_Cell_lysis.html b/WS1/module_6/3_Cell_lysis.html
index bc6f838..6484762 100755
--- a/WS1/module_6/3_Cell_lysis.html
+++ b/WS1/module_6/3_Cell_lysis.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/intro_to_ws2.html b/WS2/intro_to_ws2.html
index 3aeb504..3145046 100755
--- a/WS2/intro_to_ws2.html
+++ b/WS2/intro_to_ws2.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_1/0_intro_module_1.html b/WS2/module_1/0_intro_module_1.html
index 2493018..b87cef1 100755
--- a/WS2/module_1/0_intro_module_1.html
+++ b/WS2/module_1/0_intro_module_1.html
@@ -258,6 +258,7 @@
Module 2
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index 0371931..93364c3 100755
--- a/WS2/module_1/1_Fermentation_Scerevisiae_Lignocellulosic_Batch.html
+++ b/WS2/module_1/1_Fermentation_Scerevisiae_Lignocellulosic_Batch.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_1/2_Fermentation_Scerevisiae_Glucose_Aerobic_CSTR.html b/WS2/module_1/2_Fermentation_Scerevisiae_Glucose_Aerobic_CSTR.html
index 3ebd6cc..04e7d7f 100755
--- a/WS2/module_1/2_Fermentation_Scerevisiae_Glucose_Aerobic_CSTR.html
+++ b/WS2/module_1/2_Fermentation_Scerevisiae_Glucose_Aerobic_CSTR.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_1/3_Fermentation_MonodHerbert_aerobic.html b/WS2/module_1/3_Fermentation_MonodHerbert_aerobic.html
index 7706ae4..0987e78 100755
--- a/WS2/module_1/3_Fermentation_MonodHerbert_aerobic.html
+++ b/WS2/module_1/3_Fermentation_MonodHerbert_aerobic.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_1/4_FedBatch_Ecoli_simulation_proteinproduction.html b/WS2/module_1/4_FedBatch_Ecoli_simulation_proteinproduction.html
index 8ae07e4..d8c9a07 100755
--- a/WS2/module_1/4_FedBatch_Ecoli_simulation_proteinproduction.html
+++ b/WS2/module_1/4_FedBatch_Ecoli_simulation_proteinproduction.html
@@ -256,6 +256,7 @@
Module 2
diff --git a/WS2/module_2/0_intro_module_2.html b/WS2/module_2/0_intro_module_2.html
index 6c102a5..f78cc75 100755
--- a/WS2/module_2/0_intro_module_2.html
+++ b/WS2/module_2/0_intro_module_2.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS2/module_2/1_dd_classification.html b/WS2/module_2/1_dd_classification.html
index 3fd68dd..4abbcae 100755
--- a/WS2/module_2/1_dd_classification.html
+++ b/WS2/module_2/1_dd_classification.html
@@ -60,7 +60,7 @@
-
+
@@ -256,6 +256,7 @@
Module 2
@@ -804,11 +805,11 @@ Notice:#
diff --git a/WS2/module_2/2_dd_regression copy.html b/WS2/module_2/2_dd_regression copy.html
index a64e503..2601ec1 100755
--- a/WS2/module_2/2_dd_regression copy.html
+++ b/WS2/module_2/2_dd_regression copy.html
@@ -258,6 +258,7 @@
Module 2
diff --git a/WS2/module_2/2_pytorch_tutorial.html b/WS2/module_2/2_pytorch_tutorial.html
index adabf45..59f1f7c 100755
--- a/WS2/module_2/2_pytorch_tutorial.html
+++ b/WS2/module_2/2_pytorch_tutorial.html
@@ -60,6 +60,8 @@
+
+
@@ -122,8 +124,6 @@
-
-
@@ -226,7 +226,7 @@
Model-based Techniques (WS2)
-
+
- Introduction to workshop 2
- Module 1
-- Module 2
+- Module 2
@@ -771,22 +772,25 @@ 7. Model Training
-Epoch 0: Train Loss = 48.6153, Val Loss = 41.8169
-Epoch 10: Train Loss = 0.2252, Val Loss = 0.4560
-Epoch 20: Train Loss = 0.1035, Val Loss = 0.1433
-Epoch 30: Train Loss = 0.0848, Val Loss = 0.1144
+Epoch 0: Train Loss = 48.7267, Val Loss = 45.3895
+Epoch 10: Train Loss = 0.2846, Val Loss = 0.1482
+Epoch 20: Train Loss = 0.0872, Val Loss = 0.1037
-Epoch 40: Train Loss = 0.0653, Val Loss = 0.0906
-Epoch 50: Train Loss = 0.0516, Val Loss = 0.0735
-Epoch 60: Train Loss = 0.0482, Val Loss = 0.0600
+Epoch 30: Train Loss = 0.0676, Val Loss = 0.0645
+Epoch 40: Train Loss = 0.0530, Val Loss = 0.0498
+Epoch 50: Train Loss = 0.0488, Val Loss = 0.0478
-Epoch 70: Train Loss = 0.0398, Val Loss = 0.0514
-Epoch 80: Train Loss = 0.0376, Val Loss = 0.0505
-Epoch 90: Train Loss = 0.0369, Val Loss = 0.0478
+Epoch 60: Train Loss = 0.0423, Val Loss = 0.0437
+Epoch 70: Train Loss = 0.0420, Val Loss = 0.0418
+Epoch 80: Train Loss = 0.0384, Val Loss = 0.0397
+
+
+Epoch 90: Train Loss = 0.0428, Val Loss = 0.0392
+Early stopping triggered at epoch 94
-Test Loss: 0.0503
+Test Loss: 0.0354
@@ -842,7 +846,7 @@ 9. Visualization
-
+
@@ -890,6 +894,24 @@ Next Steps
diff --git a/WS2/module_2/3_dd_regression.html b/WS2/module_2/3_dd_regression.html
index f83a85a..a501e6d 100755
--- a/WS2/module_2/3_dd_regression.html
+++ b/WS2/module_2/3_dd_regression.html
@@ -63,7 +63,7 @@
-
+
@@ -258,6 +258,7 @@
- Module 2
@@ -771,12 +772,12 @@ Process Optimization
- Module 2
diff --git a/WS2/module_3/1_hyb_regression.html b/WS2/module_3/1_hyb_regression.html
index 51abdfa..94dde0e 100755
--- a/WS2/module_3/1_hyb_regression.html
+++ b/WS2/module_3/1_hyb_regression.html
@@ -257,6 +257,7 @@
- Module 2
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diff --git a/_sources/markdown-notebooks.ipynb b/_sources/markdown-notebooks.ipynb
index 726f83f..bb5f780 100755
--- a/_sources/markdown-notebooks.ipynb
+++ b/_sources/markdown-notebooks.ipynb
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"cells": [
{
"cell_type": "markdown",
- "id": "11d864b2",
+ "id": "8eb9d217",
"metadata": {},
"source": [
"# Notebooks with MyST Markdown\n",
@@ -23,7 +23,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "5bbaec37",
+ "id": "2032f76c",
"metadata": {},
"outputs": [
{
@@ -40,7 +40,7 @@
},
{
"cell_type": "markdown",
- "id": "29ab55df",
+ "id": "8b047a20",
"metadata": {},
"source": [
"When your book is built, the contents of any `{code-cell}` blocks will be\n",
diff --git a/genindex.html b/genindex.html
index ae3540c..a4ba30c 100755
--- a/genindex.html
+++ b/genindex.html
@@ -255,6 +255,7 @@
- Module 2
diff --git a/index.html b/index.html
index 4a4cabf..00a8f96 100755
--- a/index.html
+++ b/index.html
@@ -259,6 +259,7 @@
- Module 2
diff --git a/markdown-notebooks.html b/markdown-notebooks.html
index 320801c..e254b01 100755
--- a/markdown-notebooks.html
+++ b/markdown-notebooks.html
@@ -256,6 +256,7 @@
- Module 2
diff --git a/mymarkdownfile.html b/mymarkdownfile.html
index 7c5520b..88be591 100755
--- a/mymarkdownfile.html
+++ b/mymarkdownfile.html
@@ -256,6 +256,7 @@
- Module 2
diff --git a/notebooks.html b/notebooks.html
index 2d4a0a7..cad334e 100755
--- a/notebooks.html
+++ b/notebooks.html
@@ -258,6 +258,7 @@
- Module 2
diff --git a/search.html b/search.html
index ba50b1e..5395cdb 100755
--- a/search.html
+++ b/search.html
@@ -257,6 +257,7 @@
- Module 2
diff --git a/searchindex.js b/searchindex.js
index 59c1600..3a33286 100755
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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Lists and generators": [[3, "lists-and-generators"], [5, "lists-and-generators"]], "3. Model Definition": [[42, "model-definition"]], "3. Random Forests (RF)": [[39, "random-forests-rf"]], "3. Replacing missing values": [[9, "replacing-missing-values"]], "3. Statements and Packaging": [[3, null]], "4. Compound statement": [[3, "compound-statement"]], "4. Compound statements": [[5, "compound-statements"]], "4. Conditionality and Repetition": [[4, null]], "4. Creating DataFrames from lists and dictionaries": [[9, "creating-dataframes-from-lists-and-dictionaries"]], "4. Early Stopping Implementation": [[42, "early-stopping-implementation"]], "4. Python example: solving reaction kinetics": [[34, "python-example-solving-reaction-kinetics"]], "4. XGBoost": [[39, "xgboost"]], "5. Deep Neural Networks (DNN)": [[39, "deep-neural-networks-dnn"]], "5. Groupby": [[9, "groupby"]], "5. Mechanistic Modeling in Biochemical Engineering": [[34, "mechanistic-modeling-in-biochemical-engineering"]], "5. Packaging": [[3, "packaging"], [5, "packaging"]], "5. Training Function": [[42, "training-function"]], "6. Conclusion": [[34, "conclusion"]], "6. Data Preparation": [[42, "data-preparation"]], "6. Handle duplicates": [[9, "handle-duplicates"]], "7. Model Training": [[42, "model-training"]], "9. Visualization": [[42, "visualization"]], "Aerobic fermentation model (S. cerevisiae)": [[37, null]], "An example cell": [[47, "an-example-cell"]], "Assignment 1": [[26, "assignment-1"], [27, "assignment-1"]], "Bead mill": [[32, "bead-mill"]], "Cell Lysis modelling": [[32, null]], "Chemical Reaction Engineering - Assignment 1": [[26, null], [27, null]], "Citations": [[48, "citations"]], "Classification using Data Driven Approaches": [[40, null]], "Code blocks and outputs": [[49, "code-blocks-and-outputs"]], "Conditionality": [[4, "conditionality"]], "Constants": [[14, "constants"]], "Content": [[46, "content"]], "Content with notebooks": [[49, null]], "Context": [[41, "context"], [43, "context"], [45, "context"]], "Continue and Break": [[4, "continue-and-break"]], "Continuous reactor model": [[30, "continuous-reactor-model"]], "Create a NumPy array": [[10, "create-a-numpy-array"]], "Create a notebook with MyST Markdown": [[47, "create-a-notebook-with-myst-markdown"]], "Create an array according to a distribution": [[10, "create-an-array-according-to-a-distribution"]], "Create the figure": [[38, "create-the-figure"]], "Creating a dictionary": [[8, "creating-a-dictionary"]], "Data Visualization": [[11, null]], "Data generation": [[41, "data-generation"], [43, "data-generation"]], "Data preprocessing": [[40, "data-preprocessing"]], "Data-driven Modelling": [[39, null]], "DataFrames, arrays and plotting": [[12, "dataframes-arrays-and-plotting"]], "Dates": [[46, "dates"]], "Define initial conditions and process parameters": [[38, "define-initial-conditions-and-process-parameters"]], "Define the model equations": [[38, "define-the-model-equations"], [38, "id1"]], "Define timesteps": [[38, "define-timesteps"]], "Diafiltration": [[31, null]], "Dictionaries": [[8, "dictionaries"]], "Dictionaries and Sets": [[8, null]], "Dictionaries and sets": [[12, "dictionaries-and-sets"]], "Dig4Bio workshops": [[46, null]], "Dimentionality Reduction": [[40, "dimentionality-reduction"]], "E. coli Fed-batch fermentation model, including recombinant protein production": [[38, null]], "Energy balance for a laboratory equipment batch reactor for chemical synthesis": [[22, null], [23, null]], "Equations": [[14, "equations"]], "Example 1:": [[18, "example-1"]], "Example 2:": [[18, "example-2"]], "Example 3:": [[18, "example-3"]], "Example 4:": [[18, "example-4"]], "Exercise: Binary to English translation": [[6, "exercise-binary-to-english-translation"]], "Exercise: Remove all outliers": [[6, "exercise-remove-all-outliers"]], "Exercises about dictionaries, sets, dataframes, arrays and visualizations": [[12, null]], "Exercises about statements, assignments, lists and generators, control flow and packaging": [[5, null]], "Exploartory data Analysis": [[40, "exploartory-data-analysis"]], "Extract results and make plots": [[35, "extract-results-and-make-plots"], [36, "extract-results-and-make-plots"], [37, "extract-results-and-make-plots"]], "Extract the relevant variables": [[38, 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