Pyomo. DoE: Sensitivity initialization #3639

smondal13 · 2025-06-23T14:45:35Z

Fixes # .

Summary/Motivation:

Initializing the model to a previously solved point in the design space can help the model converge at another point in the design space for sensitivity analysis
Better error messages in the method can help the user in debugging
Saving the file can be helpful if the model takes a long time to solve or if the user wants it.
The pattern generator in the utils.py file can be used in other cases where it can help with the initialization
Correlation matrix computation functionality will be helpful in computing correlation among the parameters

Changes proposed in this PR:

Added a new method compute_FIM_factorial() in Pyomo.DoE for sensitivity initialization
Added snake_traversal_grid_sampling() and compute_correlation_matrix() in utils.py

Legal Acknowledgement

By contributing to this software project, I have read the contribution guide and agree to the following terms and conditions for my contribution:

I agree my contributions are submitted under the BSD license.
I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer.

…pected. Now, I need to add cases when some of the design variables are not changed.

…mo into sensitivity-initialization

… use compute_FIM_metrics() method. Added both the nested for loop and change_one_design_at_a_time argument to compute_FIM_factorial() in doe.py. Everything is working fine.

…gn_values` does not need to be in the same order as the `experiment_inputs` as long as the key matches, we are good. Also, if we don't want to change a design variable, just not passing it as a key in the `design_values` dictionary will do the trick. Tested with the `reactor_example.py`

smondal13 · 2025-06-23T14:46:47Z

@adowling2 @djlaky, this draft PR is ready for initial review.

adowling2 · 2025-06-24T10:55:38Z

Does this PR depend on changes in #3575?

adowling2

@smondal13 I left some initial comments.

adowling2 · 2025-06-24T10:57:24Z

pyomo/contrib/doe/utils_updated.py

@@ -0,0 +1,267 @@
+#  ___________________________________________________________________________


@smondal13 Why are your creating a new utils file instead of updating the current one? There might be a point of confusion regarding branches in git.

This issue is resolved now. merged the utils file from my previous PR # 3525.

adowling2 · 2025-06-24T10:58:40Z

pyomo/contrib/doe/doe.py

@@ -1617,6 +1628,221 @@ def compute_FIM_full_factorial(

        return self.fim_factorial_results

+    def compute_FIM_factorial(


Was this function already in Pyomo.DoE somewhere else?

No, I created this method. I do not see the same name anywhere else.

@adowling2, we have compute_FIM_full_factorial(). I have not changed that method, rather I have added a new method. Maybe we can show a deprecation warning for compute_FIM_full_factorial()

Yes, a depreciation warning sounds reasonable.

adowling2 · 2025-06-24T11:00:22Z

pyomo/contrib/doe/doe.py

+        # design_map_keys so that design_point can be constructed correctly in the loop.
+        des_ranges = [design_values[k.name] for k in design_map_keys]
+        if change_one_design_at_a_time:
+            factorial_points = generate_snake_zigzag_pattern(*des_ranges)


Let's brainstorm different sensitivity analysis sequences we might use. We can then define an enum.

adowling2 · 2025-06-24T11:00:52Z

pyomo/contrib/doe/utils.py

@@ -100,3 +100,43 @@ def rescale_FIM(FIM, param_vals):
 #             pass  # ToDo: Write error for suffix keys that aren't ParamData or VarData
 #
 #     return param_list
+
+
+def generate_snake_zigzag_pattern(*lists):


Let's come up with a better name. I do not think of "snake" as a technical term.

adowling2 · 2025-06-24T11:01:49Z

pyomo/contrib/doe/utils.py

+                yield (value,) + sub_pattern
+
+    # Start the recursion at the first list (depth 0) with an initial sum of 0.
+    yield from _generate_recursive(depth=0, index_sum=0)


How are we going to test this function? IMO, the next step is to develop some tests for this. That way, as you try to run the sensitivity analysis for an example, you are least know this part of the code is correct.

@adowling2 , I did check it manually before. I have recently added a test for this in test_utils.py for up to 3 variables, and also for different array-like structures. From the test, it works the way we want.

Also added test for patter generator

…mo into sensitivity-initialization

…updated.py file

…ensitivity-initialization

…f. The code is run by using a simple model.

smondal13 · 2025-07-01T18:18:24Z

@adowling2 , @djlaky, @blnicho This PR is ready for design review.

…ation

…mo into sensitivity-initialization

added a new correlation matrix computation in doe/utils.py, added TODOs.

…statement

… return statement" This reverts commit a063c33.

…n return statement" This reverts commit 9af160d.

…ser provided design variables

…ization

…ed conflict of doe/utils.py

adowling2 · 2025-09-17T19:45:37Z

pyomo/contrib/doe/doe.py

@@ -1617,6 +1628,221 @@ def compute_FIM_full_factorial(

        return self.fim_factorial_results

+    def compute_FIM_factorial(


Yes, a depreciation warning sounds reasonable.

adowling2 · 2025-09-17T19:46:29Z

pyomo/contrib/doe/doe.py

+        file_name: str = None,
+    ):
+        """Will run a simulation-based factorial exploration of the experimental input
+        space (i.e., a ``grid search`` or ``parameter sweep``) to understand how the


Instead of "i.e." should this be "a.k.a." (also knowns as)

adowling2 · 2025-09-17T19:51:18Z

pyomo/contrib/doe/doe.py

+            factorial_points = snake_traversal_grid_sampling(*design_values)
+        elif scheme_enum == SensitivityInitialization.nested_for_loop:
+            factorial_points = product(*design_values)
+


Does it make sense to split the function here? That way, we can do extensive testing on the results of factorial_points without running the rest of the function.

adowling2 · 2025-09-17T19:55:27Z

pyomo/contrib/doe/doe.py

+        ----------
+        model : DoE model, optional
+            The model to perform the full factorial exploration on. Default: None
+        design_vals : dict,


After reading this doc string, I do not fully appreciate all of options. I do not think we are looking at all of the edge cases with the tests.

adowling2 · 2025-09-19T12:02:06Z

@smondal13 As a next step, I suggest you create a Google Doc as a mock-up for the documentation you plan to write for this new feature. In the mock-up, you can provide example usage to show the programmatic interface. I would set the Google Doc to allow for anonymous commenting and post the link here. Alternatively, you could do this in a markdown .md file that you add to this PR. Then, at the next Pyomo dev meeting, you can present the draft documentation and get feedback. This will facilitate the design review process.

smondal13 added 9 commits June 16, 2025 16:29

added zigzag in utils and compute fim in doe.py

a4a1ade

Merge branch 'Pyomo:main' into sensitivity-initialization

58c3663

The compute_FIM_factorial() using zigzag pattern is now working as ex…

26f8cd3

…pected. Now, I need to add cases when some of the design variables are not changed.

Merge branch 'sensitivity-initialization' of github.com:smondal13/pyo…

4dab155

…mo into sensitivity-initialization

Added utils.py as utils_updated.py from adding_eigen_values branch to…

55bfeae

… use compute_FIM_metrics() method. Added both the nested for loop and change_one_design_at_a_time argument to compute_FIM_factorial() in doe.py. Everything is working fine.

Changed documentation and improved the error message

0eb9791

Merge branch 'Pyomo:main' into sensitivity-initialization

66cdd0c

updated comments

d75e667

adowling2 reviewed Jun 24, 2025

View reviewed changes

smondal13 added 5 commits June 24, 2025 14:40

Added argument checking for generate zigzag pattern.

e5b2e73

Also added test for patter generator

changed the name of the pattern generator

13848fa

Merge branch 'adding_eigen_values' into sensitivity-initialization

bd53282

Merge branch 'Pyomo:main' into sensitivity-initialization

e40c6bc

Merge branch 'sensitivity-initialization' of github.com:smondal13/pyo…

75acdd2

…mo into sensitivity-initialization

smondal13 changed the title ~~Sensitivity initialization in Pyomo. DoE~~ Pyomo. DoE: Sensitivity initialization Jun 25, 2025

Changed the name of the grid sampling function and deleted the utils_…

0c87484

…updated.py file

sscini moved this to Todo in ParmEst & Pyomo.DoE Development Jun 27, 2025

sscini added this to ParmEst & Pyomo.DoE Development Jun 27, 2025

sscini moved this from Todo to Development in ParmEst & Pyomo.DoE Development Jun 27, 2025

sscini mentioned this pull request Jun 27, 2025

Add update_model utility to utils.py for updating suffix values in Pyomo.DoE #3650

Merged

smondal13 added 5 commits June 27, 2025 16:04

Merge remote-tracking branch 'sscini/add-update-model-utility' into s…

7cdba5b

…ensitivity-initialization

added rel_change and abs_change for change in design

6db9e66

added update_suffix function in compute the sensitivity

f12d908

working code. added design vals and also changed the settings of pd d…

fda812e

…f. The code is run by using a simple model.

Merge branch 'Pyomo:main' into sensitivity-initialization

ccfca8c

changed some minor comments and docstrings

043e7de

updated with sscini's utils.py.

33e1bd0

smondal13 marked this pull request as ready for review July 7, 2025 13:26

smondal13 moved this from Development to Ready for design review in ParmEst & Pyomo.DoE Development Jul 7, 2025

smondal13 added 12 commits July 7, 2025 09:39

Merge branch 'main' into sensitivity-initialization

c95f41d

Merge remote-tracking branch 'origin/main' into sensitivity-initializ…

e9e878d

…ation

Merge branch 'sensitivity-initialization' of github.com:smondal13/pyo…

caf6bae

…mo into sensitivity-initialization

Merge branch 'Pyomo:main' into sensitivity-initialization

dd1fdcd

added new func and changed test files

553ab82

added a new correlation matrix computation in doe/utils.py, added TODOs.

changed if statement to ternary operator and minor changes in return …

a063c33

…statement

Revert "changed if statement to ternary operator and minor changes in…

9af160d

… return statement" This reverts commit a063c33.

Reapply "changed if statement to ternary operator and minor changes i…

1f849a0

…n return statement" This reverts commit 9af160d.

deleted test_solve

da91f2f

added a strategy to compute the fractional factorial as well.

fd8d3ea

Created a temporary suffix design_suff to contain the keys of the u…

0ee6856

…ser provided design variables

Merge branch 'Pyomo:main' into sensitivity-initialization

01fc6ed

blnicho self-requested a review September 16, 2025 19:42

smondal13 added 3 commits September 16, 2025 21:32

Merge remote-tracking branch 'upstream/main' into sensitivity-initial…

ab7f31f

…ization

changed the import location for update_model_from_suffix and resolv…

c6e81ea

…ed conflict of doe/utils.py

cleaned doe/utils.py

aa3961f

adowling2 suggested changes Sep 17, 2025

View reviewed changes

		@@ -0,0 +1,267 @@
		# ___________________________________________________________________________

		@@ -1617,6 +1628,221 @@ def compute_FIM_full_factorial(

		return self.fim_factorial_results

		def compute_FIM_factorial(

Pyomo. DoE: Sensitivity initialization #3639

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Pyomo. DoE: Sensitivity initialization #3639

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smondal13 commented Jun 23, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Fixes # .

Summary/Motivation:

Changes proposed in this PR:

Legal Acknowledgement

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smondal13 commented Jun 23, 2025

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adowling2 commented Jun 24, 2025

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smondal13 Jul 1, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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smondal13 commented Jul 1, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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adowling2 commented Sep 19, 2025

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smondal13 commented Jun 23, 2025 •

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