Pyomo. DoE: Sensitivity initialization by smondal13 · Pull Request #3639 · Pyomo/pyomo

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

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I agree my contributions are submitted under the BSD license.
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…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


        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.

pyomo/contrib/doe/utils.py

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.

…ser provided design variables

…ization

…ed conflict of doe/utils.py

adowling2 · 2025-09-17T19:45:37Z

pyomo/contrib/doe/doe.py


        return self.fim_factorial_results

+    def compute_FIM_factorial(


Yes, a depreciation warning sounds reasonable.

pyomo/contrib/doe/doe.py

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 · 2025-09-22T14:48:11Z

To see the Google Doc that shows the documentation and example of this feature, click here

…)` in utils.py. 2. Raised error instead of warning if the DesignSpaceTraversal is wrong in doe.py

…mo into sensitivity-initialization

adowling2

Please see my requested changes.

adowling2 · 2026-02-06T18:50:10Z

pyomo/contrib/doe/doe.py

+        traversal_scheme="snake_traversal",
+        file_name: str = None,
+    ):
+        """Will run a simulation-based factorial exploration of the experimental input


Change "will run" to "performs"

adowling2 · 2026-02-06T18:52:28Z

pyomo/contrib/doe/doe.py

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


@mrmundt @blnicho Do you have any suggestions for avoiding string-based names? I know that we want to avoid string-based names, but I do not have any good ideas of how to do that in a way that is convenient for the user.

pyomo/contrib/doe/doe.py

adowling2 · 2026-02-06T18:56:56Z

pyomo/contrib/doe/doe.py

+
+        return self.factorial_results
+
    # TODO: Overhaul plotting functions to not use strings


Do we still want to overhaul the plotting functions to not use strings? Or do we just want this function to be consistent with our user interface above? In other words, if we use string-based names above, I think it it okay to use string-based names here.

adowling2 · 2026-02-06T18:58:26Z

pyomo/contrib/doe/doe.py

    def draw_factorial_figure(
        self,
        results=None,
        sensitivity_design_variables=None,


Let's update this user interface to match the function above. It appears that design variables as specified differently in these two functions. Likewise, this function should do design variable name error checking similar to the function above.

adowling2 · 2026-02-06T19:01:25Z

pyomo/contrib/doe/utils.py

+
+
+def compute_correlation_matrix(
+    covariance_matrix, var_name: list = None, significant_digits=3


Please make the default for significant digits None.

adowling2 · 2026-02-06T19:01:58Z

pyomo/contrib/doe/utils.py

+    var_name : list, optional
+        List of variable names corresponding to the rows/columns of the covariance matrix.
+    significant_digits : int, optional
+        Number of significant digits to round the correlation matrix to. Default: 3.


Number of significant digits for rounding entries of the correlation matrix. Default: None (no rounding)

adowling2 · 2026-02-06T19:02:47Z

pyomo/contrib/doe/utils.py

+    ----------
+    covariance_matrix : numpy.ndarray
+        2D array representing the covariance matrix.
+    var_name : list, optional


What happens if this optional argument is not provided? The doc string does not tell me what happens with this information or the consequences of not providing it.

adowling2 · 2026-02-06T19:03:28Z

pyomo/contrib/doe/utils.py

+
+    Parameters
+    ----------
+    covariance_matrix : numpy.ndarray


Can this be a square DataFrame? If yes, what type of error checking should we do on the column and row names?

adowling2 · 2026-02-06T19:04:37Z

pyomo/contrib/doe/utils.py

+    # Set the index to the variable names if provided,
+    corr_df = (
+        pd.DataFrame(correlation_matrix, index=var_name, columns=var_name)
+        if var_name


What is this logic doing here?

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

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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…

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…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

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smondal13 added 4 commits July 9, 2025 08:01

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…

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…ser provided design variables

Merge branch 'Pyomo:main' into sensitivity-initialization

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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

smondal13 and others added 8 commits September 23, 2025 10:59

changed the docstring

555a307

implemented suggestions from 9/23 pyomo dev meeting.

40ac36c

Merge branch 'main' into sensitivity-initialization

b2ed61d

Merge branch 'main' into sensitivity-initialization

daf01c7

Merge branch 'main' into sensitivity-initialization

8664ea6

1. removed the argument check_positive_definite from `check_matrix(…

9393dde

…)` in utils.py. 2. Raised error instead of warning if the DesignSpaceTraversal is wrong in doe.py

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

b27d89d

…mo into sensitivity-initialization

Merge branch 'main' into sensitivity-initialization

964446b

blnicho added this to Pyomo 6.10 Nov 11, 2025

github-project-automation bot moved this to Todo in Pyomo 6.10 Nov 11, 2025

smondal13 added 2 commits November 24, 2025 11:57

Merge branch 'main' into sensitivity-initialization

39a3d2b

Merge branch 'main' into sensitivity-initialization

8e823e4

mrmundt requested review from adowling2 and mrmundt January 27, 2026 19:49

Merge branch 'main' into sensitivity-initialization

3d58a30

adowling2 suggested changes Feb 6, 2026

View reviewed changes

smondal13 added 3 commits February 6, 2026 16:48

Merge branch 'main' into sensitivity-initialization

87b6c24

Remove TODO and modify docstring.

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Merge branch 'main' into sensitivity-initialization

401e661

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


		return self.factorial_results

		# TODO: Overhaul plotting functions to not use strings



		def compute_correlation_matrix(
		covariance_matrix, var_name: list = None, significant_digits=3

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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 Sep 19, 2025

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smondal13 commented Jun 23, 2025 •

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