Adding adaptive mutation and crossover to Genetic Algorithms #11

GEONKIM1 · 2024-03-18T18:07:03Z

This is a new methodology about adaptive mutation and crossover.
Adaptive mutation : DHM/ILC, ILM/DHC(Linearly increasing or decreasing) , quadratic function method, step function method.
Adaptive crossover : DHM/ILC, ILM/DHC(Linearly increasing or decreasing) , quadratic function method

Pull Request Description

What issue does this change request address? (Use "#" before the issue to link it, i.e., idaholab#42.

Closes idaholab#2286

What are the significant changes in functionality due to this change request?

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The following review must be completed by an authorized member of the Change Control Board.

1. Review all computer code.
2. If any changes occur to the input syntax, there must be an accompanying change to the user manual and xsd schema. If the input syntax change deprecates existing input files, a conversion script needs to be added (see Conversion Scripts).
3. Make sure the Python code and commenting standards are respected (camelBack, etc.) - See on the wiki for details.
4. Automated Tests should pass, including run_tests, pylint, manual building and xsd tests. If there are changes to Simulation.py or JobHandler.py the qsub tests must pass.
5. If significant functionality is added, there must be tests added to check this. Tests should cover all possible options. Multiple short tests are preferred over one large test. If new development on the internal JobHandler parallel system is performed, a cluster test must be added setting, in XML block, the node <internalParallel> to True.
6. If the change modifies or adds a requirement or a requirement based test case, the Change Control Board's Chair or designee also needs to approve the change. The requirements and the requirements test shall be in sync.
7. The merge request must reference an issue. If the issue is closed, the issue close checklist shall be done.
8. If an analytic test is changed/added is the the analytic documentation updated/added?
9. If any test used as a basis for documentation examples (currently found in raven/tests/framework/user_guide and raven/docs/workshop) have been changed, the associated documentation must be reviewed and assured the text matches the example.

…unction method), and Adaptive crossover(ILM/DHC, DHM/ILC, Quadratic function, Step function method

….py to create adaptive quadratic methodology

…0327

ravenframework/Optimizers/GeneticAlgorithm.py

Jimmy-INL · 2024-04-10T22:14:40Z

ravenframework/Optimizers/crossOverOperators/crossovers.py

  for ind,parent in enumerate(parentsPairs):
    parent = np.array(parent).reshape(2,-1) # two parents at a time
-
-    if randomUtils.random(dim=1,samples=1) <= crossoverProb:
+    if randomUtils.random(dim=1,samples=1) <= kwargs['crossoverProb']:
      if (kwargs['points'] == None) or ('points' not in kwargs.keys()):


Why is this changed? Could you please remind me?

Jimmy-INL · 2024-04-10T22:18:42Z

ravenframework/Optimizers/crossOverOperators/crossovers.py

@@ -215,3 +212,49 @@ def uniformCrossoverMethod(parent1,parent2,crossoverProb):
      children2[pos] = parent2[pos]

  return children1,children2
+
+def twoPointsCrossoverMethod2(parent1,parent2,locL,locU):
+  """


Is this a new function? Why is that? When will it be called?

ravenframework/Optimizers/GeneticAlgorithm.py

In some cases, it was finding mamba, when the new environment was created mamba was not available in the environment, causing install failures.

This fixes install where only python3 is available.

Jimmy-INL · 2024-04-12T20:36:42Z

tests/framework/Optimizers/GeneticAlgorithms/continuous/unconstrained/ZDT1.xml

@@ -91,7 +91,7 @@
  <Samplers>
    <MonteCarlo name="MC_samp">
      <samplerInit>
-        <limit>10</limit>
+        <limit>20</limit>
        <initialSeed>050877</initialSeed>
      </samplerInit>
      <variable name="x1">


Is this the test? This doesn't test the adaptive crossover/mutation!!
Please modify this and compare the results, if this reaches convergence faster, please regold.

Jimmy-INL · 2024-04-12T20:40:14Z

ravenframework/Optimizers/GeneticAlgorithm.py

        printPriority=108,
        descr=r""" The probability governing the crossover step, i.e., the probability that if exceeded crossover will occur.""")
+    crossoverProbability.addParam("type", InputTypes.makeEnumType('crossoverProbability','crossoverProbabilityType',['static','adaptive']), True,
+                       descr="type of crossover operation to be used (e.g., static,adaptive)")


Please update description for more details. For instance, give more information about what static means and what adaptive means, and state that adaptive only accepts linear (explain and give the equation) and quadratic (explain and give the equation)

Jimmy-INL · 2024-04-12T20:41:06Z

ravenframework/Optimizers/GeneticAlgorithm.py

        printPriority=108,
        descr=r""" The probability governing the mutation step, i.e., the probability that if exceeded mutation will occur.""")
+    mutationProbability.addParam("type", InputTypes.makeEnumType('mutationProbability','mutationProbabilityType',['static','adaptive']), True,
+                       descr="type of mutation probability operation to be used (e.g., static, adaptive)")
    mutation.addSub(mutationProbability)


same as above.

Jimmy-INL · 2024-04-12T22:02:02Z

ravenframework/Optimizers/GeneticAlgorithm.py

+      if(self._crossoverProbType == "static"):
+        crossOverProb = self._crossoverProb
+      if(self._crossoverProb == "linear"):
+        crossOverProb = getLinearCrossoverProbability(self.getIteration(traj),self.limit)


What happens if the user enter's Linear instead of linear. when we spoke before I showed you that in the if statement you can add .lower() to convert the whole word to lower case. (e.g., if(self._crossoverProb.lower() == "linear"):).
In addition, what if the user entered something else other than linear or quadratic, their should be a final else that raises an error. self.raiseAnError(IOError, "{} is not implemeted!. Currently only 'linear' and 'quadratic' are implemented".format(self._crossoverProb))

…obablity defaults to static the hard way

…hinks it converged after 1 iteration

Geon Kim added 8 commits March 18, 2024 10:34

Modified methodology: Adaptive mutation(ILM/DHC, DHM/ILC, Quadratic f…

74d4c1f

…unction method), and Adaptive crossover(ILM/DHC, DHM/ILC, Quadratic function, Step function method

Changing the inputtype of crossover (float >> floatorString)

1b20f56

adding the adaptiveCrossoverProbability to crossover.py

723ed0b

New methodology about adaptive mutation and modified GeneticAlgorithm…

822796c

….py to create adaptive quadratic methodology

Modified adaptive mutation and crossover only linear 240327

a0c4ddc

Modified adaptive mutation and crossover add quadratic 240327

9ba1b0b

Modified adaptive mutation and crossover add quadratic (bug fixed) 24…

e2cb552

…0327

Modified adaptive mutation and crossover add static 240328

4aaf126

Jimmy-INL requested changes Apr 1, 2024

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Adaptive mutation and crossover 240401(apply comment)

98160fe

GEONKIM1 requested a review from Jimmy-INL April 1, 2024 21:08

Jimmy-INL requested changes Apr 3, 2024

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GEONKIM1 force-pushed the Geon-Adaptive_mutation_and_crossover_method branch from a5bfe23 to 98160fe Compare April 3, 2024 19:00

Adaptive mutation and crossover 240403 - Add description

77aea58

GEONKIM1 requested a review from Jimmy-INL April 3, 2024 19:03

Jimmy-INL reviewed Apr 10, 2024

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Adaptive mutation and crossover 240410

7c04100

GEONKIM1 requested a review from Jimmy-INL April 10, 2024 22:51

PaulTalbot-INL and others added 6 commits April 12, 2024 12:59

update HERON submod for poly transfer func

cf91fe2

Only do lapack override on x86 machine. (idaholab#2260)

34f9759

Removing MAMBA_SKIP because it causes problems. (idaholab#2270)

2bdc91d

In some cases, it was finding mamba, when the new environment was created mamba was not available in the environment, causing install failures.

Use the WORKING_PYTHON_COMMAND during create_libraries (idaholab#2266)

07f29dd

This fixes install where only python3 is available.

submod update

1ee14ab

one sentence to the objective description in optimizers.py

3b3907f

Jimmy-INL requested changes Apr 12, 2024

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Jimmy-INL reviewed Apr 12, 2024

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Jimmy-INL added 3 commits April 13, 2024 10:27

addressing some of my comments on Geons PR, making the type of the pr…

85e9604

…obablity defaults to static the hard way

changing order of fuctions in fitness and mutations

631bdd8

Found a bug if mutation and crossover Prob = 0, hence the optimizer t…

86e280e

…hinks it converged after 1 iteration

Jimmy-INL added 2 commits April 13, 2024 15:32

fixing overwritten lines in crossover

4b3dd4f

fixing crossover unit tests

65ca176

Jimmy-INL force-pushed the Geon-Adaptive_mutation_and_crossover_method branch from 7bb293f to 65ca176 Compare April 16, 2024 01:06

GEONKIM1 requested a review from Jimmy-INL April 22, 2024 19:34

Adding tests, still need to gold

9bb29bc

Jimmy-INL force-pushed the Geon-Adaptive_mutation_and_crossover_method branch from ceb167b to 9bb29bc Compare April 27, 2024 15:44

Jimmy-INL changed the base branch from JunyungKim-Junyung-Jimmy-NSGAII_RegressionTest_UnitTest_Fix to devel May 19, 2024 03:47

Jimmy-INL changed the title ~~Modified methodology: Adaptive mutation and crossover~~ Adding adaptive mutation and crossover to Genetic Algorithms May 19, 2024

Jimmy-INL changed the base branch from devel to JimmyTestingAdaptiveMutation-crossover May 20, 2024 19:37

Jimmy-INL changed the base branch from JimmyTestingAdaptiveMutation-crossover to JunyungKim-Junyung-Jimmy-NSGAII_RegressionTest_UnitTest_Fix May 20, 2024 19:39

regolding adaptive tests

24ec18f

Jimmy-INL changed the base branch from JunyungKim-Junyung-Jimmy-NSGAII_RegressionTest_UnitTest_Fix to devel May 21, 2024 20:47

Jimmy-INL changed the base branch from devel to JunyungKim-Junyung-Jimmy-NSGAII_RegressionTest_UnitTest_Fix May 21, 2024 20:48

joshua-cogliati-inl added 3 commits May 21, 2024 15:22

Switch back to devel version of HERON and TEAL

add4e88

Fixing .gitmodules as well.

a03226e

Switching to devel version of submodules.

f9d89da

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Adding adaptive mutation and crossover to Genetic Algorithms #11

Adding adaptive mutation and crossover to Genetic Algorithms #11

GEONKIM1 commented Mar 18, 2024 •

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Adding adaptive mutation and crossover to Genetic Algorithms #11

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Adding adaptive mutation and crossover to Genetic Algorithms #11

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GEONKIM1 commented Mar 18, 2024 • edited Loading

This is a new methodology about adaptive mutation and crossover. Adaptive mutation : DHM/ILC, ILM/DHC(Linearly increasing or decreasing) , quadratic function method, step function method. Adaptive crossover : DHM/ILC, ILM/DHC(Linearly increasing or decreasing) , quadratic function method

Pull Request Description

What issue does this change request address? (Use "#" before the issue to link it, i.e., idaholab#42.

What are the significant changes in functionality due to this change request?

For Change Control Board: Change Request Review

Jimmy-INL Apr 10, 2024

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Jimmy-INL Apr 12, 2024

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GEONKIM1 commented Mar 18, 2024 •

edited

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This is a new methodology about adaptive mutation and crossover.
Adaptive mutation : DHM/ILC, ILM/DHC(Linearly increasing or decreasing) , quadratic function method, step function method.
Adaptive crossover : DHM/ILC, ILM/DHC(Linearly increasing or decreasing) , quadratic function method