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bugs\r\n\r\n* implemented wc model\r\n\r\n* oc wc implemented and partially tested\r\n\r\n* - improved performance of cost functions and derivatives (derivative_precision_cost x7, precision_cost x2 with better readability), all tests passed\r\n\r\n* functional version wc optimal control\r\n\r\n* remove file\r\n\r\n* - remove explicit passing of parameter \"N\" to precision_cost function\r\n- update of docstrings\r\n\r\n* - simplified function, passes tests\r\n\r\n* - fix: adjoint_state[t=0] was never computed\r\n\r\n* - added function 'update_control_with_limit' to limit the absolute value of the control strength at all points in time. Passes tests.\r\n- added new attribute 'maximum_control_strength' to the 'OC' class to set the absolute maximum value for the control strength\r\n- test cases for the new function 'update_control_with_limit'\r\n\r\n* - fix: added missing 'maximum_control_strength' as parameter in the derived oc-classes\r\n\r\n* - fix: added scaling by time step of precision- and energy cost, added parameter in function calls\r\n- adjusted corresponding test cases\r\n\r\n* corrected background missing\r\n\r\n* - interval in which precision cost is now positional argument to avoid repeated checks of specification and allow notation with \"negative indices\" in Oc-object initialization\r\n- added 'convert_interval' to allow for the different ways of interval specification\r\n- updated function calls accordingly\r\n- changed test structure: separate tests for the interval-specification\r\n\r\n* - added: apply maximal-absolute-control-strength constraint even before first optimization\r\n- added: new test cases; passes all tests\r\n- minor fixes\r\n\r\n* - additional assertions for interval specification\r\n- checks for repeated calls of \".optimize()\"\r\n- new test cases\r\n- removed unused variable and old comments\r\n\r\n* merged cost_functions_numba branch\r\n\r\n* merged cost_functions_numba branch\r\n\r\n* - adjusted to naming 'Duh' for Jacobian\r\n- jit the compute_gradient-functions\r\n- added documentation & docstrings\r\n\r\n* removed unnecessary line of code\r\n\r\n* remove background from oc.py\r\n\r\n* - adaptive step size computation:\r\n     * adaptive step-size reduction or -increment, reduces relevance of hyperparameter for initial step size\r\n     * memorize last step, heavily increases efficiency in many cases\r\n- added very generic test case for step-size computation based on derived OcWc-class\r\n- \"convert_interval\" not further numba-compiled\r\n- improved documentation, added type-description in model specific OC classes\r\n- added todo-hints for automated control-adjustments\r\n- set default of \"precision_cost_interval\" in OcWc to same values as for the the other models\r\n\r\n* - add counter=0 in case of zero gradient\r\n- remove distinction (not-)noisy step within the noise-free step size computation, that is not required at this point\r\n- add test case for zero-step\r\n\r\n* - combine the step-size combination for the noisy and the noise free setting in the adaptive step-size algorithm\r\n\r\n* - shared \"factor_down\" for noisy and deterministic case\r\n- \"factor_down**2\" in loop for finding numerically stable regime for faster exit of loop\r\n- call the new step-size function for noisy case and delete unused method\r\n-> passes all tests in test-oc and test-fhn-noisy\r\n- adjust parameters in test case to range [0,1] in Cmat\r\n\r\n* - revision of documentation\r\n- changed variable names for clarity\r\n\r\n* - revision of docstrings for clean documentation build\r\n- fix typos and add comments\r\n- rename variables and functions for clarity\r\n\r\n* - fix mistake in equation\r\n\r\n* implemented network delays for fhn, hopf, wc/ added tests for all three models\r\n\r\n* update notebooks, fixed typo in oc.py\r\n\r\n* removed commented debug code\r\n\r\n* removed file accidentially imported from other branch\r\n\r\n* Revert \"removed file accidentially imported from other branch\"\r\n\r\nThis reverts commit 0543c8ac45a840994396367795775c2698c4ffb7.\r\n\r\n* - add comments\r\n- variable naming for clarity\r\n- remove unused code and comments\r\n- use fixed seed in test-cases for reproducibility in all cases\r\n\r\n* corrected small mistake in delay test\r\n\r\n* delay test cases\r\n\r\n* cleaned branch, remove files from experiments\r\n\r\n* - restructure project\r\n\r\n* - move example file\r\n\r\n* - adjust imports in example to new project structure\r\n\r\n* corrected failing test\r\n\r\n* corrected failing test\r\n\r\n* - move the calculation of Jacobian matrices to neurolib core modules and adjust imports in the OC submodule\r\n\r\n* - create subfolders for oc-tests and -examples and adjust naming\r\n\r\n* fixed issue in step size reduction\r\n\r\n* fixed issue in step size reduction\r\n\r\n* - restore documentation-updates:\r\n   + improved docstrings and comments\r\n   + better aligned to PEP\r\n   + clear variable naming\r\n\r\n* fixed bug in time delay\r\n\r\n* delete check zero in cmat/ run model once at initilaization/ revise example notebooks/ fix bugs in step_size and delay\r\n\r\n* revise test files\r\n\r\n* correct typo in jacobian\r\n\r\n* correct typo in jacobian\r\n\r\n* cost functional restructure\r\n\r\n* update test wc\r\n\r\n* update test wc\r\n\r\n* update test wc\r\n\r\n* update test wc\r\n\r\n* changed chdir in control examples\r\n\r\n* revision\r\n\r\n* added test for weights dictionary\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Delete CONTRIBUTING.md\r\n\r\n* Delete README.md\r\n\r\n* start implementation oc aln\r\n\r\n* implemeted bug fixes: aln delayed exc feedback, wc noise, wc&fhn&hopf copy params\r\n\r\n* time seires variables\r\n\r\n* fixed bug in aln implementation\r\n\r\n* time dependent variables\r\n\r\n* fixed mistake\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* time dependend variables and init\r\n\r\n* notebook description\r\n\r\n* implementation\r\n\r\n* aln implementation\r\n\r\n* added gradient as self.gradient\r\n\r\n* aln imp\r\n\r\n* implementation without params.Dmat_ndt\r\n\r\n* functioning implementation except for sigmas, adaptation\r\n\r\n* functioning implementation except for sigmas, adaptation\r\n\r\n* sigma implementation, IA missing\r\n\r\n* apparently works with adaptation\r\n\r\n* minimal version of adaptation control\r\n\r\n* finish aln implementation including adaptation current\r\n\r\n* finish aln implementation including adaptation current\r\n\r\n* refactoring\r\n\r\n* merge neurolib updates\r\n\r\n* network implementation\r\n\r\n* finalize(?) aln\r\n\r\n* remove files\r\n\r\n* refactor implementation and finish example notebook\r\n\r\n* finalize tests\r\n\r\n* replace Vmean with analytical function\r\n\r\n* finish test cases\r\n\r\n* finalize aln implmentation\r\n\r\n* added Dxdoth in hopf and fhn\r\n\r\n* adjust fhn, hopf, wc model_params as in aln\r\n\r\n* pass N, V, T for iterations\r\n\r\n* refactor compute_gradient function\r\n\r\n* update comments\r\n\r\n* fix bug in network input aln\r\n\r\n* revise example notebooks\r\n\r\n* initialize. for implementation, wait for aln\r\n\r\n* merge aln into OCdev\r\n\r\n* cleaned up repository\r\n\r\n* clean up\r\n\r\n* Delete workflow.txt\r\n\r\n* move zero_ste_encountered in deterministic computation\r\n\r\n* implemented cost interval and added test\r\n\r\n* checkout files from master\r\n\r\n* fixed solve_adjoint\r\n\r\n* differentiate static and time-dependent inputs\r\n\r\n* update example\r\n\r\n* revert example change\r\n\r\n* update wc for baseline and dynamical inputs\r\n\r\n* revise test wc\r\n\r\n* revise test wc\r\n\r\n* revised cost functional tests\r\n\r\n* revised remaining test files\r\n\r\n* moved get_xs, get_xs_delay and update_input to oc.py\r\n\r\n* refactoring tests\r\n\r\n* state vars as dict\r\n\r\n* remove test notebook\r\n\r\n* update aln model with correct input_vars\r\n\r\n* merging\r\n\r\n* finish test revision\r\n\r\n* indexing in time_integration file via dictionary in all models\r\n\r\n* remove comments\r\n\r\n* add adjust shape method for inputs, refactoring\r\n\r\n* moved example files to main folder\r\n\r\n* refactor aln oc test\r\n\r\n* refactor etst cases\r\n\r\n* remove unnecessary parameter\r\n\r\n* solve_adjoint revision, WC notebook\r\n\r\n* refactor tests\r\n\r\n* Update timeIntegration.py\r\n\r\n* Update plot_oc.py\r\n\r\n* shorten example runtime\r\n\r\n* Delete examples/example-5.6-oc-aln-model-noisy.ipynb\r\n\r\n* Delete examples/example-5.2-oc-phenomenological-model-noisy.ipynb\r\n\r\n* Update plot_oc.py\r\n\r\n* Update cost_functions.py\r\n\r\n* added test for solve_adjoint\r\n\r\n* Update test_oc.py\r\n\r\n* Update oc.py\r\n\r\n* Update oc.py\r\n\r\n* fix bug in WC jacobian\r\n\r\n* Rename example-5.3-oc-wc-model-deterministic.ipynb to example-5.2-oc-wc-model-deterministic.ipynb\r\n\r\n* Rename example-5.4-oc-wc-model-noisy.ipynb to example-5.3-oc-wc-model-noisy.ipynb\r\n\r\n* Rename example-5.5-oc-aln-model-deterministic.ipynb to example-5.4-oc-aln-model-deterministic.ipynb\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\nCo-authored-by: Caglar Cakan <caglorithm@gmail.com>\r\n\r\n* move plot_oc to neurolib.utils\r\n\r\n* restore plot_oc.py in correct form\r\n\r\n---------\r\n\r\nCo-authored-by: Martin <martinkrueck@gmx.de>\r\nCo-authored-by: Caglar Cakan <caglorithm@gmail.com>","shortMessageHtmlLink":"Optimal Control extension (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" 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