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Implement e-prop plasticity #2867

Merged
merged 416 commits into from
Feb 28, 2024
Merged

Implement e-prop plasticity #2867

merged 416 commits into from
Feb 28, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Nov 7, 2023

  1. Use auto instead of explicit HistEntryEprop types 

    Co-authored-by: JesusEV <[email protected]>
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  2. Initialize n_spikes in the constructor 

    Co-authored-by: JesusEV <[email protected]>
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  3. Improve naming of iterators 

    Co-authored-by: JesusEV <[email protected]>
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  4. Unify retrieval of eprop, update and firing rate reg history 

    Co-authored-by: JesusEV <[email protected]>
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  5. Remove unneeded empty vector guards 

    Co-authored-by: JesusEV <[email protected]>
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  6. Change order of history vectors for consistency 

    Co-authored-by: JesusEV <[email protected]>
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  7. Hike clang-format version to 17 and activate InsertBraces

    @heplesser @akorgor
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  8. Prescribe exact clang-format version

    @heplesser @akorgor
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  9. Insert braces around single-line blocks.

    @heplesser @akorgor
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  10. Add const where needed and remove unneeded 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
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  11. Re-add necessary checks for empty containers

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Commits on Nov 8, 2023

  1. Merge branch 'eprop_feature' of github.com:jstapmanns/nest-simulator … 

    …into fix-guards
    @heplesser
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  2. Fix formatting

    @heplesser
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  3. Merge pull request #35 from heplesser/fix-guards 

    Fix guards (new try)
    @akorgor
    akorgor authored Nov 8, 2023
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Commits on Nov 9, 2023

  1. Improve optimize functions 

      * remove underscores for non-attributes
  * do not pass class attributes to function
    @akorgor
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  2. Fix loops and types in learning signal handling

    @akorgor
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  3. Remove unneeded brackets

    @akorgor
    akorgor committed Nov 9, 2023
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  4. Introduce option to average gradient

    @akorgor
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  5. Make get_shift virtual and implement in neurons

    @akorgor
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  6. Avoid type casting in firing rate reg

    @akorgor
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  7. Remove blank line

    @akorgor
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  8. Lift restriction resolution = 1 ms

    @akorgor
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  9. Change type of z and add description

    @akorgor
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  10. Make the tests full-scale

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  11. Write to history only if eprop neuron receives eprop synapses

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Commits on Nov 10, 2023

  1. Make examples more robust and informative.

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  2. Merge branch 'verification_problem' into add-synapse-registration

    @heplesser
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  3. Fix flake8 problem

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  4. Merge branch 'verification_problem' into add-synapse-registration

    @heplesser
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  5. Fix learning-signal readout for empty history

    @heplesser
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  6. Make examples more robust and informative.

    @heplesser @akorgor
    heplesser authored and akorgor committed Nov 10, 2023
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  7. Fix flake8 problem

    @heplesser @akorgor
    heplesser authored and akorgor committed Nov 10, 2023
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  8. Fix comment on removing spikes in 0th time step

    @akorgor
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  9. Compare in tests with rtol instead of atol 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
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  10. Add links to NEST and TF reference implementation 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
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  11. Fix condition in write_update_history 

    Co-authored-by: JesusEV <[email protected]>
    @akorgor @JesusEV
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  12. Let linter ignore too long line

    @akorgor
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  13. Let linter ignore too long line (second try)

    @akorgor
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  14. Add comment on why decreasing the access counter

    @akorgor
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  15. Let linter ignore too long line (third try)

    @akorgor
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  16. Resolve discrepancy between implementation and name of write_learning… 

    …_signal_to_history
    @akorgor
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  17. Add doxygen comments to eprop archiving node 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser committed Nov 10, 2023
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Commits on Nov 12, 2023

  1. Protect verification from case len(loss) < len(loss_verification)

    @JesusEV
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  2. Add missing BadProperty checks

    @JesusEV
    JesusEV committed Nov 12, 2023
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  3. Improve accuracy of decreasing counter comment 

    * add more comments throughout
    @JesusEV
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  4. Fix formatting

    @JesusEV
    JesusEV committed Nov 12, 2023
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  5. Improve readability of gradient_change functions 

    * Refactor to make the application of low pass filters more obvious
* Demonstrate the role of binary variable z
* Add comments
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  6. Refactor erase_unneeded_eprop_history() function via lambda function 

    * add comments explaining function's logic
    @JesusEV
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  7. Add comprehensive comments to erase_unneeded* functions

    @JesusEV
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  8. Add comments to init_update_history() function

    @JesusEV
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  9. Add comments to write_learning_signal_to_history() function

    @JesusEV
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  10. Add comments to functions 

    * add comments to write_surrogate_gradient_to_history()
* add comments to write_error_signal_to_history()
    @JesusEV
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  11. Add comments to functions 

    * get_shift()
* get_update_history()
* get_get_eprop_history()
* get_firing_rate_reg_history()
    @JesusEV
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  12. Add comments to functions count_spike() and reset_spike_count()

    @JesusEV
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  13. Improve comment

    @JesusEV
    JesusEV committed Nov 12, 2023
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  14. Improve comment

    @JesusEV
    JesusEV committed Nov 12, 2023
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  15. Improve comment

    @JesusEV
    JesusEV committed Nov 12, 2023
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  16. Fix typo

    @JesusEV
    JesusEV committed Nov 12, 2023
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Commits on Nov 13, 2023

  1. Update comments in eprop_archiving_node

    @JesusEV
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  2. Update comments in gradient_change() functions

    @JesusEV
    JesusEV committed Nov 13, 2023
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  3. Fix formatting

    @JesusEV
    JesusEV committed Nov 13, 2023
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  4. Fix wrong identation error in userdocs compilation

    @akorgor
    akorgor committed Nov 13, 2023
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  5. Fix dt-dependence of firing rate regularization

    @akorgor
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  6. Make unit-conversion comment more precise

    @akorgor
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  7. Fix pylint line-too-long error

    @akorgor
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  8. Refactor erase_unneeded_eprop_history() function

    @JesusEV
    JesusEV committed Nov 13, 2023
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  9. Improve iterator security during histories cleanup

    @JesusEV @akorgor
    JesusEV authored and akorgor committed Nov 13, 2023
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  10. Replace propagator_idx with descriptive and restrictive str variable

    @JesusEV
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  11. Improve variable name

    @JesusEV
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Commits on Nov 14, 2023

  1. Merge pull request #39 from jstapmanns/remove-propagator-idx 

    Replace propagator_idx with descriptive and restrictive str variable
    @JesusEV
    JesusEV authored Nov 14, 2023
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  2. Fix malformed tables

    @akorgor
    akorgor committed Nov 14, 2023
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  3. Create skeleton for doxygen comments

    @akorgor
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  4. Merge branch 'eprop_feature' into add-synapse-registration

    @JesusEV
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  5. Merge pull request #37 from heplesser/add-synapse-registration 

    Register eprop-related histories only when eprop_synapses are present
    @JesusEV
    JesusEV authored Nov 14, 2023
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  6. Fix formatting

    @JesusEV
    JesusEV committed Nov 14, 2023
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Commits on Nov 15, 2023

  1. Make piecewise_linear funcs more readable and marginally more efficient

    @JesusEV
    JesusEV committed Nov 15, 2023
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  2. Fix bug in tutorial regression script 

    * regression tutorial now accepts batch size different than 1
    @JesusEV
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Commits on Nov 16, 2023

  1. Fix BadProperty checks 

      * introduce additional ones based on restrictions from literature
  * make format consistent
    @akorgor
    akorgor committed Nov 16, 2023
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  2. Remove restriction on eta

    @akorgor
    akorgor committed Nov 16, 2023
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  3. Initialize z in the constructor

    @akorgor
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  4. Remove remaining "leak constant complement"

    @akorgor
    akorgor committed Nov 16, 2023
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  5. Increase readability wrt to identity propagator

    @akorgor
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Commits on Nov 18, 2023

  1. Unify namescape nest scopes

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  2. Disentangle propagators by introducing alpha

    @akorgor
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  3. Replace leak_propagator_complement with alpha_complement

    @akorgor
    akorgor committed Nov 18, 2023
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  4. Fix format

    @akorgor
    akorgor committed Nov 18, 2023
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  5. Merge branch 'eprop_feature' into wip-eprop-doxygen

    @akorgor
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  6. State doxygen descriptions more precisely

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Commits on Nov 20, 2023

  1. Replace identity with unity

    @JesusEV
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  2. Remove remaining eprop_regression

    @akorgor
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  3. Add missing identity-unity renaming

    @akorgor
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  4. Merge branch 'eprop_feature' into wip-eprop-doxygen

    @akorgor
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Commits on Nov 22, 2023

  1. Add start to multimeters of recurrent neurons

    @akorgor
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  2. Include initial weight in weight plotting

    @akorgor
    akorgor committed Nov 22, 2023
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  3. Emphasize difference to iaf_psc_delta 

    Co-authored-by: JesusEV <[email protected]>
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    akorgor and JesusEV committed Nov 22, 2023
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  4. Remove unnecessary n_compare comments

    @akorgor
    akorgor committed Nov 22, 2023
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  5. Declare variables in gradient_change earlier

    @akorgor
    akorgor committed Nov 22, 2023
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  6. Rename requires_buffer to avoid ambiguity

    @akorgor
    akorgor committed Nov 22, 2023
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  7. Merge branch 'eprop_feature' into wip-eprop-doxygen

    @akorgor
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  8. Merge pull request #41 from akorgor/wip-eprop-doxygen 

    Add doxygen comments
    @akorgor
    akorgor authored Nov 22, 2023
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Commits on Nov 23, 2023

  1. Remove loss from cross_entropy_loss

    @akorgor
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  2. Add/remove blank lines and typo

    @akorgor
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Commits on Nov 24, 2023

  1. First version of eprop optimizer as classes; compiles but fails under… 

    … some circumstances
    @heplesser
    heplesser committed Nov 24, 2023
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  2. Fixing bugs

    @heplesser
    heplesser committed Nov 24, 2023
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Commits on Nov 27, 2023

  1. Rename propagators and associated variables

    @akorgor
    akorgor committed Nov 27, 2023
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  2. Rename v_ to v_m_

    @akorgor
    akorgor committed Nov 27, 2023
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  3. Rename a_ to adapt_

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  4. Match order of z, z_in to header file

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  5. Set multimeter stop to exclude forced spike

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Commits on Nov 28, 2023

  1. Fix generation of input spikes for regression for n_batch > 1 

    Co-authored-by: akorgor <[email protected]>
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  2. Fix learning signal getter

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  3. Add missing initialization of v_th_adapt

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  4. Add check eprop_learning_window_new > eprop_update_interval_

    @JesusEV
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  5. Fix typo

    @JesusEV
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Commits on Nov 30, 2023

  1. Simplify tutorials and test

    @akorgor
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  2. Rename tutorials

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Commits on Dec 1, 2023

  1. Prepare adding more tutorials

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Commits on Dec 2, 2023

  1. Remove flake8 in front of noqa

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Commits on Dec 4, 2023

  1. Add handwriting and infinite loop task

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  2. Add erase_unneeded_* functions to eprop_readout

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Commits on Dec 5, 2023

  1. Split optimizers on common and synapse-specific part; does not work f… 

    …ully yet.
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  2. Fix eprop synapse copy and assignment

    @heplesser
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  3. Add assertion

    @heplesser
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  4. Update eprop examples

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  5. Add minimal modelset for eprop examples

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  6. Fix bugs in optimizer class implementation

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  7. Merge branch 'master' of github.com:nest/nest-simulator into jstap-eprop

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  8. Merge branch 'jstap-eprop' into optimizer-class

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  9. Adapt eprop tests to new parameter settings approach

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  10. Adapt eprop examples to new parameter settings approach

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  11. Fix pylint

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  12. Place optimizer properties in subdict; work in progress

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Commits on Dec 6, 2023

  1. Merge pull request #46 from heplesser/jstap-eprop 

    Merging master
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Commits on Dec 7, 2023

  1. Add move constructor and assignment to blockvector and connector

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  2. Set optimizer for all instances of eprop_synapse and add move semantics

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  3. Remove accidentally added debug output

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  4. Fix NEST random seed for examples

    @akorgor
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  5. Merge branch 'optimizer-class-nested-dict' into optimizer-class

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  6. Introduce derived EpropArchivingNode classes 

    Co-authored-by: JesusEV <[email protected]>
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  7. Replace get_name with is_eprop_recurrent_node 

    Co-authored-by: JesusEV <[email protected]>
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  8. Fix copyright header

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  9. Replace get_name with is_eprop_recurrent_node

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  10. Trigger eprop update only after t_next_update + shift

    @JesusEV
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  11. Add additional checks against user errors

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  12. Merge branch 'jstap-eprop' into optimizer-class

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  13. Merge branch 'master' of github.com:nest/nest-simulator into optimize… 

    …r-class
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  14. Fix merge error

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  15. Add missing return

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Commits on Dec 8, 2023

  1. Move management of eprop optimizer object to Connector class with spe… 

    …cialisations; still some debugging code in this commit.
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  2. Merge branch 'optimizer-bugfix' into optimizer-class

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Commits on Dec 9, 2023

  1. Fix formatting in documentation 

    Co-authored-by: Jessica Mitchell <[email protected]>
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  2. Correct index formatting in docs

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    akorgor committed Dec 9, 2023
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Commits on Dec 10, 2023

  1. Fix generation of modelsmodule to include necessary headers

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  2. Allow setting of nested optimizer parameters

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  3. Convert eprop code, test and examples to nested dict with optimizer t… 

    …ype in subdict
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  4. Adapt test to modified eprop_synapse optimizer settings

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Commits on Dec 11, 2023

  1. Rename surrogate_gradient to avoid name clash

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  2. Add more variables to state::get

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Commits on Dec 12, 2023

  1. Link to eprop_plasticity/index

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Commits on Dec 13, 2023

  1. Apply suggestions from code review 

    Co-authored-by: Agnes Korcsak-Gorzo <[email protected]>
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  2. Name changes based on review

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  3. Merge branch 'optimizer-class' of github.com:heplesser/nest-simulator… 

    … into optimizer-class
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  4. Place Wmin before Wmax in examples

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  5. Now single modelset for eprop

    @heplesser
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  6. Renamed EpropOptimizer* to WeightOptimizer*

    @heplesser
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  7. Making optimizer_ member of eprop_synapse private; remove debugging o… 

    …utput.
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  8. Convert last remaining EpropOptimizer... to WeightOptimizer...

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  9. Update modelsets/eprop 

    Co-authored-by: Agnes Korcsak-Gorzo <[email protected]>
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Commits on Dec 14, 2023

  1. Merge branch 'eprop_feature' of github.com:jstapmanns/nest-simulator … 

    …into optimizer-class
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  2. Fix E_L adjustment of adaptive threshold

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  3. Merge pull request #47 from heplesser/optimizer-class 

    Optimizer class / merge #46 first!
    @akorgor
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  4. Merge branch 'master' of github.com:nest/nest-simulator into jstap-eprop

    @heplesser
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  5. Merge pull request #48 from heplesser/jstap-eprop 

    Merged master past nest#2990
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  6. Fix compilation in absence of eprop_synapse

    @heplesser
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  7. Much cleaner implementation of Conncetor template specialisations for… 

    … eprop_synapse
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  8. Merge pull request #49 from heplesser/jstap-eprop 

    Tidying up
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  9. Rename adapting_threshold to V_th_adapt 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
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  10. Make BadProperty messages consistent

    @akorgor
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  11. Refactor synapse dictionaries in tutorials

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  12. Instead of resolution=1ms, set delay=resolution in tests

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  13. Add _to_history to get_learning_signal to avoid name clash

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Commits on Dec 15, 2023

  1. Initialize dynamic variables of Adam optimizer

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  2. Match access specifiers between base and derived node classes

    @akorgor
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  3. Add technical comments

    @heplesser
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  4. Merge pull request #50 from heplesser/jstap-eprop 

    Add technical comments
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  5. Reorganize user documentation and update parameters

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  6. Add more information to e-prop functions in node

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  7. List criteria to erase in erase functions

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Commits on Dec 16, 2023

  1. Add _from to name get_learning_signal_history

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  2. Rename beta1, beta2 to beta_1, beta_2

    @akorgor
    akorgor committed Dec 16, 2023
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  3. Simplify comment

    @akorgor
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  4. Add more doxygen class headers

    @akorgor
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  5. Add more doxygen comments

    @akorgor
    akorgor committed Dec 16, 2023
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  6. Update user documentation

    @akorgor
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  7. Make developer comments consistent

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Commits on Dec 19, 2023

  1. Adjust learning rate validation in weight_optimizer

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  2. Adjust lower bound of weight range in WeightOptimizer 

    Co-authored-by: akorgor <[email protected]>
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  3. Rename gradient_change to compute_gradient across eprop models 

    Co-authored-by: akorgor <[email protected]>
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    JesusEV and akorgor committed Dec 19, 2023
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Commits on Dec 20, 2023

  1. Update eprop example images

    @JesusEV
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  2. Renamed eprop models to include _bsshslm_2020; compiles, examples and… 

    … tests not adapted yet
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  3. Tests adapted to renamed eprop models

    @heplesser
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  4. Adjusted examples to renamed eprop models

    @heplesser
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  5. Renamed test file

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  6. Renamed eprop_iaf_bsshslm_2020_adapt to eprop_iaf_adapt_bsshslm_2020 … 

    …and fixed minor errors.

Co-authored-by: akorgor <[email protected]>
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  7. Remove verification from tutorials

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  8. Add info in what's new 

    Co-authored-by: JesusEV <[email protected]>
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  9. Merge branch 'eprop_feature' of github.com:jstapmanns/nest-simulator … 

    …into jstap-eprop
    @heplesser
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  10. Apply suggestions from code review 

    Co-authored-by: Agnes Korcsak-Gorzo <[email protected]>
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  11. Merge branch 'jstap-eprop' of github.com:heplesser/nest-simulator int… 

    …o jstap-eprop
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  12. Fix modelsets

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Commits on Dec 21, 2023

  1. Merge branch 'master' of github.com:nest/nest-simulator into jstap-eprop

    @heplesser
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  2. Merge pull request #51 from heplesser/jstap-eprop 

    Change model names
    @akorgor
    akorgor authored Dec 21, 2023
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  3. Add explanation of _bsshslm_2020 to user documentation

    @akorgor
    akorgor committed Dec 21, 2023
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  4. Turn plotting on in tutorials

    @akorgor
    akorgor committed Dec 21, 2023
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  5. Fix rendering of math equations 

    Co-authored-by: jessica-mitchell <[email protected]>
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    akorgor and jessica-mitchell committed Dec 21, 2023
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  6. Adjust note on similarity to iaf_psc_delta

    @akorgor
    akorgor committed Dec 21, 2023
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Commits on Jan 12, 2024

  1. Fix type of learning window

    @akorgor
    akorgor committed Jan 12, 2024
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  2. Fix developer comment on error signal

    @akorgor
    akorgor committed Jan 12, 2024
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  3. Add missing arg average_gradient in compute_gradient declaration

    @akorgor
    akorgor committed Jan 12, 2024
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  4. Fix type of t in HistEntryEpropReadout

    @akorgor
    akorgor committed Jan 12, 2024
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Commits on Jan 17, 2024

  1. Rename erase_unneeded* to erase_used* 

    Co-authored-by: JesusEV <[email protected]>
    @akorgor @JesusEV
    akorgor and JesusEV committed Jan 17, 2024
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  2. Fix typo

    @akorgor
    akorgor committed Jan 17, 2024
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  3. Turn KernelException into an IllegalConnection

    @akorgor
    akorgor committed Jan 17, 2024
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Commits on Jan 18, 2024

  1. Rename alpha_t to alpha

    @akorgor
    akorgor committed Jan 18, 2024
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Commits on Jan 19, 2024

  1. Order variables alphabetically

    @akorgor
    akorgor committed Jan 19, 2024
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  2. Add protection for n_record, n_record == 0 

    Co-authored-by: JesusEV <[email protected]>
    @akorgor @JesusEV
    akorgor and JesusEV committed Jan 19, 2024
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Commits on Jan 25, 2024

  1. Remove else which is not needed because of return

    @akorgor
    akorgor committed Jan 25, 2024
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Commits on Feb 14, 2024

  1. Merge branch 'master' into eprop_feature

    @akorgor
    akorgor authored Feb 14, 2024
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  2. Make leak / resting membrane potential naming consistent

    @akorgor
    akorgor committed Feb 14, 2024
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Commits on Feb 15, 2024

  1. Update models/eprop_synapse_bsshslm_2020.h 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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  2. Update nestkernel/histentry.h 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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  3. Update models/eprop_synapse_bsshslm_2020.h 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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  4. Update nestkernel/histentry.h 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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  5. Update nestkernel/histentry.h 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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  6. Update nestkernel/eprop_archiving_node.h 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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  7. Update nestkernel/eprop_archiving_node.h 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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  8. Update models/weight_optimizer.h 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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  9. Update models/weight_optimizer.h 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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  10. Update models/eprop_iaf_adapt_bsshslm_2020.cpp 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser authored Feb 15, 2024
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Commits on Feb 16, 2024

  1. Complete regular_spike_arrival framework 

    Co-authored-by: Hans Ekkehard Plesser <[email protected]>
    @akorgor @heplesser
    akorgor and heplesser committed Feb 16, 2024
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  2. Fix docs on regular_spike_arrival

    @akorgor
    akorgor committed Feb 16, 2024
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Commits on Feb 23, 2024

  1. Fix typo

    @akorgor
    akorgor committed Feb 23, 2024
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Commits on Feb 26, 2024

  1. Fix spelling

    @akorgor
    akorgor committed Feb 26, 2024
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  2. Add n_record note to all tutorials

    @akorgor
    akorgor committed Feb 26, 2024
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  3. Add start and stop to spike and weight recorder

    @akorgor
    akorgor committed Feb 26, 2024
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  4. Remove old n_record setting

    @akorgor
    akorgor committed Feb 26, 2024
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Commits on Feb 27, 2024

  1. Avoid unnecessary elements in loop to accelerate plotting

    @akorgor
    akorgor committed Feb 27, 2024
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  2. Turn f- into r-strings to fix flake8 error

    @akorgor
    akorgor committed Feb 27, 2024
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Commits on Feb 28, 2024

  1. Add missing information to the user documentation

    @akorgor
    akorgor committed Feb 28, 2024
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  2. Merge branch 'master' into eprop_feature

    @akorgor
    akorgor committed Feb 28, 2024
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