[MRG] Add method to modify synaptic gain #897

ntolley · 2024-09-23T16:40:23Z

Closes #885. This PR allows updating synaptic weights by a scalar gain parameter. Synaptic weights are grouped by E/I connections types (EE, EI, IE, II).

Updates can be performed as:

# In place modification
net.update_weights(e_e=2.0, copy=False)

# Return a copy with updated gains
net2 = net.update_weights(e_e=2.0, copy=True

jasmainak · 2024-09-23T17:36:17Z

hnn_core/network.py

+            Synaptic gain of inhibitory to inhibitory connections (default 1.0)
+        copy : bool
+            If True, create a copy of the network. If False, update the network
+            in place (default True)


gtdang

Looks good! Had a few suggestions for additional tests.

hnn_core/tests/test_network.py

hnn_core/network_builder.py

ntolley · 2024-09-23T18:32:04Z

@gtdang I'm realizing now that our io tests are rather brittle. If any future PR's modify attributes of the network, the default .json files will also need to be updated, perhaps we should look into streamlining this a bit more?

gtdang · 2024-09-23T18:51:40Z

@gtdang I'm realizing now that our io tests are rather brittle. If any future PR's modify attributes of the network, the default .json files will also need to be updated, perhaps we should look into streamlining this a bit more?

There's a function a the top of the tests called generate_test_files that will regenerate the json. You have to run it manually and commit the updated file with the PR though. We could made it a fixture that regenerates it every time the file is run, but the tradeoff is a longer runtime. Or we can put it at the very top and add a note that it must be re-run if the Network structure is changed.

Ultimately if the network structure is altered, we'll likely also need to update the IO functions that read/write the network to file, so the IO tests should break.

… in the __eq__ method of the Network class

This function is a stand-in function for the __eq__ method used only in the tests.

…d correctly by the set gains

gtdang

Everything looks good to me. Though I think we did discuss about changing the method so that it only reassigns the gains specified instead of resetting the unspecified ones to 1. Is that something we still want to do?

gtdang

Looks good to me! Was there anything more you wanted to do with this PR? Otherwise I'm ok with merging.

gtdang · 2024-09-27T19:21:52Z

hnn_core/network.py

@@ -1428,6 +1431,75 @@ def add_electrode_array(self, name, electrode_pos, *, conductivity=0.3,
                                     method=method,
                                     min_distance=min_distance)})

+    def update_weights(self, e_e=None, e_i=None,
+                       i_e=None, i_i=None, copy=True):


Should the default behavior of the method be copy=False? Will most use cases be updating the weights in-place or saving to a new object?

agreed! will change to false and then good to merge

jasmainak · 2024-10-18T19:50:11Z

hnn_core/network.py

@@ -1428,6 +1431,76 @@ def add_electrode_array(self, name, electrode_pos, *, conductivity=0.3,
                                     method=method,
                                     min_distance=min_distance)})

+    def update_weights(self, e_e=None, e_i=None,
+                       i_e=None, i_i=None, copy=False):


something I realized late ... might be worth adding this to an example to show off that it's possible to do. Otherwise it's kind of hidden from the user.

ntolley requested review from gtdang and jasmainak September 23, 2024 16:42

jasmainak reviewed Sep 23, 2024

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gtdang requested changes Sep 23, 2024

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ntolley changed the title ~~WIP: Add method to modify synaptic gain~~ [MRG] Add method to modify synaptic gain Sep 27, 2024

ntolley and others added 10 commits September 27, 2024 11:38

add tests and type checks for synaptic gains

543d94a

tests: updated test asset jones2009_3x3_drives.json

1f040db

test: added gain to test_conn_to_dict

70d1e6e

fix: added the update_weights method to the attributes to ignore list…

0486a40

… in the __eq__ method of the Network class

refactor: removed code for generation of unused test asset file

35f601e

test: updated check_equal_networks of test_gui.py

8401a0c

This function is a stand-in function for the __eq__ method used only in the tests.

test: refactored and added comments to test_synaptic_gains

cac9ebf

test: added test for changing two gains

918b4a4

test: added spot check to see if NetworkBuilder weights are multiplie…

a4c6a8b

…d correctly by the set gains

refactor: flake8

0159408

ntolley force-pushed the syn_gains branch from c2b96e5 to 0159408 Compare September 27, 2024 15:38

update whats_new

e271d2e

gtdang self-requested a review September 27, 2024 16:05

gtdang approved these changes Sep 27, 2024

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ntolley added 2 commits September 27, 2024 14:05

Pass None as default

7acf56d

docstring spacing

ba48c62

gtdang self-requested a review September 27, 2024 19:15

gtdang approved these changes Sep 27, 2024

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gtdang self-requested a review September 27, 2024 19:19

gtdang reviewed Sep 27, 2024

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copy default to false

1bc8eb0

gtdang merged commit 7c4d560 into jonescompneurolab:master Sep 27, 2024
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jasmainak reviewed Oct 18, 2024

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[MRG] Add method to modify synaptic gain #897

[MRG] Add method to modify synaptic gain #897

ntolley commented Sep 23, 2024 •

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[MRG] Add method to modify synaptic gain #897

[MRG] Add method to modify synaptic gain #897

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