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Circuit simulation widget #2117

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Circuit simulation widget #2117

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clbarnes
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@clbarnes clbarnes commented May 19, 2021 •
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Resurrected Albert's efforts from a few years ago, now as a draft PR to make it easier to find.

This implements Casey's rate models (I believe from https://www.sciencedirect.com/science/article/pii/S0092867416312429 , implemented in https://github.com/ceesem/fb_feedback_model ) in the frontend.

Example units here: https://gist.github.com/clbarnes/7b22409a41f9272c201653937df63d1b

@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch 2 times, most recently from 113c92a to b79f233 Compare May 24, 2021 13:15
@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch from b79f233 to e64c503 Compare June 7, 2021 09:38
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clbarnes commented Jun 10, 2021 •
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UI thoughts:

global controls

  • Units are created by adding as single skeletons (uses skeleton names) or as a group (popup asking for group name, pre-populated with e.g. comma-separated names)
    • removal done via the unit dynamics table
  • total time
  • advanced settings collapsed (or tabbed)
    • max iterations per timestep
    • termination criteria? hard to do right
  • Checkbox for "resimulate on change"
    • performance-dependent
    • could automatically cut out at certain complexity level (e.g. n_edges * timesteps * maxit); this could be controlled in advanced settings
  • Button for "normalise weights": ensure that the largest is 1 and scale appropriately
    • Could be a checkbox to do this onchange
  • Button for "populate weights" to get from synapse count
    • checkbox or popup for "normalise by input fraction" (hover: "only for complete skeletons")
    • warning if weights are non-empty
  • buttons for import/ export JSON
  • lock all inputs during execution
  • button to export traces

Tables

All tables collapsible, otherwise the controls are going to be huge. Alternatively, tables could go into content.

  • Unit dynamics table

    • Checkbox for selection: act as skeleton source
    • Each added skeleton/group has a row with columns colourpicker, k, th, I_tonic, scaling, tau
      • additionally, a special top row allowing setting for all selected
    • "Remove unit" button which also clears from weight and stimulation tables
    • Allow renaming? With skeleton names as a hover
    • export as CSV

  • Weight table

    • row and column added for each unit
    • each cell has a num box
    • colour cell background by relative weight?
    • export as CSV

  • Stimulation table:

    • Empty by default with "add row" button for stimulation: drop-down for unit, num boxes for strength, start, stop
    • Same unit can appear multiple times for chains of stimulation
    • Allow sorting by values
    • export as CSV

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Additional features

  • Parameter sweeping
    • UI to run many simulations with small changes to parameters, somehow visualise them
  • "Simulate circuit" button in graph widget (respecting groups etc.)

@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch 2 times, most recently from cb74be4 to db642bf Compare July 20, 2021 17:00
@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch from db642bf to 423053a Compare August 10, 2021 08:30
@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch from 423053a to 6685da4 Compare August 18, 2021 13:45
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Current status

  • fixed a bug which meant the plot's time series was warped
  • simulation units can be uploaded from a JSON file
  • results can be exported as JSON

@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch 2 times, most recently from ce58325 to c5f3a99 Compare September 3, 2021 12:39
@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch from c5f3a99 to 61547fe Compare September 8, 2021 09:55
@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch from 61547fe to 5c4e049 Compare September 23, 2021 15:22
@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch from 5c4e049 to a2688ff Compare October 19, 2021 18:13
@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch from a2688ff to 45e9ee5 Compare November 4, 2021 11:40
@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch 3 times, most recently from 27cad8b to df33ba7 Compare December 21, 2021 13:50
clbarnes and others added 11 commits April 12, 2022 11:25
@clbarnes @acardona @lauralungum
SVGUtil.insertMultiLinePlot: show name on mouseover
0272c5e 
When mouse is passed over a line, if the line has a name, show it in the
title.

Co-authored-by: Albert Cardona <[email protected]>
Co-authored-by: Laura Lungu <[email protected]>
@clbarnes @acardona @lauralungum
SVGUtil.insertMultiLinePlot: add legend.
a7bd6b0 
Co-authored-by: Albert Cardona <[email protected]>
Co-authored-by: Laura Lungu <[email protected]>
@clbarnes @acardona @lauralungum
CircuitSimulation: rate models of circuits
bc6a86f 
Integration is defined as a logistic function.
The activity of neurons is plotted as a function of time.

Based completely on Casey Schneider-Mizell's conceptualization and code.

Includes WIP on parameter UI.

Co-authored-by: Albert Cardona <[email protected]>
Co-authored-by: Laura Lungu <[email protected]>
@clbarnes @acardona @lauralungum
tracing-tool: add CircuitSimulation widget
748b996 
Co-authored-by: Albert Cardona <[email protected]>
Co-authored-by: Laura Lungu <[email protected]>
@clbarnes
circuit-sim: jshint ignore vendored dopri fn
9767368
@clbarnes
circuit sim: converge on this.units as array
05bcc7d
@clbarnes
circuit sim: load units from JSON
1d72140
@clbarnes
Circuit sim: adjust logistic function
8234908 
Prevents the asymptotic nature of logistic functions causing output
where there is no input.

Co-authored-by: Andre Ferreira Castro <[email protected]>
@clbarnes
circuit sim: error handling for JSON file
b100dc3
@clbarnes
circuit sim: docs for units
be5cb06
@clbarnes
circuit sim: fix time scaling
e4335f7 
Previously, the time series was assumed to be 0,1,2...,
where the dopri solver actually uses dynamic time steps.
This resulted in a weird-looking graph.
clbarnes added 6 commits April 12, 2022 11:25
@clbarnes
circuit sim: save results
73ca3e6 
Also allow "Load JSON" to accept results-like JSON.

Minor: set default time to 1000
@clbarnes
circuit sim: improve behaviour of results saving
f3f7142
@clbarnes
circuit-sim: major refactor
a0baf40 
* use ES6 class syntax
* compose over skel source rather than inherit
* prettify
@clbarnes
circuit-sim minor: use new dateToString util
fb9c746
@clbarnes
js tools: zip
9ab2c8d
@clbarnes
WIP circuit sim classes
f0c8863
@clbarnes clbarnes force-pushed the feature/circuit-simulation2 branch from df33ba7 to f0c8863 Compare April 12, 2022 10:25
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