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kinaseq updated, working for standard equations; will try to optimize…
… summary function to save compute cost
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| NDrives = 3 | ||
| Paradigm = "GroupGoodBad" | ||
| LengthRange.Min = 4 | ||
| LengthRange.Max = 12 | ||
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| // Copyright (c) 2023, The Emergent Authors. All rights reserved. | ||
| // Use of this source code is governed by a BSD-style | ||
| // license that can be found in the LICENSE file. | ||
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| package main | ||
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| // ParamConfig has config parameters related to sim params | ||
| type ParamConfig struct { | ||
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| // gain multiplier on spike for computing CaSpk: increasing this directly affects the magnitude of the trace values, learning rate in Target layers, and other factors that depend on CaSpk values: RLRate, UpdateThr. Path.KinaseCa.SpikeG provides an additional gain factor specific to the synapse-level trace factors, without affecting neuron-level CaSpk values. Larger networks require higher gain factors at the neuron level -- 12, vs 8 for smaller. | ||
| SpikeG float32 `default:"8"` | ||
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| // time constant for integrating spike-driven calcium trace at sender and recv neurons, CaSyn, which then drives synapse-level integration of the joint pre * post synapse-level activity, in cycles (msec). Note: if this param is changed, then there will be a change in effective learning rate that can be compensated for by multiplying PathParams.Learn.KinaseCa.SpikeG by sqrt(30 / sqrt(SynTau) | ||
| SynTau float32 `default:"30" min:"1"` | ||
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| // rate = 1 / tau | ||
| SynDt float32 `view:"-" json:"-" xml:"-" edit:"-"` | ||
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| // network parameters | ||
| Network map[string]any | ||
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| // Extra Param Sheet name(s) to use (space separated if multiple) -- must be valid name as listed in compiled-in params or loaded params | ||
| Sheet string | ||
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| // extra tag to add to file names and logs saved from this run | ||
| Tag string | ||
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| // user note -- describe the run params etc -- like a git commit message for the run | ||
| Note string | ||
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| // Name of the JSON file to input saved parameters from. | ||
| File string `nest:"+"` | ||
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| // Save a snapshot of all current param and config settings in a directory named params_<datestamp> (or _good if Good is true), then quit -- useful for comparing to later changes and seeing multiple views of current params | ||
| SaveAll bool `nest:"+"` | ||
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| // for SaveAll, save to params_good for a known good params state. This can be done prior to making a new release after all tests are passing -- add results to git to provide a full diff record of all params over time. | ||
| Good bool `nest:"+"` | ||
| } | ||
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| func (pc *ParamConfig) Update() { | ||
| pc.SynDt = 1.0 / pc.SynTau | ||
| } | ||
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| // RunConfig has config parameters related to running the sim | ||
| type RunConfig struct { | ||
| // Neuron runs the standard Neuron update equations, vs. Kinase experimental equations | ||
| Neuron bool `default:"false"` | ||
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| // use the GPU for computation -- only for testing in this model -- not faster | ||
| GPU bool `default:"false"` | ||
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| // number of parallel threads for CPU computation -- 0 = use default | ||
| NThreads int `default:"2"` | ||
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| // starting run number -- determines the random seed -- runs counts from there -- can do all runs in parallel by launching separate jobs with each run, runs = 1 | ||
| Run int `default:"0"` | ||
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| // total number of runs to do when running Train | ||
| NRuns int `default:"1" min:"1"` | ||
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| // total number of epochs per run | ||
| NEpochs int `default:"1"` | ||
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| // total number of epochs per run | ||
| NTrials int `default:"10"` // 1000 | ||
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| MinusMSec int `default:"150"` | ||
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| PlusMSec int `default:"50"` | ||
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| ISIMSec int `default:"200"` | ||
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| // firing rate, for testing | ||
| MinusHz, PlusHz float32 `default:"50"` | ||
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| // additive difference in sending firing frequency relative to recv (recv has basic minus, plus) | ||
| SendDiffHz float32 | ||
| } | ||
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| // LogConfig has config parameters related to logging data | ||
| type LogConfig struct { | ||
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| // if true, save final weights after each run | ||
| SaveWts bool | ||
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| // if true, save cycle log to file, as .cyc.tsv typically | ||
| Cycle bool `default:"true" nest:"+"` | ||
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| // if true, save network activation etc data from testing trials, for later viewing in netview | ||
| NetData bool | ||
| } | ||
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| // Config is a standard Sim config -- use as a starting point. | ||
| type Config struct { | ||
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| // clamp constant Ge value -- otherwise drive discrete spiking input | ||
| GeClamp bool `default:"false"` | ||
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| // frequency of input spiking for !GeClamp mode | ||
| SpikeHz float32 `default:"50"` | ||
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| // Raw synaptic excitatory conductance | ||
| Ge float32 `min:"0" step:"0.01" default:"2.0"` | ||
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| // Inhibitory conductance | ||
| Gi float32 `min:"0" step:"0.01" default:"0.1"` | ||
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| // total number of cycles to run | ||
| NCycles int `min:"10" default:"200"` | ||
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| // when does excitatory input into neuron come on? | ||
| OnCycle int `min:"0" default:"10"` | ||
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| // when does excitatory input into neuron go off? | ||
| OffCycle int `min:"0" default:"190"` | ||
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| // how often to update display (in cycles) | ||
| UpdateInterval int `min:"1" default:"10"` | ||
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| // specify include files here, and after configuration, it contains list of include files added | ||
| Includes []string | ||
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| // open the GUI -- does not automatically run -- if false, then runs automatically and quits | ||
| GUI bool `default:"true"` | ||
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| // log debugging information | ||
| Debug bool | ||
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| // parameter related configuration options | ||
| Params ParamConfig `view:"add-fields"` | ||
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| // sim running related configuration options | ||
| Run RunConfig `view:"add-fields"` | ||
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| // data logging related configuration options | ||
| Log LogConfig `view:"add-fields"` | ||
| } | ||
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| func (cfg *Config) IncludesPtr() *[]string { return &cfg.Includes } |
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