diff --git a/Manifest.toml b/Manifest.toml index 3b3da9f..027e941 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -627,9 +627,9 @@ version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "4b138e4643b577ccf355377c2bc70fa975af25de" +git-tree-sha1 = "7901a6117656e29fa2c74a58adb682f380922c47" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.115" +version = "0.25.116" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" diff --git a/assets/literate/DCM.md b/assets/literate/DCM.md index 5b46a24..67b8584 100644 --- a/assets/literate/DCM.md +++ b/assets/literate/DCM.md @@ -293,7 +293,7 @@ Prepare the DCM. This function will setup the computation of the Dynamic Causal with_stack(f, n) = fetch(schedule(Task(f, n))); ```` -We are now ready to run the optimization procedure! :) +We are now ready to run the optimization procedure! That is we loop over run_sDCM_iteration! which will alter `state` after each optimization iteration. It essentially computes the Variational Laplace estimation of expectation and variance of the tunable parameters. ````julia:ex26 diff --git a/assets/pages/CS_circuit/code/output/cort_asc_stack.svg b/assets/pages/CS_circuit/code/output/cort_asc_stack.svg index 9a4f102..b3366e0 100644 --- a/assets/pages/CS_circuit/code/output/cort_asc_stack.svg +++ b/assets/pages/CS_circuit/code/output/cort_asc_stack.svg @@ -2,66 +2,66 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -72,127 +72,127 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/assets/pages/CS_circuit/code/output/cort_meanfield.svg b/assets/pages/CS_circuit/code/output/cort_meanfield.svg index 3b001b7..31beda0 100644 --- a/assets/pages/CS_circuit/code/output/cort_meanfield.svg +++ b/assets/pages/CS_circuit/code/output/cort_meanfield.svg @@ -2,115 +2,106 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - + - - - - + - + - - - - + + + + @@ -118,152 +109,141 @@ - - - - - - - - - - - - - - + + + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - + + + + diff --git a/assets/pages/CS_circuit/code/output/cort_power.svg b/assets/pages/CS_circuit/code/output/cort_power.svg index 7fb454f..40f433f 100644 --- a/assets/pages/CS_circuit/code/output/cort_power.svg +++ b/assets/pages/CS_circuit/code/output/cort_power.svg @@ -2,177 +2,183 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + + + + - + - + + + + - + - + - + - + - + - + - + @@ -188,219 +194,220 @@ - - - - + + + + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - + - + - + - + - + - + - + @@ -412,10 +419,11 @@ - - - - + + + + + diff --git a/assets/pages/CS_circuit/code/output/cort_stack.svg b/assets/pages/CS_circuit/code/output/cort_stack.svg index 578b5e9..16bcbe8 100644 --- a/assets/pages/CS_circuit/code/output/cort_stack.svg +++ b/assets/pages/CS_circuit/code/output/cort_stack.svg @@ -2,66 +2,66 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -72,138 +72,138 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/assets/pages/CS_circuit/code/output/wta_stack.svg b/assets/pages/CS_circuit/code/output/wta_stack.svg index b3deeb9..90be86b 100644 --- a/assets/pages/CS_circuit/code/output/wta_stack.svg +++ b/assets/pages/CS_circuit/code/output/wta_stack.svg @@ -2,66 +2,66 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -72,83 +72,83 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - + + + + + + diff --git a/assets/pages/CS_circuit/code/output/wta_wta_stack.svg b/assets/pages/CS_circuit/code/output/wta_wta_stack.svg index 600acda..9be748a 100644 --- a/assets/pages/CS_circuit/code/output/wta_wta_stack.svg +++ b/assets/pages/CS_circuit/code/output/wta_wta_stack.svg @@ -2,66 +2,66 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -72,89 +72,89 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - + + + + + + + + + + + + diff --git a/assets/pages/custom/code/output/ex6.res b/assets/pages/custom/code/output/ex6.res index c478aae..a865d54 100644 --- a/assets/pages/custom/code/output/ex6.res +++ b/assets/pages/custom/code/output/ex6.res @@ -1,4 +1,4 @@ -Main.FD_SANDBOX_13439752999271061286.IzhNeuron(ModelingToolkit.ODESystem(0x0000000000002013, Symbolics.Equation[Differential(t)(V(t)) ~ 145 + jcn - u(t) + 5V(t) + 0.04(V(t)^2), Differential(t)(u(t)) ~ a*(-u(t) + b*V(t))], t, SymbolicUtils.BasicSymbolic{Real}[V(t), u(t), jcn], SymbolicUtils.BasicSymbolic{Real}[a, b, V_reset, d, θ], nothing, Dict{Any, Any}(:a => a, :b => b, :d => d, :V => V(t), :jcn => jcn, :u => u(t), :θ => θ, :V_reset => V_reset), Any[], Symbolics.Equation[], Base.RefValue{Vector{Symbolics.Num}}(Symbolics.Num[]), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), :izh, "", ModelingToolkit.ODESystem[], Dict{Any, Any}(a => 0.02, V_reset => -50, d => 2, u(t) => -13, V(t) => -65, b => 0.2, θ => 30), Dict{Any, Any}(), nothing, nothing, Symbolics.Equation[], nothing, nothing, nothing, ModelingToolkit.SymbolicContinuousCallback[], ModelingToolkit.SymbolicDiscreteCallback[condition: V(t) > θ +Main.FD_SANDBOX_13439752999271061286.IzhNeuron(ModelingToolkit.ODESystem(0x0000000000001fed, Symbolics.Equation[Differential(t)(V(t)) ~ 145 + jcn - u(t) + 5V(t) + 0.04(V(t)^2), Differential(t)(u(t)) ~ a*(-u(t) + b*V(t))], t, SymbolicUtils.BasicSymbolic{Real}[V(t), u(t), jcn], SymbolicUtils.BasicSymbolic{Real}[a, b, V_reset, d, θ], nothing, Dict{Any, Any}(:a => a, :b => b, :d => d, :V => V(t), :jcn => jcn, :u => u(t), :θ => θ, :V_reset => V_reset), Any[], Symbolics.Equation[], Base.RefValue{Vector{Symbolics.Num}}(Symbolics.Num[]), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), :izh, "", ModelingToolkit.ODESystem[], Dict{Any, Any}(a => 0.02, V_reset => -50, d => 2, u(t) => -13, V(t) => -65, b => 0.2, θ => 30), Dict{Any, Any}(), nothing, nothing, Symbolics.Equation[], nothing, nothing, nothing, ModelingToolkit.SymbolicContinuousCallback[], ModelingToolkit.SymbolicDiscreteCallback[condition: V(t) > θ affects: u(t) ~ d + u(t) V(t) ~ V_reset diff --git a/assets/pages/learning/code/output/adj_RL.svg b/assets/pages/learning/code/output/adj_RL.svg index 110fa40..29327fa 100644 --- a/assets/pages/learning/code/output/adj_RL.svg +++ b/assets/pages/learning/code/output/adj_RL.svg @@ -2,2269 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + @@ -7771,24 +7769,24 @@ - - + + - - + + - - + + - - + + - - + + @@ -7797,23 +7795,23 @@ - + - - + + - + @@ -7822,20 +7820,24 @@ + + + - - + + + @@ -7844,24 +7846,22 @@ + - - - + - - + + - @@ -7870,24 +7870,20 @@ - - + - - - - + diff --git a/assets/pages/learning/code/output/ex3.out b/assets/pages/learning/code/output/ex3.out index 18f8d86..6a13261 100644 --- a/assets/pages/learning/code/output/ex3.out +++ b/assets/pages/learning/code/output/ex3.out @@ -1,100 +1,100 @@ -Trial = 1, Category choice = 1, Response = False +Trial = 1, Category choice = 2, Response = Correct Trial = 2, Category choice = 2, Response = False Trial = 3, Category choice = 2, Response = False Trial = 4, Category choice = 2, Response = Correct -Trial = 5, Category choice = 2, Response = False -Trial = 6, Category choice = 2, Response = Correct -Trial = 7, Category choice = 2, Response = Correct -Trial = 8, Category choice = 2, Response = Correct -Trial = 9, Category choice = 2, Response = Correct +Trial = 5, Category choice = 1, Response = Correct +Trial = 6, Category choice = 1, Response = False +Trial = 7, Category choice = 1, Response = False +Trial = 8, Category choice = 1, Response = False +Trial = 9, Category choice = 1, Response = False Trial = 10, Category choice = 1, Response = False -Trial = 11, Category choice = 1, Response = False +Trial = 11, Category choice = 2, Response = Correct Trial = 12, Category choice = 1, Response = False -Trial = 13, Category choice = 2, Response = False -Trial = 14, Category choice = 2, Response = Correct -Trial = 15, Category choice = 1, Response = Correct -Trial = 16, Category choice = 1, Response = Correct -Trial = 17, Category choice = 2, Response = False -Trial = 18, Category choice = 2, Response = False +Trial = 13, Category choice = 1, Response = Correct +Trial = 14, Category choice = 1, Response = False +Trial = 15, Category choice = 2, Response = False +Trial = 16, Category choice = 2, Response = False +Trial = 17, Category choice = 1, Response = Correct +Trial = 18, Category choice = 1, Response = Correct Trial = 19, Category choice = 2, Response = False -Trial = 20, Category choice = 2, Response = Correct +Trial = 20, Category choice = 1, Response = False Trial = 21, Category choice = 1, Response = Correct Trial = 22, Category choice = 1, Response = Correct -Trial = 23, Category choice = 1, Response = Correct +Trial = 23, Category choice = 2, Response = False Trial = 24, Category choice = 2, Response = Correct -Trial = 25, Category choice = 2, Response = False -Trial = 26, Category choice = 2, Response = False +Trial = 25, Category choice = 1, Response = Correct +Trial = 26, Category choice = 1, Response = Correct Trial = 27, Category choice = 2, Response = False -Trial = 28, Category choice = 2, Response = False +Trial = 28, Category choice = 1, Response = Correct Trial = 29, Category choice = 2, Response = Correct Trial = 30, Category choice = 1, Response = Correct -Trial = 31, Category choice = 1, Response = False -Trial = 32, Category choice = 1, Response = Correct -Trial = 33, Category choice = 2, Response = Correct +Trial = 31, Category choice = 2, Response = Correct +Trial = 32, Category choice = 2, Response = False +Trial = 33, Category choice = 1, Response = False Trial = 34, Category choice = 2, Response = Correct Trial = 35, Category choice = 1, Response = False Trial = 36, Category choice = 2, Response = False Trial = 37, Category choice = 1, Response = Correct -Trial = 38, Category choice = 1, Response = Correct -Trial = 39, Category choice = 1, Response = False -Trial = 40, Category choice = 1, Response = Correct -Trial = 41, Category choice = 2, Response = Correct +Trial = 38, Category choice = 2, Response = False +Trial = 39, Category choice = 2, Response = Correct +Trial = 40, Category choice = 2, Response = False +Trial = 41, Category choice = 1, Response = False Trial = 42, Category choice = 2, Response = False -Trial = 43, Category choice = 2, Response = False -Trial = 44, Category choice = 2, Response = Correct -Trial = 45, Category choice = 1, Response = Correct -Trial = 46, Category choice = 1, Response = Correct +Trial = 43, Category choice = 1, Response = Correct +Trial = 44, Category choice = 1, Response = False +Trial = 45, Category choice = 2, Response = False +Trial = 46, Category choice = 2, Response = False Trial = 47, Category choice = 1, Response = Correct -Trial = 48, Category choice = 2, Response = Correct -Trial = 49, Category choice = 2, Response = Correct +Trial = 48, Category choice = 1, Response = False +Trial = 49, Category choice = 1, Response = False Trial = 50, Category choice = 1, Response = False -Trial = 51, Category choice = 2, Response = False +Trial = 51, Category choice = 1, Response = Correct Trial = 52, Category choice = 2, Response = False Trial = 53, Category choice = 2, Response = Correct -Trial = 54, Category choice = 2, Response = Correct -Trial = 55, Category choice = 2, Response = Correct -Trial = 56, Category choice = 2, Response = Correct -Trial = 57, Category choice = 2, Response = False +Trial = 54, Category choice = 1, Response = False +Trial = 55, Category choice = 1, Response = False +Trial = 56, Category choice = 1, Response = False +Trial = 57, Category choice = 1, Response = Correct Trial = 58, Category choice = 1, Response = Correct -Trial = 59, Category choice = 2, Response = False +Trial = 59, Category choice = 1, Response = Correct Trial = 60, Category choice = 1, Response = Correct Trial = 61, Category choice = 2, Response = Correct Trial = 62, Category choice = 1, Response = False Trial = 63, Category choice = 2, Response = Correct -Trial = 64, Category choice = 2, Response = False +Trial = 64, Category choice = 1, Response = Correct Trial = 65, Category choice = 1, Response = Correct -Trial = 66, Category choice = 2, Response = Correct +Trial = 66, Category choice = 1, Response = False Trial = 67, Category choice = 2, Response = False -Trial = 68, Category choice = 2, Response = Correct -Trial = 69, Category choice = 2, Response = Correct +Trial = 68, Category choice = 1, Response = False +Trial = 69, Category choice = 1, Response = False Trial = 70, Category choice = 2, Response = False Trial = 71, Category choice = 1, Response = Correct -Trial = 72, Category choice = 2, Response = Correct +Trial = 72, Category choice = 1, Response = False Trial = 73, Category choice = 1, Response = False -Trial = 74, Category choice = 2, Response = False +Trial = 74, Category choice = 1, Response = Correct Trial = 75, Category choice = 1, Response = Correct Trial = 76, Category choice = 2, Response = Correct -Trial = 77, Category choice = 2, Response = False +Trial = 77, Category choice = 1, Response = Correct Trial = 78, Category choice = 1, Response = Correct Trial = 79, Category choice = 1, Response = Correct -Trial = 80, Category choice = 2, Response = False -Trial = 81, Category choice = 2, Response = Correct -Trial = 82, Category choice = 1, Response = Correct +Trial = 80, Category choice = 1, Response = Correct +Trial = 81, Category choice = 1, Response = False +Trial = 82, Category choice = 2, Response = False Trial = 83, Category choice = 2, Response = False -Trial = 84, Category choice = 1, Response = False +Trial = 84, Category choice = 2, Response = Correct Trial = 85, Category choice = 1, Response = False Trial = 86, Category choice = 2, Response = False Trial = 87, Category choice = 2, Response = False -Trial = 88, Category choice = 2, Response = False -Trial = 89, Category choice = 2, Response = Correct +Trial = 88, Category choice = 1, Response = Correct +Trial = 89, Category choice = 1, Response = False Trial = 90, Category choice = 2, Response = False Trial = 91, Category choice = 2, Response = Correct -Trial = 92, Category choice = 1, Response = Correct -Trial = 93, Category choice = 2, Response = Correct +Trial = 92, Category choice = 2, Response = False +Trial = 93, Category choice = 1, Response = False Trial = 94, Category choice = 1, Response = False Trial = 95, Category choice = 2, Response = False -Trial = 96, Category choice = 1, Response = False -Trial = 97, Category choice = 1, Response = False +Trial = 96, Category choice = 2, Response = Correct +Trial = 97, Category choice = 2, Response = Correct Trial = 98, Category choice = 1, Response = False -Trial = 99, Category choice = 2, Response = False +Trial = 99, Category choice = 1, Response = Correct Trial = 100, Category choice = 1, Response = Correct diff --git a/assets/pages/learning/code/output/ex3.res b/assets/pages/learning/code/output/ex3.res index d3a2d5f..05fe882 100644 --- a/assets/pages/learning/code/output/ex3.res +++ b/assets/pages/learning/code/output/ex3.res @@ -1 +1 @@ -(trial = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100], correct = Bool[0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1], action = [1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 1, 2, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 2, 2, 2, 2, 1, 2, 1, 2, 1, 2, 2, 1, 1, 2, 2, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 1, 2, 1, 2, 1, 1, 1, 2, 1]) \ No newline at end of file +(trial = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100], correct = Bool[1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1], action = [2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 1, 2, 2, 2, 1, 2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 1, 1, 1, 2, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1]) \ No newline at end of file diff --git a/pages/DCM/index.html b/pages/DCM/index.html index 0ac434e..2515c67 100644 --- a/pages/DCM/index.html +++ b/pages/DCM/index.html @@ -300,7 +300,7 @@

Se # HACK: on machines with very small amounts of RAM, Julia can run out of stack space while compiling the code called in this loop # this should be rewritten to abuse the compiler less, but for now, an easy solution is just to run it with more allocated stack space. with_stack(f, n) = fetch(schedule(Task(f, n))); -

We are now ready to run the optimization procedure! :) That is we loop over runsDCMiteration! which will alter state after each optimization iteration. It essentially computes the Variational Laplace estimation of expectation and variance of the tunable parameters.

+

We are now ready to run the optimization procedure! That is we loop over runsDCMiteration! which will alter state after each optimization iteration. It essentially computes the Variational Laplace estimation of expectation and variance of the tunable parameters.

with_stack(5_000_000) do  # 5MB of stack space
     for iter in 1:max_iter
         state.iter = iter
diff --git a/pages/custom/index.html b/pages/custom/index.html
index 54fcc0a..e60f528 100644
--- a/pages/custom/index.html
+++ b/pages/custom/index.html
@@ -49,7 +49,7 @@
 
         new(sys, namespace)
     end
-end

NOTE: In IzhNeuron the jcn variable does not get a default value, only the [input=true] tag. This means that other Bloxs will connect to a IzhNeuron through jcn.

Neuroblox automatically initializes a jcn ~ 0 equation and then accumulates connection terms in it. This happens with all input variables of Bloxs.

Similarly the [output=true] tag designates the V variable as the output variable. It is necessary for every Blox to have one if they rely on generic connection rules that fetch the output variable and add it to the connection equation.

Both input and output tags are also useful to note which variables should be used when writing connection rules to or from our Blox.

Now we are ready to define the first object of IzhNeuron and connect it with the LIFNeuron we created above.

@named izh = IzhNeuron()
IzhNeuron(ModelingToolkit.ODESystem(0x0000000000002013, Symbolics.Equation[Differential(t)(V(t)) ~ 145 + jcn - u(t) + 5V(t) + 0.04(V(t)^2), Differential(t)(u(t)) ~ a*(-u(t) + b*V(t))], t, SymbolicUtils.BasicSymbolic{Real}[V(t), u(t), jcn], SymbolicUtils.BasicSymbolic{Real}[a, b, V_reset, d, θ], nothing, Dict{Any, Any}(:a => a, :b => b, :d => d, :V => V(t), :jcn => jcn, :u => u(t), :θ => θ, :V_reset => V_reset), Any[], Symbolics.Equation[], Base.RefValue{Vector{Symbolics.Num}}(Symbolics.Num[]), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), :izh, "", ModelingToolkit.ODESystem[], Dict{Any, Any}(a => 0.02, V_reset => -50, d => 2, u(t) => -13, V(t) => -65, b => 0.2, θ => 30), Dict{Any, Any}(), nothing, nothing, Symbolics.Equation[], nothing, nothing, nothing, ModelingToolkit.SymbolicContinuousCallback[], ModelingToolkit.SymbolicDiscreteCallback[condition: V(t) > θ
+end

NOTE: In IzhNeuron the jcn variable does not get a default value, only the [input=true] tag. This means that other Bloxs will connect to a IzhNeuron through jcn.

Neuroblox automatically initializes a jcn ~ 0 equation and then accumulates connection terms in it. This happens with all input variables of Bloxs.

Similarly the [output=true] tag designates the V variable as the output variable. It is necessary for every Blox to have one if they rely on generic connection rules that fetch the output variable and add it to the connection equation.

Both input and output tags are also useful to note which variables should be used when writing connection rules to or from our Blox.

Now we are ready to define the first object of IzhNeuron and connect it with the LIFNeuron we created above.

@named izh = IzhNeuron()
IzhNeuron(ModelingToolkit.ODESystem(0x0000000000001fed, Symbolics.Equation[Differential(t)(V(t)) ~ 145 + jcn - u(t) + 5V(t) + 0.04(V(t)^2), Differential(t)(u(t)) ~ a*(-u(t) + b*V(t))], t, SymbolicUtils.BasicSymbolic{Real}[V(t), u(t), jcn], SymbolicUtils.BasicSymbolic{Real}[a, b, V_reset, d, θ], nothing, Dict{Any, Any}(:a => a, :b => b, :d => d, :V => V(t), :jcn => jcn, :u => u(t), :θ => θ, :V_reset => V_reset), Any[], Symbolics.Equation[], Base.RefValue{Vector{Symbolics.Num}}(Symbolics.Num[]), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), :izh, "", ModelingToolkit.ODESystem[], Dict{Any, Any}(a => 0.02, V_reset => -50, d => 2, u(t) => -13, V(t) => -65, b => 0.2, θ => 30), Dict{Any, Any}(), nothing, nothing, Symbolics.Equation[], nothing, nothing, nothing, ModelingToolkit.SymbolicContinuousCallback[], ModelingToolkit.SymbolicDiscreteCallback[condition: V(t) > θ
 affects:
   u(t) ~ d + u(t)
   V(t) ~ V_reset
diff --git a/pages/learning/index.html b/pages/learning/index.html
index d815f0b..d6ed779 100644
--- a/pages/learning/index.html
+++ b/pages/learning/index.html
@@ -103,107 +103,107 @@
 
 adjacency(fig[1,1], agent; title = "Before Learning", colorrange=(0,10))
 
-trace = run_experiment!(agent, env; t_warmup=200.0, alg=Vern7(), verbose=true)
Trial = 1, Category choice = 1, Response = False
+trace = run_experiment!(agent, env; t_warmup=200.0, alg=Vern7(), verbose=true)
Trial = 1, Category choice = 2, Response = Correct
 Trial = 2, Category choice = 2, Response = False
 Trial = 3, Category choice = 2, Response = False
 Trial = 4, Category choice = 2, Response = Correct
-Trial = 5, Category choice = 2, Response = False
-Trial = 6, Category choice = 2, Response = Correct
-Trial = 7, Category choice = 2, Response = Correct
-Trial = 8, Category choice = 2, Response = Correct
-Trial = 9, Category choice = 2, Response = Correct
+Trial = 5, Category choice = 1, Response = Correct
+Trial = 6, Category choice = 1, Response = False
+Trial = 7, Category choice = 1, Response = False
+Trial = 8, Category choice = 1, Response = False
+Trial = 9, Category choice = 1, Response = False
 Trial = 10, Category choice = 1, Response = False
-Trial = 11, Category choice = 1, Response = False
+Trial = 11, Category choice = 2, Response = Correct
 Trial = 12, Category choice = 1, Response = False
-Trial = 13, Category choice = 2, Response = False
-Trial = 14, Category choice = 2, Response = Correct
-Trial = 15, Category choice = 1, Response = Correct
-Trial = 16, Category choice = 1, Response = Correct
-Trial = 17, Category choice = 2, Response = False
-Trial = 18, Category choice = 2, Response = False
+Trial = 13, Category choice = 1, Response = Correct
+Trial = 14, Category choice = 1, Response = False
+Trial = 15, Category choice = 2, Response = False
+Trial = 16, Category choice = 2, Response = False
+Trial = 17, Category choice = 1, Response = Correct
+Trial = 18, Category choice = 1, Response = Correct
 Trial = 19, Category choice = 2, Response = False
-Trial = 20, Category choice = 2, Response = Correct
+Trial = 20, Category choice = 1, Response = False
 Trial = 21, Category choice = 1, Response = Correct
 Trial = 22, Category choice = 1, Response = Correct
-Trial = 23, Category choice = 1, Response = Correct
+Trial = 23, Category choice = 2, Response = False
 Trial = 24, Category choice = 2, Response = Correct
-Trial = 25, Category choice = 2, Response = False
-Trial = 26, Category choice = 2, Response = False
+Trial = 25, Category choice = 1, Response = Correct
+Trial = 26, Category choice = 1, Response = Correct
 Trial = 27, Category choice = 2, Response = False
-Trial = 28, Category choice = 2, Response = False
+Trial = 28, Category choice = 1, Response = Correct
 Trial = 29, Category choice = 2, Response = Correct
 Trial = 30, Category choice = 1, Response = Correct
-Trial = 31, Category choice = 1, Response = False
-Trial = 32, Category choice = 1, Response = Correct
-Trial = 33, Category choice = 2, Response = Correct
+Trial = 31, Category choice = 2, Response = Correct
+Trial = 32, Category choice = 2, Response = False
+Trial = 33, Category choice = 1, Response = False
 Trial = 34, Category choice = 2, Response = Correct
 Trial = 35, Category choice = 1, Response = False
 Trial = 36, Category choice = 2, Response = False
 Trial = 37, Category choice = 1, Response = Correct
-Trial = 38, Category choice = 1, Response = Correct
-Trial = 39, Category choice = 1, Response = False
-Trial = 40, Category choice = 1, Response = Correct
-Trial = 41, Category choice = 2, Response = Correct
+Trial = 38, Category choice = 2, Response = False
+Trial = 39, Category choice = 2, Response = Correct
+Trial = 40, Category choice = 2, Response = False
+Trial = 41, Category choice = 1, Response = False
 Trial = 42, Category choice = 2, Response = False
-Trial = 43, Category choice = 2, Response = False
-Trial = 44, Category choice = 2, Response = Correct
-Trial = 45, Category choice = 1, Response = Correct
-Trial = 46, Category choice = 1, Response = Correct
+Trial = 43, Category choice = 1, Response = Correct
+Trial = 44, Category choice = 1, Response = False
+Trial = 45, Category choice = 2, Response = False
+Trial = 46, Category choice = 2, Response = False
 Trial = 47, Category choice = 1, Response = Correct
-Trial = 48, Category choice = 2, Response = Correct
-Trial = 49, Category choice = 2, Response = Correct
+Trial = 48, Category choice = 1, Response = False
+Trial = 49, Category choice = 1, Response = False
 Trial = 50, Category choice = 1, Response = False
-Trial = 51, Category choice = 2, Response = False
+Trial = 51, Category choice = 1, Response = Correct
 Trial = 52, Category choice = 2, Response = False
 Trial = 53, Category choice = 2, Response = Correct
-Trial = 54, Category choice = 2, Response = Correct
-Trial = 55, Category choice = 2, Response = Correct
-Trial = 56, Category choice = 2, Response = Correct
-Trial = 57, Category choice = 2, Response = False
+Trial = 54, Category choice = 1, Response = False
+Trial = 55, Category choice = 1, Response = False
+Trial = 56, Category choice = 1, Response = False
+Trial = 57, Category choice = 1, Response = Correct
 Trial = 58, Category choice = 1, Response = Correct
-Trial = 59, Category choice = 2, Response = False
+Trial = 59, Category choice = 1, Response = Correct
 Trial = 60, Category choice = 1, Response = Correct
 Trial = 61, Category choice = 2, Response = Correct
 Trial = 62, Category choice = 1, Response = False
 Trial = 63, Category choice = 2, Response = Correct
-Trial = 64, Category choice = 2, Response = False
+Trial = 64, Category choice = 1, Response = Correct
 Trial = 65, Category choice = 1, Response = Correct
-Trial = 66, Category choice = 2, Response = Correct
+Trial = 66, Category choice = 1, Response = False
 Trial = 67, Category choice = 2, Response = False
-Trial = 68, Category choice = 2, Response = Correct
-Trial = 69, Category choice = 2, Response = Correct
+Trial = 68, Category choice = 1, Response = False
+Trial = 69, Category choice = 1, Response = False
 Trial = 70, Category choice = 2, Response = False
 Trial = 71, Category choice = 1, Response = Correct
-Trial = 72, Category choice = 2, Response = Correct
+Trial = 72, Category choice = 1, Response = False
 Trial = 73, Category choice = 1, Response = False
-Trial = 74, Category choice = 2, Response = False
+Trial = 74, Category choice = 1, Response = Correct
 Trial = 75, Category choice = 1, Response = Correct
 Trial = 76, Category choice = 2, Response = Correct
-Trial = 77, Category choice = 2, Response = False
+Trial = 77, Category choice = 1, Response = Correct
 Trial = 78, Category choice = 1, Response = Correct
 Trial = 79, Category choice = 1, Response = Correct
-Trial = 80, Category choice = 2, Response = False
-Trial = 81, Category choice = 2, Response = Correct
-Trial = 82, Category choice = 1, Response = Correct
+Trial = 80, Category choice = 1, Response = Correct
+Trial = 81, Category choice = 1, Response = False
+Trial = 82, Category choice = 2, Response = False
 Trial = 83, Category choice = 2, Response = False
-Trial = 84, Category choice = 1, Response = False
+Trial = 84, Category choice = 2, Response = Correct
 Trial = 85, Category choice = 1, Response = False
 Trial = 86, Category choice = 2, Response = False
 Trial = 87, Category choice = 2, Response = False
-Trial = 88, Category choice = 2, Response = False
-Trial = 89, Category choice = 2, Response = Correct
+Trial = 88, Category choice = 1, Response = Correct
+Trial = 89, Category choice = 1, Response = False
 Trial = 90, Category choice = 2, Response = False
 Trial = 91, Category choice = 2, Response = Correct
-Trial = 92, Category choice = 1, Response = Correct
-Trial = 93, Category choice = 2, Response = Correct
+Trial = 92, Category choice = 2, Response = False
+Trial = 93, Category choice = 1, Response = False
 Trial = 94, Category choice = 1, Response = False
 Trial = 95, Category choice = 2, Response = False
-Trial = 96, Category choice = 1, Response = False
-Trial = 97, Category choice = 1, Response = False
+Trial = 96, Category choice = 2, Response = Correct
+Trial = 97, Category choice = 2, Response = Correct
 Trial = 98, Category choice = 1, Response = False
-Trial = 99, Category choice = 2, Response = False
+Trial = 99, Category choice = 1, Response = Correct
 Trial = 100, Category choice = 1, Response = Correct
-(trial = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100], correct = Bool[0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1], action = [1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 1, 2, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 2, 2, 2, 2, 1, 2, 1, 2, 1, 2, 2, 1, 1, 2, 2, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 1, 2, 1, 2, 1, 1, 1, 2, 1])

trace is a NamedTuple containing useful outcomes for each trial of the experiment:

trace.trial ## trial indices
+(trial = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100], correct = Bool[1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1], action = [2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 1, 2, 2, 2, 1, 2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 1, 1, 1, 2, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1])

trace is a NamedTuple containing useful outcomes for each trial of the experiment:

trace.trial ## trial indices
 trace.correct ## whether the response was correct or not on each trial
 trace.action; ## what responce was made on each trial, 1 is left and 2 is right