change from end of sample learning to online learning

Manifest.toml

@@ -16,9 +16,9 @@ weakdeps = ["ChainRulesCore"]
 
 [[deps.Accessors]]
 deps = ["Compat", "CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "Test"]
-git-tree-sha1 = "a4f8669e46c8cdf68661fe6bb0f7b89f51dd23cf"
+git-tree-sha1 = "2b301c2388067d655fe5e4ca6d4aa53b61f895b4"
 uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
-version = "0.1.30"
+version = "0.1.31"
 
     [deps.Accessors.extensions]
     AccessorsAxisKeysExt = "AxisKeys"
@@ -67,10 +67,24 @@ uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b"
 version = "0.4.2"
 
 [[deps.BangBang]]
-deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"]
+deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"]
-git-tree-sha1 = "7fe6d92c4f281cf4ca6f2fba0ce7b299742da7ca"
+git-tree-sha1 = "54b00d1b93791f8e19e31584bd30f2cb6004614b"
 uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66"
-version = "0.3.37"
+version = "0.3.38"
+
+    [deps.BangBang.extensions]
+    BangBangChainRulesCoreExt = "ChainRulesCore"
+    BangBangDataFramesExt = "DataFrames"
+    BangBangStaticArraysExt = "StaticArrays"
+    BangBangStructArraysExt = "StructArrays"
+    BangBangTypedTablesExt = "TypedTables"
+
+    [deps.BangBang.weakdeps]
+    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+    StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+    StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+    TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9"
 
 [[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -155,9 +169,13 @@ uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
 version = "1.0.2+0"
 
 [[deps.CompositionsBase]]
-git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769"
+git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad"
 uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b"
-version = "0.1.1"
+version = "0.1.2"
+weakdeps = ["InverseFunctions"]
+
+    [deps.CompositionsBase.extensions]
+    CompositionsBaseInverseFunctionsExt = "InverseFunctions"
 
 [[deps.ConstructionBase]]
 deps = ["LinearAlgebra"]
@@ -340,13 +358,13 @@ version = "0.1.4"
 
 [[deps.GPUCompiler]]
 deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"]
-git-tree-sha1 = "e9a9173cd77e16509cdf9c1663fda19b22a518b7"
+git-tree-sha1 = "5737dc242dadd392d934ee330c69ceff47f0259c"
 uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
-version = "0.19.3"
+version = "0.19.4"
 
 [[deps.GeneralUtils]]
 deps = ["DataStructures", "Distributions", "JSON3"]
-path = "/home/ton/.julia/dev/GeneralUtils"
+path = "C:\\Users\\naraw\\.julia\\dev\\GeneralUtils"
 uuid = "c6c72f09-b708-4ac8-ac7c-2084d70108fe"
 version = "0.1.0"
 
@@ -750,9 +768,9 @@ version = "0.1.15"
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "c262c8e978048c2b095be1672c9bee55b4619521"
+git-tree-sha1 = "8982b3607a212b070a5e46eea83eb62b4744ae12"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.5.24"
+version = "1.5.25"
 
 [[deps.StaticArraysCore]]
 git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a"

src/Ironpen.jl

@@ -25,16 +25,16 @@ using .forward
 include("learn.jl")
 using .learn
 
-include("readout.jl")
+# include("readout.jl")
-using .readout
+# using .readout
 
-include("interface.jl")
+# include("interface.jl")
-using .interface
+# using .interface
 #------------------------------------------------------------------------------------------------100
 
 """ 
     Todo:
-        [*1] add maximum weight cap of each connection
+        
         [2] implement connection strength based on right or wrong answer
         [4] implement dormant connection
         [3] Δweight * connection strength 
@@ -63,6 +63,7 @@ using .interface
         [DONE] neuroplasticity() i.e. change connection
         [DONE] add multi threads
         [DONE] during 0 training if 1-9 output neuron fires, adjust weight only those neurons
+        [DONE] add maximum weight cap of each connection
 
     Change from version:    v06_36a
         - 

src/forward.jl

@@ -1,8 +1,6 @@
 module forward
 
-using Flux.Optimise: apply!
+using Statistics, Random, LinearAlgebra, JSON3
-
-using Statistics, Flux, Random, LinearAlgebra, JSON3
 using GeneralUtils
 using ..types, ..snn_utils
 
@@ -77,19 +75,17 @@ function (kfn::kfn_1)(m::model, input_data::AbstractVector)
 
     kfn.firedNeurons_t0 = [n.z_t for n in kfn.neuronsArray]    #TODO check if it is used?
 
-    Threads.@threads for n in kfn.neuronsArray
+    # Threads.@threads for n in kfn.neuronsArray
-    # for n in kfn.neuronsArray
+    for n in kfn.neuronsArray
         n(kfn)
     end
 
     kfn.firedNeurons_t1 = [n.z_t1 for n in kfn.neuronsArray]
     append!(kfn.firedNeurons, findall(kfn.firedNeurons_t1)) # store id of neuron that fires
-    if kfn.learningStage == "end_learning" 
+    kfn.firedNeurons |> unique!    # use for random new neuron connection
-        kfn.firedNeurons |> unique!    # use for random new neuron connection
-    end
 
-    Threads.@threads for n in kfn.outputNeuronsArray
+    # Threads.@threads for n in kfn.outputNeuronsArray
-    # for n in kfn.outputNeuronsArray
+    for n in kfn.outputNeuronsArray
         n(kfn)
     end
 

src/learn.jl

@@ -1,8 +1,6 @@
 module learn
 
-using Flux.Optimise: apply!
+using Statistics, Random, LinearAlgebra, JSON3
-
-using Statistics, Flux, Random, LinearAlgebra, JSON3
 using GeneralUtils
 using ..types, ..snn_utils
 
@@ -12,7 +10,7 @@ export learn!
 
 function learn!(m::model, modelRespond::Vector{Bool}, correctAnswer::Union{AbstractVector, Nothing})
     if correctAnswer === nothing
-        correctAnswer_I = BitArray(undef, length(modelRespond))
+        correctAnswer_I = BitArray(zeros(length(modelRespond)))
     else
         correctAnswer_I = Bool.(correctAnswer) # correct answer for kfn I
     end
@@ -43,76 +41,43 @@ function learn!(kfn::kfn_1, correctAnswer::BitVector)
     outs = [n.z_t1 for n in kfn.outputNeuronsArray]
     for (i, out) in enumerate(outs)
         if out != correctAnswer[i]   # need to adjust weight
-            kfnError = ( (kfn.outputNeuronsArray[i].v_th - kfn.outputNeuronsArray[i].vError) / 
+            kfnError = ( (kfn.outputNeuronsArray[i].v_th - kfn.outputNeuronsArray[i].vError) * 100.0 / 
                             kfn.outputNeuronsArray[i].v_th )
             if correctAnswer[i] == 1    # output neuron that associated with correctAnswer
-                Threads.@threads for n in kfn.neuronsArray
+                Threads.@threads for n in kfn.neuronsArray # multithread is not atomic and causing error
                 # for n in kfn.neuronsArray
-                    learn!(n, kfnError)
+                    compute_wRecChange!(n, kfnError)
+                    learn!(n, kfn.firedNeurons, kfn.nExInType)
                 end
-
+                compute_wRecChange!(kfn.outputNeuronsArray[i], kfnError)
-                learn!(kfn.outputNeuronsArray[i], kfnError)     
+                learn!(kfn.outputNeuronsArray[i], kfn.firedNeurons, kfn.nExInType, 
+                        kfn.kfnParams[:totalInputPort])
             else    # output neuron that is NOT associated with correctAnswer
-                learn!(kfn.outputNeuronsArray[i], kfnError)
+                compute_wRecChange!(kfn.outputNeuronsArray[i], kfnError)
+                learn!(kfn.outputNeuronsArray[i], kfn.firedNeurons, kfn.nExInType, 
+                        kfn.kfnParams[:totalInputPort])
             end
         end
     end
     
     # wrap up learning session
     if kfn.learningStage == "end_learning"
-        Threads.@threads for n in kfn.neuronsArray
-        # for n in kfn.neuronsArray
-            if typeof(n) <: computeNeuron
-                wSign_0 = sign.(n.wRec) # original sign
-                n.wRec += n.wRecChange  # merge wRecChange into wRec
-                wSign_1 = sign.(n.wRec)   # check for fliped sign, 1 indicates non-fliped sign
-                nonFlipedSign = isequal.(wSign_0, wSign_1)  # 1 not fliped, 0 fliped
-                # normalize wRec peak to prevent input signal overwhelming neuron
-                normalizePeak!(n.wRec, n.wRecChange, 2)
-                # set weight that fliped sign to 0 for random new connection
-                n.wRec .*= nonFlipedSign 
-                capMaxWeight!(n.wRec)   # cap maximum weight
-
-                synapticConnStrength!(n)
-                neuroplasticity!(n, kfn.firedNeurons, kfn.nExInType)
-            end
-        end
-
-        for n in kfn.outputNeuronsArray   # merge wRecChange into wRec
-            wSign_0 = sign.(n.wRec) # original sign
-            n.wRec += n.wRecChange
-            wSign_1 = sign.(n.wRec)   # check for fliped sign, 1 indicates non-fliped sign
-            nonFlipedSign = isequal.(wSign_0, wSign_1)  # 1 not fliped, 0 fliped
-            normalizePeak!(n.wRec, n.wRecChange, 2)
-            n.wRec .*= nonFlipedSign  # set weight that fliped sign to 0 for random new connection
-            capMaxWeight!(n.wRec)   # cap maximum weight
-
-            synapticConnStrength!(n)
-            neuroplasticity!(n, kfn.firedNeurons, kfn.nExInType, kfn.kfnParams[:totalInputPort])
-        end
-
         kfn.learningStage = "inference"
     end
 end
 
-""" passthroughNeuron learn()
+function compute_wRecChange!(n::passthroughNeuron, error::Float64)
-"""
-function learn!(n::passthroughNeuron, error::Float64)
     # skip
 end
 
-""" lif learn()
+function compute_wRecChange!(n::lifNeuron, error::Float64)
-"""
-function learn!(n::lifNeuron, error::Float64)
     n.eRec = n.phi * n.epsilonRec
     ΔwRecChange = n.eta * error * n.eRec
     n.wRecChange .+= ΔwRecChange
     reset_epsilonRec!(n)
 end
 
-""" alifNeuron learn()
+function compute_wRecChange!(n::alifNeuron, error::Float64)
-"""
-function learn!(n::alifNeuron, error::Float64)
     n.eRec_v = n.phi * n.epsilonRec
     n.eRec_a = -n.phi * n.beta * n.epsilonRecA
     n.eRec = n.eRec_v + n.eRec_a
@@ -122,14 +87,71 @@ function learn!(n::alifNeuron, error::Float64)
     reset_epsilonRecA!(n)
 end
 
-""" linearNeuron learn()
+function compute_wRecChange!(n::linearNeuron, error::Float64)
-"""
-function learn!(n::linearNeuron, error::Float64)
     n.eRec = n.phi * n.epsilonRec
     ΔwRecChange = n.eta * error * n.eRec
     n.wRecChange .+= ΔwRecChange
     reset_epsilonRec!(n)
 end
+
+function learn!(n::T, firedNeurons, nExInType) where T<:inputNeuron
+    # skip
+end
+
+function learn!(n::T, firedNeurons, nExInType) where T<:computeNeuron
+    wSign_0 = sign.(n.wRec) # original sign
+    n.wRec += n.wRecChange  # merge wRecChange into wRec
+    reset_wRecChange!(n)
+    wSign_1 = sign.(n.wRec)   # check for fliped sign, 1 indicates non-fliped sign
+    nonFlipedSign = isequal.(wSign_0, wSign_1)  # 1 not fliped, 0 fliped
+    # normalize wRec peak to prevent input signal overwhelming neuron
+    normalizePeak!(n.wRec, n.wRecChange, 2)
+    # set weight that fliped sign to 0 for random new connection
+    n.wRec .*= nonFlipedSign 
+    capMaxWeight!(n.wRec)   # cap maximum weight
+
+    synapticConnStrength!(n)
+    neuroplasticity!(n, firedNeurons, nExInType)
+end
+
+function learn!(n::T, firedNeurons, nExInType, totalInputPort) where T<:outputNeuron
+    wSign_0 = sign.(n.wRec) # original sign
+    n.wRec += n.wRecChange
+    reset_wRecChange!(n)
+    wSign_1 = sign.(n.wRec)   # check for fliped sign, 1 indicates non-fliped sign
+    nonFlipedSign = isequal.(wSign_0, wSign_1)  # 1 not fliped, 0 fliped
+    # normalize wRec peak to prevent input signal overwhelming neuron
+    normalizePeak!(n.wRec, n.wRecChange, 2)
+    # set weight that fliped sign to 0 for random new connection
+    n.wRec .*= nonFlipedSign  
+    capMaxWeight!(n.wRec)   # cap maximum weight
+
+    synapticConnStrength!(n)
+    neuroplasticity!(n,firedNeurons, nExInType, totalInputPort)
+end
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 
 
 

src/snn_utils.jl

@@ -1,10 +1,9 @@
 module snn_utils
 
-using Flux.Optimise: apply!
 export calculate_α, calculate_ρ, calculate_k, timestep_forward!, init_neuron, no_negative!,
         precision, calculate_w_change!, store_knowledgefn_error!, interneurons_adjustment!, 
         reset_z_t!, resetLearningParams!, reset_learning_history_params!, reset_epsilonRec!,
-        reset_epsilonRecA!, synapticConnStrength!, normalizePeak!,
+        reset_epsilonRecA!, synapticConnStrength!, normalizePeak!, reset_wRecChange!,
         firing_rate_error!, firing_rate_regulator!, update_Bn!, cal_firing_reg!,
         neuroplasticity!, shakeup!, reset_learning_no_wchange!, adjust_internal_learning_rate!,
         gradient_withloss, capMaxWeight!
@@ -253,6 +252,11 @@ function adjust_internal_learning_rate!(n::computeNeuron)
                                 n.internal_learning_rate * 1.005
 end
 
+function connStrengthAdjust(currentStrength::Float64)
+    Δstrength = (1.0 - sigmoid(currentStrength))
+    return Δstrength::Float64
+end
+
 """ compute synaptic connection strength. bias will shift currentStrength to fit into
     sigmoid operating range which centred at 0 and range is -37 to 37.
     # Example
@@ -260,21 +264,15 @@ end
     one may use bias = -5 to transform synaptic strength into range -5 to 5
     the return value is shifted back to original scale
 """
-function synapticConnStrength(currentStrength::AbstractFloat, updown::String, bias::Number=0)::Float64
+function synapticConnStrength(currentStrength::Float64, updown::String)
-    currentStrength += bias
+    Δstrength = connStrengthAdjust(currentStrength)
-    if currentStrength > 0
-        Δstrength = (1.0 - sigmoid(currentStrength))
-    else
-        Δstrength = sigmoid(currentStrength)
-    end
 
     if updown == "up"
         updatedStrength = currentStrength + Δstrength
     else
         updatedStrength = currentStrength - Δstrength
     end
-    updatedStrength -= bias
+    return updatedStrength::Float64
-    return updatedStrength 
 end
 
 """ Compute all synaptic connection strength of a neuron. Also mark n.wRec to 0 if wRec goes
@@ -318,47 +316,6 @@ function normalizePeak!(v1::Vector, v2::Vector, radius::Integer=2)
     normalize!(subvector, 1)
 end
 
-""" rewire of neuron synaptic connection that has 0 weight. With connection's excitatory and 
-    inhabitory ratio constraint.
-"""
-# function neuroplasticity!(n::Union{computeNeuron, outputNeuron}, firedNeurons::Vector,
-#                     nExcitatory::Vector, nInhabitory::Vector, excitatoryPercent::Integer)
-#     # if there is 0-weight then replace it with new connection
-#     zeroWeightConnIndex = findall(iszero.(n.wRec))   # connection that has 0 weight
-#     desiredEx = Int(floor((excitatoryPercent / 100) * length(n.subscriptionList)))
-#     desiredIn = length(n.subscriptionList) - desiredEx
-#     wRecSign = sign.(n.wRec)
-#     inConn = sum(isequal.(wRecSign, -1))
-
-#     # random new synaptic connection
-#     inConnToAdd = desiredIn - inConn
-#     if inConnToAdd <= 0
-#         # skip  all new Conn will be excitatory type
-#     else
-#         newConnVecSign = ones(length(zeroWeightConnIndex))
-#         newConnVecSign = view(newConnVecSign, 1:inConnToAdd) * -1
-#     end
-
-#     # new synaptic connection must sample fron neuron that fires
-#     inPool = nInhabitory ∩ firedNeurons
-#     filter!(x -> x ∉ [n.id], inPool)  # exclude this neuron id from the list
-#     filter!(x -> x ∉ n.subscriptionList, inPool) # exclude this neuron's subscriptionList from the list
-#     exPool = nExcitatory ∩ firedNeurons
-#     filter!(x -> x ∉ [n.id], exPool)  # exclude this neuron id from the list
-#     filter!(x -> x ∉ n.subscriptionList, exPool) # exclude this neuron's subscriptionList from the list
-
-#     w = [rand(0.01:0.01:0.2, length(zeroWeightConnIndex))] .* newConnVecSign
-#     synapticStrength = [rand(-5:0.01:-4, length(zeroWeightConnIndex))]
-
-#     # add new synaptic connection to neuron
-#     for (i, connIndex) in enumerate(zeroWeightConnIndex)
-#         n.subscriptionList[connIndex] = newConnVecSign[i] < 0 ? pop!(inPool) : pop!(exPool)
-#         n.wRec[connIndex] = w[i]
-#         n.synapticStrength[connIndex] = synapticStrength[i]
-#     end
-# end
-
-
 """ rewire of neuron synaptic connection that has 0 weight. Without connection's excitatory and 
     inhabitory ratio constraint.
 """

src/types.jl

@@ -9,7 +9,7 @@ export
     instantiate_custom_types, init_neuron, populate_neuron,    
     add_neuron!
 
-using Random, Flux, LinearAlgebra
+using Random, LinearAlgebra
 
 #------------------------------------------------------------------------------------------------100
 
@@ -350,7 +350,7 @@ Base.@kwdef mutable struct lifNeuron <: computeNeuron
     refractoryDuration::Int64 = 3     # neuron's refratory period in millisecond
     refractoryCounter::Int64 = 0
     tau_m::Float64 = 0.0        # τ_m, membrane time constant  in millisecond
-    eta::Float64 = 0.0001        # η, learning rate
+    eta::Float64 = 0.01        # η, learning rate
     wRecChange::Array{Float64} = Float64[]     # Δw_rec, cumulated wRec change
     recSignal::Float64 = 0.0    # incoming recurrent signal
     alpha_v_t::Float64 = 0.0  # alpha * v_t
@@ -438,7 +438,7 @@ Base.@kwdef mutable struct alifNeuron <: computeNeuron
     eRec_v::Array{Float64} = Float64[]    # a component of neuron's eligibility trace resulted from v_t
     eRec_a::Array{Float64} = Float64[]    # a component of neuron's eligibility trace resulted from av_th
     eRec::Array{Float64} = Float64[]    # neuron's eligibility trace
-    eta::Float64 = 0.0001        # eta, learning rate
+    eta::Float64 = 0.01        # eta, learning rate
     gammaPd::Float64 = 0.3      # γ_pd, discount factor, value from paper
     phi::Float64 = 0.0          # ϕ, psuedo derivative
     refractoryDuration::Int64 = 3     # neuron's refractory period in millisecond
@@ -448,7 +448,7 @@ Base.@kwdef mutable struct alifNeuron <: computeNeuron
     recSignal::Float64 = 0.0    # incoming recurrent signal
     alpha_v_t::Float64 = 0.0  # alpha * v_t
     error::Float64 = 0.0   # local neuron error
-    optimiser::Union{Any,Nothing} = load_optimiser("AdaBelief") # Flux optimizer
+    # optimiser::Union{Any,Nothing} = load_optimiser("AdaBelief") # Flux optimizer
 
     firingCounter::Int64 = 0 # store how many times neuron fires 
     firingRateTarget::Float64 = 20.0 # neuron's target firing rate in Hz
@@ -548,7 +548,7 @@ Base.@kwdef mutable struct linearNeuron <: outputNeuron
     refractoryDuration::Int64 = 3     # neuron's refratory period in millisecond
     refractoryCounter::Int64 = 0
     tau_out::Float64 = 0.0        # τ_out, membrane time constant  in millisecond
-    eta::Float64 = 0.0001        # η, learning rate
+    eta::Float64 = 0.01        # η, learning rate
     wRecChange::Array{Float64} = Float64[]     # Δw_rec, cumulated wRec change
     recSignal::Float64 = 0.0    # incoming recurrent signal
     alpha_v_t::Float64 = 0.0  # alpha * v_t
@@ -588,21 +588,21 @@ end
 
 #------------------------------------------------------------------------------------------------100
 
-function load_optimiser(optimiser_name::String; params::Union{Dict,Nothing} = nothing)
+# function load_optimiser(optimiser_name::String; params::Union{Dict,Nothing} = nothing)
-    if optimiser_name == "AdaBelief"
+#     if optimiser_name == "AdaBelief"
-        params = (0.01, (0.9, 0.8))
+#         params = (0.01, (0.9, 0.8))
-        return Flux.Optimise.AdaBelief(params...)
+#         return Flux.Optimise.AdaBelief(params...)
-    elseif optimiser_name == "AdaBelief2"
+#     elseif optimiser_name == "AdaBelief2"
-        # output neuron requires slower change pace so η is lower than compute neuron at 0.007
+#         # output neuron requires slower change pace so η is lower than compute neuron at 0.007
-            # because if w_out change too fast, compute neuron will not able to 
+#             # because if w_out change too fast, compute neuron will not able to 
-            # grapse output neuron moving direction i.e. both compute neuron's direction and
+#             # grapse output neuron moving direction i.e. both compute neuron's direction and
-            # output neuron direction are out of sync.
+#             # output neuron direction are out of sync.
-        params = (0.007, (0.9, 0.8))    
+#         params = (0.007, (0.9, 0.8))    
-        return Flux.Optimise.AdaBelief(params...)
+#         return Flux.Optimise.AdaBelief(params...)
-    else
+#     else
-        error("optimiser is not defined yet in load_optimiser()")
+#         error("optimiser is not defined yet in load_optimiser()")
-    end
+#     end
-end
+# end
 
 function init_neuron!(id::Int64, n::passthroughNeuron, n_params::Dict, kfnParams::Dict)
     n.id = id