Merge branch 'master' into ap/trigger

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.23.1 
+        uses: crate-ci/typos@v1.24.1 

docs/Project.toml

@@ -44,9 +44,9 @@ MethodOfLines = "0.11"
 ModelingToolkit = "9.7"
 MonteCarloMeasurements = "1"
 NeuralPDE = "5.14"
-Optimization = "3.24"
-OptimizationOptimJL = "0.2.1, 0.3"
-OptimizationOptimisers = "0.2.1"
+Optimization = "3.24, 4"
+OptimizationOptimJL = "0.2.1, 0.3, 0.4"
+OptimizationOptimisers = "0.2.1, 0.3"
 OptimizationPolyalgorithms = "0.2"
 OrdinaryDiffEq = "6.74"
 Plots = "1.36"

src/BPINN_ode.jl

@@ -100,6 +100,8 @@ struct BNNODE{C, K, IT <: NamedTuple,
     init_params::I
     Adaptorkwargs::A
     Integratorkwargs::IT
+    numensemble::Int64
+    estim_collocate::Bool
     autodiff::Bool
     progress::Bool
     verbose::Bool
@@ -112,6 +114,8 @@ function BNNODE(chain, Kernel = HMC; strategy = nothing, draw_samples = 2000,
             Metric = DiagEuclideanMetric,
             targetacceptancerate = 0.8),
         Integratorkwargs = (Integrator = Leapfrog,),
+        numensemble = floor(Int, draw_samples / 3),
+        estim_collocate = false,
         autodiff = false, progress = false, verbose = false)
     !(chain isa Lux.AbstractExplicitLayer) &&
         (chain = adapt(FromFluxAdaptor(false, false), chain))
@@ -120,6 +124,7 @@ function BNNODE(chain, Kernel = HMC; strategy = nothing, draw_samples = 2000,
         phystd, dataset, physdt, MCMCkwargs,
         nchains, init_params,
         Adaptorkwargs, Integratorkwargs,
+        numensemble, estim_collocate,
         autodiff, progress, verbose)
 end
 
@@ -186,7 +191,8 @@ function SciMLBase.__solve(prob::SciMLBase.ODEProblem,
     @unpack chain, l2std, phystd, param, priorsNNw, Kernel, strategy,
     draw_samples, dataset, init_params,
     nchains, physdt, Adaptorkwargs, Integratorkwargs,
-    MCMCkwargs, autodiff, progress, verbose = alg
+    MCMCkwargs, numensemble, estim_collocate, autodiff, progress,
+    verbose = alg
 
     # ahmc_bayesian_pinn_ode needs param=[] for easier vcat operation for full vector of parameters
     param = param === nothing ? [] : param
@@ -211,7 +217,8 @@ function SciMLBase.__solve(prob::SciMLBase.ODEProblem,
         Integratorkwargs = Integratorkwargs,
         MCMCkwargs = MCMCkwargs,
         progress = progress,
-        verbose = verbose)
+        verbose = verbose,
+        estim_collocate = estim_collocate)
 
     fullsolution = BPINNstats(mcmcchain, samples, statistics)
     ninv = length(param)
@@ -220,7 +227,8 @@ function SciMLBase.__solve(prob::SciMLBase.ODEProblem,
     if chain isa Lux.AbstractExplicitLayer
         θinit, st = Lux.setup(Random.default_rng(), chain)
         θ = [vector_to_parameters(samples[i][1:(end - ninv)], θinit)
-             for i in (draw_samples - numensemble):draw_samples]
+             for i in 1:max(draw_samples - draw_samples ÷ 10, draw_samples - 1000)]
+
         luxar = [chain(t', θ[i], st)[1] for i in 1:numensemble]
         # only need for size
         θinit = collect(ComponentArrays.ComponentArray(θinit))

src/PDE_BPINN.jl

@@ -69,11 +69,6 @@ function LogDensityProblems.logdensity(Tar::PDELogTargetDensity, θ)
     # + L2loss2(Tar, θ)
 end
 
-# function L2loss2(Tar::PDELogTargetDensity, θ)
-#     return Tar.full_loglikelihood(setparameters(Tar, θ),
-#         Tar.allstd)
-# end
-
 function setparameters(Tar::PDELogTargetDensity, θ)
     names = Tar.names
     ps_new = θ[1:(end - Tar.extraparams)]

src/advancedHMC_MCMC.jl

@@ -16,11 +16,12 @@ mutable struct LogTargetDensity{C, S, ST <: AbstractTrainingStrategy, I,
     physdt::Float64
     extraparams::Int
     init_params::I
+    estim_collocate::Bool
 
     function LogTargetDensity(dim, prob, chain::Optimisers.Restructure, st, strategy,
             dataset,
             priors, phystd, l2std, autodiff, physdt, extraparams,
-            init_params::AbstractVector)
+            init_params::AbstractVector, estim_collocate)
         new{
             typeof(chain),
             Nothing,
@@ -39,12 +40,13 @@ mutable struct LogTargetDensity{C, S, ST <: AbstractTrainingStrategy, I,
             autodiff,
             physdt,
             extraparams,
-            init_params)
+            init_params,
+            estim_collocate)
     end
     function LogTargetDensity(dim, prob, chain::Lux.AbstractExplicitLayer, st, strategy,
             dataset,
             priors, phystd, l2std, autodiff, physdt, extraparams,
-            init_params::NamedTuple)
+            init_params::NamedTuple, estim_collocate)
         new{
             typeof(chain),
             typeof(st),
@@ -60,7 +62,8 @@ mutable struct LogTargetDensity{C, S, ST <: AbstractTrainingStrategy, I,
             autodiff,
             physdt,
             extraparams,
-            init_params)
+            init_params,
+            estim_collocate)
     end
 end
 
@@ -83,7 +86,12 @@ end
 vector_to_parameters(ps_new::AbstractVector, ps::AbstractVector) = ps_new
 
 function LogDensityProblems.logdensity(Tar::LogTargetDensity, θ)
-    return physloglikelihood(Tar, θ) + priorweights(Tar, θ) + L2LossData(Tar, θ)
+    if Tar.estim_collocate
+        return physloglikelihood(Tar, θ) + priorweights(Tar, θ) + L2LossData(Tar, θ) +
+               L2loss2(Tar, θ)
+    else
+        return physloglikelihood(Tar, θ) + priorweights(Tar, θ) + L2LossData(Tar, θ)
+    end
 end
 
 LogDensityProblems.dimension(Tar::LogTargetDensity) = Tar.dim
@@ -92,6 +100,55 @@ function LogDensityProblems.capabilities(::LogTargetDensity)
     LogDensityProblems.LogDensityOrder{1}()
 end
 
+"""
+suggested extra loss function for ODE solver case
+"""
+function L2loss2(Tar::LogTargetDensity, θ)
+    f = Tar.prob.f
+
+    # parameter estimation chosen or not
+    if Tar.extraparams > 0
+        autodiff = Tar.autodiff
+        # Timepoints to enforce Physics 
+        t = Tar.dataset[end]
+        u1 = Tar.dataset[2]
+        û = Tar.dataset[1]
+
+        nnsol = NNodederi(Tar, t, θ[1:(length(θ) - Tar.extraparams)], autodiff)
+
+        ode_params = Tar.extraparams == 1 ?
+                     θ[((length(θ) - Tar.extraparams) + 1):length(θ)][1] :
+                     θ[((length(θ) - Tar.extraparams) + 1):length(θ)]
+
+        if length(Tar.prob.u0) == 1
+            physsol = [f(û[i],
+                ode_params,
+                t[i])
+                       for i in 1:length(û[:, 1])]
+        else
+            physsol = [f([û[i], u1[i]],
+                ode_params,
+                t[i])
+                       for i in 1:length(û)]
+        end
+        #form of NN output matrix output dim x n 
+        deri_physsol = reduce(hcat, physsol)
+
+        physlogprob = 0
+        for i in 1:length(Tar.prob.u0)
+            # can add phystd[i] for u[i] 
+            physlogprob += logpdf(MvNormal(deri_physsol[i, :],
+                    LinearAlgebra.Diagonal(map(abs2,
+                        (Tar.l2std[i] * 4.0) .*
+                        ones(length(nnsol[i, :]))))),
+                nnsol[i, :])
+        end
+        return physlogprob
+    else
+        return 0
+    end
+end
+
 """
 L2 loss loglikelihood(needed for ODE parameter estimation).
 """
@@ -247,7 +304,7 @@ function innerdiff(Tar::LogTargetDensity, f, autodiff::Bool, t::AbstractVector,
 
     vals = nnsol .- physsol
 
-    # N dimensional vector if N outputs for NN(each row has logpdf of i[i] where u is vector of dependant variables)
+    # N dimensional vector if N outputs for NN(each row has logpdf of u[i] where u is vector of dependant variables)
     return [logpdf(
                 MvNormal(vals[i, :],
                     LinearAlgebra.Diagonal(abs2.(Tar.phystd[i] .*
@@ -442,7 +499,8 @@ function ahmc_bayesian_pinn_ode(prob::SciMLBase.ODEProblem, chain;
             Metric = DiagEuclideanMetric, targetacceptancerate = 0.8),
         Integratorkwargs = (Integrator = Leapfrog,),
         MCMCkwargs = (n_leapfrog = 30,),
-        progress = false, verbose = false)
+        progress = false, verbose = false,
+        estim_collocate = false)
     !(chain isa Lux.AbstractExplicitLayer) &&
         (chain = adapt(FromFluxAdaptor(false, false), chain))
     # NN parameter prior mean and variance(PriorsNN must be a tuple)
@@ -467,7 +525,7 @@ function ahmc_bayesian_pinn_ode(prob::SciMLBase.ODEProblem, chain;
         # Lux-Named Tuple
         initial_nnθ, recon, st = generate_Tar(chain, init_params)
     else
-        error("Only Lux.AbstractExplicitLayer neural networks are supported")
+        error("Only Lux.AbstractExplicitLayer Neural networks are supported")
     end
 
     if nchains > Threads.nthreads()
@@ -500,7 +558,7 @@ function ahmc_bayesian_pinn_ode(prob::SciMLBase.ODEProblem, chain;
     t0 = prob.tspan[1]
     # dimensions would be total no of params,initial_nnθ for Lux namedTuples
     ℓπ = LogTargetDensity(nparameters, prob, recon, st, strategy, dataset, priors,
-        phystd, l2std, autodiff, physdt, ninv, initial_nnθ)
+        phystd, l2std, autodiff, physdt, ninv, initial_nnθ, estim_collocate)
 
     try
         ℓπ(t0, initial_θ[1:(nparameters - ninv)])
@@ -515,6 +573,9 @@ function ahmc_bayesian_pinn_ode(prob::SciMLBase.ODEProblem, chain;
     @info("Current Physics Log-likelihood : ", physloglikelihood(ℓπ, initial_θ))
     @info("Current Prior Log-likelihood : ", priorweights(ℓπ, initial_θ))
     @info("Current MSE against dataset Log-likelihood : ", L2LossData(ℓπ, initial_θ))
+    if estim_collocate
+        @info("Current gradient loss against dataset Log-likelihood : ", L2loss2(ℓπ, initial_θ))
+    end
 
     Adaptor, Metric, targetacceptancerate = Adaptorkwargs[:Adaptor],
     Adaptorkwargs[:Metric], Adaptorkwargs[:targetacceptancerate]
@@ -565,12 +626,14 @@ function ahmc_bayesian_pinn_ode(prob::SciMLBase.ODEProblem, chain;
         @info("Sampling Complete.")
         @info("Current Physics Log-likelihood : ", physloglikelihood(ℓπ, samples[end]))
         @info("Current Prior Log-likelihood : ", priorweights(ℓπ, samples[end]))
-        @info("Current MSE against dataset Log-likelihood : ",
-            L2LossData(ℓπ, samples[end]))
+        @info("Current MSE against dataset Log-likelihood : ", L2LossData(ℓπ, samples[end]))
+        if estim_collocate
+            @info("Current gradient loss against dataset Log-likelihood : ", L2loss2(ℓπ, samples[end]))
+        end
 
         # return a chain(basic chain),samples and stats
-        matrix_samples = hcat(samples...)
-        mcmc_chain = MCMCChains.Chains(matrix_samples')
+        matrix_samples = reshape(hcat(samples...), (length(samples[1]), length(samples), 1))
+        mcmc_chain = MCMCChains.Chains(matrix_samples)
         return mcmc_chain, samples, stats
     end
 end

test/BPINN_PDEinvsol_tests.jl

@@ -7,7 +7,7 @@ using ComponentArrays
 
 Random.seed!(100)
 
-@testset "Example 1: 2D Periodic System with parameter estimation" begin
+@testset "Example 1: 1D Periodic System with parameter estimation" begin
     # Cos(pi*t) periodic curve
     @parameters t, p
     @variables u(..)
@@ -59,17 +59,7 @@ Random.seed!(100)
         saveats = [1 / 50.0],
         param = [LogNormal(6.0, 0.5)])
 
-    discretization = BayesianPINN([chainl], QuadratureTraining(), param_estim = true,
-        dataset = [dataset, nothing])
-
-    ahmc_bayesian_pinn_pde(pde_system,
-        discretization;
-        draw_samples = 1500,
-        bcstd = [0.05],
-        phystd = [0.01], l2std = [0.01],
-        priorsNNw = (0.0, 1.0),
-        saveats = [1 / 50.0],
-        param = [LogNormal(6.0, 0.5)])
+        # alternative to QuadratureTraining [WIP]
 
     discretization = BayesianPINN([chainl], GridTraining([0.02]), param_estim = true,
         dataset = [dataset, nothing])