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May 4, 2020 13:45
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# This file is machine-generated - editing it directly is not advised | |
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[[PDMats]] | |
deps = ["Arpack", "LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"] | |
git-tree-sha1 = "2fc6f50ddd959e462f0a2dbc802ddf2a539c6e35" | |
uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" | |
version = "0.9.12" | |
[[PaddedViews]] | |
deps = ["OffsetArrays"] | |
git-tree-sha1 = "100195a79b577d5747db98bf1732c3686285fa1e" | |
uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" | |
version = "0.5.5" | |
[[Parameters]] | |
deps = ["OrderedCollections"] | |
git-tree-sha1 = "b62b2558efb1eef1fa44e4be5ff58a515c287e38" | |
uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" | |
version = "0.12.0" | |
[[Parsers]] | |
deps = ["Dates", "Test"] | |
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uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" | |
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[[Pkg]] | |
deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"] | |
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" | |
[[PoissonRandom]] | |
deps = ["Random", "Statistics", "Test"] | |
git-tree-sha1 = "44d018211a56626288b5d3f8c6497d28c26dc850" | |
uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" | |
version = "0.4.0" | |
[[PositiveFactorizations]] | |
deps = ["LinearAlgebra", "Test"] | |
git-tree-sha1 = "127c47b91990c101ee3752291c4f45640eeb03d1" | |
uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" | |
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[[Printf]] | |
deps = ["Unicode"] | |
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" | |
[[Profile]] | |
deps = ["Printf"] | |
uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" | |
[[ProgressLogging]] | |
deps = ["Logging", "SHA", "UUIDs"] | |
git-tree-sha1 = "e47914361d124d8760f5e356403daeb7f3b81633" | |
uuid = "33c8b6b6-d38a-422a-b730-caa89a2f386c" | |
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[[ProgressMeter]] | |
deps = ["Distributed", "Printf"] | |
git-tree-sha1 = "ea1f4fa0ff5e8b771bf130d87af5b7ef400760bd" | |
uuid = "92933f4c-e287-5a05-a399-4b506db050ca" | |
version = "1.2.0" | |
[[QuadGK]] | |
deps = ["DataStructures", "LinearAlgebra"] | |
git-tree-sha1 = "dc84e810393cfc6294248c9032a9cdacc14a3db4" | |
uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" | |
version = "2.3.1" | |
[[QuasiMonteCarlo]] | |
deps = ["Distributions", "LatinHypercubeSampling", "Sobol"] | |
git-tree-sha1 = "b90f9ff53b4c1f14eee512626cd8e7f9791b20a2" | |
uuid = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b" | |
version = "0.2.0" | |
[[REPL]] | |
deps = ["InteractiveUtils", "Markdown", "Sockets"] | |
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" | |
[[Random]] | |
deps = ["Serialization"] | |
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" | |
[[RandomNumbers]] | |
deps = ["Random", "Requires"] | |
git-tree-sha1 = "441e6fc35597524ada7f85e13df1f4e10137d16f" | |
uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" | |
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[[RangeArrays]] | |
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uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d" | |
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[[Ratios]] | |
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uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" | |
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[[RecipesBase]] | |
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uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" | |
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git-tree-sha1 = "01af091d2e62b907f6bb65ea2e7c12208131cf17" | |
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[[Reexport]] | |
deps = ["Pkg"] | |
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uuid = "189a3867-3050-52da-a836-e630ba90ab69" | |
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[[Requires]] | |
deps = ["UUIDs"] | |
git-tree-sha1 = "d37400976e98018ee840e0ca4f9d20baa231dc6b" | |
uuid = "ae029012-a4dd-5104-9daa-d747884805df" | |
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[[ResettableStacks]] | |
deps = ["StaticArrays"] | |
git-tree-sha1 = "d19e9c93de6020a96dbb2820567c78d0ab8f7248" | |
uuid = "ae5879a3-cd67-5da8-be7f-38c6eb64a37b" | |
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[[ReverseDiff]] | |
deps = ["DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] | |
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git-tree-sha1 = "2bbddcb984a1d08612d0c4abb5b4774883f6fa98" | |
uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" | |
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[[Roots]] | |
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[[SHA]] | |
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[[SharedArrays]] | |
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uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" | |
[[Showoff]] | |
deps = ["Dates"] | |
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[[Sobol]] | |
deps = ["Random"] | |
git-tree-sha1 = "f8afbde90f4e2d5e579dae4b0e71f931b2e194ca" | |
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[[Sockets]] | |
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[[SortingAlgorithms]] | |
deps = ["DataStructures", "Random", "Test"] | |
git-tree-sha1 = "03f5898c9959f8115e30bc7226ada7d0df554ddd" | |
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[[SparseArrays]] | |
deps = ["LinearAlgebra", "Random"] | |
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[[SparseDiffTools]] | |
deps = ["Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "InteractiveUtils", "LightGraphs", "LinearAlgebra", "Requires", "SparseArrays", "VertexSafeGraphs"] | |
git-tree-sha1 = "132c55cf302f1faf1d0d1c8205453764066cb018" | |
uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" | |
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[[SpatialIndexing]] | |
deps = ["Printf", "Random", "Test"] | |
git-tree-sha1 = "7bc6fc5c363aae476ec2c8bc527aef104b90c779" | |
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[[SpecialFunctions]] | |
deps = ["BinDeps", "BinaryProvider", "Libdl"] | |
git-tree-sha1 = "3bdd374b6fd78faf0119b8c5d538788dbf910c6e" | |
uuid = "276daf66-3868-5448-9aa4-cd146d93841b" | |
version = "0.8.0" | |
[[StaticArrays]] | |
deps = ["LinearAlgebra", "Random", "Statistics"] | |
git-tree-sha1 = "5a3bcb6233adabde68ebc97be66e95dcb787424c" | |
uuid = "90137ffa-7385-5640-81b9-e52037218182" | |
version = "0.12.1" | |
[[Statistics]] | |
deps = ["LinearAlgebra", "SparseArrays"] | |
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" | |
[[StatsBase]] | |
deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"] | |
git-tree-sha1 = "19bfcb46245f69ff4013b3df3b977a289852c3a1" | |
uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" | |
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[[StatsFuns]] | |
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git-tree-sha1 = "9a2de84a1618e1702dbb95ebdbb84dbf7f24d1ab" | |
uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" | |
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[[StochasticDiffEq]] | |
deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "FillArrays", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "Parameters", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays"] | |
git-tree-sha1 = "d87e6bdb20f822ee5840dc3efe0b6285c0710100" | |
uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" | |
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[[SuiteSparse]] | |
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[[Sundials]] | |
deps = ["BinaryProvider", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SparseArrays", "SuiteSparse"] | |
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uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" | |
version = "3.8.3" | |
[[TableTraits]] | |
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uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" | |
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[[TerminalLoggers]] | |
deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] | |
git-tree-sha1 = "8c05be75dfe73d90e5dfb6293e0c852013f7282d" | |
uuid = "5d786b92-1e48-4d6f-9151-6b4477ca9bed" | |
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git-tree-sha1 = "98693daea9bb49aba71eaad6b168b152d2310358" | |
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[[TimerOutputs]] | |
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[[Tracker]] | |
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[[TranscodingStreams]] | |
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git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c" | |
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" | |
version = "0.9.5" | |
[[TreeViews]] | |
deps = ["Test"] | |
git-tree-sha1 = "8d0d7a3fe2f30d6a7f833a5f19f7c7a5b396eae6" | |
uuid = "a2a6695c-b41b-5b7d-aed9-dbfdeacea5d7" | |
version = "0.3.0" | |
[[URIParser]] | |
deps = ["Unicode"] | |
git-tree-sha1 = "53a9f49546b8d2dd2e688d216421d050c9a31d0d" | |
uuid = "30578b45-9adc-5946-b283-645ec420af67" | |
version = "0.4.1" | |
[[UUIDs]] | |
deps = ["Random", "SHA"] | |
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" | |
[[Unicode]] | |
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" | |
[[VersionParsing]] | |
git-tree-sha1 = "80229be1f670524750d905f8fc8148e5a8c4537f" | |
uuid = "81def892-9a0e-5fdd-b105-ffc91e053289" | |
version = "1.2.0" | |
[[VertexSafeGraphs]] | |
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git-tree-sha1 = "35060f8047a2b79bdc8e4961bbbd2b7e30e62709" | |
uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f" | |
version = "0.1.1" | |
[[WoodburyMatrices]] | |
deps = ["LinearAlgebra", "SparseArrays"] | |
git-tree-sha1 = "28ffe06d28b1ba8fdb2f36ec7bb079fac81bac0d" | |
uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" | |
version = "0.5.2" | |
[[ZipFile]] | |
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git-tree-sha1 = "7fbfbc51c186f0ccdbe091f32d3dff8608973f8e" | |
uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea" | |
version = "0.8.4" | |
[[Zygote]] | |
deps = ["AbstractFFTs", "ArrayLayouts", "DiffRules", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NNlib", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"] | |
git-tree-sha1 = "08ee0b7796c4c9ce644b9ecc326f3e047486baeb" | |
uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" | |
version = "0.4.17" | |
[[ZygoteRules]] | |
deps = ["MacroTools"] | |
git-tree-sha1 = "b3b4882cc9accf6731a08cc39543fbc6b669dca8" | |
uuid = "700de1a5-db45-46bc-99cf-38207098b444" | |
version = "0.2.0" |
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[deps] | |
BlackBoxOptim = "a134a8b2-14d6-55f6-9291-3336d3ab0209" | |
CuArrays = "3a865a2d-5b23-5a0f-bc46-62713ec82fae" | |
DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" | |
DiffEqFlux = "aae7a2af-3d4f-5e19-a356-7da93b79d9d0" | |
DiffEqJump = "c894b116-72e5-5b58-be3c-e6d8d4ac2b12" | |
DiffEqMonteCarlo = "78ddff82-25fc-5f2b-89aa-309469cbf16f" | |
DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" | |
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" | |
Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" | |
Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004" | |
HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" | |
Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0" | |
JLD = "4138dd39-2aa7-5051-a626-17a0bb65d9c8" | |
Juno = "e5e0dc1b-0480-54bc-9374-aad01c23163d" | |
KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" | |
LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" | |
MAT = "23992714-dd62-5051-b70f-ba57cb901cac" | |
Metalhead = "dbeba491-748d-5e0e-a39e-b530a07fa0cc" | |
Optim = "429524aa-4258-5aef-a3af-852621145aeb" | |
OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" | |
QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" | |
RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" | |
StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" | |
SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" | |
StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" | |
Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" | |
Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" |
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using DifferentialEquations, DiffEqFlux, OrdinaryDiffEq, Flux, StatsBase, LinearAlgebra, CuArrays | |
CuArrays.allowscalar(false) | |
u0 = Float32[2.; 0.] | |
datasize = 100 | |
tspan = (0.0f0,1.0f0) | |
function trueODEfunc(du,u,p,t) | |
true_A = [-0.1 2.0; -2.0 -0.1] | |
du .= ((u.^3)'true_A)' | |
end | |
t = range(tspan[1],tspan[2],length=datasize) | |
prob = ODEProblem(trueODEfunc,u0,tspan) | |
ode_data = Array(solve(prob,Tsit5(),saveat=t)) |> gpu | |
f = Chain(Dense(2,1000, tanh), Dense(1000,2)) |> gpu # using FastChain/FastDense in this example throws a "scalar getindex is disallowed" error | |
g = Chain(Dense(2,100), GRU(100,100), Dense(100,2)) |> gpu | |
p1, fre = Flux.destructure(f) | |
p2, gre = Flux.destructure(g) | |
θ = Float32.([p1;p2]) | |
n_ode = NeuralODE(f, tspan, Tsit5(), saveat=t) | |
function loss_n_ode(p) | |
z0 = gre(p[length(p1)+1:end])(ode_data)[:, end] | |
pred = Array(n_ode(z0, p[1:length(p1)])) | |
loss = sum(abs2,ode_data .- pred) | |
loss,pred | |
end | |
cb = function (p,l,pred;doplot=false) #callback function to observe training | |
return false | |
end | |
res1 = DiffEqFlux.sciml_train(loss_n_ode, θ, ADAM(0.05), cb = cb, maxiters = 300) | |
cb(res1.minimizer,loss_n_ode(res1.minimizer)...;doplot=false) |
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