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Remove view() in Bayesian NN doc, see compintell/Mooncake.jl#423
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@penelopeysm
penelopeysm committed Dec 14, 2024
1 parent 78730de commit b0445a7
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149 changes: 79 additions & 70 deletions Manifest.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -101,10 +101,10 @@ version = "0.6.4"
OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"

[[deps.AdvancedMH]]
deps = ["AbstractMCMC", "Distributions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"]
git-tree-sha1 = "b5f8159bffa2e6af9e080c11c4e6da8c5b05f079"
deps = ["AbstractMCMC", "Distributions", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"]
git-tree-sha1 = "6e3d18037861bf220ed77f1a2c5f24a21a68d4b7"
uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
version = "0.8.4"
version = "0.8.5"
weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"]

[deps.AdvancedMH.extensions]
Expand Down Expand Up @@ -170,9 +170,9 @@ version = "3.5.1+1"

[[deps.ArrayInterface]]
deps = ["Adapt", "LinearAlgebra"]
git-tree-sha1 = "d5140b60b87473df18cf4fe66382b7c3596df047"
git-tree-sha1 = "017fcb757f8e921fb44ee063a7aafe5f89b86dd1"
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version = "7.17.1"
version = "7.18.0"

[deps.ArrayInterface.extensions]
ArrayInterfaceBandedMatricesExt = "BandedMatrices"
Expand Down Expand Up @@ -216,9 +216,9 @@ version = "1.11.0"

[[deps.Atomix]]
deps = ["UnsafeAtomics"]
git-tree-sha1 = "14e254ef74e44cd6ed27fbb751d4e1f9bbf085cc"
git-tree-sha1 = "c3b238aa28c1bebd4b5ea4988bebf27e9a01b72b"
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version = "1.0.0"
version = "1.0.1"

[deps.Atomix.extensions]
AtomixCUDAExt = "CUDA"
Expand Down Expand Up @@ -547,9 +547,9 @@ version = "0.2.3"

[[deps.ConcurrentUtilities]]
deps = ["Serialization", "Sockets"]
git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1"
git-tree-sha1 = "f36e5e8fdffcb5646ea5da81495a5a7566005127"
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version = "2.4.3"

[[deps.ConsoleProgressMonitor]]
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Expand Down Expand Up @@ -799,9 +799,9 @@ version = "1.11.0"

[[deps.Distributions]]
deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
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git-tree-sha1 = "9d9e93d19c912ee6f0f3543af0d8839079dbd0d7"
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version = "0.25.114"
weakdeps = ["ChainRulesCore", "DensityInterface", "Test"]

[deps.Distributions.extensions]
Expand Down Expand Up @@ -841,19 +841,28 @@ version = "3.4.7"

[[deps.DynamicPPL]]
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DynamicPPLEnzymeCoreExt = ["EnzymeCore"]
DynamicPPLForwardDiffExt = ["ForwardDiff"]
DynamicPPLJETExt = ["JET"]
DynamicPPLMCMCChainsExt = ["MCMCChains"]
DynamicPPLReverseDiffExt = ["ReverseDiff"]
DynamicPPLMooncakeExt = ["Mooncake"]
DynamicPPLZygoteRulesExt = ["ZygoteRules"]

[deps.DynamicPPL.weakdeps]
ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"

[[deps.EllipticalSliceSampling]]
deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"]
git-tree-sha1 = "e611b7fdfbfb5b18d5e98776c30daede41b44542"
Expand All @@ -867,9 +876,9 @@ version = "1.0.4"

[[deps.Enzyme]]
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version = "0.13.22"

[deps.Enzyme.extensions]
EnzymeBFloat16sExt = "BFloat16s"
Expand Down Expand Up @@ -1121,9 +1130,9 @@ version = "0.2.10"

[[deps.Fontconfig_jll]]
deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
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git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc"
Expand Down Expand Up @@ -1277,15 +1286,15 @@ version = "1.14.2+1"

[[deps.HTTP]]
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version = "1.10.14"

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[[deps.HostCPUFeatures]]
deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"]
Expand Down Expand Up @@ -1398,9 +1407,9 @@ weakdeps = ["Dates", "Test"]
InverseFunctionsTestExt = "Test"

[[deps.InvertedIndices]]
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Expand Down Expand Up @@ -1461,10 +1470,10 @@ uuid = "ef3ab10e-7fda-4108-b977-705223b18434"
version = "0.6.0"

[[deps.KernelAbstractions]]
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[deps.KernelAbstractions.extensions]
Expand Down Expand Up @@ -1582,9 +1591,9 @@ version = "0.1.17"

[[deps.LazyArrays]]
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[deps.LazyArrays.extensions]
LazyArraysBandedMatricesExt = "BandedMatrices"
Expand Down Expand Up @@ -1803,9 +1812,9 @@ version = "1.13.0"

[[deps.LogExpFunctions]]
deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
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version = "0.3.29"
weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"]

[deps.LogExpFunctions.extensions]
Expand Down Expand Up @@ -2150,14 +2159,13 @@ version = "0.8.1"

[[deps.Mooncake]]
deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DiffTests", "ExprTools", "FunctionWrappers", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Setfield", "Test"]
git-tree-sha1 = "0914d23f446ee9770be16528ee4a3f0bad4a4fb7"
git-tree-sha1 = "46c0f7c9cbe46232d0f4f2145126bf7b3499ffd0"
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[deps.Mooncake.extensions]
MooncakeAllocCheckExt = "AllocCheck"
MooncakeCUDAExt = "CUDA"
MooncakeDynamicPPLExt = "DynamicPPL"
MooncakeJETExt = "JET"
MooncakeLuxLibExt = "LuxLib"
MooncakeLuxLibSLEEFPiratesExtension = ["LuxLib", "SLEEFPirates"]
Expand All @@ -2167,7 +2175,6 @@ version = "0.4.58"
[deps.Mooncake.weakdeps]
AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a"
CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
LuxLib = "82251201-b29d-42c6-8e01-566dec8acb11"
NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
Expand Down Expand Up @@ -2668,9 +2675,9 @@ version = "0.11.31"

[[deps.PSIS]]
deps = ["LinearAlgebra", "LogExpFunctions", "Printf", "RecipesBase", "Statistics"]
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Expand Down Expand Up @@ -2698,9 +2705,9 @@ version = "2.8.1"

[[deps.Pathfinder]]
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[deps.Pathfinder.extensions]
Expand Down Expand Up @@ -3079,9 +3086,9 @@ version = "0.1.1"

[[deps.SciMLBase]]
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[deps.SciMLBase.extensions]
SciMLBaseChainRulesCoreExt = "ChainRulesCore"
Expand Down Expand Up @@ -3121,9 +3128,13 @@ weakdeps = ["SparseArrays", "StaticArraysCore"]

[[deps.SciMLSensitivity]]
deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"]
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[deps.SciMLSensitivity.extensions]
SciMLSensitivityMooncakeExt = "Mooncake"

[[deps.SciMLStructures]]
deps = ["ArrayInterface"]
Expand All @@ -3144,9 +3155,9 @@ version = "1.2.1"

[[deps.SentinelArrays]]
deps = ["Dates", "Random"]
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[[deps.Serialization]]
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Expand Down Expand Up @@ -3287,9 +3298,9 @@ version = "0.3.9"

[[deps.SpecialFunctions]]
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[deps.SpecialFunctions.extensions]
Expand Down Expand Up @@ -3398,10 +3409,10 @@ uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
version = "2.4.1"

[[deps.StochasticDiffEq]]
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Expand Down Expand Up @@ -3693,15 +3704,13 @@ uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728"
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Expand Down Expand Up @@ -3856,22 +3865,22 @@ uuid = "a51aa0fd-4e3c-5386-b890-e753decda492"
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Expand All @@ -3887,9 +3896,9 @@ version = "1.17.0+1"

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[[deps.Xorg_xcb_util_cursor_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"]
Expand Down Expand Up @@ -3929,9 +3938,9 @@ version = "0.4.1+1"

[[deps.Xorg_xkbcomp_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"]
git-tree-sha1 = "330f955bc41bb8f5270a369c473fc4a5a4e4d3cb"
git-tree-sha1 = "ab2221d309eda71020cdda67a973aa582aa85d69"
uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4"
version = "1.4.6+0"
version = "1.4.6+1"

[[deps.Xorg_xkeyboard_config_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"]
Expand Down
6 changes: 3 additions & 3 deletions tutorials/03-bayesian-neural-network/index.qmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ function vector_to_parameters(ps_new::AbstractVector, ps::NamedTuple)
@assert length(ps_new) == Lux.parameterlength(ps)
i = 1
function get_ps(x)
z = reshape(view(ps_new, i:(i + length(x) - 1)), size(x))
z = reshape(ps_new[i:(i + length(x) - 1)], size(x))
i += length(x)
return z
end
Expand Down Expand Up @@ -207,8 +207,8 @@ setprogress!(false)

```{julia}
# Perform inference.
N = 2_000
ch = sample(bayes_nn(reduce(hcat, xs), ts), NUTS(; adtype=AutoMooncake(; config=nothing)), N);
n_iters = 2_000
ch = sample(bayes_nn(reduce(hcat, xs), ts), NUTS(; adtype=AutoMooncake(; config=nothing)), n_iters);
```

Now we extract the parameter samples from the sampled chain as `θ` (this is of size `5000 x 20` where `5000` is the number of iterations and `20` is the number of parameters).
Expand Down

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