diff --git a/.github/workflows/docs.yml b/.github/workflows/tests_and_docs.yml similarity index 80% rename from .github/workflows/docs.yml rename to .github/workflows/tests_and_docs.yml index 74c78f2..a96a108 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/tests_and_docs.yml @@ -1,4 +1,4 @@ -name: doctests +name: tests_and_docs on: push: @@ -22,9 +22,9 @@ jobs: run: | python -m pip install --upgrade pip pip install matplotlib - julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' - name: Build and deploy env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key - run: julia --project=docs/ docs/make.jl + timeout-minutes: 30 + run: julia --project=. -e 'using Pkg; Pkg.test(); include("docs/make.jl")' diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9438b1e --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +scratch/ +Manifest.toml +.vscode \ No newline at end of file diff --git a/README.md b/README.md index 1799adf..42689d9 100644 --- a/README.md +++ b/README.md @@ -2,14 +2,16 @@ [![](https://img.shields.io/badge/documentation-latest-blue.svg)](https://cosmicmar.com/MuseInference.jl/latest) [![](https://img.shields.io/badge/source-github-blue)](https://github.com/marius311/MuseInference.jl) -[![](https://github.com/marius311/MuseInference.jl/actions/workflows/docs.yml/badge.svg)](https://github.com/marius311/MuseInference.jl/actions/workflows/docs.yml) +[![](https://github.com/marius311/MuseInference.jl/actions/workflows/tests_and_docs.yml/badge.svg)](https://github.com/marius311/MuseInference.jl/actions/workflows/tests_and_docs.yml) -Marginal unbiased score expansion (MUSE) estimation in Julia, with interface to Turing.jl. +Marginal unbiased score expansion (MUSE) estimation in Julia, with interface to [Turing.jl](https://turing.ml) and [Soss.jl](https://github.com/cscherrer/Soss.jl). + +For the Python package, see: https://github.com/marius311/muse_inference ## Install ``` -pkg> add https://github.com/marius311/MuseInference.jl +pkg> add MuseInference ``` ## Usage diff --git a/docs/Manifest.toml b/docs/Manifest.toml deleted file mode 100644 index 7a90195..0000000 --- a/docs/Manifest.toml +++ /dev/null @@ -1,1016 +0,0 @@ -# This file is machine-generated - 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-[[deps.ZygoteRules]] -deps = ["MacroTools"] -git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.2" - -[[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" - -[[deps.nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" - -[[deps.p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" diff --git a/docs/Manifest.toml b/docs/Manifest.toml new file mode 120000 index 0000000..c4d2acd --- /dev/null +++ b/docs/Manifest.toml @@ -0,0 +1 @@ +../test/Manifest.toml \ No newline at end of file diff --git a/docs/Project.toml b/docs/Project.toml deleted file mode 100644 index 819a731..0000000 --- a/docs/Project.toml +++ /dev/null @@ -1,7 +0,0 @@ -[deps] -Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -MCMCDiagnosticTools = "be115224-59cd-429b-ad48-344e309966f0" -MuseInference = "43b88160-90c7-4f71-933b-9d65205cd921" -PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/docs/Project.toml b/docs/Project.toml new file mode 120000 index 0000000..3af89b2 --- /dev/null +++ b/docs/Project.toml @@ -0,0 +1 @@ +../test/Project.toml \ No newline at end of file diff --git a/src/interface.jl b/src/interface.jl index d9059f7..978520f 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -192,7 +192,7 @@ function check_self_consistency( prob, θ; fdm = central_fdm(3, 1), - atol = 1e-3, + atol = 1e-2, rng = Random.default_rng(), has_volume_factor = true ) diff --git a/src/muse.jl b/src/muse.jl index 4ba4409..b37981e 100644 --- a/src/muse.jl +++ b/src/muse.jl @@ -73,7 +73,7 @@ Optional keyword arguments: * `rng` — Random number generator to use. Taken from `result.rng` or `Random.default_rng()` if not passed. * `z₀` — Starting guess for the latent space MAP. * `maxsteps = 50` — Maximum number of iterations. -* `θ_rtol = 1e-1` — Error tolerance on $\theta$ relative to its standard deviation. +* `θ_rtol = 1e-2` — Error tolerance on $\theta$ relative to its standard deviation. * `∇z_logLike_atol = 1e-2` — Absolute tolerance on the $z$-gradient at the MAP solution. * `nsims = 100` — Number of simulations. * `α = 0.7` — Step size for root-finder. @@ -96,7 +96,7 @@ function muse!( rng = nothing, z₀ = nothing, maxsteps = 50, - θ_rtol = 1e-1, + θ_rtol = 1e-2, ∇z_logLike_atol = 1e-2, nsims = 100, α = 0.7, diff --git a/src/soss.jl b/src/soss.jl index 75dba97..0255d95 100644 --- a/src/soss.jl +++ b/src/soss.jl @@ -1,6 +1,5 @@ - -using .Soss +import .Soss import .Soss.TransformVariables as TV export SossMuseProblem @@ -23,13 +22,14 @@ function SossMuseProblem( autodiff = ForwardDiffBackend() ) x = model.obs + !isempty(x) || error("Model must be conditioned on observed data.") sim = rand(model) observed_vars = keys(x) hyper_vars = params latent_vars = keys(delete(sim, (observed_vars..., hyper_vars...))) - model_for_prior = likelihood(Model(model), hyper_vars...)(argvals(model)) - xform_z = xform(model | select(sim, hyper_vars)) - xform_θ = xform(model | select(sim, latent_vars)) + model_for_prior = Soss.likelihood(Soss.Model(model), hyper_vars...)(Soss.argvals(model)) + xform_z = Soss.xform(model | select(sim, hyper_vars)) + xform_θ = Soss.xform(model | select(sim, latent_vars)) SossMuseProblem( autodiff, model, @@ -52,7 +52,7 @@ function inv_transform_θ(prob::SossMuseProblem, θ) end function logPriorθ(prob::SossMuseProblem, θ::ComponentVector, ::UnTransformedθ) - logdensity(prob.model_for_prior(_namedtuple(θ))) + Soss.logdensity(prob.model_for_prior(_namedtuple(θ))) end function logPriorθ(prob::SossMuseProblem, θ::AbstractVector, ::Transformedθ) logPriorθ(prob, inv_transform_θ(prob, θ), UnTransformedθ()) @@ -60,20 +60,20 @@ end function ∇θ_logLike(prob::SossMuseProblem, x, z::AbstractVector, θ::ComponentVector, ::UnTransformedθ) like = prob.model | (;_namedtuple(x)..., TV.transform(prob.xform_z, z)...) - first(AD.gradient(prob.autodiff, θ -> logdensity(like, _namedtuple(θ)), θ)) + first(AD.gradient(prob.autodiff, θ -> Soss.logdensity(like, _namedtuple(θ)), θ)) end function ∇θ_logLike(prob::SossMuseProblem, x, z::AbstractVector, θ::AbstractVector, ::Transformedθ) like = prob.model | (;_namedtuple(x)..., TV.transform(prob.xform_z, z)...) - first(AD.gradient(prob.autodiff, θ -> logdensity(like, _namedtuple(inv_transform_θ(prob, θ))), θ)) + first(AD.gradient(prob.autodiff, θ -> Soss.logdensity(like, _namedtuple(inv_transform_θ(prob, θ))), θ)) end function logLike_and_∇z_logLike(prob::SossMuseProblem, x, z, θ) - first.(AD.value_and_gradient(prob.autodiff, z -> logdensity(prob.model | (;_namedtuple(x)..., _namedtuple(θ)...), TV.transform(prob.xform_z, z)), z)) + first.(AD.value_and_gradient(prob.autodiff, z -> Soss.logdensity(prob.model | (;_namedtuple(x)..., _namedtuple(θ)...), TV.transform(prob.xform_z, z)), z)) end function sample_x_z(prob::SossMuseProblem, rng::AbstractRNG, θ) - sim = predict(rng, prob.model, _namedtuple(θ)) + sim = Soss.predict(rng, prob.model, _namedtuple(θ)) x = ComponentVector(select(sim, prob.observed_vars)) z = TV.inverse(prob.xform_z, select(sim, prob.latent_vars)) (;x, z) @@ -94,4 +94,4 @@ function get_J!(result::MuseResult, model::Soss.ConditionalModel, θ₀ = result end function get_H!(result::MuseResult, model::Soss.ConditionalModel, θ₀ = result.θ; kwargs...) get_H!(result, SossMuseProblem(model, params=_params_from_θ₀(θ₀)), θ₀; kwargs...) -end +end \ No newline at end of file diff --git a/src/turing.jl b/src/turing.jl index 5cb904c..f523970 100644 --- a/src/turing.jl +++ b/src/turing.jl @@ -2,19 +2,11 @@ ### Turing interface import .Turing -using .Turing: VarInfo, TypedVarInfo, tonamedtuple, decondition, logprior, - logjoint, VarName, SampleFromPrior, link!, invlink!, MAP, OptimLogDensity, - DefaultContext, SimpleVarInfo, LikelihoodContext, condition -using .Turing.ModeEstimation: transform! -using .Turing.DynamicPPL: evaluate!!, setval!, settrans!, Model, Metadata, getlogp - -import .Turing.DynamicPPL: VarInfo, condition - +import .Turing.DynamicPPL as DynPPL import ComponentArrays: ComponentVector export TuringMuseProblem - struct TuringMuseProblem{A<:AD.AbstractBackend, M<:Turing.Model} <: AbstractMuseProblem autodiff :: A @@ -89,23 +81,23 @@ function TuringMuseProblem( x = ComponentVector(model.context.values) # figure out variable names observed = keys(x) - latent = keys(delete(_namedtuple(VarInfo(model)), (observed..., params...))) + latent = keys(delete(_namedtuple(DynPPL.VarInfo(model)), (observed..., params...))) # VarInfo for (z,θ) with both transformed - vi_z′_θ′ = VarInfo(model) - settrans!.((vi_z′_θ′,), true, VarName.((latent..., params...))) + vi_z′_θ′ = DynPPL.VarInfo(model) + DynPPL.settrans!.((vi_z′_θ′,), true, DynPPL.VarName.((latent..., params...))) # VarInfo for (z,θ) with only z transformed - vi_z′_θ = VarInfo(model) - settrans!.((vi_z′_θ,), true, VarName.(latent)) + vi_z′_θ = DynPPL.VarInfo(model) + DynPPL.settrans!.((vi_z′_θ,), true, DynPPL.VarName.(latent)) # model with all vars free - model = decondition(model) + model = DynPPL.decondition(model) # model for computing prior, just need any values for (x,z) to condition on here - vars = _namedtuple(evaluate!!(model)[2]) + vars = _namedtuple(DynPPL.evaluate!!(model)[2]) model_for_prior = model | select(vars, (observed..., latent...)) # VarInfo for θ - vi_θ = VarInfo(model_for_prior) + vi_θ = DynPPL.VarInfo(model_for_prior) # VarInfo for transformed θ vi_θ′ = deepcopy(vi_θ) - settrans!.((vi_θ′,), true, VarName.(params)) + DynPPL.settrans!.((vi_θ′,), true, DynPPL.VarName.(params)) TuringMuseProblem( autodiff, @@ -125,18 +117,18 @@ end function transform_θ(prob::TuringMuseProblem, θ) vi = deepcopy(prob.vi_θ) - setval!(vi, θ) - link!(vi, SampleFromPrior()) + DynPPL.setval!(vi, θ) + DynPPL.link!(vi, DynPPL.SampleFromPrior()) ComponentVector(vi) end function inv_transform_θ(prob::TuringMuseProblem, θ) vi = deepcopy(prob.vi_θ) - setval!(vi, θ) + DynPPL.setval!(vi, θ) for k in keys(θ) - settrans!(vi, true, VarName(k)) + DynPPL.settrans!(vi, true, DynPPL.VarName(k)) end - invlink!(vi, SampleFromPrior()) + DynPPL.invlink!(vi, DynPPL.SampleFromPrior()) ComponentVector(vi) end @@ -146,28 +138,28 @@ standardizeθ(prob::TuringMuseProblem, θ::Number) = function logPriorθ(prob::TuringMuseProblem, θ, θ_space) vi = is_transformed(θ_space) ? prob.vi_θ′ : prob.vi_θ - logprior(prob.model_for_prior, VarInfo(vi, θ)) + DynPPL.logprior(prob.model_for_prior, DynPPL.VarInfo(vi, θ)) end function ∇θ_logLike(prob::TuringMuseProblem, x, z, θ, θ_space) - model = condition(prob.model, x) + model = DynPPL.condition(prob.model, x) vi = is_transformed(θ_space) ? prob.vi_z′_θ′ : prob.vi_z′_θ - first(AD.gradient(prob.autodiff, θ -> logjoint(model, VarInfo(vi, z, θ)), θ)) + first(AD.gradient(prob.autodiff, θ -> DynPPL.logjoint(model, DynPPL.VarInfo(vi, z, θ)), θ)) end function ẑ_at_θ(prob::TuringMuseProblem, x, z₀, θ; ∇z_logLike_atol) - model = condition(prob.model, x) - neglogp(z) = -logjoint(model, VarInfo(prob.vi_z′_θ, z, θ)) + model = DynPPL.condition(prob.model, x) + neglogp(z) = -DynPPL.logjoint(model, DynPPL.VarInfo(prob.vi_z′_θ, z, θ)) soln = Optim.optimize(optim_only_fg!(neglogp, prob.autodiff), z₀, Optim.LBFGS(), Optim.Options(g_tol=∇z_logLike_atol)) _check_optim_soln(soln) soln.minimizer, soln end function sample_x_z(prob::TuringMuseProblem, rng::AbstractRNG, θ) - model = condition(prob.model, θ) - vi = VarInfo(rng, model) + model = DynPPL.condition(prob.model, θ) + vi = DynPPL.VarInfo(rng, model) vars_untransformed = map(copy, _namedtuple(vi)) - link!(vi, SampleFromPrior()) + DynPPL.link!(vi, DynPPL.SampleFromPrior()) vars_transformed = map(copy, _namedtuple(vi)) (; x = ComponentVector(select(vars_untransformed, prob.observed_vars)), @@ -179,9 +171,9 @@ end # helped to extract parameters from a sampled model. feels like there # should be a less hacky way to do this... -function _namedtuple(vi::VarInfo) - map(TypedVarInfo(vi).metadata) do m - if m.vns[1] isa VarName{<:Any,Setfield.IdentityLens} && length(m.vals)==1 +function _namedtuple(vi::DynPPL.VarInfo) + map(DynPPL.TypedVarInfo(vi).metadata) do m + if m.vns[1] isa DynPPL.VarName{<:Any,Setfield.IdentityLens} && length(m.vals)==1 m.vals[1] else m.vals @@ -189,17 +181,17 @@ function _namedtuple(vi::VarInfo) end end -ComponentVector(vi::VarInfo) = ComponentVector(_namedtuple(vi)) +ComponentVector(vi::DynPPL.VarInfo) = ComponentVector(_namedtuple(vi)) -function VarInfo(vi::TypedVarInfo, x::Union{NamedTuple,ComponentVector}, xs::Union{NamedTuple,ComponentVector}...) - VarInfo(vi, merge(map(_namedtuple, (x, xs...))...)) +function DynPPL.VarInfo(vi::DynPPL.TypedVarInfo, x::Union{NamedTuple,ComponentVector}, xs::Union{NamedTuple,ComponentVector}...) + DynPPL.VarInfo(vi, merge(map(_namedtuple, (x, xs...))...)) end -function VarInfo(vi::TypedVarInfo, x::NamedTuple) +function DynPPL.VarInfo(vi::DynPPL.TypedVarInfo, x::NamedTuple) T = promote_type(map(eltype, values(x))..., map(eltype, _namedtuple(values(vi)))...) # if x is ForwardDiff Duals - VarInfo( + DynPPL.VarInfo( NamedTuple{keys(vi.metadata)}(map(keys(vi.metadata),values(vi.metadata)) do k,v - Metadata( + DynPPL.Metadata( v.idcs, v.vns, v.ranges, @@ -210,12 +202,12 @@ function VarInfo(vi::TypedVarInfo, x::NamedTuple) v.flags, ) end), - Base.RefValue{T}(getlogp(vi)), + Base.RefValue{T}(DynPPL.getlogp(vi)), vi.num_produce ) end -condition(model::Model, x::ComponentVector) = condition(model, _namedtuple(x)) +DynPPL.condition(model::DynPPL.Model, x::ComponentVector) = DynPPL.condition(model, _namedtuple(x)) atleast1d(x::Number) = [x] atleast1d(x::AbstractVector) = x @@ -223,12 +215,12 @@ atleast1d(x::AbstractVector) = x _params_from_θ₀(θ₀::Number) = (:θ,) _params_from_θ₀(θ₀) = keys(θ₀) -function muse!(result::MuseResult, model::Turing.Model, θ₀ = result.θ; kwargs...) +function muse!(result::MuseResult, model::DynPPL.Model, θ₀ = result.θ; kwargs...) muse!(result, TuringMuseProblem(model, params=_params_from_θ₀(θ₀)), θ₀; kwargs...) end -function get_J!(result::MuseResult, model::Turing.Model, θ₀ = result.θ; kwargs...) +function get_J!(result::MuseResult, model::DynPPL.Model, θ₀ = result.θ; kwargs...) get_J!(result, TuringMuseProblem(model, params=_params_from_θ₀(θ₀)), θ₀; kwargs...) end -function get_H!(result::MuseResult, model::Turing.Model, θ₀ = result.θ; kwargs...) +function get_H!(result::MuseResult, model::DynPPL.Model, θ₀ = result.θ; kwargs...) get_H!(result, TuringMuseProblem(model, params=_params_from_θ₀(θ₀)), θ₀; kwargs...) end diff --git a/test/Manifest.toml b/test/Manifest.toml new file mode 100644 index 0000000..1386461 --- /dev/null +++ b/test/Manifest.toml 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0000000..9356dee --- /dev/null +++ b/test/Project.toml @@ -0,0 +1,18 @@ +[deps] +ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" +DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb" +ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" +MCMCDiagnosticTools = "be115224-59cd-429b-ad48-344e309966f0" +MeasureTheory = "eadaa1a4-d27c-401d-8699-e962e1bbc33b" +MuseInference = "43b88160-90c7-4f71-933b-9d65205cd921" +PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +SampleChainsDynamicHMC = "6d9fd711-e8b2-4778-9c70-c1dfb499d4c4" +Soss = "8ce77f84-9b61-11e8-39ff-d17a774bf41c" +StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" +Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +TransformVariables = "84d833dd-6860-57f9-a1a7-6da5db126cff" +Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" +Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/test/runtests.jl b/test/runtests.jl new file mode 100644 index 0000000..c4da352 --- /dev/null +++ b/test/runtests.jl @@ -0,0 +1,82 @@ + +using MuseInference, Soss, Turing, Distributions, Random, + Zygote, MeasureTheory, Test, StableRNGs + +## + +rng = StableRNG(0) + +@testset "MuseInference" begin + + @testset "Turing w/ Distributions" begin + + Turing.@model function turing_funnel() + θ ~ Distributions.Normal(0, 3) + z ~ Distributions.MvNormal(512, exp(θ/2)) + x ~ Distributions.MvNormal(z, 1) + end + + @testset "$name" for (name,autodiff) in [ + ("ForwardDiff", MuseInference.ForwardDiffBackend()), + ("Zygote", MuseInference.ZygoteBackend()) + ] + + (;x) = rand(copy(rng), turing_funnel() | (θ=0,)) + prob = TuringMuseProblem(turing_funnel() | (;x); autodiff) + MuseInference.check_self_consistency(prob, (θ=1,), has_volume_factor=true, rng=copy(rng)) + result = muse(prob, (θ=1,); rng=copy(rng), get_covariance=true) + @test result.dist.μ / result.dist.σ < 1 + + end + + end + + ## + + @testset "Soss w/ Distributions" begin + + soss_funnel = Soss.@model (σ) begin + θ ~ Distributions.Normal(0, σ) + z ~ Distributions.MvNormal(512, exp(θ/2)) + x ~ Distributions.MvNormal(z, 1) + end + + @testset "$name" for (name,autodiff) in [ + ("ForwardDiff", MuseInference.ForwardDiffBackend()), + ("Zygote", MuseInference.ZygoteBackend()) + ] + (;x) = Soss.predict(copy(rng), soss_funnel(3), θ=0) + prob = SossMuseProblem(soss_funnel(3) | (;x); autodiff) + MuseInference.check_self_consistency(prob, (θ=1,), has_volume_factor=false, rng=copy(rng)) + result = muse(prob, (θ=1,); rng=copy(rng), get_covariance=true) + @test result.dist.μ / result.dist.σ < 1 + + end + + end + + @testset "Soss w/ MeasureTheory" begin + + soss_funnel = Soss.@model (σ) begin + θ ~ MeasureTheory.Normal(0, σ) + z ~ MeasureTheory.Normal(0, exp(θ/2)) ^ 512 + x ~ For(z) do zᵢ + MeasureTheory.Normal(zᵢ, 1) + end + end + + @testset "$name" for (name,autodiff) in [ + ("ForwardDiff", MuseInference.ForwardDiffBackend()), + # ("Zygote", MuseInference.ZygoteBackend()) # broken + ] + (;x) = Soss.predict(copy(rng), soss_funnel(3), θ=0) + prob = SossMuseProblem(soss_funnel(3) | (;x); autodiff) + MuseInference.check_self_consistency(prob, (θ=1,), has_volume_factor=false, rng=copy(rng)) + result = muse(prob, (θ=1,); rng=copy(rng), get_covariance=true) + @test result.dist.μ / result.dist.σ < 1 + + end + + end + +end \ No newline at end of file