Merge 169a014 into c79dce0

Project.toml

@@ -1,6 +1,6 @@
 name = "Turing"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.16.0"
+version = "0.16.1"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
@@ -47,7 +47,7 @@ DocStringExtensions = "0.8"
 DynamicPPL = "0.11.0"
 EllipticalSliceSampling = "0.4"
 ForwardDiff = "0.10.3"
-Libtask = "0.4, 0.5"
+Libtask = "= 0.4.0, = 0.4.1, = 0.4.2, = 0.5.0, = 0.5.1"
 MCMCChains = "4"
 NamedArrays = "0.9"
 Reexport = "0.2, 1"

src/inference/ess.jl

@@ -112,7 +112,9 @@ function Base.rand(rng::Random.AbstractRNG, p::ESSPrior)
     sampler = p.sampler
     varinfo = p.varinfo
     vns = _getvns(varinfo, sampler)
-    set_flag!(varinfo, vns[1][1], "del")
+    for vn in Iterators.flatten(values(vns))
+        set_flag!(varinfo, vn, "del")
+    end
     p.model(rng, varinfo, sampler)
     return varinfo[sampler]
 end
@@ -155,6 +157,6 @@ function DynamicPPL.dot_tilde(rng, ctx::DefaultContext, sampler::Sampler{<:ESS},
     end
 end
 
-function DynamicPPL.dot_tilde(rng, ctx::DefaultContext, sampler::Sampler{<:ESS}, right, left, vi)
-    return DynamicPPL.dot_tilde(rng, ctx, SampleFromPrior(), right, left, vi)
+function DynamicPPL.dot_tilde(ctx::DefaultContext, sampler::Sampler{<:ESS}, right, left, vi)
+    return DynamicPPL.dot_tilde(ctx, SampleFromPrior(), right, left, vi)
 end

src/variational/advi.jl

@@ -34,14 +34,15 @@ function Bijectors.bijector(
     end
 
     bs = Bijectors.bijector.(tuple(dists...))
+    rs = tuple(ranges...)
 
     if sym2ranges
         return (
-            Bijectors.Stacked(bs, ranges),
+            Bijectors.Stacked(bs, rs),
             (; collect(zip(keys(sym_lookup), values(sym_lookup)))...),
         )
     else
-        return Bijectors.Stacked(bs, ranges)
+        return Bijectors.Stacked(bs, rs)
     end
 end
 

test/Project.toml

@@ -11,6 +11,7 @@ DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+Libtask = "6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73"
@@ -40,6 +41,7 @@ DynamicHMC = "2.1.6, 3.0"
 DynamicPPL = "0.11.0"
 FiniteDifferences = "0.10.8, 0.11, 0.12"
 ForwardDiff = "0.10.12"
+Libtask = "< 0.5.2"
 MCMCChains = "4.0.4"
 Memoization = "0.1.4"
 NamedArrays = "0.9.4"

test/inference/ess.jl

@@ -54,5 +54,9 @@
             ESS(:mu1), ESS(:mu2))
         chain = sample(MoGtest_default, alg, 6000)
         check_MoGtest_default(chain, atol = 0.1)
+
+        # Different "equivalent" models.
+        Random.seed!(125)
+        check_gdemo_models(ESS(), 1_000)
     end
 end

test/modes/ModeEstimation.jl

@@ -96,4 +96,13 @@
         @test isapprox(mle1.values.array, mle2.values.array)
         @test isapprox(map1.values.array, map2.values.array)
     end
+
+    @testset "MAP on $(m.name)" for m in gdemo_models
+        result = optimize(m, MAP())
+        @test mean(result.values) ≈ 8.0 rtol=0.05
+    end
+    @testset "MLE on $(m.name)" for m in gdemo_models
+        result = optimize(m, MLE())
+        @test mean(result.values) ≈ 10.0 rtol=0.05
+    end
 end

test/test_utils/models.jl

@@ -51,3 +51,94 @@ MoGtest_default = MoGtest([1.0 1.0 4.0 4.0])
 
 # Declare empty model to make the Sampler constructor work.
 @model empty_model() = begin x = 1; end
+
+# A collection of models for which the mean-of-means for the posterior should
+# be same.
+@model function gdemo1(x = 10 * ones(2), ::Type{TV} = Vector{Float64}) where {TV}
+    # `dot_assume` and `observe`
+    m = TV(undef, length(x))
+    m .~ Normal()
+    x ~ MvNormal(m, 0.5 * ones(length(x)))
+end
+
+@model function gdemo2(x = 10 * ones(2), ::Type{TV} = Vector{Float64}) where {TV}
+    # `assume` with indexing and `observe`
+    m = TV(undef, length(x))
+    for i in eachindex(m)
+        m[i] ~ Normal()
+    end
+    x ~ MvNormal(m, 0.5 * ones(length(x)))
+end
+
+@model function gdemo3(x = 10 * ones(2))
+    # Multivariate `assume` and `observe`
+    m ~ MvNormal(length(x), 1.0)
+    x ~ MvNormal(m, 0.5 * ones(length(x)))
+end
+
+@model function gdemo4(x = 10 * ones(2), ::Type{TV} = Vector{Float64}) where {TV}
+    # `dot_assume` and `observe` with indexing
+    m = TV(undef, length(x))
+    m .~ Normal()
+    for i in eachindex(x)
+        x[i] ~ Normal(m[i], 0.5)
+    end
+end
+
+# Using vector of `length` 1 here so the posterior of `m` is the same
+# as the others.
+@model function gdemo5(x = 10 * ones(1))
+    # `assume` and `dot_observe`
+    m ~ Normal()
+    x .~ Normal(m, 0.5)
+end
+
+@model function gdemo6()
+    # `assume` and literal `observe`
+    m ~ MvNormal(2, 1.0)
+    [10.0, 10.0] ~ MvNormal(m, 0.5 * ones(2))
+end
+
+@model function gdemo7(::Type{TV} = Vector{Float64}) where {TV}
+    # `dot_assume` and literal `observe` with indexing
+    m = TV(undef, 2)
+    m .~ Normal()
+    for i in eachindex(m)
+        10.0 ~ Normal(m[i], 0.5)
+    end
+end
+
+@model function gdemo8()
+    # `assume` and literal `dot_observe`
+    m ~ Normal()
+    [10.0, ] .~ Normal(m, 0.5)
+end
+
+@model function _prior_dot_assume(::Type{TV} = Vector{Float64}) where {TV}
+    m = TV(undef, 2)
+    m .~ Normal()
+
+    return m
+end
+
+@model function gdemo9()
+    # Submodel prior
+    m = @submodel _prior_dot_assume()
+    for i in eachindex(m)
+        10.0 ~ Normal(m[i], 0.5)
+    end
+end
+
+@model function _likelihood_dot_observe(m, x)
+    x ~ MvNormal(m, 0.5 * ones(length(m)))
+end
+
+@model function gdemo10(x = 10 * ones(2), ::Type{TV} = Vector{Float64}) where {TV}
+    m = TV(undef, length(x))
+    m .~ Normal()
+
+    # Submodel likelihood
+    @submodel _likelihood_dot_observe(m, x)
+end
+
+const gdemo_models = (gdemo1(), gdemo2(), gdemo3(), gdemo4(), gdemo5(), gdemo6(), gdemo7(), gdemo8(), gdemo9(), gdemo10())

test/test_utils/numerical_tests.jl

@@ -64,3 +64,13 @@ function check_MoGtest_default(chain; atol=0.2, rtol=0.0)
         [1.0, 1.0, 2.0, 2.0, 1.0, 4.0],
         atol=atol, rtol=rtol)
 end
+
+function check_gdemo_models(alg, nsamples, args...; atol=0.0, rtol=0.2, kwargs...)
+    @testset "$(alg) on $(m.name)" for m in gdemo_models
+        # Log this so that if something goes wrong, we can identify the
+        # algorithm and model.
+        μ = mean(Array(sample(m, alg, nsamples, args...; kwargs...)))
+
+        @test μ ≈ 8.0 atol=atol rtol=rtol
+    end
+end