Fix for HMCs dot_assume (#1758)

* fixed dot_assume for hmc * copy-pasted tests from dynamicppl integration tests * inspecting what in the world is going on with tests * trying again * skip failing test for TrackerAD * bump patch version * fixed typo in tests * Rename `Turing.Core` to `Turing.Essential` * Deprecate Turing.Core Co-authored-by: Tor Erlend Fjelde <[email protected]> * fixed a numerical test * version bump Co-authored-by: David Widmann <[email protected]> Co-authored-by: David Widmann <[email protected]>
TuringLang · Jan 26, 2022 · f87f455 · f87f455
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diff --git a/Project.toml b/Project.toml
@@ -1,6 +1,6 @@
 name = "Turing"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.19.4"
+version = "0.19.5"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"

diff --git a/src/inference/hmc.jl b/src/inference/hmc.jl
@@ -503,7 +503,7 @@ function DynamicPPL.dot_assume(
     var::AbstractArray,
     vi,
 )
-    DynamicPPL.updategid!(Ref(vi), vns, Ref(spl))
+    DynamicPPL.updategid!.(Ref(vi), vns, Ref(spl))
     return DynamicPPL.dot_assume(dists, var, vns, vi)
 end
 

diff --git a/test/inference/Inference.jl b/test/inference/Inference.jl
@@ -151,4 +151,348 @@
             @test range(chain) == range(6; step=2, length=10)
         end
     end
+
+    # Copy-paste from integration tests in DynamicPPL.
+    @testset "assume" begin
+        @model function test_assume()
+            x ~ Bernoulli(1)
+            y ~ Bernoulli(x / 2)
+            return x, y
+        end
+
+        smc = SMC()
+        pg = PG(10)
+
+        res1 = sample(test_assume(), smc, 1000)
+        res2 = sample(test_assume(), pg, 1000)
+
+        check_numerical(res1, [:y], [0.5]; atol=0.1)
+        check_numerical(res2, [:y], [0.5]; atol=0.1)
+
+        # Check that all xs are 1.
+        @test all(isone, res1[:x])
+        @test all(isone, res2[:x])
+    end
+    @testset "beta binomial" begin
+        prior = Beta(2, 2)
+        obs = [0, 1, 0, 1, 1, 1, 1, 1, 1, 1]
+        exact = Beta(prior.α + sum(obs), prior.β + length(obs) - sum(obs))
+        meanp = exact.α / (exact.α + exact.β)
+
+        @model function testbb(obs)
+            p ~ Beta(2, 2)
+            x ~ Bernoulli(p)
+            for i in 1:length(obs)
+                obs[i] ~ Bernoulli(p)
+            end
+            return p, x
+        end
+
+        smc = SMC()
+        pg = PG(10)
+        gibbs = Gibbs(HMC(0.2, 3, :p), PG(10, :x))
+
+        chn_s = sample(testbb(obs), smc, 1000)
+        chn_p = sample(testbb(obs), pg, 2000)
+        chn_g = sample(testbb(obs), gibbs, 1500)
+
+        check_numerical(chn_s, [:p], [meanp]; atol=0.05)
+        check_numerical(chn_p, [:x], [meanp]; atol=0.1)
+        check_numerical(chn_g, [:x], [meanp]; atol=0.1)
+    end
+    @testset "forbid global" begin
+        xs = [1.5 2.0]
+        # xx = 1
+
+        @model function fggibbstest(xs)
+            s ~ InverseGamma(2, 3)
+            m ~ Normal(0, sqrt(s))
+            # xx ~ Normal(m, sqrt(s)) # this is illegal
+
+            for i in 1:length(xs)
+                xs[i] ~ Normal(m, sqrt(s))
+                # for xx in xs
+                # xx ~ Normal(m, sqrt(s))
+            end
+            return s, m
+        end
+
+        gibbs = Gibbs(PG(10, :s), HMC(0.4, 8, :m))
+        chain = sample(fggibbstest(xs), gibbs, 2)
+    end
+    @testset "new grammar" begin
+        x = Float64[1 2]
+
+        @model function gauss(x)
+            priors = TArray{Float64}(2)
+            priors[1] ~ InverseGamma(2, 3)         # s
+            priors[2] ~ Normal(0, sqrt(priors[1])) # m
+            for i in 1:length(x)
+                x[i] ~ Normal(priors[2], sqrt(priors[1]))
+            end
+            return priors
+        end
+
+        chain = sample(gauss(x), PG(10), 10)
+        chain = sample(gauss(x), SMC(), 10)
+
+        @model function gauss2(::Type{TV}=Vector{Float64}; x) where {TV}
+            priors = TV(undef, 2)
+            priors[1] ~ InverseGamma(2, 3)         # s
+            priors[2] ~ Normal(0, sqrt(priors[1])) # m
+            for i in 1:length(x)
+                x[i] ~ Normal(priors[2], sqrt(priors[1]))
+            end
+            return priors
+        end
+
+        chain = sample(gauss2(; x=x), PG(10), 10)
+        chain = sample(gauss2(; x=x), SMC(), 10)
+
+        chain = sample(gauss2(Vector{Float64}; x=x), PG(10), 10)
+        chain = sample(gauss2(Vector{Float64}; x=x), SMC(), 10)
+    end
+    @testset "new interface" begin
+        obs = [0, 1, 0, 1, 1, 1, 1, 1, 1, 1]
+
+        @model function newinterface(obs)
+            p ~ Beta(2, 2)
+            for i in 1:length(obs)
+                obs[i] ~ Bernoulli(p)
+            end
+            return p
+        end
+
+        chain = sample(
+            newinterface(obs), HMC{Turing.ForwardDiffAD{2}}(0.75, 3, :p, :x), 100
+        )
+    end
+    @testset "no return" begin
+        @model function noreturn(x)
+            s ~ InverseGamma(2, 3)
+            m ~ Normal(0, sqrt(s))
+            for i in 1:length(x)
+                x[i] ~ Normal(m, sqrt(s))
+            end
+        end
+
+        chain = sample(noreturn([1.5 2.0]), HMC(0.1, 10), 4000)
+        check_numerical(chain, [:s, :m], [49 / 24, 7 / 6])
+    end
+    @testset "observe" begin
+        @model function test()
+            z ~ Normal(0, 1)
+            x ~ Bernoulli(1)
+            1 ~ Bernoulli(x / 2)
+            0 ~ Bernoulli(x / 2)
+            return x
+        end
+
+        is = IS()
+        smc = SMC()
+        pg = PG(10)
+
+        res_is = sample(test(), is, 10000)
+        res_smc = sample(test(), smc, 1000)
+        res_pg = sample(test(), pg, 100)
+
+        @test all(isone, res_is[:x])
+        @test res_is.logevidence ≈ 2 * log(0.5)
+
+        @test all(isone, res_smc[:x])
+        @test res_smc.logevidence ≈ 2 * log(0.5)
+
+        @test all(isone, res_pg[:x])
+    end
+    @testset "sample" begin
+        alg = Gibbs(HMC(0.2, 3, :m), PG(10, :s))
+        chn = sample(gdemo_default, alg, 1000)
+    end
+    @testset "vectorization @." begin
+        # https://github.com/FluxML/Tracker.jl/issues/119
+        if Turing.Core.ADBackend() !== Turing.Core.TrackerAD
+            @model function vdemo1(x)
+                s ~ InverseGamma(2, 3)
+                m ~ Normal(0, sqrt(s))
+                @. x ~ Normal(m, sqrt(s))
+                return s, m
+            end
+
+            alg = HMC(0.01, 5)
+            x = randn(100)
+            res = sample(vdemo1(x), alg, 250)
+
+            @model function vdemo1b(x)
+                s ~ InverseGamma(2, 3)
+                m ~ Normal(0, sqrt(s))
+                @. x ~ Normal(m, $(sqrt(s)))
+                return s, m
+            end
+
+            res = sample(vdemo1b(x), alg, 250)
+
+            @model function vdemo2(x)
+                μ ~ MvNormal(zeros(size(x, 1)), I)
+                @. x ~ $(MvNormal(μ, I))
+            end
+
+            D = 2
+            alg = HMC(0.01, 5)
+            res = sample(vdemo2(randn(D, 100)), alg, 250)
+
+            # Vector assumptions
+            N = 10
+            setchunksize(N)
+            alg = HMC(0.2, 4)
+
+            @model function vdemo3()
+                x = Vector{Real}(undef, N)
+                for i in 1:N
+                    x[i] ~ Normal(0, sqrt(4))
+                end
+            end
+
+            t_loop = @elapsed res = sample(vdemo3(), alg, 1000)
+
+            # Test for vectorize UnivariateDistribution
+            @model function vdemo4()
+                x = Vector{Real}(undef, N)
+                @. x ~ Normal(0, 2)
+            end
+
+            t_vec = @elapsed res = sample(vdemo4(), alg, 1000)
+
+            @model vdemo5() = x ~ MvNormal(zeros(N), 4 * I)
+
+            t_mv = @elapsed res = sample(vdemo5(), alg, 1000)
+
+            println("Time for")
+            println("  Loop : ", t_loop)
+            println("  Vec  : ", t_vec)
+            println("  Mv   : ", t_mv)
+
+            # Transformed test
+            @model function vdemo6()
+                x = Vector{Real}(undef, N)
+                @. x ~ InverseGamma(2, 3)
+            end
+
+            sample(vdemo6(), alg, 1000)
+
+            N = 3
+            @model function vdemo7()
+                x = Array{Real}(undef, N, N)
+                @. x ~ [InverseGamma(2, 3) for i in 1:N]
+            end
+
+            sample(vdemo7(), alg, 1000)
+        end
+    end
+    @testset "vectorization .~" begin
+        @model function vdemo1(x)
+            s ~ InverseGamma(2, 3)
+            m ~ Normal(0, sqrt(s))
+            x .~ Normal(m, sqrt(s))
+            return s, m
+        end
+
+        alg = HMC(0.01, 5)
+        x = randn(100)
+        res = sample(vdemo1(x), alg, 250)
+
+        @model function vdemo2(x)
+            μ ~ MvNormal(zeros(size(x, 1)), I)
+            return x .~ MvNormal(μ, I)
+        end
+
+        D = 2
+        alg = HMC(0.01, 5)
+        res = sample(vdemo2(randn(D, 100)), alg, 250)
+
+        # Vector assumptions
+        N = 10
+        setchunksize(N)
+        alg = HMC(0.2, 4)
+
+        @model function vdemo3()
+            x = Vector{Real}(undef, N)
+            for i in 1:N
+                x[i] ~ Normal(0, sqrt(4))
+            end
+        end
+
+        t_loop = @elapsed res = sample(vdemo3(), alg, 1000)
+
+        # Test for vectorize UnivariateDistribution
+        @model function vdemo4()
+            x = Vector{Real}(undef, N)
+            return x .~ Normal(0, 2)
+        end
+
+        t_vec = @elapsed res = sample(vdemo4(), alg, 1000)
+
+        @model vdemo5() = x ~ MvNormal(zeros(N), 4 * I)
+
+        t_mv = @elapsed res = sample(vdemo5(), alg, 1000)
+
+        println("Time for")
+        println("  Loop : ", t_loop)
+        println("  Vec  : ", t_vec)
+        println("  Mv   : ", t_mv)
+
+        # Transformed test
+        @model function vdemo6()
+            x = Vector{Real}(undef, N)
+            return x .~ InverseGamma(2, 3)
+        end
+
+        sample(vdemo6(), alg, 1000)
+
+        @model function vdemo7()
+            x = Array{Real}(undef, N, N)
+            return x .~ [InverseGamma(2, 3) for i in 1:N]
+        end
+
+        sample(vdemo7(), alg, 1000)
+    end
+    @testset "Type parameters" begin
+        N = 10
+        setchunksize(N)
+        alg = HMC(0.01, 5)
+        x = randn(1000)
+        @model function vdemo1(::Type{T}=Float64) where {T}
+            x = Vector{T}(undef, N)
+            for i in 1:N
+                x[i] ~ Normal(0, sqrt(4))
+            end
+        end
+
+        t_loop = @elapsed res = sample(vdemo1(), alg, 250)
+        t_loop = @elapsed res = sample(vdemo1(Float64), alg, 250)
+
+        vdemo1kw(; T) = vdemo1(T)
+        t_loop = @elapsed res = sample(vdemo1kw(; T=Float64), alg, 250)
+
+        @model function vdemo2(::Type{T}=Float64) where {T<:Real}
+            x = Vector{T}(undef, N)
+            @. x ~ Normal(0, 2)
+        end
+
+        t_vec = @elapsed res = sample(vdemo2(), alg, 250)
+        t_vec = @elapsed res = sample(vdemo2(Float64), alg, 250)
+
+        vdemo2kw(; T) = vdemo2(T)
+        t_vec = @elapsed res = sample(vdemo2kw(; T=Float64), alg, 250)
+
+        @model function vdemo3(::Type{TV}=Vector{Float64}) where {TV<:AbstractVector}
+            x = TV(undef, N)
+            @. x ~ InverseGamma(2, 3)
+        end
+
+        sample(vdemo3(), alg, 250)
+        sample(vdemo3(Vector{Float64}), alg, 250)
+
+        vdemo3kw(; T) = vdemo3(T)
+        sample(vdemo3kw(; T=Vector{Float64}), alg, 250)
+    end
 end