Merge branch 'master' into tgf/softmax_docs

Project.toml

@@ -1,7 +1,7 @@
 name = "GPLikelihoods"
 uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40"
 authors = ["JuliaGaussianProcesses Team"]
-version = "0.4.3"
+version = "0.4.5"
 
 [deps]
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
@@ -20,7 +20,7 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 ChainRulesCore = "1.7"
 Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
 FastGaussQuadrature = "0.4"
-Functors = "0.1, 0.2"
+Functors = "0.1, 0.2, 0.3"
 InverseFunctions = "0.1.2"
 IrrationalConstants = "0.1"
 SpecialFunctions = "1, 2"

src/expectations.jl

@@ -87,25 +87,13 @@ function expected_loglikelihood(
     # Compute the expectation via Gauss-Hermite quadrature
     # using a reparameterisation by change of variable
     # (see e.g. en.wikipedia.org/wiki/Gauss%E2%80%93Hermite_quadrature)
-    return sum(Broadcast.instantiate(
-        Broadcast.broadcasted(y, q_f) do yᵢ, q_fᵢ  # Loop over every pair
-            # of marginal distribution q(fᵢ) and observation yᵢ
-            expected_loglikelihood(gh, lik, q_fᵢ, yᵢ)
-        end,
-    ))
-end
-
-# Compute the expected_loglikelihood for one observation and a marginal distributions
-function expected_loglikelihood(gh::GaussHermiteExpectation, lik, q_f::Normal, y)
-    μ = mean(q_f)
-    σ̃ = sqrt2 * std(q_f)
-    return invsqrtπ * sum(Broadcast.instantiate(
-        Broadcast.broadcasted(gh.xs, gh.ws) do x, w # Loop over every
-            # pair of Gauss-Hermite point x with weight w
-            f = σ̃ * x + μ
-            loglikelihood(lik(f), y) * w
-        end,
-    ))
+    # PR #90 introduces eager instead of lazy broadcast over observations
+    # and Gauss-Hermit points and weights in order to make the function
+    # type stable. Compared to other type stable implementations, e.g.
+    # using a custom two-argument pairwise sum, this is faster to
+    # differentiate using Zygote.
+    A = loglikelihood.(lik.(sqrt2 .* std.(q_f) .* gh.xs' .+ mean.(q_f)), y) .* gh.ws'
+    return invsqrtπ * sum(A)
 end
 
 function expected_loglikelihood(

src/likelihoods/negativebinomial.jl

@@ -147,9 +147,11 @@ struct NBParamII{T} <: NBParamMean
 end
 
 function (l::NegativeBinomialLikelihood{<:NBParamII})(f::Real)
-    μ = l.invlink(f)
-    ev = l.params.α * μ
-    return NegativeBinomial(_nb_mean_excessvar_to_r_p(μ, ev)...)
+    # Simplify parameter conversions and avoid splatting
+    α = l.params.α
+    r = inv(α)
+    p = inv(one(α) + α * l.invlink(f))
+    return NegativeBinomial(r, p)
 end
 
 """

test/Project.toml

@@ -8,7 +8,7 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
 Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
-Functors = "0.1, 0.2"
+Functors = "0.1, 0.2, 0.3"
 StatsFuns = "0.9, 1"
 Zygote = "0.6"
 julia = "1.3"

test/expectations.jl

@@ -1,14 +1,17 @@
 @testset "expectations" begin
-    # Test that the various methods of computing expectations return the same
-    # result.
     rng = MersenneTwister(123456)
     q_f = Normal.(zeros(10), ones(10))
 
     likelihoods_to_test = [
+        BernoulliLikelihood(),
         ExponentialLikelihood(),
         GammaLikelihood(),
-        PoissonLikelihood(),
         GaussianLikelihood(),
+        NegativeBinomialLikelihood(NBParamSuccess(1.0)),
+        NegativeBinomialLikelihood(NBParamFailure(1.0)),
+        NegativeBinomialLikelihood(NBParamI(1.0)),
+        NegativeBinomialLikelihood(NBParamII(1.0)),
+        PoissonLikelihood(),
     ]
 
     @testset "testing all analytic implementations" begin
@@ -30,30 +33,50 @@
         end
     end
 
-    @testset "$(nameof(typeof(lik)))" for lik in likelihoods_to_test
-        methods = [
-            GaussHermiteExpectation(100),
-            MonteCarloExpectation(1e7),
-            GPLikelihoods.DefaultExpectationMethod(),
-        ]
-        def = GPLikelihoods.default_expectation_method(lik)
-        if def isa GPLikelihoods.AnalyticExpectation
-            push!(methods, def)
-        end
-        y = rand.(rng, lik.(zeros(10)))
+    @testset "testing consistency of different expectation methods" begin
+        @testset "$(nameof(typeof(lik)))" for lik in likelihoods_to_test
+            # Test that the various methods of computing expectations return the same
+            # result.
+            methods = [
+                GaussHermiteExpectation(100),
+                MonteCarloExpectation(1e7),
+                GPLikelihoods.DefaultExpectationMethod(),
+            ]
+            def = GPLikelihoods.default_expectation_method(lik)
+            if def isa GPLikelihoods.AnalyticExpectation
+                push!(methods, def)
+            end
+            y = rand.(rng, lik.(zeros(10)))
 
-        results = map(m -> GPLikelihoods.expected_loglikelihood(m, lik, q_f, y), methods)
-        @test all(x -> isapprox(x, results[end]; atol=1e-6, rtol=1e-3), results)
+            results = map(
+                m -> GPLikelihoods.expected_loglikelihood(m, lik, q_f, y), methods
+            )
+            @test all(x -> isapprox(x, results[end]; atol=1e-6, rtol=1e-3), results)
+        end
     end
 
-    @test GPLikelihoods.expected_loglikelihood(
-        MonteCarloExpectation(1), GaussianLikelihood(), q_f, zeros(10)
-    ) isa Real
-    @test GPLikelihoods.expected_loglikelihood(
-        GaussHermiteExpectation(1), GaussianLikelihood(), q_f, zeros(10)
-    ) isa Real
-    @test GPLikelihoods.default_expectation_method(θ -> Normal(0, θ)) isa
-        GaussHermiteExpectation
+    @testset "testing return types and type stability" begin
+        @test GPLikelihoods.expected_loglikelihood(
+            MonteCarloExpectation(1), GaussianLikelihood(), q_f, zeros(10)
+        ) isa Real
+        @test GPLikelihoods.expected_loglikelihood(
+            GaussHermiteExpectation(1), GaussianLikelihood(), q_f, zeros(10)
+        ) isa Real
+        @test GPLikelihoods.default_expectation_method(θ -> Normal(0, θ)) isa
+            GaussHermiteExpectation
+
+        @testset "$(nameof(typeof(lik)))" for lik in likelihoods_to_test
+            # Test that `expectec_loglikelihood` is type-stable
+            y = rand.(rng, lik.(zeros(10)))
+            for method in [
+                MonteCarloExpectation(100),
+                GaussHermiteExpectation(100),
+                GPLikelihoods.DefaultExpectationMethod(),
+            ]
+                @test (@inferred expected_loglikelihood(method, lik, q_f, y)) isa Real
+            end
+        end
+    end
 
     # see https://github.com/JuliaGaussianProcesses/ApproximateGPs.jl/issues/82
     @testset "testing Zygote compatibility with GaussHermiteExpectation" begin