Merge pull request #114 from theogf/test_AD

Series of tests for AD

.github/workflows/CompatHelper.yml

@@ -16,4 +16,4 @@ jobs:
       - name: CompatHelper.main()
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+        run: julia -e 'using CompatHelper; CompatHelper.main(; subdirs = ["", "test"])'

Project.toml

@@ -22,15 +22,3 @@ StatsBase = "0.32, 0.33"
 StatsFuns = "0.8, 0.9"
 ZygoteRules = "0.2"
 julia = "1.3"
-
-[extras]
-FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
-Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
-Kronecker = "2c470bb0-bcc8-11e8-3dad-c9649493f05e"
-PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
-
-[targets]
-test = ["Random", "Test", "FiniteDifferences", "Zygote", "PDMats", "Kronecker", "Flux"]

src/KernelFunctions.jl

@@ -34,8 +34,8 @@ export spectral_mixture_kernel, spectral_mixture_product_kernel
 using Compat
 using Requires
 using Distances, LinearAlgebra
-using SpecialFunctions: logabsgamma, besselk
-using ZygoteRules: @adjoint
+using SpecialFunctions: logabsgamma, besselk, polygamma
+using ZygoteRules: @adjoint, pullback
 using StatsFuns: logtwo
 using InteractiveUtils: subtypes
 using StatsBase

src/basekernels/matern.jl

@@ -17,12 +17,11 @@ end
 
 @inline function kappa(κ::MaternKernel, d::Real)
     ν = first(κ.ν)
-    iszero(d) ? one(d) :
-    exp(
-        (one(d) - ν) * logtwo - logabsgamma(ν)[1] +
-        ν * log(sqrt(2ν) * d) +
-        log(besselk(ν, sqrt(2ν) * d))
-    )
+    iszero(d) ? one(d) : _matern(ν, d)
+end
+
+function _matern(ν::Real, d::Real)
+    exp((one(d) - ν) * logtwo - loggamma(ν) + ν * log(sqrt(2ν) * d) + log(besselk(ν, sqrt(2ν) * d)))
 end
 
 metric(::MaternKernel) = Euclidean()

src/distances/delta.jl

@@ -1,12 +1,14 @@
 struct Delta <: Distances.PreMetric
 end
 
-@inline function Distances._evaluate(::Delta,a::AbstractVector{T},b::AbstractVector{T}) where {T}
+@inline function Distances._evaluate(::Delta, a::AbstractVector, b::AbstractVector) where {T}
     @boundscheck if length(a) != length(b)
         throw(DimensionMismatch("first array has length $(length(a)) which does not match the length of the second, $(length(b))."))
     end
     return a == b
 end
 
+Distances.result_type(::Delta, Ta::Type, Tb::Type) = promote_type(Ta, Tb)
+
 @inline (dist::Delta)(a::AbstractArray, b::AbstractArray) = Distances._evaluate(dist, a, b)
-@inline (dist::Delta)(a::Number,b::Number) = a == b
+@inline (dist::Delta)(a::Number, b::Number) = a == b

src/distances/dotproduct.jl

@@ -1,13 +1,15 @@
 struct DotProduct <: Distances.PreMetric end
 # struct DotProduct <: Distances.UnionSemiMetric end
 
-@inline function Distances._evaluate(::DotProduct, a::AbstractVector{T}, b::AbstractVector{T}) where {T}
+@inline function Distances._evaluate(::DotProduct, a::AbstractVector, b::AbstractVector)
     @boundscheck if length(a) != length(b)
         throw(DimensionMismatch("first array has length $(length(a)) which does not match the length of the second, $(length(b))."))
     end
     return dot(a,b)
 end
 
+Distances.result_type(::DotProduct, Ta::Type, Tb::Type) = promote_type(Ta, Tb)
+
 @inline Distances.eval_op(::DotProduct, a::Real, b::Real) = a * b
 @inline (dist::DotProduct)(a::AbstractArray,b::AbstractArray) = Distances._evaluate(dist, a, b)
 @inline (dist::DotProduct)(a::Number,b::Number) = a * b

src/distances/sinus.jl

@@ -8,7 +8,9 @@ Distances.parameters(d::Sinus) = d.r
 @inline (dist::Sinus)(a::AbstractArray, b::AbstractArray) = Distances._evaluate(dist, a, b)
 @inline (dist::Sinus)(a::Number, b::Number) = abs2(sinpi(a - b) / first(dist.r))
 
-@inline function Distances._evaluate(d::Sinus, a::AbstractVector{T}, b::AbstractVector{T}) where {T}
+Distances.result_type(::Sinus{T}, Ta::Type, Tb::Type) where {T} = promote_type(T, Ta, Tb)
+
+@inline function Distances._evaluate(d::Sinus, a::AbstractVector, b::AbstractVector) where {T}
     @boundscheck if (length(a) != length(b)) || length(a) != length(d.r)
         throw(DimensionMismatch("Dimensions of the inputs are not matching : a = $(length(a)), b = $(length(b)), r = $(length(d.r))"))
     end

src/transform/ardtransform.jl

@@ -24,9 +24,9 @@ dim(t::ARDTransform) = length(t.v)
 (t::ARDTransform)(x::Real) = first(t.v) * x
 (t::ARDTransform)(x) = t.v .* x
 
-Base.map(t::ARDTransform, x::AbstractVector{<:Real}) = t.v' .* x
-Base.map(t::ARDTransform, x::ColVecs) = ColVecs(t.v .* x.X)
-Base.map(t::ARDTransform, x::RowVecs) = RowVecs(t.v' .* x.X)
+_map(t::ARDTransform, x::AbstractVector{<:Real}) = t.v' .* x
+_map(t::ARDTransform, x::ColVecs) = ColVecs(t.v .* x.X)
+_map(t::ARDTransform, x::RowVecs) = RowVecs(t.v' .* x.X)
 
 Base.isequal(t::ARDTransform, t2::ARDTransform) = isequal(t.v, t2.v)
 

src/transform/chaintransform.jl

@@ -27,7 +27,7 @@ Base.:∘(tc::ChainTransform, t::Transform) = ChainTransform(vcat(t, tc.transfor
 
 (t::ChainTransform)(x) = foldl((x, t) -> t(x), t.transforms; init=x)
 
-function Base.map(t::ChainTransform, x::AbstractVector)
+function _map(t::ChainTransform, x::AbstractVector)
     return foldl((x, t) -> map(t, x), t.transforms; init=x)
 end
 

src/transform/functiontransform.jl

@@ -15,9 +15,9 @@ end
 
 (t::FunctionTransform)(x) = t.f(x)
 
-Base.map(t::FunctionTransform, x::AbstractVector{<:Real}) = map(t.f, x)
-Base.map(t::FunctionTransform, x::ColVecs) = ColVecs(mapslices(t.f, x.X; dims=1))
-Base.map(t::FunctionTransform, x::RowVecs) = RowVecs(mapslices(t.f, x.X; dims=2))
+_map(t::FunctionTransform, x::AbstractVector{<:Real}) = map(t.f, x)
+_map(t::FunctionTransform, x::ColVecs) = ColVecs(mapslices(t.f, x.X; dims=1))
+_map(t::FunctionTransform, x::RowVecs) = RowVecs(mapslices(t.f, x.X; dims=2))
 
 duplicate(t::FunctionTransform,f) = FunctionTransform(f)
 

src/transform/lineartransform.jl

@@ -27,9 +27,9 @@ end
 (t::LinearTransform)(x::Real) = vec(t.A * x)
 (t::LinearTransform)(x::AbstractVector{<:Real}) = t.A * x
 
-Base.map(t::LinearTransform, x::AbstractVector{<:Real}) = ColVecs(t.A * x')
-Base.map(t::LinearTransform, x::ColVecs) = ColVecs(t.A * x.X)
-Base.map(t::LinearTransform, x::RowVecs) = RowVecs(x.X * t.A')
+_map(t::LinearTransform, x::AbstractVector{<:Real}) = ColVecs(t.A * x')
+_map(t::LinearTransform, x::ColVecs) = ColVecs(t.A * x.X)
+_map(t::LinearTransform, x::RowVecs) = RowVecs(x.X * t.A')
 
 function Base.show(io::IO, t::LinearTransform)
     print(io::IO, "Linear transform (size(A) = ", size(t.A), ")")

src/transform/scaletransform.jl

@@ -19,9 +19,9 @@ set!(t::ScaleTransform,ρ::Real) = t.s .= [ρ]
 
 (t::ScaleTransform)(x) = first(t.s) .* x
 
-Base.map(t::ScaleTransform, x::AbstractVector{<:Real}) = first(t.s) .* x
-Base.map(t::ScaleTransform, x::ColVecs) = ColVecs(first(t.s) .* x.X)
-Base.map(t::ScaleTransform, x::RowVecs) = RowVecs(first(t.s) .* x.X)
+_map(t::ScaleTransform, x::AbstractVector{<:Real}) = first(t.s) .* x
+_map(t::ScaleTransform, x::ColVecs) = ColVecs(first(t.s) .* x.X)
+_map(t::ScaleTransform, x::RowVecs) = RowVecs(first(t.s) .* x.X)
 
 Base.isequal(t::ScaleTransform,t2::ScaleTransform) = isequal(first(t.s),first(t2.s))
 

src/transform/selecttransform.jl

@@ -25,7 +25,7 @@ duplicate(t::SelectTransform,θ) = t
 
 (t::SelectTransform)(x::AbstractVector) = view(x, t.select)
 
-Base.map(t::SelectTransform, x::ColVecs) = ColVecs(view(x.X, t.select, :))
-Base.map(t::SelectTransform, x::RowVecs) = RowVecs(view(x.X, :, t.select))
+_map(t::SelectTransform, x::ColVecs) = ColVecs(view(x.X, t.select, :))
+_map(t::SelectTransform, x::RowVecs) = RowVecs(view(x.X, :, t.select))
 
 Base.show(io::IO, t::SelectTransform) = print(io, "Select Transform (dims: ", t.select, ")")

src/transform/transform.jl

@@ -5,12 +5,8 @@ include("functiontransform.jl")
 include("selecttransform.jl")
 include("chaintransform.jl")
 
-"""
-    apply(t::Transform, x; obsdim::Int=defaultobs)
 
-Apply the transform `t` vector-wise on the array `x`
-"""
-apply
+Base.map(t::Transform, x::AbstractVector) = _map(t, x)
 
 """
     IdentityTransform()
@@ -20,7 +16,7 @@ Return exactly the input
 struct IdentityTransform <: Transform end
 
 (t::IdentityTransform)(x) = x
-Base.map(::IdentityTransform, x::AbstractVector) = x
+_map(::IdentityTransform, x::AbstractVector) = x
 
 ### TODO Maybe defining adjoints could help but so far it's not working
 

src/utils.jl

@@ -1,5 +1,7 @@
 hadamard(x, y) = x .* y
 
+loggamma(x) = first(logabsgamma(x))
+
 # Macro for checking arguments
 macro check_args(K, param, cond, desc=string(cond))
     quote
@@ -124,4 +126,3 @@ function validate_dims(x::AbstractVector, y::AbstractVector)
         ))
     end
 end
-

src/zygote_adjoints.jl

@@ -1,9 +1,78 @@
+## Adjoints Delta
+@adjoint function evaluate(s::Delta, x::AbstractVector, y::AbstractVector)
+  evaluate(s, x, y), Δ -> begin
+    (nothing, nothing, nothing)
+  end
+end
+
+@adjoint function pairwise(d::Delta, X::AbstractMatrix, Y::AbstractMatrix; dims=2)
+  D = pairwise(d, X, Y; dims = dims)
+  if dims == 1
+      return D, Δ -> (nothing, nothing, nothing)
+  else
+      return D, Δ -> (nothing, nothing, nothing)
+  end
+end
+
+@adjoint function pairwise(d::Delta, X::AbstractMatrix; dims=2)
+  D = pairwise(d, X; dims = dims)
+  if dims == 1
+      return D, Δ -> (nothing, nothing)
+  else
+      return D, Δ -> (nothing, nothing)
+  end
+end
+
+## Adjoints DotProduct
 @adjoint function evaluate(s::DotProduct, x::AbstractVector, y::AbstractVector)
   dot(x, y), Δ -> begin
     (nothing, Δ .* y, Δ .* x)
   end
 end
 
+@adjoint function pairwise(d::DotProduct, X::AbstractMatrix, Y::AbstractMatrix; dims=2)
+  D = pairwise(d, X, Y; dims = dims)
+  if dims == 1
+      return D, Δ -> (nothing, Δ * Y, (X' * Δ)')
+  else
+      return D, Δ -> (nothing, (Δ * Y')', X * Δ)
+  end
+end
+
+@adjoint function pairwise(d::DotProduct, X::AbstractMatrix; dims=2)
+  D = pairwise(d, X; dims = dims)
+  if dims == 1
+      return D, Δ -> (nothing, 2 * Δ * X)
+  else
+      return D, Δ -> (nothing, 2 * X * Δ)
+  end
+end
+
+## Adjoints Sinus
+@adjoint function evaluate(s::Sinus, x::AbstractVector, y::AbstractVector)
+  d = (x - y)
+  sind = sinpi.(d)
+  val = sum(abs2, sind ./ s.r)
+  gradx = 2π .* cospi.(d) .* sind ./ (s.r .^ 2)
+  val, Δ -> begin
+    ((r = -2Δ .* abs2.(sind) ./ s.r,), Δ * gradx, - Δ * gradx)
+  end
+end
+
+@adjoint function loggamma(x)
+    first(logabsgamma(x)) , Δ -> (Δ .* polygamma(0, x), )
+end
+
+@adjoint function kappa(κ::MaternKernel, d::Real)
+    ν = first(κ.ν)
+    val, grad = pullback(_matern, ν, d)
+    return ((iszero(d) ? one(d) : val),
+    Δ -> begin
+        ∇ = grad(Δ)
+        return ((ν = [∇[1]],), iszero(d) ? zero(d) : ∇[2])
+    end)
+end
+
 @adjoint function ColVecs(X::AbstractMatrix)
     back(Δ::NamedTuple) = (Δ.X,)
     back(Δ::AbstractMatrix) = (Δ,)
@@ -22,10 +91,10 @@ end
     return RowVecs(X), back
 end
 
-# @adjoint function evaluate(s::Sinus, x::AbstractVector, y::AbstractVector)
-#   d = evaluate(s, x, y)
-#   s = sum(sin.(π*(x-y)))
-#   d, Δ -> begin
-#     (Sinus(Δ ./ s.r), 2Δ .* cos.(x - y) * d, -2Δ .* cos.(x - y) * d)
-#   end
-# end
+@adjoint function Base.map(t::Transform, X::ColVecs)
+    pullback(_map, t, X)
+end
+
+@adjoint function Base.map(t::Transform, X::RowVecs)
+    pullback(_map, t, X)
+end

test/Project.toml

@@ -0,0 +1,24 @@
+[deps]
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+Kronecker = "2c470bb0-bcc8-11e8-3dad-c9649493f05e"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
+
+[compat]
+Distances = "0.9"
+FiniteDifferences = "0.10"
+Flux = "0.10"
+ForwardDiff = "0.10"
+Kronecker = "0.4"
+PDMats = "0.9"
+ReverseDiff = "1.2"
+SpecialFunctions = "0.10"
+Zygote = "0.4"

test/basekernels/constant.jl

@@ -5,6 +5,7 @@
         @test kappa(k,2.0) == 0.0
         @test KernelFunctions.metric(ZeroKernel()) == KernelFunctions.Delta()
         @test repr(k) == "Zero Kernel"
+        test_ADs(ZeroKernel)
     end
     @testset "WhiteKernel" begin
         k = WhiteKernel()
@@ -14,6 +15,7 @@
         @test EyeKernel == WhiteKernel
         @test metric(WhiteKernel()) == KernelFunctions.Delta()
         @test repr(k) == "White Kernel"
+        test_ADs(WhiteKernel)
     end
     @testset "ConstantKernel" begin
         c = 2.0
@@ -24,5 +26,6 @@
         @test metric(ConstantKernel()) == KernelFunctions.Delta()
         @test metric(ConstantKernel(c=2.0)) == KernelFunctions.Delta()
         @test repr(k) == "Constant Kernel (c = $(c))"
+        test_ADs(c->ConstantKernel(c=first(c)), [c])
     end
 end

test/basekernels/cosine.jl

@@ -12,4 +12,5 @@
     @test kappa(k,x) ≈ cospi(x) atol=1e-5
     @test k(v1, v2) ≈ cospi(sqrt(sum(abs2.(v1-v2)))) atol=1e-5
     @test repr(k) == "Cosine Kernel"
+    test_ADs(CosineKernel)
 end

test/basekernels/exponential.jl

@@ -14,6 +14,7 @@
         @test SEKernel == SqExponentialKernel
         @test repr(k) == "Squared Exponential Kernel"
         @test KernelFunctions.iskroncompatible(k) == true
+        test_ADs(SEKernel)
     end
     @testset "ExponentialKernel" begin
         k = ExponentialKernel()
@@ -24,6 +25,7 @@
         @test repr(k) == "Exponential Kernel"
         @test LaplacianKernel == ExponentialKernel
         @test KernelFunctions.iskroncompatible(k) == true
+        test_ADs(ExponentialKernel)
     end
     @testset "GammaExponentialKernel" begin
         γ = 2.0
@@ -36,7 +38,8 @@
         @test metric(GammaExponentialKernel(γ=2.0)) == SqEuclidean()
         @test repr(k) == "Gamma Exponential Kernel (γ = $(γ))"
         @test KernelFunctions.iskroncompatible(k) == true
-
+        test_ADs(γ -> GammaExponentialKernel(gamma=first(γ)), [γ], ADs = [:ForwardDiff, :ReverseDiff])
+        @test_broken "Zygote gradient given γ"
         #Coherence :
         @test GammaExponentialKernel(γ=1.0)(v1,v2) ≈ SqExponentialKernel()(v1,v2)
         @test GammaExponentialKernel(γ=0.5)(v1,v2) ≈ ExponentialKernel()(v1,v2)

test/basekernels/exponentiated.jl

@@ -10,4 +10,5 @@
     @test k(v1,v2) ≈ exp(dot(v1,v2))
     @test metric(ExponentiatedKernel()) == KernelFunctions.DotProduct()
     @test repr(k) == "Exponentiated Kernel"
+    test_ADs(ExponentiatedKernel)
 end