Eigenpooling

src/AtomicGraphNets.jl

@@ -1,8 +1,8 @@
 module AtomicGraphNets
 
 export AGNConv, AGNPool#, AGNConvDEQ
-include("layers.jl")
-using .Layers: AGNConv, AGNPool
+include("layers/layers.jl")
+export AGNConv, AGNPool
 
 include("models.jl")
 export build_CGCNN, build_SGCNN

src/layers/conv/agnconv.jl

@@ -0,0 +1,102 @@
+using Flux
+using Flux: glorot_uniform, normalise, @functor#, destructure
+using Zygote: @adjoint, @nograd
+using LinearAlgebra, SparseArrays
+using Statistics
+using ChemistryFeaturization
+#using DifferentialEquations, DiffEqSensitivity
+
+"""
+    AGNConv(in=>out)
+
+Atomic graph convolutional layer. Almost identical to GCNConv from GeometricFlux but adapted to be most similar to Tian's original AGNN structure, so explicitly has self and convolutional weights separately.
+
+# Fields
+- `selfweight::Array{T,2}`: weights applied to features at a node
+- `convweight::Array{T,2}`: convolutional weights
+- `bias::Array{T,2}`: additive bias (second dimension is always 1 because only learnable per-feature, not per-node)
+- `σ::F`: activation function (will be applied before `reg_norm` to outputs), defaults to softplus
+
+# Arguments
+- `in::Integer`: the dimension of input features.
+- `out::Integer`: the dimension of output features.
+- `σ=softplus`: activation function
+- `initW=glorot_uniform`: initialization function for weights
+- `initb=zeros`: initialization function for biases
+
+"""
+struct AGNConv{T,F}
+    selfweight::Array{T,2}
+    convweight::Array{T,2}
+    bias::Array{T,2}
+    σ::F
+end
+
+function AGNConv(
+    ch::Pair{<:Integer,<:Integer},
+    σ = softplus;
+    initW = glorot_uniform,
+    initb = zeros,
+    T::DataType = Float64,
+)
+    selfweight = T.(initW(ch[2], ch[1]))
+    convweight = T.(initW(ch[2], ch[1]))
+    b = T.(initb(ch[2], 1))
+    AGNConv(selfweight, convweight, b, σ)
+end
+
+@functor AGNConv
+
+"""
+ Define action of layer on inputs: do a graph convolution, add this (weighted by convolutional weight) to the features themselves (weighted by self weight) and the per-feature bias (concatenated to match number of nodes in graph).
+
+# Arguments
+- input: a FeaturizedAtoms object, or graph_laplacian, encoded_features
+
+# Note
+In the case of providing two matrices, the following conditions must hold:
+- `lapl` must be square and of dimension N x N where N is the number of nodes in the graph
+- `X` (encoded features) must be of dimension M x N, where M is `size(l.convweight)[2]` (or equivalently, `size(l.selfweight)[2]`)
+"""
+function (l::AGNConv{T,F})(lapl::Matrix{<:Real}, X::Matrix{<:Real}) where {T<:Real,F}
+    # should we put dimension checks here? Could allow more informative errors, but would likely introduce performance penalty. For now it's just in docstring.
+    out_mat =
+        T.(
+            normalise(
+                l.σ.(
+                    l.convweight * X * lapl +
+                    l.selfweight * X +
+                    reduce(hcat, l.bias for i = 1:size(X, 2)),
+                ),
+                dims = [1, 2],
+            ),
+        )
+    lapl, out_mat
+end
+
+# alternate signature so FeaturizedAtoms can be fed into first layer
+(l::AGNConv)(a::FeaturizedAtoms{AtomGraph,GraphNodeFeaturization}) =
+    l(a.atoms.laplacian, a.encoded_features)
+
+# signature to splat appropriately
+(l::AGNConv)(t::Tuple{Matrix{R1},Matrix{R2}}) where {R1<:Real,R2<:Real} = l(t...)
+
+# fixes from Dhairya so backprop works
+@adjoint function SparseMatrixCSC{T,N}(arr) where {T,N}
+    SparseMatrixCSC{T,N}(arr), Δ -> (collect(Δ),)
+end
+@nograd LinearAlgebra.diagm
+
+@adjoint function Broadcast.broadcasted(Float32, a::SparseMatrixCSC{T,N}) where {T,N}
+    Float32.(a), Δ -> (nothing, T.(Δ))
+end
+@nograd issymmetric
+
+@adjoint function Broadcast.broadcasted(Float64, a::SparseMatrixCSC{T,N}) where {T,N}
+    Float64.(a), Δ -> (nothing, T.(Δ))
+end
+
+@adjoint function softplus(x::Real)
+    y = softplus(x)
+    return y, Δ -> (Δ * σ(x),)
+end

src/layers/layers.jl

@@ -0,0 +1,44 @@
+#using DifferentialEquations, DiffEqSensitivity
+
+include("conv/agnconv.jl")
+include("pool/agnpool.jl")
+
+# following commented out for now because it only runs suuuuper slowly but slows down precompilation a lot
+"""
+# DEQ-style model where we treat the convolution as a SteadyStateProblem
+struct AGNConvDEQ{T,F}
+    conv::AGNConv{T,F}
+end
+
+function AGNConvDEQ(ch::Pair{<:Integer,<:Integer}, σ=softplus; initW=glorot_uniform, initb=glorot_uniform, T::DataType=Float32, bias::Bool=true)
+    conv = AGNConv(ch, σ; initW=initW, initb=initb, T=T)
+    AGNConvDEQ(conv)
+end
+
+@functor AGNConvDEQ
+
+# set up SteadyStateProblem where the derivative is the convolution operation
+# (we want the "fixed point" of the convolution)
+# need it in the form f(u,p,t) (but t doesn't matter)
+# u is the features, p is the parameters of conv
+# re(p) reconstructs the convolution with new parameters p
+function (l::AGNConvDEQ)(fa::FeaturizedAtoms)
+    p,re = Flux.destructure(l.conv)
+    # do one convolution to get initial guess
+    guess = l.conv(gr)[2]
+
+    f = function (dfeat,feat,p,t)
+        input = gr
+        input.encoded_features = reshape(feat,size(guess))
+        output = re(p)(input)
+        dfeat .= vec(output[2]) .- vec(input.encoded_features)
+    end
+
+    prob = SteadyStateProblem{true}(f, vec(guess), p)
+    #return solve(prob, DynamicSS(Tsit5())).u
+    alg = SSRootfind()
+    #alg = SSRootfind(nlsolve = (f,u0,abstol) -> (res=SteadyStateDiffEq.NLsolve.nlsolve(f,u0,autodiff=:forward,method=:anderson,iterations=Int(1e6),ftol=abstol);res.zero))
+    out_mat = reshape(solve(prob, alg, sensealg = SteadyStateAdjoint(autodiff = false, autojacvec = ZygoteVJP())).u,size(guess))
+    return AtomGraph(gr.graph, gr.elements, out_mat, gr.featurization)
+end
+"""