Merge pull request #46 from CarloLucibello/cl/dev

implement ResGatedGraphConv and support Parallel in GNNChain

Author: CarloLucibello

Project.toml

@@ -4,6 +4,7 @@ authors = ["Carlo Lucibello and contributors"]
 version = "0.1.1"
 
 [deps]
+Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
@@ -20,6 +21,7 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
+Adapt = "3"
 CUDA = "3.3"
 ChainRulesCore = "1"
 DataStructures = "0.18"

docs/src/models.md

@@ -78,11 +78,26 @@ X = randn(Float32, din, 10)
 model = GNNChain(GCNConv(din => d),
                  BatchNorm(d),
                  x -> relu.(x),
-                 GraphConv(d => d, relu),
+                 GCNConv(d => d, relu),
                  Dropout(0.5),
                  Dense(d, dout))
 
-y = model(g, X)
+y = model(g, X)  # output size: (dout, g.num_nodes)
 ```
 
 The `GNNChain` only propagates the graph and the node features. More complex scenarios, e.g. when also edge features are updated, have to be handled using the explicit definition of the forward pass. 
+
+A `GNNChain` oppurtunely propagates the graph into the branches created by the `Flux.Parallel` layer:
+
+```julia
+AddResidual(l) = Parallel(+, identity, l)  # implementing a skip/residual connection
+
+model = GNNChain( ResGatedGraphConv(din => d, relu),
+                  AddResidual(ResGatedGraphConv(d => d, relu)),
+                  AddResidual(ResGatedGraphConv(d => d, relu)),
+                  AddResidual(ResGatedGraphConv(d => d, relu)),
+                  GlobalPooling(mean),
+                  Dense(d, dout))
+
+y = model(g, X) # output size: (dout, g.num_graphs)
+```

src/GraphNeuralNetworks.jl

@@ -46,6 +46,7 @@ export
     GINConv,
     GraphConv,
     NNConv,
+    ResGatedGraphConv,
     SAGEConv,
 
     # layers/pool
@@ -62,5 +63,6 @@ include("msgpass.jl")
 include("layers/basic.jl")
 include("layers/conv.jl")
 include("layers/pool.jl")
+include("deprecations.jl")
 
 end

src/deprecations.jl

@@ -0,0 +1,3 @@
+# Deprecated in v0.1 
+
+@deprecate GINConv(nn; eps=0, aggr=+)  GINConv(nn, eps; aggr)

src/layers/basic.jl

@@ -63,6 +63,12 @@ Flux.functor(::Type{<:GNNChain}, c) = c.layers, ls -> GNNChain(ls...)
 applylayer(l, g::GNNGraph, x) = l(x)
 applylayer(l::GNNLayer, g::GNNGraph, x) = l(g, x)
 
+# Handle Flux.Parallel
+applylayer(l::Parallel, g::GNNGraph, x::AbstractArray) = mapreduce(f -> applylayer(f, g, x), l.connection, l.layers)
+applylayer(l::Parallel, g::GNNGraph, xs::Vararg{<:AbstractArray}) = mapreduce((f, x) -> applylayer(f, g, x), l.connection, l.layers, xs)
+applylayer(l::Parallel, g::GNNGraph, xs::Tuple) = applylayer(l, g, xs...)
+
+
 applychain(::Tuple{}, g::GNNGraph, x) = x
 applychain(fs::Tuple, g::GNNGraph, x) = applychain(tail(fs), g, applylayer(first(fs), g, x))
 

src/layers/conv.jl

@@ -224,7 +224,7 @@ with ``z_i`` a normalization factor.
 
 - `in`: The dimension of input features.
 - `out`: The dimension of output features.
-- `bias::Bool`: Keyword argument, whether to learn the additive bias.
+- `bias`: Learn the additive bias if true.
 - `heads`: Number attention heads.
 - `concat`: Concatenate layer output or not. If not, layer output is averaged over the heads.
 - `negative_slope`: The parameter of LeakyReLU.
@@ -407,7 +407,7 @@ end
 
 
 @doc raw"""
-    GINConv(f; eps = 0f0)
+    GINConv(f, ϵ; aggr=+)
 
 Graph Isomorphism convolutional layer from paper [How Powerful are Graph Neural Networks?](https://arxiv.org/pdf/1810.00826.pdf)
 
@@ -420,30 +420,38 @@ where ``f_\Theta`` typically denotes a learnable function, e.g. a linear layer o
 # Arguments
 
 - `f`: A (possibly learnable) function acting on node features. 
-- `eps`: Weighting factor.
+- `ϵ`: Weighting factor.
 """
 struct GINConv{R<:Real} <: GNNLayer
     nn
-    eps::R
+    ϵ::R
+    aggr
 end
 
 @functor GINConv
-Flux.trainable(l::GINConv) = (nn=l.nn,)
+Flux.trainable(l::GINConv) = (l.nn,)
+
+GINConv(nn, ϵ; aggr=+) = GINConv(nn, ϵ, aggr)
 
-function GINConv(nn; eps=0f0)
-    GINConv(nn, eps)
-end
 
 compute_message(l::GINConv, x_i, x_j, e_ij) = x_j 
-update_node(l::GINConv, m, x) = l.nn((1 + l.eps) * x + m)
+update_node(l::GINConv, m, x) = l.nn((1 + ofeltype(x, l.ϵ)) * x + m)
 
 function (l::GINConv)(g::GNNGraph, X::AbstractMatrix)
     check_num_nodes(g, X)
-    X, _ = propagate(l, g, +, X)
+    X, _ = propagate(l, g, l.aggr, X)
     X
 end
 
 
+function Base.show(io::IO, l::GINConv)
+    print(io, "GINConv($(l.nn)")
+    print(io, ", $(l.ϵ)")
+    print(io, ")")
+end
+
+
+
 @doc raw"""
     NNConv(in => out, f, σ=identity; aggr=+, bias=true, init=glorot_uniform)
 
@@ -572,3 +580,77 @@ function Base.show(io::IO, l::SAGEConv)
     print(io, ", aggr=", l.aggr)
     print(io, ")")
 end
+
+
+@doc raw"""
+    ResGatedGraphConv(in => out, act=identity; init=glorot_uniform, bias=true)
+
+The residual gated graph convolutional operator from the [Residual Gated Graph ConvNets]((https://arxiv.org/abs/1711.07553)) paper.
+
+The layer's forward pass is given by
+
+```math
+\mathbf{x}_i' = act\big(U\mathbf{xhttps://github.com/ArtLabBocconi/deepJuliaNN}_i + \sum_{j \in N(i)} \eta_{ij} V \mathbf{x}_j\big),
+```
+where the edge gates ``\eta_{ij}`` are given by
+
+```math
+\eta_{ij} = sigmoid(A\mathbf{x}_i + B\mathbf{x}_j).
+```
+
+# Arguments
+
+- `in`: The dimension of input features.
+- `out`: The dimension of output features.
+- `act`: Activation function.
+- `init`: Weight matrices' initializing function. 
+- `bias`: Learn an additive bias if true.
+"""
+struct ResGatedGraphConv <: GNNLayer
+    A
+    B
+    U
+    V
+    bias
+    σ
+end
+
+@functor ResGatedGraphConv
+
+function ResGatedGraphConv(ch::Pair{Int,Int}, σ=identity;
+                      init=glorot_uniform, bias::Bool=true)
+    in, out = ch             
+    A = init(out, in)
+    B = init(out, in)
+    U = init(out, in)
+    V = init(out, in)
+    b = bias ? Flux.create_bias(A, true, out) : false
+    return ResGatedGraphConv(A, B, U, V, b, σ)
+end
+
+function compute_message(l::ResGatedGraphConv, di, dj)
+    η = sigmoid.(di.Ax .+ dj.Bx)
+    return η .* dj.Vx
+end
+
+update_node(l::ResGatedGraphConv, m, x) = m
+
+function (l::ResGatedGraphConv)(g::GNNGraph, x::AbstractMatrix)
+    check_num_nodes(g, x)
+
+    Ax = l.A * x
+    Bx = l.B * x
+    Vx = l.V * x
+    
+    m, _ = propagate(l, g, +, (; Ax, Bx, Vx))
+
+    return l.σ.(l.U*x .+ m .+ l.bias)                                      
+end
+
+
+function Base.show(io::IO, l::ResGatedGraphConv)
+    out_channel, in_channel = size(l.A)
+    print(io, "ResGatedGraphConv(", in_channel, "=>", out_channel)
+    l.σ == identity || print(io, ", ", l.σ)
+    print(io, ")")
+end

src/utils.jl

@@ -67,3 +67,6 @@ function normalize_graphdata(data::NamedTuple; default_name, n, duplicate_if_nee
     end
     return data
 end
+
+
+ofeltype(x, y) = convert(float(eltype(x)), y)

test/examples/node_classification_cora.jl

@@ -17,11 +17,11 @@ end
 
 # arguments for the `train` function 
 Base.@kwdef mutable struct Args
-    η = 1f-3             # learning rate
-    epochs = 20         # number of epochs
+    η = 5f-3             # learning rate
+    epochs = 10         # number of epochs
     seed = 17             # set seed > 0 for reproducibility
     usecuda = false      # if true use cuda (if available)
-    nhidden = 128        # dimension of hidden features
+    nhidden = 64        # dimension of hidden features
 end
 
 function train(Layer; verbose=false, kws...)
@@ -49,7 +49,7 @@ function train(Layer; verbose=false, kws...)
 
     ## DEFINE MODEL
     model = GNNChain(Layer(nin, nhidden),
-                     Dropout(0.5),
+                    #  Dropout(0.5),
                      Layer(nhidden, nhidden), 
                      Dense(nhidden, nout))  |> device
 
@@ -70,8 +70,8 @@ function train(Layer; verbose=false, kws...)
             ŷ = model(g, X)
             logitcrossentropy(ŷ[:,train_ids], ytrain)
         end
-        verbose && report(epoch)
         Flux.Optimise.update!(opt, ps, gs)
+        verbose && report(epoch)
     end
 
     train_res = eval_loss_accuracy(X, y, train_ids, model, g)
@@ -84,15 +84,16 @@ for Layer in [
             (nin, nout) -> GraphConv(nin => nout, relu, aggr=mean),
             (nin, nout) -> SAGEConv(nin => nout, relu),
             (nin, nout) -> GATConv(nin => nout, relu),
-            (nin, nout) -> GATConv(nin => nout÷2, relu, heads=2),
-            (nin, nout) -> GINConv(Dense(nin, nout, relu)),
-            (nin, nout) -> ChebConv(nin => nout, 3),
+            (nin, nout) -> GINConv(Dense(nin, nout, relu), 0.01, aggr=mean),
+            (nin, nout) -> ChebConv(nin => nout, 2),
+            (nin, nout) -> ResGatedGraphConv(nin => nout, relu),        
             # (nin, nout) -> NNConv(nin => nout),  # needs edge features
             # (nin, nout) -> GatedGraphConv(nout, 2),  # needs nin = nout
             # (nin, nout) -> EdgeConv(Dense(2nin, nout, relu)), # Fits the traning set but does not generalize well
               ]
-    train_res, test_res = train(Layer, verbose=true)
-    # @show Layer(2,2) train_res, test_res
+
+    # @show Layer(2,2)
+    train_res, test_res = train(Layer, verbose=false)
     @test train_res.acc > 95
     @test test_res.acc > 70
 end

test/layers/basic.jl

@@ -2,32 +2,34 @@
     @testset "GNNChain" begin
         n, din, d, dout = 10, 3, 4, 2
 
-        g = GNNGraph(random_regular_graph(n, 4), graph_type=GRAPH_T)
+        g = GNNGraph(random_regular_graph(n, 4), 
+                    graph_type=GRAPH_T,
+                    ndata= randn(Float32, din, n))
 
         gnn = GNNChain(GCNConv(din => d),
                        BatchNorm(d),
-                       x -> relu.(x),
-                       GraphConv(d => d, relu),
+                       x -> tanh.(x),
+                       GraphConv(d => d, tanh),
                        Dropout(0.5),
                        Dense(d, dout))
+
+        testmode!(gnn)
 
-        X = randn(Float32, din, n)
+        test_layer(gnn, g, rtol=1e-5)
 
-        y = gnn(g, X)
-  
-        @test y isa Matrix{Float32}
-        @test size(y) == (dout, n)
 
-        @test length(params(gnn)) == 9
-        
-        gs = gradient(x -> sum(gnn(g, x)), X)[1]
-        @test gs isa Matrix{Float32}
-        @test size(gs) == size(X) 
+        @testset "Parallel" begin
+            AddResidual(l) = Parallel(+, identity, l) 
+
+            gnn = GNNChain(ResGatedGraphConv(din => d, tanh),
+                           BatchNorm(d),
+                           AddResidual(ResGatedGraphConv(d => d, tanh)),
+                           BatchNorm(d),
+                           Dense(d, dout))
 
-        gs = gradient(() -> sum(gnn(g, X)), Flux.params(gnn))
-        for p in Flux.params(gnn)
-            @test eltype(gs[p]) == Float32
-            @test size(gs[p]) == size(p)
+            testmode!(gnn)
+                           
+            test_layer(gnn, g, rtol=1e-5)
         end
     end
 end

test/layers/conv.jl

@@ -111,10 +111,10 @@
 
     @testset "GINConv" begin
         nn = Dense(in_channel, out_channel)
-        eps = 0.001f0
-        l = GINConv(nn, eps=eps)
+        
+        l = GINConv(nn, 0.01f0, aggr=mean)
         for g in test_graphs
-            test_layer(l, g, rtol=1e-5, outsize=(out_channel, g.num_nodes), exclude_grad_fields=[:eps]) 
+            test_layer(l, g, rtol=1e-5, outsize=(out_channel, g.num_nodes)) 
         end
 
         @test !in(:eps, Flux.trainable(l))
@@ -149,4 +149,17 @@
             test_layer(l, g, rtol=1e-5, outsize=(out_channel, g.num_nodes)) 
         end
     end
+
+
+    @testset "ResGatedGraphConv" begin
+        l = ResGatedGraphConv(in_channel => out_channel)
+        for g in test_graphs
+            test_layer(l, g, rtol=1e-5,)
+        end
+
+        l = ResGatedGraphConv(in_channel => out_channel, tanh, bias=false)
+        for g in test_graphs
+            test_layer(l, g, rtol=1e-5,)
+        end
+    end
 end