JuliaGraphs / JuliaGraphs/GraphNeuralNetworks.jl
GATConv doesn't work on hetero graphs with empty edge arrays or during backpropagation
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Description
e.g. (The dropout defaults to a 64-bit float which causes more problems but can be easily fixed)
using GNNGraphs, GraphNeuralNetworks, NNlib, Flux
graph = GNNHeteroGraph(
Dict(
(:A, :a, :B) => ([1, 2], [3, 4]),
(:B, :a, :A) => ([1], [2]),
(:C, :a, :A) => (Int[], Int[]),
(:A, :a, :C) => (Int[], Int[]),
(:D, :a, :A) => (Int[], Int[]),
(:E, :a, :A) => (Int[], Int[]),
(:E, :a, :D) => (Int[], Int[]),
(:D, :a, :E) => (Int[], Int[]),
);
num_nodes = Dict(:A => 3, :B => 5, :C => 7, :D => 0, :E => 0)
)
layer = HeteroGraphConv(
[
(src, edge, dst) => GATConv(4 => 4, NNlib.elu; dropout = Float32(0.25)) for
(src, edge, dst) in keys(graph.edata)
];
)
layer2 = HeteroGraphConv(
[
(src, edge, dst) => GATConv(4 => 4, NNlib.elu; dropout = Float32(0.25)) for
(src, edge, dst) in keys(graph.edata)
];
)
x = (
A = rand(Float32, 4, 3),
B = rand(Float32, 4, 5),
C = rand(Float32, 4, 7),
D = rand(Float32, 4, 0),
E = rand(Float32, 4, 0),
)
x1 = layer(graph, x)
x2 = layer2(graph, x1)
@info "$x2"
g = Flux.gradient(x) do x
y = layer(graph, x)
sum(y[:A])
end
The error is
ERROR: LoadError: DimensionMismatch: arrays could not be broadcast to a common size: a has axes Base.OneTo(0) and b has axes Base.OneTo(4)
Stacktrace:
[1] _bcs1
@ ./broadcast.jl:535 [inlined]
[2] _bcs
@ ./broadcast.jl:529 [inlined]
[3] broadcast_shape
@ ./broadcast.jl:523 [inlined]
[4] combine_axes
@ ./broadcast.jl:504 [inlined]
[5] _axes
@ ./broadcast.jl:240 [inlined]
[6] axes
@ ./broadcast.jl:238 [inlined]
[7] combine_axes
@ ./broadcast.jl:505 [inlined]
[8] instantiate
@ ./broadcast.jl:313 [inlined]
[9] materialize
@ ./broadcast.jl:894 [inlined]
[10] gat_conv(l::GATConv{Flux.Dense{typeof(identity), Matrix{Float32}, Bool}, Nothing, Float32, Float32, Matrix{Float32}, typeof(elu), Vector{Float32}}, g::GNNHeteroGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}, x::Tuple{Matrix{Float32}, Matrix{Float32}}, e::Nothing)
@ GNNlib ~/.julia/packages/GNNlib/wxiDz/src/layers/conv.jl:147
[11] GATConv
@ ~/.julia/packages/GraphNeuralNetworks/XGIXF/src/layers/conv.jl:346 [inlined]
[12] (::GATConv{Flux.Dense{typeof(identity), Matrix{Float32}, Bool}, Nothing, Float32, Float32, Matrix{Float32}, typeof(elu), Vector{Float32}})(g::GNNHeteroGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}, x::Tuple{Matrix{Float32}, Matrix{Float32}})
@ GraphNeuralNetworks ~/.julia/packages/GraphNeuralNetworks/XGIXF/src/layers/conv.jl:346
[13] (::GraphNeuralNetworks.var"#forw#forw##0"{GNNHeteroGraph{Tuple{T, T, Union{Nothing, AbstractVector}} where T<:(AbstractVector{<:Integer})}, @NamedTuple{A::Matrix{Float32}, B::Matrix{Float32}, C::Matrix{Float32}, D::Matrix{Float32}, E::Matrix{Float32}}})(l::GATConv{Flux.Dense{typeof(identity), Matrix{Float32}, Bool}, Nothing, Float32, Float32, Matrix{Float32}, typeof(elu), Vector{Float32}}, et::Tuple{Symbol, Symbol, Symbol})
@ GraphNeuralNetworks ~/.julia/packages/GraphNeuralNetworks/XGIXF/src/layers/heteroconv.jl:63
[14] #60
@ ./none:-1 [inlined]
[15] iterate
@ ./generator.jl:48 [inlined]
[16] collect(itr::Base.Generator{Base.Iterators.Zip{Tuple{Vector{GATConv{Flux.Dense{typeof(identity), Matrix{Float32}, Bool}, Nothing, Float32, Float32, Matrix{Float32}, typeof(elu), Vector{Float32}}}, Vector{Tuple{Symbol, Symbol, Symbol}}}}, GraphNeuralNetworks.var"#60#61"{GraphNeuralNetworks.var"#forw#forw##0"{GNNHeteroGraph{Tuple{T, T, Union{Nothing, AbstractVector}} where T<:(AbstractVector{<:Integer})}, @NamedTuple{A::Matrix{Float32}, B::Matrix{Float32}, C::Matrix{Float32}, D::Matrix{Float32}, E::Matrix{Float32}}}}})
@ Base ./array.jl:790
[17] (::HeteroGraphConv)(g::GNNHeteroGraph{Tuple{T, T, Union{Nothing, AbstractVector}} where T<:(AbstractVector{<:Integer})}, x::@NamedTuple{A::Matrix{Float32}, B::Matrix{Float32}, C::Matrix{Float32}, D::Matrix{Float32}, E::Matrix{Float32}})
@ GraphNeuralNetworks ~/.julia/packages/GraphNeuralNetworks/XGIXF/src/layers/heteroconv.jl:65
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Research direction
Run the Julia reproducer first, then inspect GNNlib/src/layers/conv.jl:147 and GraphNeuralNetworks/src/layers/conv.jl:346, with heteroconv.jl:63 showing the dispatch path. Check behavior for empty edge arrays and the Flux.gradient case. Done means the shown heterograph works through both forward calls and backpropagation without the DimensionMismatch error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- julia
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100