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changes for Flux v0.15 #550

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merged 7 commits into from
Dec 9, 2024
Merged

changes for Flux v0.15 #550

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8c4e15b
adapt to flux 0.15
CarloLucibello Dec 7, 2024
69e64a6
finish TGCN
CarloLucibello Dec 7, 2024
83c1c31
fix gradient
CarloLucibello Dec 7, 2024
b7b773e
fix gated graph conv
CarloLucibello Dec 7, 2024
628da46
fix lstm
CarloLucibello Dec 7, 2024
00e802d
cleanup
CarloLucibello Dec 9, 2024
9b379d7
packages
CarloLucibello Dec 9, 2024
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4 changes: 2 additions & 2 deletions GNNGraphs/Project.toml
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@@ -1,7 +1,7 @@
name = "GNNGraphs"
uuid = "aed8fd31-079b-4b5a-b342-a13352159b8c"
authors = ["Carlo Lucibello and contributors"]
version = "1.3.1"
version = "1.4.0-DEV"

[deps]
Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
Expand Down Expand Up @@ -31,7 +31,7 @@ GNNGraphsSimpleWeightedGraphsExt = "SimpleWeightedGraphs"
Adapt = "4"
CUDA = "5"
ChainRulesCore = "1"
Functors = "0.4.1, 0.5"
Functors = "0.5"
Graphs = "1.4"
KrylovKit = "0.8"
LinearAlgebra = "1"
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2 changes: 0 additions & 2 deletions GNNGraphs/src/GNNGraphs.jl
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@@ -1,7 +1,6 @@
module GNNGraphs

using SparseArrays
using Functors: @functor
import Graphs
using Graphs: AbstractGraph, outneighbors, inneighbors, adjacency_matrix, degree,
has_self_loops, is_directed, induced_subgraph, has_edge
Expand All @@ -13,7 +12,6 @@ using ChainRulesCore
using LinearAlgebra, Random, Statistics
import MLUtils
using MLUtils: getobs, numobs, ones_like, zeros_like, chunk, batch, rand_like
import Functors
using MLDataDevices: get_device, cpu_device, CPUDevice

include("chainrules.jl") # hacks for differentiability
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2 changes: 0 additions & 2 deletions GNNGraphs/src/datastore.jl
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Expand Up @@ -70,8 +70,6 @@ struct DataStore
end
end

@functor DataStore

DataStore(data) = DataStore(-1, data)
DataStore(n::Int, data::NamedTuple) = DataStore(n, Dict{Symbol, Any}(pairs(data)))
DataStore(n::Int, data) = DataStore(n, Dict{Symbol, Any}(data))
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2 changes: 0 additions & 2 deletions GNNGraphs/src/gnngraph.jl
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Expand Up @@ -116,8 +116,6 @@ struct GNNGraph{T <: Union{COO_T, ADJMAT_T}} <: AbstractGNNGraph{T}
gdata::DataStore
end

@functor GNNGraph

function GNNGraph(data::D;
num_nodes = nothing,
graph_indicator = nothing,
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2 changes: 0 additions & 2 deletions GNNGraphs/src/gnnheterograph/gnnheterograph.jl
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Expand Up @@ -95,8 +95,6 @@ struct GNNHeteroGraph{T <: Union{COO_T, ADJMAT_T}} <: AbstractGNNGraph{T}
etypes::Vector{EType}
end

@functor GNNHeteroGraph

GNNHeteroGraph(data; kws...) = GNNHeteroGraph(Dict(data); kws...)
GNNHeteroGraph(data::Pair...; kws...) = GNNHeteroGraph(Dict(data...); kws...)

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2 changes: 0 additions & 2 deletions GNNGraphs/src/temporalsnapshotsgnngraph.jl
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Expand Up @@ -240,5 +240,3 @@ function print_feature_t(io::IO, feature)
print(io, "no")
end
end

@functor TemporalSnapshotsGNNGraph
2 changes: 1 addition & 1 deletion GNNGraphs/test/runtests.jl
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@@ -1,7 +1,7 @@
using CUDA, cuDNN
using GNNGraphs
using GNNGraphs: getn, getdata
using Functors
using Functors: Functors
using LinearAlgebra, Statistics, Random
using NNlib
import MLUtils
Expand Down
6 changes: 3 additions & 3 deletions GNNLux/Project.toml
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@@ -1,7 +1,7 @@
name = "GNNLux"
uuid = "e8545f4d-a905-48ac-a8c4-ca114b98986d"
authors = ["Carlo Lucibello and contributors"]
version = "0.1.1"
version = "0.2.0-DEV"

[deps]
ConcreteStructs = "2569d6c7-a4a2-43d3-a901-331e8e4be471"
Expand All @@ -17,8 +17,8 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[compat]
ConcreteStructs = "0.2.3"
GNNGraphs = "1.3"
GNNlib = "0.2.3"
GNNGraphs = "1.4"
GNNlib = "1"
Lux = "1"
LuxCore = "1"
NNlib = "0.9.21"
Expand Down
8 changes: 5 additions & 3 deletions GNNLux/docs/make.jl
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@@ -1,8 +1,10 @@
using Pkg
Pkg.activate(@__DIR__)
Pkg.develop(path=joinpath(@__DIR__, "..", "..", "GNNGraphs"))
Pkg.develop(path=joinpath(@__DIR__, "..", "..", "GNNlib"))
Pkg.develop(path=joinpath(@__DIR__, ".."))
Pkg.develop([
PackageSpec(path=joinpath(@__DIR__, "..", "..", "GNNGraphs")),
PackageSpec(path=joinpath(@__DIR__, "..", "..", "GNNlib")),
PackageSpec(path=joinpath(@__DIR__, "..")),
])
Pkg.instantiate()

using Documenter
Expand Down
2 changes: 1 addition & 1 deletion GNNLux/src/layers/conv.jl
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Expand Up @@ -1261,7 +1261,7 @@ LuxCore.parameterlength(l::GatedGraphConv) = parameterlength(l.gru) + l.dims^2*l

function (l::GatedGraphConv)(g, x, ps, st)
gru = StatefulLuxLayer{true}(l.gru, ps.gru, _getstate(st, :gru))
fgru = (h, x) -> gru((x, (h,))) # make the forward compatible with Flux.GRUCell style
fgru = (x, h) -> gru((x, (h,)))[1] # make the forward compatible with Flux.GRUCell style
m = (; gru=fgru, ps.weight, l.num_layers, l.aggr, l.dims)
return GNNlib.gated_graph_conv(m, g, x), st
end
Expand Down
8 changes: 8 additions & 0 deletions GNNLux/test/runtests.jl
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@@ -1,3 +1,11 @@
## The test environment is instantiated as follows:
# using Pkg
# Pkg.activate(@__DIR__)
# Pkg.develop(path=joinpath(@__DIR__, "..", "..", "GNNGraphs"))
# Pkg.develop(path=joinpath(@__DIR__, "..", "..", "GNNlib"))
# Pkg.develop(path=joinpath(@__DIR__, ".."))
# Pkg.instantiate()

using TestItemRunner

## See https://www.julia-vscode.org/docs/stable/userguide/testitems/
Expand Down
6 changes: 3 additions & 3 deletions GNNlib/Project.toml
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@@ -1,7 +1,7 @@
name = "GNNlib"
uuid = "a6a84749-d869-43f8-aacc-be26a1996e48"
authors = ["Carlo Lucibello and contributors"]
version = "0.2.5"
version = "1.0.0-DEV"

[deps]
ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
Expand All @@ -28,10 +28,10 @@ GNNlibCUDAExt = "CUDA"

[compat]
AMDGPU = "1"
CUDA = "4, 5"
CUDA = "5"
ChainRulesCore = "1.24"
DataStructures = "0.18"
GNNGraphs = "1.0"
GNNGraphs = "1.4"
GPUArraysCore = "0.1"
LinearAlgebra = "1"
MLUtils = "0.4"
Expand Down
6 changes: 4 additions & 2 deletions GNNlib/docs/make.jl
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@@ -1,7 +1,9 @@
using Pkg
Pkg.activate(@__DIR__)
Pkg.develop(path=joinpath(@__DIR__, "..", "..", "GNNGraphs"))
Pkg.develop(path=joinpath(@__DIR__, ".."))
Pkg.develop([
PackageSpec(path=joinpath(@__DIR__, "..", "..", "GNNGraphs")),
PackageSpec(path=joinpath(@__DIR__, "..")),
])
Pkg.instantiate()

using Documenter
Expand Down
2 changes: 1 addition & 1 deletion GNNlib/src/layers/conv.jl
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Expand Up @@ -228,7 +228,7 @@ function gated_graph_conv(l, g::GNNGraph, x::AbstractMatrix)
m = view(l.weight, :, :, i) * h
m = propagate(copy_xj, g, l.aggr; xj = m)
# in gru forward, hidden state is first argument, input is second
h, _ = l.gru(h, m)
h = l.gru(m, h)
end
return h
end
Expand Down
5 changes: 4 additions & 1 deletion GNNlib/src/layers/pool.jl
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Expand Up @@ -29,8 +29,11 @@ topk_index(y::Adjoint, k::Int) = topk_index(y', k)
function set2set_pool(l, g::GNNGraph, x::AbstractMatrix)
n_in = size(x, 1)
qstar = zeros_like(x, (2*n_in, g.num_graphs))
h = zeros_like(l.lstm.Wh, size(l.lstm.Wh, 2))
c = zeros_like(l.lstm.Wh, size(l.lstm.Wh, 2))
for t in 1:l.num_iters
q = l.lstm(qstar) # [n_in, n_graphs]
h, c = l.lstm(qstar, (h, c)) # [n_in, n_graphs]
q = h
qn = broadcast_nodes(g, q) # [n_in, n_nodes]
α = softmax_nodes(g, sum(qn .* x, dims = 1)) # [1, n_nodes]
r = reduce_nodes(+, g, x .* α) # [n_in, n_graphs]
Expand Down
7 changes: 7 additions & 0 deletions GNNlib/test/runtests.jl
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@@ -1,3 +1,10 @@
## The test environment is instantiated as follows:
# using Pkg
# Pkg.activate(@__DIR__)
# Pkg.develop(path=joinpath(@__DIR__, "..", "..", "GNNGraphs"))
# Pkg.develop(path=joinpath(@__DIR__, ".."))
# Pkg.instantiate()

using TestItemRunner

## See https://www.julia-vscode.org/docs/stable/userguide/testitems/
Expand Down
8 changes: 4 additions & 4 deletions GraphNeuralNetworks/Project.toml
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@@ -1,7 +1,7 @@
name = "GraphNeuralNetworks"
uuid = "cffab07f-9bc2-4db1-8861-388f63bf7694"
authors = ["Carlo Lucibello and contributors"]
version = "0.6.23"
version = "1.0.0-DEV"

[deps]
ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
Expand All @@ -18,9 +18,9 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[compat]
ChainRulesCore = "1"
Flux = "0.14"
GNNGraphs = "1.0"
GNNlib = "0.2"
Flux = "0.15"
GNNGraphs = "1.4"
GNNlib = "1"
LinearAlgebra = "1"
MLUtils = "0.4"
MacroTools = "0.5"
Expand Down
8 changes: 5 additions & 3 deletions GraphNeuralNetworks/docs/make.jl
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@@ -1,8 +1,10 @@
using Pkg
Pkg.activate(@__DIR__)
Pkg.develop(path=joinpath(@__DIR__, "..", "..", "GNNGraphs"))
Pkg.develop(path=joinpath(@__DIR__, "..", "..", "GNNlib"))
Pkg.develop(path=joinpath(@__DIR__, ".."))
Pkg.develop([
PackageSpec(path=joinpath(@__DIR__, "..", "..", "GNNGraphs")),
PackageSpec(path=joinpath(@__DIR__, "..", "..", "GNNlib")),
PackageSpec(path=joinpath(@__DIR__, "..")),
])
Pkg.instantiate()

using Documenter
Expand Down
21 changes: 8 additions & 13 deletions GraphNeuralNetworks/src/layers/pool.jl
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Expand Up @@ -149,24 +149,19 @@ end
Flux.@layer Set2Set

function Set2Set(n_in::Int, n_iters::Int, n_layers::Int = 1)
@assert n_layers >= 1
@assert n_layers == 1 "multiple layers not implemented yet" #TODO
n_out = 2 * n_in

if n_layers == 1
lstm = LSTM(n_out => n_in)
else
layers = [LSTM(n_out => n_in)]
for _ in 2:n_layers
push!(layers, LSTM(n_in => n_in))
end
lstm = Chain(layers...)
end

lstm = LSTMCell(n_out => n_in)
return Set2Set(lstm, n_iters)
end

function initialstates(cell::LSTMCell)
h = zeros_like(cell.Wh, size(cell.Wh, 2))
c = zeros_like(cell.Wh, size(cell.Wh, 2))
return h, c
end

function (l::Set2Set)(g, x)
Flux.reset!(l.lstm)
return GNNlib.set2set_pool(l, g, x)
end

Expand Down
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