GNNGraph

Documentation page for the graph type GNNGraph provided by GraphNeuralNetworks.jl and related methods.

Besides the methods documented here, one can rely on the large set of functionalities given by Graphs.jl thanks to the fact that GNNGraph inherits from Graphs.AbstractGraph.

Index

GNNGraph type

GraphNeuralNetworks.GNNGraphs.GNNGraphType
GNNGraph(data; [graph_type, ndata, edata, gdata, num_nodes, graph_indicator, dir])
GNNGraph(g::GNNGraph; [ndata, edata, gdata])

A type representing a graph structure that also stores feature arrays associated to nodes, edges, and the graph itself.

A GNNGraph can be constructed out of different data objects expressing the connections inside the graph. The internal representation type is determined by graph_type.

When constructed from another GNNGraph, the internal graph representation is preserved and shared. The node/edge/graph features are retained as well, unless explicitely set by the keyword arguments ndata, edata, and gdata.

A GNNGraph can also represent multiple graphs batched togheter (see Flux.batch or SparseArrays.blockdiag). The field g.graph_indicator contains the graph membership of each node.

GNNGraphs are always directed graphs, therefore each edge is defined by a source node and a target node (see edge_index). Self loops (edges connecting a node to itself) and multiple edges (more than one edge between the same pair of nodes) are supported.

A GNNGraph is a Graphs.jl's AbstractGraph, therefore it supports most functionality from that library.

Arguments

  • data: Some data representing the graph topology. Possible type are
    • An adjacency matrix
    • An adjacency list.
    • A tuple containing the source and target vectors (COO representation)
    • A Graphs.jl' graph.
  • graph_type: A keyword argument that specifies the underlying representation used by the GNNGraph. Currently supported values are
    • :coo. Graph represented as a tuple (source, target), such that the k-th edge connects the node source[k] to node target[k]. Optionally, also edge weights can be given: (source, target, weights).
    • :sparse. A sparse adjacency matrix representation.
    • :dense. A dense adjacency matrix representation.
    Defaults to :coo, currently the most supported type.
  • dir: The assumed edge direction when given adjacency matrix or adjacency list input data g. Possible values are :out and :in. Default :out.
  • num_nodes: The number of nodes. If not specified, inferred from g. Default nothing.
  • graph_indicator: For batched graphs, a vector containing the graph assignment of each node. Default nothing.
  • ndata: Node features. An array or named tuple of arrays whose last dimension has size num_nodes.
  • edata: Edge features. An array or named tuple of arrays whose last dimension has size num_edges.
  • gdata: Graph features. An array or named tuple of arrays whose last dimension has size num_graphs.

Examples

using Flux, GraphNeuralNetworks

# Construct from adjacency list representation
data = [[2,3], [1,4,5], [1], [2,5], [2,4]]
g = GNNGraph(data)

# Number of nodes, edges, and batched graphs
g.num_nodes  # 5
g.num_edges  # 10 
g.num_graphs # 1 

# Same graph in COO representation
s = [1,1,2,2,2,3,4,4,5,5]
t = [2,3,1,4,5,3,2,5,2,4]
g = GNNGraph(s, t)

# From a Graphs' graph
g = GNNGraph(erdos_renyi(100, 20))

# Add 2 node feature arrays
g = GNNGraph(g, ndata = (x=rand(100, g.num_nodes), y=rand(g.num_nodes)))

# Add node features and edge features with default names `x` and `e` 
g = GNNGraph(g, ndata = rand(100, g.num_nodes), edata = rand(16, g.num_edges))

g.ndata.x # or just g.x
g.ndata.e # or just g.e

# Send to gpu
g = g |> gpu

# Collect edges' source and target nodes.
# Both source and target are vectors of length num_edges
source, target = edge_index(g)
source

Query

GraphNeuralNetworks.GNNGraphs.adjacency_listMethod
adjacency_list(g; dir=:out)
adjacency_list(g, nodes; dir=:out)

Return the adjacency list representation (a vector of vectors) of the graph g.

Calling a the adjacency list, if dir=:out than a[i] will contain the neighbors of node i through outgoing edges. If dir=:in, it will contain neighbors from incoming edges instead.

If nodes is given, return the neighborhood of the nodes in nodes only.

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GraphNeuralNetworks.GNNGraphs.normalized_laplacianFunction
normalized_laplacian(g, T=Float32; add_self_loops=false, dir=:out)

Normalized Laplacian matrix of graph g.

Arguments

  • g: A GNNGraph.
  • T: result element type.
  • add_self_loops: add self-loops while calculating the matrix.
  • dir: the edge directionality considered (:out, :in, :both).
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GraphNeuralNetworks.GNNGraphs.scaled_laplacianFunction
scaled_laplacian(g, T=Float32; dir=:out)

Scaled Laplacian matrix of graph g, defined as $\hat{L} = \frac{2}{\lambda_{max}} L - I$ where $L$ is the normalized Laplacian matrix.

Arguments

  • g: A GNNGraph.
  • T: result element type.
  • dir: the edge directionality considered (:out, :in, :both).
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Graphs.LinAlg.adjacency_matrixFunction
adjacency_matrix(g::GNNGraph, T=eltype(g); dir=:out, weighted=true)

Return the adjacency matrix A for the graph g.

If dir=:out, A[i,j] > 0 denotes the presence of an edge from node i to node j. If dir=:in instead, A[i,j] > 0 denotes the presence of an edge from node j to node i.

User may specify the eltype T of the returned matrix.

If weighted=true, the A will contain the edge weights if any, otherwise the elements of A will be either 0 or 1.

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Graphs.degreeMethod
degree(g::GNNGraph, T=nothing; dir=:out, edge_weight=true)

Return a vector containing the degrees of the nodes in g.

Arguments

  • g: A graph.
  • T: Element type of the returned vector. If nothing, is chosen based on the graph type and will be an integer if edge_weight=false.
  • dir: For dir=:out the degree of a node is counted based on the outgoing edges. For dir=:in, the ingoing edges are used. If dir=:both we have the sum of the two.
  • edge_weight: If true and the graph contains weighted edges, the degree will be weighted. Set to false instead to just count the number of outgoing/ingoing edges. In alternative, you can also pass a vector of weights to be used instead of the graph's own weights.
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Graphs.outneighborsFunction
outneighbors(g, v)

Return a list of all neighbors connected to vertex v by an outgoing edge.

Implementation Notes

Returns a reference to the current graph's internal structures, not a copy. Do not modify result. If the graph is modified, the behavior is undefined: the array behind this reference may be modified too, but this is not guaranteed.

Examples

julia> g = SimpleDiGraph([0 1 0 0 0; 0 0 1 0 0; 1 0 0 1 0; 0 0 0 0 1; 0 0 0 1 0]);

julia> outneighbors(g, 4)
1-element Array{Int64,1}:
 5
Graphs.inneighborsFunction
inneighbors(g, v)

Return a list of all neighbors connected to vertex v by an incoming edge.

Implementation Notes

Returns a reference to the current graph's internal structures, not a copy. Do not modify result. If the graph is modified, the behavior is undefined: the array behind this reference may be modified too, but this is not guaranteed.

Examples

julia> g = SimpleDiGraph([0 1 0 0 0; 0 0 1 0 0; 1 0 0 1 0; 0 0 0 0 1; 0 0 0 1 0]);

julia> inneighbors(g, 4)
2-element Array{Int64,1}:
 3
 5

Transform

GraphNeuralNetworks.GNNGraphs.add_edgesMethod
add_edges(g::GNNGraph, s::AbstractVector, t::AbstractVector; [edata])

Add to graph g the edges with source nodes s and target nodes t. Optionally, pass the features edata for the new edges.

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GraphNeuralNetworks.GNNGraphs.add_self_loopsMethod
add_self_loops(g::GNNGraph)

Return a graph with the same features as g but also adding edges connecting the nodes to themselves.

Nodes with already existing self-loops will obtain a second self-loop.

If the graphs has edge weights, the new edges will have weight 1.

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GraphNeuralNetworks.GNNGraphs.getgraphMethod
getgraph(g::GNNGraph, i; nmap=false)

Return the subgraph of g induced by those nodes j for which g.graph_indicator[j] == i or, if i is a collection, g.graph_indicator[j] ∈ i. In other words, it extract the component graphs from a batched graph.

If nmap=true, return also a vector v mapping the new nodes to the old ones. The node i in the subgraph will correspond to the node v[i] in g.

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GraphNeuralNetworks.GNNGraphs.negative_sampleMethod
negative_sample(g::GNNGraph; 
                num_neg_edges = g.num_edges, 
                bidirected = is_bidirected(g))

Return a graph containing random negative edges (i.e. non-edges) from graph g as edges.

If bidirected=true, the output graph will be bidirected and there will be no leakage from the origin graph.

See also is_bidirected.

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GraphNeuralNetworks.GNNGraphs.rand_edge_splitMethod
rand_edge_split(g::GNNGraph, frac; bidirected=is_bidirected(g)) -> g1, g2

Randomly partition the edges in g to form two graphs, g1 and g2. Both will have the same number of nodes as g. g1 will contain a fraction frac of the original edges, while g2 wil contain the rest.

If bidirected = true makes sure that an edge and its reverse go into the same split. This option is supported only for bidirected graphs with no self-loops and multi-edges.

rand_edge_split is tipically used to create train/test splits in link prediction tasks.

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GraphNeuralNetworks.GNNGraphs.to_bidirectedMethod
to_bidirected(g)

Adds a reverse edge for each edge in the graph, then calls remove_multi_edges with mean aggregation to simplify the graph.

See also is_bidirected.

Examples

julia> s, t = [1, 2, 3, 3, 4], [2, 3, 4, 4, 4];

julia> w = [1.0, 2.0, 3.0, 4.0, 5.0];

julia> e = [10.0, 20.0, 30.0, 40.0, 50.0];

julia> g = GNNGraph(s, t, w, edata = e)
GNNGraph:
    num_nodes = 4
    num_edges = 5
    edata:
        e => (5,)

julia> g2 = to_bidirected(g)
GNNGraph:
    num_nodes = 4
    num_edges = 7
    edata:
        e => (7,)

julia> edge_index(g2)
([1, 2, 2, 3, 3, 4, 4], [2, 1, 3, 2, 4, 3, 4])

julia> get_edge_weight(g2)
7-element Vector{Float64}:
 1.0
 1.0
 2.0
 2.0
 3.5
 3.5
 5.0

julia> g2.edata.e
7-element Vector{Float64}:
 10.0
 10.0
 20.0
 20.0
 35.0
 35.0
 50.0
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MLUtils.batchMethod
batch(gs::Vector{<:GNNGraph})

Batch together multiple GNNGraphs into a single one containing the total number of original nodes and edges.

Equivalent to SparseArrays.blockdiag. See also Flux.unbatch.

Examples

julia> g1 = rand_graph(4, 6, ndata=ones(8, 4))
GNNGraph:
    num_nodes = 4
    num_edges = 6
    ndata:
        x => (8, 4)

julia> g2 = rand_graph(7, 4, ndata=zeros(8, 7))
GNNGraph:
    num_nodes = 7
    num_edges = 4
    ndata:
        x => (8, 7)

julia> g12 = Flux.batch([g1, g2])
GNNGraph:
    num_nodes = 11
    num_edges = 10
    num_graphs = 2
    ndata:
        x => (8, 11)

julia> g12.ndata.x
8×11 Matrix{Float64}:
 1.0  1.0  1.0  1.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 1.0  1.0  1.0  1.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 1.0  1.0  1.0  1.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 1.0  1.0  1.0  1.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 1.0  1.0  1.0  1.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 1.0  1.0  1.0  1.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 1.0  1.0  1.0  1.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
 1.0  1.0  1.0  1.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
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MLUtils.unbatchMethod
unbatch(g::GNNGraph)

Opposite of the Flux.batch operation, returns an array of the individual graphs batched together in g.

See also Flux.batch and getgraph.

Examples

julia> gbatched = Flux.batch([rand_graph(5, 6), rand_graph(10, 8), rand_graph(4,2)])
GNNGraph:
    num_nodes = 19
    num_edges = 16
    num_graphs = 3

julia> Flux.unbatch(gbatched)
3-element Vector{GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}}:
 GNNGraph:
    num_nodes = 5
    num_edges = 6

 GNNGraph:
    num_nodes = 10
    num_edges = 8

 GNNGraph:
    num_nodes = 4
    num_edges = 2
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Generate

GraphNeuralNetworks.GNNGraphs.knn_graphMethod
knn_graph(points::AbstractMatrix, 
          k::Int; 
          graph_indicator = nothing,
          self_loops = false, 
          dir = :in, 
          kws...)

Create a k-nearest neighbor graph where each node is linked to its k closest points.

Arguments

  • points: A numfeatures × numnodes matrix storing the Euclidean positions of the nodes.
  • k: The number of neighbors considered in the kNN algorithm.
  • graph_indicator: Either nothing or a vector containing the graph assignment of each node, in which case the returned graph will be a batch of graphs.
  • self_loops: If true, consider the node itself among its k nearest neighbors, in which case the graph will contain self-loops.
  • dir: The direction of the edges. If dir=:in edges go from the k neighbors to the central node. If dir=:out we have the opposite direction.
  • kws: Further keyword arguments will be passed to the GNNGraph constructor.

Examples

julia> n, k = 10, 3;

julia> x = rand(3, n);

julia> g = knn_graph(x, k)
GNNGraph:
    num_nodes = 10
    num_edges = 30

julia> graph_indicator = [1,1,1,1,1,2,2,2,2,2];

julia> g = knn_graph(x, k; graph_indicator)
GNNGraph:
    num_nodes = 10
    num_edges = 30
    num_graphs = 2
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GraphNeuralNetworks.GNNGraphs.radius_graphMethod
radius_graph(points::AbstractMatrix, 
             r::AbstractFloat; 
             graph_indicator = nothing,
             self_loops = false, 
             dir = :in, 
             kws...)

Create a graph where each node is linked to its neighbors within a given distance r.

Arguments

  • points: A numfeatures × numnodes matrix storing the Euclidean positions of the nodes.
  • r: The radius.
  • graph_indicator: Either nothing or a vector containing the graph assignment of each node, in which case the returned graph will be a batch of graphs.
  • self_loops: If true, consider the node itself among its neighbors, in which case the graph will contain self-loops.
  • dir: The direction of the edges. If dir=:in edges go from the neighbors to the central node. If dir=:out we have the opposite direction.
  • kws: Further keyword arguments will be passed to the GNNGraph constructor.

Examples

julia> n, r = 10, 0.75;

julia> x = rand(3, n);

julia> g = radius_graph(x, r)
GNNGraph:
    num_nodes = 10
    num_edges = 46

julia> graph_indicator = [1,1,1,1,1,2,2,2,2,2];

julia> g = radius_graph(x, r; graph_indicator)
GNNGraph:
    num_nodes = 10
    num_edges = 20
    num_graphs = 2
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GraphNeuralNetworks.GNNGraphs.rand_graphMethod
rand_graph(n, m; bidirected=true, seed=-1, kws...)

Generate a random (Erdós-Renyi) GNNGraph with n nodes and m edges.

If bidirected=true the reverse edge of each edge will be present. If bidirected=false instead, m unrelated edges are generated. In any case, the output graph will contain no self-loops or multi-edges.

Use a seed > 0 for reproducibility.

Additional keyword arguments will be passed to the GNNGraph constructor.

Examples

julia> g = rand_graph(5, 4, bidirected=false)
GNNGraph:
    num_nodes = 5
    num_edges = 4

julia> edge_index(g)
([1, 3, 3, 4], [5, 4, 5, 2])

# In the bidirected case, edge data will be duplicated on the reverse edges if needed.
julia> g = rand_graph(5, 4, edata=rand(16, 2))
GNNGraph:
    num_nodes = 5
    num_edges = 4
    edata:
        e => (16, 4)

# Each edge has a reverse
julia> edge_index(g)
([1, 3, 3, 4], [3, 4, 1, 3])
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Operators

Base.intersectFunction
intersect(g, h)

Return a graph with edges that are only in both graph g and graph h.

Implementation Notes

This function may produce a graph with 0-degree vertices. Preserves the eltype of the input graph.

Examples

julia> g1 = SimpleDiGraph([0 1 0 0 0; 0 0 1 0 0; 1 0 0 1 0; 0 0 0 0 1; 0 0 0 1 0]);

julia> g2 = SimpleDiGraph([0 1 0; 0 0 1; 1 0 0]);

julia> foreach(println, edges(intersect(g1, g2)))
Edge 1 => 2
Edge 2 => 3
Edge 3 => 1

Sampling

GraphNeuralNetworks.GNNGraphs.sample_neighborsFunction
sample_neighbors(g, nodes, K=-1; dir=:in, replace=false, dropnodes=false)

Sample neighboring edges of the given nodes and return the induced subgraph. For each node, a number of inbound (or outbound when dir = :out) edges will be randomly chosen. Ifdropnodes=false`, the graph returned will then contain all the nodes in the original graph, but only the sampled edges.

The returned graph will contain an edge feature EID corresponding to the id of the edge in the original graph. If dropnodes=true, it will also contain a node feature NID with the node ids in the original graph.

Arguments

  • g. The graph.
  • nodes. A list of node IDs to sample neighbors from.
  • K. The maximum number of edges to be sampled for each node. If -1, all the neighboring edges will be selected.
  • dir. Determines whether to sample inbound (:in) or outbound (`:out) edges (Default :in).
  • replace. If true, sample with replacement.
  • dropnodes. If true, the resulting subgraph will contain only the nodes involved in the sampled edges.

Examples

julia> g = rand_graph(20, 100)
GNNGraph:
    num_nodes = 20
    num_edges = 100

julia> sample_neighbors(g, 2:3)
GNNGraph:
    num_nodes = 20
    num_edges = 9
    edata:
        EID => (9,)

julia> sg = sample_neighbors(g, 2:3, dropnodes=true)
GNNGraph:
    num_nodes = 10
    num_edges = 9
    ndata:
        NID => (10,)
    edata:
        EID => (9,)

julia> sg.ndata.NID
10-element Vector{Int64}:
  2
  3
 17
 14
 18
 15
 16
 20
  7
 10

julia> sample_neighbors(g, 2:3, 5, replace=true)
GNNGraph:
    num_nodes = 20
    num_edges = 10
    edata:
        EID => (10,)
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