feat: add induced_subgraph functionality (#499)

* feat: add induced_subgraph functionality * fix: fix tests * fix: fix tests * Update GNNGraphs/src/sampling.jl Co-authored-by: Carlo Lucibello <[email protected]> * Update GNNGraphs/src/GNNGraphs.jl Co-authored-by: Carlo Lucibello <[email protected]> * Update GNNGraphs/src/sampling.jl Co-authored-by: Carlo Lucibello <[email protected]> * Update GNNGraphs/src/sampling.jl Co-authored-by: Carlo Lucibello <[email protected]> * feat: add edata&ndata support for induced_subgraph * chore: export induced_subgraph * fix: fix naming for induced_subgraph * fix: fix typo * fix: revert naming for induced_subgraph * fix: fix test * fix: don't export induced subgraph * fix: don't export induced subgraph * fix: amend docstring * fix: amend docstring * fix: fix docstring * fix: add Graphs.induced_subgraph to docs --------- Co-authored-by: Carlo Lucibello <[email protected]>
JuliaGraphs · Oct 12, 2024 · 8dbac17 · 8dbac17
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diff --git a/GNNGraphs/src/GNNGraphs.jl b/GNNGraphs/src/GNNGraphs.jl
@@ -4,7 +4,7 @@ using SparseArrays
 using Functors: @functor
 import Graphs
 using Graphs: AbstractGraph, outneighbors, inneighbors, adjacency_matrix, degree, 
-              has_self_loops, is_directed
+              has_self_loops, is_directed, induced_subgraph
 import NearestNeighbors
 import NNlib
 import StatsBase

diff --git a/GNNGraphs/src/sampling.jl b/GNNGraphs/src/sampling.jl
@@ -116,3 +116,87 @@ function sample_neighbors(g::GNNGraph{<:COO_T}, nodes, K = -1;
     end
     return gnew
 end
+
+
+"""
+    induced_subgraph(graph, nodes)
+
+Generates a subgraph from the original graph using the provided `nodes`. 
+The function includes the nodes' neighbors and creates edges between nodes that are connected in the original graph. 
+If a node has no neighbors, an isolated node will be added to the subgraph. 
+Returns A new `GNNGraph` containing the subgraph with the specified nodes and their features.
+
+# Arguments
+
+- `graph`. The original GNNGraph containing nodes, edges, and node features.
+- `nodes``. A vector of node indices to include in the subgraph.
+     
+# Examples
+
+```julia
+julia> s = [1, 2]
+2-element Vector{Int64}:
+ 1
+ 2
+
+julia> t = [2, 3]
+2-element Vector{Int64}:
+ 2
+ 3
+
+julia> graph = GNNGraph((s, t), ndata = (; x=rand(Float32, 32, 3), y=rand(Float32, 3)), edata = rand(Float32, 2))
+GNNGraph:
+  num_nodes: 3
+  num_edges: 2
+  ndata:
+        y = 3-element Vector{Float32}
+        x = 32×3 Matrix{Float32}
+  edata:
+        e = 2-element Vector{Float32}
+
+julia> nodes = [1, 2]
+2-element Vector{Int64}:
+ 1
+ 2
+
+julia> subgraph = Graphs.induced_subgraph(graph, nodes)
+GNNGraph:
+  num_nodes: 2
+  num_edges: 1
+  ndata:
+        y = 2-element Vector{Float32}
+        x = 32×2 Matrix{Float32}
+  edata:
+        e = 1-element Vector{Float32}
+```
+"""
+function Graphs.induced_subgraph(graph::GNNGraph, nodes::Vector{Int})
+    if isempty(nodes)
+        return GNNGraph()  # Return empty graph if no nodes are provided
+    end
+
+    node_map = Dict(node => i for (i, node) in enumerate(nodes))
+
+    # Collect edges to add
+    source = Int[]
+    target = Int[]
+    eindices = Int[]
+    for node in nodes
+        neighbors = Graphs.neighbors(graph, node, dir = :in)
+        for neighbor in neighbors
+            if neighbor in keys(node_map)
+                push!(target, node_map[node])
+                push!(source, node_map[neighbor])
+
+                eindex = findfirst(x -> x == [neighbor, node], edge_index(graph))
+                push!(eindices, eindex)
+            end
+        end
+    end
+
+    # Extract features for the new nodes
+    new_ndata = getobs(graph.ndata, nodes)
+    new_edata = getobs(graph.edata, eindices)
+
+    return GNNGraph(source, target, num_nodes = length(node_map), ndata = new_ndata, edata = new_edata) 
+end
diff --git a/GNNGraphs/test/sampling.jl b/GNNGraphs/test/sampling.jl
@@ -45,4 +45,36 @@ if GRAPH_T == :coo
         @test sg.ndata.x1 == g.ndata.x1[sg.ndata.NID]
         @test length(union(sg.ndata.NID)) == length(sg.ndata.NID)
     end
+
+    @testset "induced_subgraph" begin
+        s = [1, 2]
+        t = [2, 3]
+
+        graph = GNNGraph((s, t), ndata = (; x=rand(Float32, 32, 3), y=rand(Float32, 3)), edata = rand(Float32, 2))
+
+        nodes = [1, 2, 3]
+        subgraph = Graphs.induced_subgraph(graph, nodes)
+
+        @test subgraph.num_nodes == 3  
+        @test subgraph.num_edges == 2  
+        @test subgraph.ndata.x == graph.ndata.x
+        @test subgraph.ndata.y == graph.ndata.y
+        @test subgraph.edata == graph.edata
+
+        nodes = [1, 2]
+        subgraph = Graphs.induced_subgraph(graph, nodes)
+
+        @test subgraph.num_nodes == 2 
+        @test subgraph.num_edges == 1 
+        @test subgraph.ndata == getobs(graph.ndata, [1, 2])
+        @test isapprox(getobs(subgraph.edata.e, 1), getobs(graph.edata.e, 1); atol=1e-6)
+
+        graph = GNNGraph(2)
+        graph = add_edges(graph, ([2], [1]))
+        nodes = [1]
+        subgraph = Graphs.induced_subgraph(graph, nodes)
+
+        @test subgraph.num_nodes == 1 
+        @test subgraph.num_edges == 0 
+    end
 end
diff --git a/GraphNeuralNetworks/docs/src/api/gnngraph.md b/GraphNeuralNetworks/docs/src/api/gnngraph.md
@@ -88,3 +88,7 @@ Modules = [GNNGraphs]
 Pages   = ["sampling.jl"]
 Private = false
 ```
+
+```@docs
+Graphs.induced_subgraph(::GNNGraph, ::Vector{Int})
+```
diff --git a/GraphNeuralNetworks/src/GraphNeuralNetworks.jl b/GraphNeuralNetworks/src/GraphNeuralNetworks.jl
@@ -11,7 +11,7 @@ using ChainRulesCore
 using Reexport
 using MLUtils: zeros_like
 
-using GNNGraphs: COO_T, ADJMAT_T, SPARSE_T,
+using GNNGraphs:  COO_T, ADJMAT_T, SPARSE_T,
                   check_num_nodes, check_num_edges,
                   EType, NType # for heteroconvs