import mxnet as mx import networkx as nx import numpy as np import scipy as sp import dgl import dgl.nn.mxnet as nn import dgl.function as fn import backend as F from mxnet import autograd, gluon, nd def check_close(a, b): assert np.allclose(a.asnumpy(), b.asnumpy(), rtol=1e-4, atol=1e-4) def _AXWb(A, X, W, b): X = mx.nd.dot(X, W.data(X.context)) Y = mx.nd.dot(A, X.reshape(X.shape[0], -1)).reshape(X.shape) return Y + b.data(X.context) def test_graph_conv(): g = dgl.DGLGraph(nx.path_graph(3)) ctx = F.ctx() adj = g.adjacency_matrix(ctx=ctx) conv = nn.GraphConv(5, 2, norm=False, bias=True) conv.initialize(ctx=ctx) # test#1: basic h0 = F.ones((3, 5)) h1 = conv(g, h0) assert len(g.ndata) == 0 assert len(g.edata) == 0 check_close(h1, _AXWb(adj, h0, conv.weight, conv.bias)) # test#2: more-dim h0 = F.ones((3, 5, 5)) h1 = conv(g, h0) assert len(g.ndata) == 0 assert len(g.edata) == 0 check_close(h1, _AXWb(adj, h0, conv.weight, conv.bias)) conv = nn.GraphConv(5, 2) conv.initialize(ctx=ctx) # test#3: basic h0 = F.ones((3, 5)) h1 = conv(g, h0) assert len(g.ndata) == 0 assert len(g.edata) == 0 # test#4: basic h0 = F.ones((3, 5, 5)) h1 = conv(g, h0) assert len(g.ndata) == 0 assert len(g.edata) == 0 conv = nn.GraphConv(5, 2) conv.initialize(ctx=ctx) with autograd.train_mode(): # test#3: basic h0 = F.ones((3, 5)) h1 = conv(g, h0) assert len(g.ndata) == 0 assert len(g.edata) == 0 # test#4: basic h0 = F.ones((3, 5, 5)) h1 = conv(g, h0) assert len(g.ndata) == 0 assert len(g.edata) == 0 # test not override features g.ndata["h"] = 2 * F.ones((3, 1)) h1 = conv(g, h0) assert len(g.ndata) == 1 assert len(g.edata) == 0 assert "h" in g.ndata check_close(g.ndata['h'], 2 * F.ones((3, 1))) def _S2AXWb(A, N, X, W, b): X1 = X * N X1 = mx.nd.dot(A, X1.reshape(X1.shape[0], -1)) X1 = X1 * N X2 = X1 * N X2 = mx.nd.dot(A, X2.reshape(X2.shape[0], -1)) X2 = X2 * N X = mx.nd.concat(X, X1, X2, dim=-1) Y = mx.nd.dot(X, W) return Y + b def test_tagconv(): g = dgl.DGLGraph(nx.path_graph(3)) ctx = F.ctx() adj = g.adjacency_matrix(ctx=ctx) norm = mx.nd.power(g.in_degrees().astype('float32'), -0.5) conv = nn.TAGConv(5, 2, bias=True) conv.initialize(ctx=ctx) print(conv) # test#1: basic h0 = F.ones((3, 5)) h1 = conv(g, h0) assert len(g.ndata) == 0 assert len(g.edata) == 0 shp = norm.shape + (1,) * (h0.ndim - 1) norm = norm.reshape(shp).as_in_context(h0.context) assert F.allclose(h1, _S2AXWb(adj, norm, h0, conv.lin.data(ctx), conv.h_bias.data(ctx))) conv = nn.TAGConv(5, 2) conv.initialize(ctx=ctx) # test#2: basic h0 = F.ones((3, 5)) h1 = conv(g, h0) assert h1.shape[-1] == 2 def test_gat_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() gat = nn.GATConv(10, 20, 5) # n_heads = 5 gat.initialize(ctx=ctx) print(gat) # test#1: basic h0 = F.randn((20, 10)) h1 = gat(g, h0) assert h1.shape == (20, 5, 20) def test_sage_conv(): for aggre_type in ['mean', 'pool', 'gcn']: ctx = F.ctx() g = dgl.DGLGraph(sp.sparse.random(100, 100, density=0.1), readonly=True) sage = nn.SAGEConv(5, 10, aggre_type) feat = F.randn((100, 5)) sage.initialize(ctx=ctx) h = sage(g, feat) assert h.shape[-1] == 10 g = dgl.graph(sp.sparse.random(100, 100, density=0.1)) sage = nn.SAGEConv(5, 10, aggre_type) feat = F.randn((100, 5)) sage.initialize(ctx=ctx) h = sage(g, feat) assert h.shape[-1] == 10 g = dgl.bipartite(sp.sparse.random(100, 200, density=0.1)) dst_dim = 5 if aggre_type != 'gcn' else 10 sage = nn.SAGEConv((10, dst_dim), 2, aggre_type) feat = (F.randn((100, 10)), F.randn((200, dst_dim))) sage.initialize(ctx=ctx) h = sage(g, feat) assert h.shape[-1] == 2 assert h.shape[0] == 200 def test_gg_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() gg_conv = nn.GatedGraphConv(10, 20, 3, 4) # n_step = 3, n_etypes = 4 gg_conv.initialize(ctx=ctx) print(gg_conv) # test#1: basic h0 = F.randn((20, 10)) etypes = nd.random.randint(0, 4, g.number_of_edges()).as_in_context(ctx) h1 = gg_conv(g, h0, etypes) assert h1.shape == (20, 20) def test_cheb_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() cheb = nn.ChebConv(10, 20, 3) # k = 3 cheb.initialize(ctx=ctx) print(cheb) # test#1: basic h0 = F.randn((20, 10)) h1 = cheb(g, h0) assert h1.shape == (20, 20) def test_agnn_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() agnn_conv = nn.AGNNConv(0.1, True) agnn_conv.initialize(ctx=ctx) print(agnn_conv) # test#1: basic h0 = F.randn((20, 10)) h1 = agnn_conv(g, h0) assert h1.shape == (20, 10) def test_appnp_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() appnp_conv = nn.APPNPConv(3, 0.1, 0) appnp_conv.initialize(ctx=ctx) print(appnp_conv) # test#1: basic h0 = F.randn((20, 10)) h1 = appnp_conv(g, h0) assert h1.shape == (20, 10) def test_dense_cheb_conv(): for k in range(1, 4): ctx = F.ctx() g = dgl.DGLGraph(sp.sparse.random(100, 100, density=0.3), readonly=True) adj = g.adjacency_matrix(ctx=ctx).tostype('default') cheb = nn.ChebConv(5, 2, k) dense_cheb = nn.DenseChebConv(5, 2, k) cheb.initialize(ctx=ctx) dense_cheb.initialize(ctx=ctx) for i in range(len(cheb.fc)): dense_cheb.fc[i].weight.set_data( cheb.fc[i].weight.data()) if cheb.bias is not None: dense_cheb.bias.set_data( cheb.bias.data()) feat = F.randn((100, 5)) out_cheb = cheb(g, feat, [2.0]) out_dense_cheb = dense_cheb(adj, feat, 2.0) assert F.allclose(out_cheb, out_dense_cheb) def test_dense_graph_conv(): ctx = F.ctx() g = dgl.DGLGraph(sp.sparse.random(100, 100, density=0.3), readonly=True) adj = g.adjacency_matrix(ctx=ctx).tostype('default') conv = nn.GraphConv(5, 2, norm=False, bias=True) dense_conv = nn.DenseGraphConv(5, 2, norm=False, bias=True) conv.initialize(ctx=ctx) dense_conv.initialize(ctx=ctx) dense_conv.weight.set_data( conv.weight.data()) dense_conv.bias.set_data( conv.bias.data()) feat = F.randn((100, 5)) out_conv = conv(g, feat) out_dense_conv = dense_conv(adj, feat) assert F.allclose(out_conv, out_dense_conv) def test_dense_sage_conv(): ctx = F.ctx() g = dgl.DGLGraph(sp.sparse.random(100, 100, density=0.1), readonly=True) adj = g.adjacency_matrix(ctx=ctx).tostype('default') sage = nn.SAGEConv(5, 2, 'gcn') dense_sage = nn.DenseSAGEConv(5, 2) sage.initialize(ctx=ctx) dense_sage.initialize(ctx=ctx) dense_sage.fc.weight.set_data( sage.fc_neigh.weight.data()) dense_sage.fc.bias.set_data( sage.fc_neigh.bias.data()) feat = F.randn((100, 5)) out_sage = sage(g, feat) out_dense_sage = dense_sage(adj, feat) assert F.allclose(out_sage, out_dense_sage) def test_edge_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() edge_conv = nn.EdgeConv(5, 2) edge_conv.initialize(ctx=ctx) print(edge_conv) # test #1: basic h0 = F.randn((g.number_of_nodes(), 5)) h1 = edge_conv(g, h0) assert h1.shape == (g.number_of_nodes(), 2) def test_gin_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() gin_conv = nn.GINConv(lambda x: x, 'mean', 0.1) gin_conv.initialize(ctx=ctx) print(gin_conv) # test #1: basic h0 = F.randn((g.number_of_nodes(), 5)) h1 = gin_conv(g, h0) assert h1.shape == (g.number_of_nodes(), 5) def test_gmm_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() gmm_conv = nn.GMMConv(5, 2, 5, 3, 'max') gmm_conv.initialize(ctx=ctx) print(gmm_conv) # test #1: basic h0 = F.randn((g.number_of_nodes(), 5)) pseudo = F.randn((g.number_of_edges(), 5)) h1 = gmm_conv(g, h0, pseudo) assert h1.shape == (g.number_of_nodes(), 2) def test_nn_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() nn_conv = nn.NNConv(5, 2, gluon.nn.Embedding(3, 5 * 2), 'max') nn_conv.initialize(ctx=ctx) print(nn_conv) # test #1: basic h0 = F.randn((g.number_of_nodes(), 5)) etypes = nd.random.randint(0, 4, g.number_of_edges()).as_in_context(ctx) h1 = nn_conv(g, h0, etypes) assert h1.shape == (g.number_of_nodes(), 2) def test_sg_conv(): g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3)) ctx = F.ctx() sgc = nn.SGConv(5, 2, 2) sgc.initialize(ctx=ctx) print(sgc) # test #1: basic h0 = F.randn((g.number_of_nodes(), 5)) h1 = sgc(g, h0) assert h1.shape == (g.number_of_nodes(), 2) def test_set2set(): g = dgl.DGLGraph(nx.path_graph(10)) ctx = F.ctx() s2s = nn.Set2Set(5, 3, 3) # hidden size 5, 3 iters, 3 layers s2s.initialize(ctx=ctx) print(s2s) # test#1: basic h0 = F.randn((g.number_of_nodes(), 5)) h1 = s2s(g, h0) assert h1.shape[0] == 1 and h1.shape[1] == 10 and h1.ndim == 2 # test#2: batched graph bg = dgl.batch([g, g, g]) h0 = F.randn((bg.number_of_nodes(), 5)) h1 = s2s(bg, h0) assert h1.shape[0] == 3 and h1.shape[1] == 10 and h1.ndim == 2 def test_glob_att_pool(): g = dgl.DGLGraph(nx.path_graph(10)) ctx = F.ctx() gap = nn.GlobalAttentionPooling(gluon.nn.Dense(1), gluon.nn.Dense(10)) gap.initialize(ctx=ctx) print(gap) # test#1: basic h0 = F.randn((g.number_of_nodes(), 5)) h1 = gap(g, h0) assert h1.shape[0] == 1 and h1.shape[1] == 10 and h1.ndim == 2 # test#2: batched graph bg = dgl.batch([g, g, g, g]) h0 = F.randn((bg.number_of_nodes(), 5)) h1 = gap(bg, h0) assert h1.shape[0] == 4 and h1.shape[1] == 10 and h1.ndim == 2 def test_simple_pool(): g = dgl.DGLGraph(nx.path_graph(15)) sum_pool = nn.SumPooling() avg_pool = nn.AvgPooling() max_pool = nn.MaxPooling() sort_pool = nn.SortPooling(10) # k = 10 print(sum_pool, avg_pool, max_pool, sort_pool) # test#1: basic h0 = F.randn((g.number_of_nodes(), 5)) h1 = sum_pool(g, h0) check_close(F.squeeze(h1, 0), F.sum(h0, 0)) h1 = avg_pool(g, h0) check_close(F.squeeze(h1, 0), F.mean(h0, 0)) h1 = max_pool(g, h0) check_close(F.squeeze(h1, 0), F.max(h0, 0)) h1 = sort_pool(g, h0) assert h1.shape[0] == 1 and h1.shape[1] == 10 * 5 and h1.ndim == 2 # test#2: batched graph g_ = dgl.DGLGraph(nx.path_graph(5)) bg = dgl.batch([g, g_, g, g_, g]) h0 = F.randn((bg.number_of_nodes(), 5)) h1 = sum_pool(bg, h0) truth = mx.nd.stack(F.sum(h0[:15], 0), F.sum(h0[15:20], 0), F.sum(h0[20:35], 0), F.sum(h0[35:40], 0), F.sum(h0[40:55], 0), axis=0) check_close(h1, truth) h1 = avg_pool(bg, h0) truth = mx.nd.stack(F.mean(h0[:15], 0), F.mean(h0[15:20], 0), F.mean(h0[20:35], 0), F.mean(h0[35:40], 0), F.mean(h0[40:55], 0), axis=0) check_close(h1, truth) h1 = max_pool(bg, h0) truth = mx.nd.stack(F.max(h0[:15], 0), F.max(h0[15:20], 0), F.max(h0[20:35], 0), F.max(h0[35:40], 0), F.max(h0[40:55], 0), axis=0) check_close(h1, truth) h1 = sort_pool(bg, h0) assert h1.shape[0] == 5 and h1.shape[1] == 10 * 5 and h1.ndim == 2 def uniform_attention(g, shape): a = mx.nd.ones(shape) target_shape = (g.number_of_edges(),) + (1,) * (len(shape) - 1) return a / g.in_degrees(g.edges()[1]).reshape(target_shape).astype('float32') def test_edge_softmax(): # Basic g = dgl.DGLGraph(nx.path_graph(3)) edata = F.ones((g.number_of_edges(), 1)) a = nn.edge_softmax(g, edata) assert len(g.ndata) == 0 assert len(g.edata) == 0 assert np.allclose(a.asnumpy(), uniform_attention(g, a.shape).asnumpy(), 1e-4, 1e-4) # Test higher dimension case edata = F.ones((g.number_of_edges(), 3, 1)) a = nn.edge_softmax(g, edata) assert len(g.ndata) == 0 assert len(g.edata) == 0 assert np.allclose(a.asnumpy(), uniform_attention(g, a.shape).asnumpy(), 1e-4, 1e-4) def test_partial_edge_softmax(): g = dgl.DGLGraph() g.add_nodes(30) # build a complete graph for i in range(30): for j in range(30): g.add_edge(i, j) score = F.randn((300, 1)) score.attach_grad() grad = F.randn((300, 1)) import numpy as np eids = np.random.choice(900, 300, replace=False).astype('int64') eids = F.zerocopy_from_numpy(eids) # compute partial edge softmax with mx.autograd.record(): y_1 = nn.edge_softmax(g, score, eids) y_1.backward(grad) grad_1 = score.grad # compute edge softmax on edge subgraph subg = g.edge_subgraph(eids) with mx.autograd.record(): y_2 = nn.edge_softmax(subg, score) y_2.backward(grad) grad_2 = score.grad assert F.allclose(y_1, y_2) assert F.allclose(grad_1, grad_2) def test_rgcn(): ctx = F.ctx() etype = [] g = dgl.DGLGraph(sp.sparse.random(100, 100, density=0.1), readonly=True) # 5 etypes R = 5 for i in range(g.number_of_edges()): etype.append(i % 5) B = 2 I = 10 O = 8 rgc_basis = nn.RelGraphConv(I, O, R, "basis", B) rgc_basis.initialize(ctx=ctx) h = nd.random.randn(100, I, ctx=ctx) r = nd.array(etype, ctx=ctx) h_new = rgc_basis(g, h, r) assert list(h_new.shape) == [100, O] rgc_bdd = nn.RelGraphConv(I, O, R, "bdd", B) rgc_bdd.initialize(ctx=ctx) h = nd.random.randn(100, I, ctx=ctx) r = nd.array(etype, ctx=ctx) h_new = rgc_bdd(g, h, r) assert list(h_new.shape) == [100, O] # with norm norm = nd.zeros((g.number_of_edges(), 1), ctx=ctx) rgc_basis = nn.RelGraphConv(I, O, R, "basis", B) rgc_basis.initialize(ctx=ctx) h = nd.random.randn(100, I, ctx=ctx) r = nd.array(etype, ctx=ctx) h_new = rgc_basis(g, h, r, norm) assert list(h_new.shape) == [100, O] rgc_bdd = nn.RelGraphConv(I, O, R, "bdd", B) rgc_bdd.initialize(ctx=ctx) h = nd.random.randn(100, I, ctx=ctx) r = nd.array(etype, ctx=ctx) h_new = rgc_bdd(g, h, r, norm) assert list(h_new.shape) == [100, O] # id input rgc_basis = nn.RelGraphConv(I, O, R, "basis", B) rgc_basis.initialize(ctx=ctx) h = nd.random.randint(0, I, (100,), ctx=ctx) r = nd.array(etype, ctx=ctx) h_new = rgc_basis(g, h, r) assert list(h_new.shape) == [100, O] def test_sequential(): ctx = F.ctx() # test single graph class ExampleLayer(gluon.nn.Block): def __init__(self, **kwargs): super().__init__(**kwargs) def forward(self, graph, n_feat, e_feat): graph = graph.local_var() graph.ndata['h'] = n_feat graph.update_all(fn.copy_u('h', 'm'), fn.sum('m', 'h')) n_feat += graph.ndata['h'] graph.apply_edges(fn.u_add_v('h', 'h', 'e')) e_feat += graph.edata['e'] return n_feat, e_feat g = dgl.DGLGraph() g.add_nodes(3) g.add_edges([0, 1, 2, 0, 1, 2, 0, 1, 2], [0, 0, 0, 1, 1, 1, 2, 2, 2]) net = nn.Sequential() net.add(ExampleLayer()) net.add(ExampleLayer()) net.add(ExampleLayer()) net.initialize(ctx=ctx) n_feat = F.randn((3, 4)) e_feat = F.randn((9, 4)) n_feat, e_feat = net(g, n_feat, e_feat) assert n_feat.shape == (3, 4) assert e_feat.shape == (9, 4) # test multiple graphs class ExampleLayer(gluon.nn.Block): def __init__(self, **kwargs): super().__init__(**kwargs) def forward(self, graph, n_feat): graph = graph.local_var() graph.ndata['h'] = n_feat graph.update_all(fn.copy_u('h', 'm'), fn.sum('m', 'h')) n_feat += graph.ndata['h'] return n_feat.reshape(graph.number_of_nodes() // 2, 2, -1).sum(1) g1 = dgl.DGLGraph(nx.erdos_renyi_graph(32, 0.05)) g2 = dgl.DGLGraph(nx.erdos_renyi_graph(16, 0.2)) g3 = dgl.DGLGraph(nx.erdos_renyi_graph(8, 0.8)) net = nn.Sequential() net.add(ExampleLayer()) net.add(ExampleLayer()) net.add(ExampleLayer()) net.initialize(ctx=ctx) n_feat = F.randn((32, 4)) n_feat = net([g1, g2, g3], n_feat) assert n_feat.shape == (4, 4) if __name__ == '__main__': test_graph_conv() test_gat_conv() test_sage_conv() test_gg_conv() test_cheb_conv() test_agnn_conv() test_appnp_conv() test_dense_cheb_conv() test_dense_graph_conv() test_dense_sage_conv() test_edge_conv() test_gin_conv() test_gmm_conv() test_nn_conv() test_sg_conv() test_edge_softmax() test_partial_edge_softmax() test_set2set() test_glob_att_pool() test_simple_pool() test_rgcn() test_sequential()