test_nn.py

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():
    g = dgl.DGLGraph(nx.erdos_renyi_graph(20, 0.3))
    ctx = F.ctx()

    graphsage = nn.SAGEConv(10, 20)
    graphsage.initialize(ctx=ctx)
    print(graphsage)

    # test#1: basic
    h0 = F.randn((20, 10))
    h1 = graphsage(g, h0)
    assert h1.shape == (20, 20)

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()