dmlc--dgl
44b6864114
* enable use for weighted neighbor sampler and biased random walk * add unit tests * fix for mxnet/tf * fix typo
1045 行
47 KiB
Python
1045 行
47 KiB
Python
import dgl
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import backend as F
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import numpy as np
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import unittest
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from collections import defaultdict
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import pytest
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def check_random_walk(g, metapath, traces, ntypes, prob=None, trace_eids=None):
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traces = F.asnumpy(traces)
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ntypes = F.asnumpy(ntypes)
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for j in range(traces.shape[1] - 1):
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assert ntypes[j] == g.get_ntype_id(g.to_canonical_etype(metapath[j])[0])
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assert ntypes[j + 1] == g.get_ntype_id(g.to_canonical_etype(metapath[j])[2])
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for i in range(traces.shape[0]):
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for j in range(traces.shape[1] - 1):
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assert g.has_edge_between(
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traces[i, j], traces[i, j+1], etype=metapath[j])
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if prob is not None and prob in g.edges[metapath[j]].data:
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p = F.asnumpy(g.edges[metapath[j]].data['p'])
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eids = g.edge_ids(traces[i, j], traces[i, j+1], etype=metapath[j])
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assert p[eids] != 0
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if trace_eids is not None:
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u, v = g.find_edges(trace_eids[i, j], etype=metapath[j])
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assert (u == traces[i, j]) and (v == traces[i, j + 1])
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@pytest.mark.parametrize('use_uva', [True, False])
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def test_non_uniform_random_walk(use_uva):
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if use_uva:
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if F.ctx() == F.cpu():
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pytest.skip('UVA biased random walk requires a GPU.')
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if dgl.backend.backend_name != 'pytorch':
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pytest.skip('UVA biased random walk is only supported with PyTorch.')
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g2 = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 1, 1, 2, 3], [1, 2, 3, 0, 0])
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})
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g4 = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 1, 1, 2, 3], [1, 2, 3, 0, 0]),
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('user', 'view', 'item'): ([0, 0, 1, 2, 3, 3], [0, 1, 1, 2, 2, 1]),
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('item', 'viewed-by', 'user'): ([0, 1, 1, 2, 2, 1], [0, 0, 1, 2, 3, 3])
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})
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g2.edata['p'] = F.copy_to(F.tensor([3, 0, 3, 3, 3], dtype=F.float32), F.cpu())
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g2.edata['p2'] = F.copy_to(F.tensor([[3], [0], [3], [3], [3]], dtype=F.float32), F.cpu())
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g4.edges['follow'].data['p'] = F.copy_to(F.tensor([3, 0, 3, 3, 3], dtype=F.float32), F.cpu())
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g4.edges['viewed-by'].data['p'] = F.copy_to(F.tensor([1, 1, 1, 1, 1, 1], dtype=F.float32), F.cpu())
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if use_uva:
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for g in (g2, g4):
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g.create_formats_()
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g.pin_memory_()
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elif F._default_context_str == 'gpu':
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g2 = g2.to(F.ctx())
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g4 = g4.to(F.ctx())
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try:
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traces, eids, ntypes = dgl.sampling.random_walk(
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g2, F.tensor([0, 1, 2, 3, 0, 1, 2, 3], dtype=g2.idtype),
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length=4, prob='p', return_eids=True)
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check_random_walk(g2, ['follow'] * 4, traces, ntypes, 'p', trace_eids=eids)
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with pytest.raises(dgl.DGLError):
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traces, ntypes = dgl.sampling.random_walk(
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g2, F.tensor([0, 1, 2, 3, 0, 1, 2, 3], dtype=g2.idtype),
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length=4, prob='p2')
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metapath = ['follow', 'view', 'viewed-by'] * 2
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traces, eids, ntypes = dgl.sampling.random_walk(
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g4, F.tensor([0, 1, 2, 3, 0, 1, 2, 3], dtype=g4.idtype),
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metapath=metapath, prob='p', return_eids=True)
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check_random_walk(g4, metapath, traces, ntypes, 'p', trace_eids=eids)
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traces, eids, ntypes = dgl.sampling.random_walk(
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g4, F.tensor([0, 1, 2, 3, 0, 1, 2, 3], dtype=g4.idtype),
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metapath=metapath, prob='p', restart_prob=0., return_eids=True)
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check_random_walk(g4, metapath, traces, ntypes, 'p', trace_eids=eids)
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traces, eids, ntypes = dgl.sampling.random_walk(
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g4, F.tensor([0, 1, 2, 3, 0, 1, 2, 3], dtype=g4.idtype),
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metapath=metapath, prob='p',
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restart_prob=F.zeros((6,), F.float32, F.ctx()), return_eids=True)
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check_random_walk(g4, metapath, traces, ntypes, 'p', trace_eids=eids)
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traces, eids, ntypes = dgl.sampling.random_walk(
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g4, F.tensor([0, 1, 2, 3, 0, 1, 2, 3], dtype=g4.idtype),
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metapath=metapath + ['follow'], prob='p',
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restart_prob=F.tensor([0, 0, 0, 0, 0, 0, 1], F.float32), return_eids=True)
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check_random_walk(g4, metapath, traces[:, :7], ntypes[:7], 'p', trace_eids=eids)
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assert (F.asnumpy(traces[:, 7]) == -1).all()
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finally:
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for g in (g2, g4):
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g.unpin_memory_()
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@pytest.mark.parametrize('use_uva', [True, False])
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def test_uniform_random_walk(use_uva):
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if use_uva and F.ctx() == F.cpu():
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pytest.skip('UVA random walk requires a GPU.')
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g1 = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 1, 2], [1, 2, 0])
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})
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g2 = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 1, 1, 2, 3], [1, 2, 3, 0, 0])
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})
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g3 = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 1, 2], [1, 2, 0]),
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('user', 'view', 'item'): ([0, 1, 2], [0, 1, 2]),
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('item', 'viewed-by', 'user'): ([0, 1, 2], [0, 1, 2])
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})
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g4 = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 1, 1, 2, 3], [1, 2, 3, 0, 0]),
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('user', 'view', 'item'): ([0, 0, 1, 2, 3, 3], [0, 1, 1, 2, 2, 1]),
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('item', 'viewed-by', 'user'): ([0, 1, 1, 2, 2, 1], [0, 0, 1, 2, 3, 3])
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})
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if use_uva:
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for g in (g1, g2, g3, g4):
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g.create_formats_()
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g.pin_memory_()
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elif F._default_context_str == 'gpu':
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g1 = g1.to(F.ctx())
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g2 = g2.to(F.ctx())
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g3 = g3.to(F.ctx())
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g4 = g4.to(F.ctx())
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try:
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traces, eids, ntypes = dgl.sampling.random_walk(
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g1, F.tensor([0, 1, 2, 0, 1, 2], dtype=g1.idtype), length=4, return_eids=True)
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check_random_walk(g1, ['follow'] * 4, traces, ntypes, trace_eids=eids)
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if F._default_context_str == 'cpu':
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with pytest.raises(dgl.DGLError):
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dgl.sampling.random_walk(g1, F.tensor([0, 1, 2, 10], dtype=g1.idtype), length=4, return_eids=True)
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traces, eids, ntypes = dgl.sampling.random_walk(
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g1, F.tensor([0, 1, 2, 0, 1, 2], dtype=g1.idtype), length=4, restart_prob=0., return_eids=True)
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check_random_walk(g1, ['follow'] * 4, traces, ntypes, trace_eids=eids)
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traces, ntypes = dgl.sampling.random_walk(
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g1, F.tensor([0, 1, 2, 0, 1, 2], dtype=g1.idtype), length=4, restart_prob=F.zeros((4,), F.float32))
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check_random_walk(g1, ['follow'] * 4, traces, ntypes)
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traces, ntypes = dgl.sampling.random_walk(
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g1, F.tensor([0, 1, 2, 0, 1, 2], dtype=g1.idtype), length=5,
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restart_prob=F.tensor([0, 0, 0, 0, 1], dtype=F.float32))
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check_random_walk(
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g1, ['follow'] * 4, F.slice_axis(traces, 1, 0, 5), F.slice_axis(ntypes, 0, 0, 5))
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assert (F.asnumpy(traces)[:, 5] == -1).all()
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traces, eids, ntypes = dgl.sampling.random_walk(
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g2, F.tensor([0, 1, 2, 3, 0, 1, 2, 3], dtype=g2.idtype), length=4, return_eids=True)
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check_random_walk(g2, ['follow'] * 4, traces, ntypes, trace_eids=eids)
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metapath = ['follow', 'view', 'viewed-by'] * 2
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traces, eids, ntypes = dgl.sampling.random_walk(
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g3, F.tensor([0, 1, 2, 0, 1, 2], dtype=g3.idtype), metapath=metapath, return_eids=True)
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check_random_walk(g3, metapath, traces, ntypes, trace_eids=eids)
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metapath = ['follow', 'view', 'viewed-by'] * 2
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traces, eids, ntypes = dgl.sampling.random_walk(
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g4, F.tensor([0, 1, 2, 3, 0, 1, 2, 3], dtype=g4.idtype), metapath=metapath, return_eids=True)
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check_random_walk(g4, metapath, traces, ntypes, trace_eids=eids)
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traces, eids, ntypes = dgl.sampling.random_walk(
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g4, F.tensor([0, 1, 2, 0, 1, 2], dtype=g4.idtype), metapath=metapath, return_eids=True)
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check_random_walk(g4, metapath, traces, ntypes, trace_eids=eids)
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finally: # make sure to unpin the graphs even if some test fails
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for g in (g1, g2, g3, g4):
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if g.is_pinned():
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g.unpin_memory_()
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@unittest.skipIf(F._default_context_str == 'gpu', reason="GPU random walk not implemented")
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def test_node2vec():
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g1 = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 1, 2], [1, 2, 0])
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})
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g2 = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 1, 1, 2, 3], [1, 2, 3, 0, 0])
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})
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g2.edata['p'] = F.tensor([3, 0, 3, 3, 3], dtype=F.float32)
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ntypes = F.zeros((5,), dtype=F.int64)
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traces, eids = dgl.sampling.node2vec_random_walk(g1, [0, 1, 2, 0, 1, 2], 1, 1, 4, return_eids=True)
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check_random_walk(g1, ['follow'] * 4, traces, ntypes, trace_eids=eids)
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traces, eids = dgl.sampling.node2vec_random_walk(
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g2, [0, 1, 2, 3, 0, 1, 2, 3], 1, 1, 4, prob='p', return_eids=True)
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check_random_walk(g2, ['follow'] * 4, traces, ntypes, 'p', trace_eids=eids)
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@unittest.skipIf(F._default_context_str == 'gpu', reason="GPU pack traces not implemented")
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def test_pack_traces():
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traces, types = (np.array(
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[[ 0, 1, -1, -1, -1, -1, -1],
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[ 0, 1, 1, 3, 0, 0, 0]], dtype='int64'),
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np.array([0, 0, 1, 0, 0, 1, 0], dtype='int64'))
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traces = F.zerocopy_from_numpy(traces)
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types = F.zerocopy_from_numpy(types)
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result = dgl.sampling.pack_traces(traces, types)
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assert F.array_equal(result[0], F.tensor([0, 1, 0, 1, 1, 3, 0, 0, 0], dtype=F.int64))
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assert F.array_equal(result[1], F.tensor([0, 0, 0, 0, 1, 0, 0, 1, 0], dtype=F.int64))
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assert F.array_equal(result[2], F.tensor([2, 7], dtype=F.int64))
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assert F.array_equal(result[3], F.tensor([0, 2], dtype=F.int64))
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@pytest.mark.parametrize('use_uva', [True, False])
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def test_pinsage_sampling(use_uva):
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if use_uva and F.ctx() == F.cpu():
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pytest.skip('UVA sampling requires a GPU.')
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def _test_sampler(g, sampler, ntype):
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seeds = F.copy_to(F.tensor([0, 2], dtype=g.idtype), F.ctx())
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neighbor_g = sampler(seeds)
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assert neighbor_g.ntypes == [ntype]
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u, v = neighbor_g.all_edges(form='uv', order='eid')
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uv = list(zip(F.asnumpy(u).tolist(), F.asnumpy(v).tolist()))
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assert (1, 0) in uv or (0, 0) in uv
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assert (2, 2) in uv or (3, 2) in uv
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g = dgl.heterograph({
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('item', 'bought-by', 'user'): ([0, 0, 1, 1, 2, 2, 3, 3], [0, 1, 0, 1, 2, 3, 2, 3]),
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('user', 'bought', 'item'): ([0, 1, 0, 1, 2, 3, 2, 3], [0, 0, 1, 1, 2, 2, 3, 3])})
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if use_uva:
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g.create_formats_()
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g.pin_memory_()
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elif F._default_context_str == 'gpu':
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g = g.to(F.ctx())
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try:
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sampler = dgl.sampling.PinSAGESampler(g, 'item', 'user', 4, 0.5, 3, 2)
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_test_sampler(g, sampler, 'item')
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sampler = dgl.sampling.RandomWalkNeighborSampler(g, 4, 0.5, 3, 2, ['bought-by', 'bought'])
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_test_sampler(g, sampler, 'item')
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sampler = dgl.sampling.RandomWalkNeighborSampler(g, 4, 0.5, 3, 2,
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[('item', 'bought-by', 'user'), ('user', 'bought', 'item')])
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_test_sampler(g, sampler, 'item')
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finally:
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if g.is_pinned():
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g.unpin_memory_()
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g = dgl.graph(([0, 0, 1, 1, 2, 2, 3, 3],
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[0, 1, 0, 1, 2, 3, 2, 3]))
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if use_uva:
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g.create_formats_()
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g.pin_memory_()
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elif F._default_context_str == 'gpu':
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g = g.to(F.ctx())
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try:
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sampler = dgl.sampling.RandomWalkNeighborSampler(g, 4, 0.5, 3, 2)
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_test_sampler(g, sampler, g.ntypes[0])
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finally:
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if g.is_pinned():
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g.unpin_memory_()
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g = dgl.heterograph({
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('A', 'AB', 'B'): ([0, 2], [1, 3]),
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('B', 'BC', 'C'): ([1, 3], [2, 1]),
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('C', 'CA', 'A'): ([2, 1], [0, 2])})
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if use_uva:
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g.create_formats_()
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g.pin_memory_()
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elif F._default_context_str == 'gpu':
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g = g.to(F.ctx())
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try:
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sampler = dgl.sampling.RandomWalkNeighborSampler(g, 4, 0.5, 3, 2, ['AB', 'BC', 'CA'])
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_test_sampler(g, sampler, 'A')
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finally:
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if g.is_pinned():
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g.unpin_memory_()
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def _gen_neighbor_sampling_test_graph(hypersparse, reverse):
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if hypersparse:
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# should crash if allocated a CSR
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card = 1 << 50
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num_nodes_dict = {'user': card, 'game': card, 'coin': card}
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else:
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card = None
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num_nodes_dict = None
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if reverse:
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g = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 0, 0, 1, 1, 1, 2], [1, 2, 3, 0, 2, 3, 0])
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}, {'user': card if card is not None else 4})
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g = g.to(F.ctx())
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g.edata['prob'] = F.tensor([.5, .5, 0., .5, .5, 0., 1.], dtype=F.float32)
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hg = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 0, 0, 1, 1, 1, 2],
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[1, 2, 3, 0, 2, 3, 0]),
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('game', 'play', 'user'): ([0, 1, 2, 2], [0, 0, 1, 3]),
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('user', 'liked-by', 'game'): ([0, 1, 2, 0, 3, 0], [2, 2, 2, 1, 1, 0]),
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('coin', 'flips', 'user'): ([0, 0, 0, 0], [0, 1, 2, 3])
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}, num_nodes_dict)
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hg = hg.to(F.ctx())
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else:
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g = dgl.heterograph({
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('user', 'follow', 'user'): ([1, 2, 3, 0, 2, 3, 0], [0, 0, 0, 1, 1, 1, 2])
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}, {'user': card if card is not None else 4})
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g = g.to(F.ctx())
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g.edata['prob'] = F.tensor([.5, .5, 0., .5, .5, 0., 1.], dtype=F.float32)
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hg = dgl.heterograph({
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('user', 'follow', 'user'): ([1, 2, 3, 0, 2, 3, 0],
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[0, 0, 0, 1, 1, 1, 2]),
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('user', 'play', 'game'): ([0, 0, 1, 3], [0, 1, 2, 2]),
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('game', 'liked-by', 'user'): ([2, 2, 2, 1, 1, 0], [0, 1, 2, 0, 3, 0]),
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('user', 'flips', 'coin'): ([0, 1, 2, 3], [0, 0, 0, 0])
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}, num_nodes_dict)
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hg = hg.to(F.ctx())
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hg.edges['follow'].data['prob'] = F.tensor([.5, .5, 0., .5, .5, 0., 1.], dtype=F.float32)
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hg.edges['play'].data['prob'] = F.tensor([.8, .5, .5, .5], dtype=F.float32)
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hg.edges['liked-by'].data['prob'] = F.tensor([.3, .5, .2, .5, .1, .1], dtype=F.float32)
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return g, hg
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def _gen_neighbor_topk_test_graph(hypersparse, reverse):
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if hypersparse:
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# should crash if allocated a CSR
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card = 1 << 50
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else:
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card = None
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if reverse:
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g = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 0, 0, 1, 1, 1, 2], [1, 2, 3, 0, 2, 3, 0])
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})
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g.edata['weight'] = F.tensor([.5, .3, 0., -5., 22., 0., 1.], dtype=F.float32)
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hg = dgl.heterograph({
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('user', 'follow', 'user'): ([0, 0, 0, 1, 1, 1, 2],
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[1, 2, 3, 0, 2, 3, 0]),
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('game', 'play', 'user'): ([0, 1, 2, 2], [0, 0, 1, 3]),
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('user', 'liked-by', 'game'): ([0, 1, 2, 0, 3, 0], [2, 2, 2, 1, 1, 0]),
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('coin', 'flips', 'user'): ([0, 0, 0, 0], [0, 1, 2, 3])
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})
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else:
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g = dgl.heterograph({
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('user', 'follow', 'user'): ([1, 2, 3, 0, 2, 3, 0], [0, 0, 0, 1, 1, 1, 2])
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})
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g.edata['weight'] = F.tensor([.5, .3, 0., -5., 22., 0., 1.], dtype=F.float32)
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hg = dgl.heterograph({
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('user', 'follow', 'user'): ([1, 2, 3, 0, 2, 3, 0],
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[0, 0, 0, 1, 1, 1, 2]),
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('user', 'play', 'game'): ([0, 0, 1, 3], [0, 1, 2, 2]),
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('game', 'liked-by', 'user'): ([2, 2, 2, 1, 1, 0], [0, 1, 2, 0, 3, 0]),
|
|
('user', 'flips', 'coin'): ([0, 1, 2, 3], [0, 0, 0, 0])
|
|
})
|
|
hg.edges['follow'].data['weight'] = F.tensor([.5, .3, 0., -5., 22., 0., 1.], dtype=F.float32)
|
|
hg.edges['play'].data['weight'] = F.tensor([.8, .5, .4, .5], dtype=F.float32)
|
|
hg.edges['liked-by'].data['weight'] = F.tensor([.3, .5, .2, .5, .1, .1], dtype=F.float32)
|
|
hg.edges['flips'].data['weight'] = F.tensor([10, 2, 13, -1], dtype=F.float32)
|
|
return g, hg
|
|
|
|
def _test_sample_neighbors(hypersparse, prob):
|
|
g, hg = _gen_neighbor_sampling_test_graph(hypersparse, False)
|
|
|
|
def _test1(p, replace):
|
|
subg = dgl.sampling.sample_neighbors(g, [0, 1], -1, prob=p, replace=replace)
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
u, v = subg.edges()
|
|
u_ans, v_ans = subg.in_edges([0, 1])
|
|
uv = set(zip(F.asnumpy(u), F.asnumpy(v)))
|
|
uv_ans = set(zip(F.asnumpy(u_ans), F.asnumpy(v_ans)))
|
|
assert uv == uv_ans
|
|
|
|
for i in range(10):
|
|
subg = dgl.sampling.sample_neighbors(g, [0, 1], 2, prob=p, replace=replace)
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
assert subg.number_of_edges() == 4
|
|
u, v = subg.edges()
|
|
assert set(F.asnumpy(F.unique(v))) == {0, 1}
|
|
assert F.array_equal(F.astype(g.has_edges_between(u, v), F.int64), F.ones((4,), dtype=F.int64))
|
|
assert F.array_equal(g.edge_ids(u, v), subg.edata[dgl.EID])
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
if not replace:
|
|
# check no duplication
|
|
assert len(edge_set) == 4
|
|
if p is not None:
|
|
assert not (3, 0) in edge_set
|
|
assert not (3, 1) in edge_set
|
|
_test1(prob, True) # w/ replacement, uniform
|
|
_test1(prob, False) # w/o replacement, uniform
|
|
|
|
def _test2(p, replace): # fanout > #neighbors
|
|
subg = dgl.sampling.sample_neighbors(g, [0, 2], -1, prob=p, replace=replace)
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
u, v = subg.edges()
|
|
u_ans, v_ans = subg.in_edges([0, 2])
|
|
uv = set(zip(F.asnumpy(u), F.asnumpy(v)))
|
|
uv_ans = set(zip(F.asnumpy(u_ans), F.asnumpy(v_ans)))
|
|
assert uv == uv_ans
|
|
|
|
for i in range(10):
|
|
subg = dgl.sampling.sample_neighbors(g, [0, 2], 2, prob=p, replace=replace)
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
num_edges = 4 if replace else 3
|
|
assert subg.number_of_edges() == num_edges
|
|
u, v = subg.edges()
|
|
assert set(F.asnumpy(F.unique(v))) == {0, 2}
|
|
assert F.array_equal(F.astype(g.has_edges_between(u, v), F.int64), F.ones((num_edges,), dtype=F.int64))
|
|
assert F.array_equal(g.edge_ids(u, v), subg.edata[dgl.EID])
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
if not replace:
|
|
# check no duplication
|
|
assert len(edge_set) == num_edges
|
|
if p is not None:
|
|
assert not (3, 0) in edge_set
|
|
_test2(prob, True) # w/ replacement, uniform
|
|
_test2(prob, False) # w/o replacement, uniform
|
|
|
|
def _test3(p, replace):
|
|
subg = dgl.sampling.sample_neighbors(hg, {'user': [0, 1], 'game': 0}, -1, prob=p, replace=replace)
|
|
assert len(subg.ntypes) == 3
|
|
assert len(subg.etypes) == 4
|
|
assert subg['follow'].number_of_edges() == 6
|
|
assert subg['play'].number_of_edges() == 1
|
|
assert subg['liked-by'].number_of_edges() == 4
|
|
assert subg['flips'].number_of_edges() == 0
|
|
|
|
for i in range(10):
|
|
subg = dgl.sampling.sample_neighbors(hg, {'user' : [0,1], 'game' : 0}, 2, prob=p, replace=replace)
|
|
assert len(subg.ntypes) == 3
|
|
assert len(subg.etypes) == 4
|
|
assert subg['follow'].number_of_edges() == 4
|
|
assert subg['play'].number_of_edges() == 2 if replace else 1
|
|
assert subg['liked-by'].number_of_edges() == 4 if replace else 3
|
|
assert subg['flips'].number_of_edges() == 0
|
|
|
|
_test3(prob, True) # w/ replacement, uniform
|
|
_test3(prob, False) # w/o replacement, uniform
|
|
|
|
# test different fanouts for different relations
|
|
for i in range(10):
|
|
subg = dgl.sampling.sample_neighbors(
|
|
hg,
|
|
{'user' : [0,1], 'game' : 0, 'coin': 0},
|
|
{'follow': 1, 'play': 2, 'liked-by': 0, 'flips': -1},
|
|
replace=True)
|
|
assert len(subg.ntypes) == 3
|
|
assert len(subg.etypes) == 4
|
|
assert subg['follow'].number_of_edges() == 2
|
|
assert subg['play'].number_of_edges() == 2
|
|
assert subg['liked-by'].number_of_edges() == 0
|
|
assert subg['flips'].number_of_edges() == 4
|
|
|
|
def _test_sample_neighbors_outedge(hypersparse):
|
|
g, hg = _gen_neighbor_sampling_test_graph(hypersparse, True)
|
|
|
|
def _test1(p, replace):
|
|
subg = dgl.sampling.sample_neighbors(g, [0, 1], -1, prob=p, replace=replace, edge_dir='out')
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
u, v = subg.edges()
|
|
u_ans, v_ans = subg.out_edges([0, 1])
|
|
uv = set(zip(F.asnumpy(u), F.asnumpy(v)))
|
|
uv_ans = set(zip(F.asnumpy(u_ans), F.asnumpy(v_ans)))
|
|
assert uv == uv_ans
|
|
|
|
for i in range(10):
|
|
subg = dgl.sampling.sample_neighbors(g, [0, 1], 2, prob=p, replace=replace, edge_dir='out')
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
assert subg.number_of_edges() == 4
|
|
u, v = subg.edges()
|
|
assert set(F.asnumpy(F.unique(u))) == {0, 1}
|
|
assert F.array_equal(F.astype(g.has_edges_between(u, v), F.int64), F.ones((4,), dtype=F.int64))
|
|
assert F.array_equal(g.edge_ids(u, v), subg.edata[dgl.EID])
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
if not replace:
|
|
# check no duplication
|
|
assert len(edge_set) == 4
|
|
if p is not None:
|
|
assert not (0, 3) in edge_set
|
|
assert not (1, 3) in edge_set
|
|
_test1(None, True) # w/ replacement, uniform
|
|
_test1(None, False) # w/o replacement, uniform
|
|
_test1('prob', True) # w/ replacement
|
|
_test1('prob', False) # w/o replacement
|
|
|
|
def _test2(p, replace): # fanout > #neighbors
|
|
subg = dgl.sampling.sample_neighbors(g, [0, 2], -1, prob=p, replace=replace, edge_dir='out')
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
u, v = subg.edges()
|
|
u_ans, v_ans = subg.out_edges([0, 2])
|
|
uv = set(zip(F.asnumpy(u), F.asnumpy(v)))
|
|
uv_ans = set(zip(F.asnumpy(u_ans), F.asnumpy(v_ans)))
|
|
assert uv == uv_ans
|
|
|
|
for i in range(10):
|
|
subg = dgl.sampling.sample_neighbors(g, [0, 2], 2, prob=p, replace=replace, edge_dir='out')
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
num_edges = 4 if replace else 3
|
|
assert subg.number_of_edges() == num_edges
|
|
u, v = subg.edges()
|
|
assert set(F.asnumpy(F.unique(u))) == {0, 2}
|
|
assert F.array_equal(F.astype(g.has_edges_between(u, v), F.int64), F.ones((num_edges,), dtype=F.int64))
|
|
assert F.array_equal(g.edge_ids(u, v), subg.edata[dgl.EID])
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
if not replace:
|
|
# check no duplication
|
|
assert len(edge_set) == num_edges
|
|
if p is not None:
|
|
assert not (0, 3) in edge_set
|
|
_test2(None, True) # w/ replacement, uniform
|
|
_test2(None, False) # w/o replacement, uniform
|
|
_test2('prob', True) # w/ replacement
|
|
_test2('prob', False) # w/o replacement
|
|
|
|
def _test3(p, replace):
|
|
subg = dgl.sampling.sample_neighbors(hg, {'user': [0, 1], 'game': 0}, -1, prob=p, replace=replace, edge_dir='out')
|
|
assert len(subg.ntypes) == 3
|
|
assert len(subg.etypes) == 4
|
|
assert subg['follow'].number_of_edges() == 6
|
|
assert subg['play'].number_of_edges() == 1
|
|
assert subg['liked-by'].number_of_edges() == 4
|
|
assert subg['flips'].number_of_edges() == 0
|
|
|
|
for i in range(10):
|
|
subg = dgl.sampling.sample_neighbors(hg, {'user' : [0,1], 'game' : 0}, 2, prob=p, replace=replace, edge_dir='out')
|
|
assert len(subg.ntypes) == 3
|
|
assert len(subg.etypes) == 4
|
|
assert subg['follow'].number_of_edges() == 4
|
|
assert subg['play'].number_of_edges() == 2 if replace else 1
|
|
assert subg['liked-by'].number_of_edges() == 4 if replace else 3
|
|
assert subg['flips'].number_of_edges() == 0
|
|
|
|
_test3(None, True) # w/ replacement, uniform
|
|
_test3(None, False) # w/o replacement, uniform
|
|
_test3('prob', True) # w/ replacement
|
|
_test3('prob', False) # w/o replacement
|
|
|
|
def _test_sample_neighbors_topk(hypersparse):
|
|
g, hg = _gen_neighbor_topk_test_graph(hypersparse, False)
|
|
|
|
def _test1():
|
|
subg = dgl.sampling.select_topk(g, -1, 'weight', [0, 1])
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
u, v = subg.edges()
|
|
u_ans, v_ans = subg.in_edges([0, 1])
|
|
uv = set(zip(F.asnumpy(u), F.asnumpy(v)))
|
|
uv_ans = set(zip(F.asnumpy(u_ans), F.asnumpy(v_ans)))
|
|
assert uv == uv_ans
|
|
|
|
subg = dgl.sampling.select_topk(g, 2, 'weight', [0, 1])
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
assert subg.number_of_edges() == 4
|
|
u, v = subg.edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert F.array_equal(g.edge_ids(u, v), subg.edata[dgl.EID])
|
|
assert edge_set == {(2,0),(1,0),(2,1),(3,1)}
|
|
_test1()
|
|
|
|
def _test2(): # k > #neighbors
|
|
subg = dgl.sampling.select_topk(g, -1, 'weight', [0, 2])
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
u, v = subg.edges()
|
|
u_ans, v_ans = subg.in_edges([0, 2])
|
|
uv = set(zip(F.asnumpy(u), F.asnumpy(v)))
|
|
uv_ans = set(zip(F.asnumpy(u_ans), F.asnumpy(v_ans)))
|
|
assert uv == uv_ans
|
|
|
|
subg = dgl.sampling.select_topk(g, 2, 'weight', [0, 2])
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
assert subg.number_of_edges() == 3
|
|
u, v = subg.edges()
|
|
assert F.array_equal(g.edge_ids(u, v), subg.edata[dgl.EID])
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert edge_set == {(2,0),(1,0),(0,2)}
|
|
_test2()
|
|
|
|
def _test3():
|
|
subg = dgl.sampling.select_topk(hg, 2, 'weight', {'user' : [0,1], 'game' : 0})
|
|
assert len(subg.ntypes) == 3
|
|
assert len(subg.etypes) == 4
|
|
u, v = subg['follow'].edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert F.array_equal(hg['follow'].edge_ids(u, v), subg['follow'].edata[dgl.EID])
|
|
assert edge_set == {(2,0),(1,0),(2,1),(3,1)}
|
|
u, v = subg['play'].edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert F.array_equal(hg['play'].edge_ids(u, v), subg['play'].edata[dgl.EID])
|
|
assert edge_set == {(0,0)}
|
|
u, v = subg['liked-by'].edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert F.array_equal(hg['liked-by'].edge_ids(u, v), subg['liked-by'].edata[dgl.EID])
|
|
assert edge_set == {(2,0),(2,1),(1,0)}
|
|
assert subg['flips'].number_of_edges() == 0
|
|
_test3()
|
|
|
|
# test different k for different relations
|
|
subg = dgl.sampling.select_topk(
|
|
hg, {'follow': 1, 'play': 2, 'liked-by': 0, 'flips': -1}, 'weight', {'user' : [0,1], 'game' : 0, 'coin': 0})
|
|
assert len(subg.ntypes) == 3
|
|
assert len(subg.etypes) == 4
|
|
assert subg['follow'].number_of_edges() == 2
|
|
assert subg['play'].number_of_edges() == 1
|
|
assert subg['liked-by'].number_of_edges() == 0
|
|
assert subg['flips'].number_of_edges() == 4
|
|
|
|
def _test_sample_neighbors_topk_outedge(hypersparse):
|
|
g, hg = _gen_neighbor_topk_test_graph(hypersparse, True)
|
|
|
|
def _test1():
|
|
subg = dgl.sampling.select_topk(g, -1, 'weight', [0, 1], edge_dir='out')
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
u, v = subg.edges()
|
|
u_ans, v_ans = subg.out_edges([0, 1])
|
|
uv = set(zip(F.asnumpy(u), F.asnumpy(v)))
|
|
uv_ans = set(zip(F.asnumpy(u_ans), F.asnumpy(v_ans)))
|
|
assert uv == uv_ans
|
|
|
|
subg = dgl.sampling.select_topk(g, 2, 'weight', [0, 1], edge_dir='out')
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
assert subg.number_of_edges() == 4
|
|
u, v = subg.edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert F.array_equal(g.edge_ids(u, v), subg.edata[dgl.EID])
|
|
assert edge_set == {(0,2),(0,1),(1,2),(1,3)}
|
|
_test1()
|
|
|
|
def _test2(): # k > #neighbors
|
|
subg = dgl.sampling.select_topk(g, -1, 'weight', [0, 2], edge_dir='out')
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
u, v = subg.edges()
|
|
u_ans, v_ans = subg.out_edges([0, 2])
|
|
uv = set(zip(F.asnumpy(u), F.asnumpy(v)))
|
|
uv_ans = set(zip(F.asnumpy(u_ans), F.asnumpy(v_ans)))
|
|
assert uv == uv_ans
|
|
|
|
subg = dgl.sampling.select_topk(g, 2, 'weight', [0, 2], edge_dir='out')
|
|
assert subg.number_of_nodes() == g.number_of_nodes()
|
|
assert subg.number_of_edges() == 3
|
|
u, v = subg.edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert F.array_equal(g.edge_ids(u, v), subg.edata[dgl.EID])
|
|
assert edge_set == {(0,2),(0,1),(2,0)}
|
|
_test2()
|
|
|
|
def _test3():
|
|
subg = dgl.sampling.select_topk(hg, 2, 'weight', {'user' : [0,1], 'game' : 0}, edge_dir='out')
|
|
assert len(subg.ntypes) == 3
|
|
assert len(subg.etypes) == 4
|
|
u, v = subg['follow'].edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert F.array_equal(hg['follow'].edge_ids(u, v), subg['follow'].edata[dgl.EID])
|
|
assert edge_set == {(0,2),(0,1),(1,2),(1,3)}
|
|
u, v = subg['play'].edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert F.array_equal(hg['play'].edge_ids(u, v), subg['play'].edata[dgl.EID])
|
|
assert edge_set == {(0,0)}
|
|
u, v = subg['liked-by'].edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert F.array_equal(hg['liked-by'].edge_ids(u, v), subg['liked-by'].edata[dgl.EID])
|
|
assert edge_set == {(0,2),(1,2),(0,1)}
|
|
assert subg['flips'].number_of_edges() == 0
|
|
_test3()
|
|
|
|
def test_sample_neighbors_noprob():
|
|
_test_sample_neighbors(False, None)
|
|
#_test_sample_neighbors(True)
|
|
|
|
def test_sample_neighbors_prob():
|
|
_test_sample_neighbors(False, 'prob')
|
|
#_test_sample_neighbors(True)
|
|
|
|
def test_sample_neighbors_outedge():
|
|
_test_sample_neighbors_outedge(False)
|
|
#_test_sample_neighbors_outedge(True)
|
|
|
|
@unittest.skipIf(F._default_context_str == 'gpu', reason="GPU sample neighbors not implemented")
|
|
def test_sample_neighbors_topk():
|
|
_test_sample_neighbors_topk(False)
|
|
#_test_sample_neighbors_topk(True)
|
|
|
|
@unittest.skipIf(F._default_context_str == 'gpu', reason="GPU sample neighbors not implemented")
|
|
def test_sample_neighbors_topk_outedge():
|
|
_test_sample_neighbors_topk_outedge(False)
|
|
#_test_sample_neighbors_topk_outedge(True)
|
|
|
|
def test_sample_neighbors_with_0deg():
|
|
g = dgl.graph(([], []), num_nodes=5).to(F.ctx())
|
|
sg = dgl.sampling.sample_neighbors(g, F.tensor([1, 2], dtype=F.int64), 2, edge_dir='in', replace=False)
|
|
assert sg.number_of_edges() == 0
|
|
sg = dgl.sampling.sample_neighbors(g, F.tensor([1, 2], dtype=F.int64), 2, edge_dir='in', replace=True)
|
|
assert sg.number_of_edges() == 0
|
|
sg = dgl.sampling.sample_neighbors(g, F.tensor([1, 2], dtype=F.int64), 2, edge_dir='out', replace=False)
|
|
assert sg.number_of_edges() == 0
|
|
sg = dgl.sampling.sample_neighbors(g, F.tensor([1, 2], dtype=F.int64), 2, edge_dir='out', replace=True)
|
|
assert sg.number_of_edges() == 0
|
|
|
|
def create_test_graph(num_nodes, num_edges_per_node, bipartite=False):
|
|
src = np.concatenate(
|
|
[np.array([i] * num_edges_per_node) for i in range(num_nodes)])
|
|
dst = np.concatenate(
|
|
[np.random.choice(num_nodes, num_edges_per_node, replace=False) for i in range(num_nodes)]
|
|
)
|
|
if bipartite:
|
|
g = dgl.heterograph({("u", "e", "v") : (src, dst)})
|
|
else:
|
|
g = dgl.graph((src, dst))
|
|
return g
|
|
|
|
def create_etype_test_graph(num_nodes, num_edges_per_node, rare_cnt):
|
|
src = np.concatenate(
|
|
[np.random.choice(num_nodes, num_edges_per_node, replace=False) for i in range(num_nodes)]
|
|
)
|
|
dst = np.concatenate(
|
|
[np.array([i] * num_edges_per_node) for i in range(num_nodes)])
|
|
|
|
minor_src = np.concatenate(
|
|
[np.random.choice(num_nodes, 2, replace=False) for i in range(num_nodes)]
|
|
)
|
|
minor_dst = np.concatenate(
|
|
[np.array([i] * 2) for i in range(num_nodes)])
|
|
|
|
most_zero_src = np.concatenate(
|
|
[np.random.choice(num_nodes, num_edges_per_node, replace=False) for i in range(rare_cnt)]
|
|
)
|
|
most_zero_dst = np.concatenate(
|
|
[np.array([i] * num_edges_per_node) for i in range(rare_cnt)])
|
|
|
|
|
|
g = dgl.heterograph({("v", "e_major", "u") : (src, dst),
|
|
("u", "e_major_rev", "v") : (dst, src),
|
|
("v2", "e_minor", "u") : (minor_src, minor_dst),
|
|
("v2", "most_zero", "u") : (most_zero_src, most_zero_dst),
|
|
("u", "e_minor_rev", "v2") : (minor_dst, minor_src)})
|
|
|
|
return g
|
|
|
|
@unittest.skipIf(F._default_context_str == 'gpu', reason="GPU sample neighbors not implemented")
|
|
def test_sample_neighbors_biased_homogeneous():
|
|
g = create_test_graph(100, 30)
|
|
|
|
def check_num(nodes, tag):
|
|
nodes, tag = F.asnumpy(nodes), F.asnumpy(tag)
|
|
cnt = [sum(tag[nodes] == i) for i in range(4)]
|
|
# No tag 0
|
|
assert cnt[0] == 0
|
|
|
|
# very rare tag 1
|
|
assert cnt[2] > 2 * cnt[1]
|
|
assert cnt[3] > 2 * cnt[1]
|
|
|
|
tag = F.tensor(np.random.choice(4, 100))
|
|
bias = F.tensor([0, 0.1, 10, 10], dtype=F.float32)
|
|
# inedge / without replacement
|
|
g_sorted = dgl.sort_csc_by_tag(g, tag)
|
|
for _ in range(5):
|
|
subg = dgl.sampling.sample_neighbors_biased(g_sorted, g.nodes(), 5, bias, replace=False)
|
|
check_num(subg.edges()[0], tag)
|
|
u, v = subg.edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert len(edge_set) == subg.number_of_edges()
|
|
|
|
# inedge / with replacement
|
|
for _ in range(5):
|
|
subg = dgl.sampling.sample_neighbors_biased(g_sorted, g.nodes(), 5, bias, replace=True)
|
|
check_num(subg.edges()[0], tag)
|
|
|
|
# outedge / without replacement
|
|
g_sorted = dgl.sort_csr_by_tag(g, tag)
|
|
for _ in range(5):
|
|
subg = dgl.sampling.sample_neighbors_biased(g_sorted, g.nodes(), 5, bias, edge_dir='out', replace=False)
|
|
check_num(subg.edges()[1], tag)
|
|
u, v = subg.edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert len(edge_set) == subg.number_of_edges()
|
|
|
|
# outedge / with replacement
|
|
for _ in range(5):
|
|
subg = dgl.sampling.sample_neighbors_biased(g_sorted, g.nodes(), 5, bias, edge_dir='out', replace=True)
|
|
check_num(subg.edges()[1], tag)
|
|
|
|
@unittest.skipIf(F._default_context_str == 'gpu', reason="GPU sample neighbors not implemented")
|
|
def test_sample_neighbors_biased_bipartite():
|
|
g = create_test_graph(100, 30, True)
|
|
num_dst = g.number_of_dst_nodes()
|
|
bias = F.tensor([0, 0.01, 10, 10], dtype=F.float32)
|
|
def check_num(nodes, tag):
|
|
nodes, tag = F.asnumpy(nodes), F.asnumpy(tag)
|
|
cnt = [sum(tag[nodes] == i) for i in range(4)]
|
|
# No tag 0
|
|
assert cnt[0] == 0
|
|
|
|
# very rare tag 1
|
|
assert cnt[2] > 2 * cnt[1]
|
|
assert cnt[3] > 2 * cnt[1]
|
|
|
|
# inedge / without replacement
|
|
tag = F.tensor(np.random.choice(4, 100))
|
|
g_sorted = dgl.sort_csc_by_tag(g, tag)
|
|
for _ in range(5):
|
|
subg = dgl.sampling.sample_neighbors_biased(g_sorted, g.dstnodes(), 5, bias, replace=False)
|
|
check_num(subg.edges()[0], tag)
|
|
u, v = subg.edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert len(edge_set) == subg.number_of_edges()
|
|
|
|
# inedge / with replacement
|
|
for _ in range(5):
|
|
subg = dgl.sampling.sample_neighbors_biased(g_sorted, g.dstnodes(), 5, bias, replace=True)
|
|
check_num(subg.edges()[0], tag)
|
|
|
|
# outedge / without replacement
|
|
tag = F.tensor(np.random.choice(4, num_dst))
|
|
g_sorted = dgl.sort_csr_by_tag(g, tag)
|
|
for _ in range(5):
|
|
subg = dgl.sampling.sample_neighbors_biased(g_sorted, g.srcnodes(), 5, bias, edge_dir='out', replace=False)
|
|
check_num(subg.edges()[1], tag)
|
|
u, v = subg.edges()
|
|
edge_set = set(zip(list(F.asnumpy(u)), list(F.asnumpy(v))))
|
|
assert len(edge_set) == subg.number_of_edges()
|
|
|
|
# outedge / with replacement
|
|
for _ in range(5):
|
|
subg = dgl.sampling.sample_neighbors_biased(g_sorted, g.srcnodes(), 5, bias, edge_dir='out', replace=True)
|
|
check_num(subg.edges()[1], tag)
|
|
|
|
@unittest.skipIf(F._default_context_str == 'gpu', reason="GPU sample neighbors not implemented")
|
|
@pytest.mark.parametrize('format_', ['coo', 'csr', 'csc'])
|
|
@pytest.mark.parametrize('direction', ['in', 'out'])
|
|
@pytest.mark.parametrize('replace', [False, True])
|
|
def test_sample_neighbors_etype_homogeneous(format_, direction, replace):
|
|
num_nodes = 100
|
|
rare_cnt = 4
|
|
g = create_etype_test_graph(100, 30, rare_cnt)
|
|
h_g = dgl.to_homogeneous(g)
|
|
seed_ntype = g.get_ntype_id("u")
|
|
seeds = F.nonzero_1d(h_g.ndata[dgl.NTYPE] == seed_ntype)
|
|
fanouts = F.tensor([6, 5, 4, 3, 2], dtype=F.int64)
|
|
|
|
def check_num(h_g, all_src, all_dst, subg, replace, fanouts, direction):
|
|
src, dst = subg.edges()
|
|
num_etypes = F.asnumpy(h_g.edata[dgl.ETYPE]).max()
|
|
etype_array = F.asnumpy(subg.edata[dgl.ETYPE])
|
|
src = F.asnumpy(src)
|
|
dst = F.asnumpy(dst)
|
|
fanouts = F.asnumpy(fanouts)
|
|
|
|
all_etype_array = F.asnumpy(h_g.edata[dgl.ETYPE])
|
|
all_src = F.asnumpy(all_src)
|
|
all_dst = F.asnumpy(all_dst)
|
|
|
|
src_per_etype = []
|
|
dst_per_etype = []
|
|
for etype in range(num_etypes):
|
|
src_per_etype.append(src[etype_array == etype])
|
|
dst_per_etype.append(dst[etype_array == etype])
|
|
|
|
if replace:
|
|
if direction == 'in':
|
|
in_degree_per_etype = [np.bincount(d) for d in dst_per_etype]
|
|
for in_degree, fanout in zip(in_degree_per_etype, fanouts):
|
|
assert np.all(in_degree == fanout)
|
|
else:
|
|
out_degree_per_etype = [np.bincount(s) for s in src_per_etype]
|
|
for out_degree, fanout in zip(out_degree_per_etype, fanouts):
|
|
assert np.all(out_degree == fanout)
|
|
else:
|
|
if direction == 'in':
|
|
for v in set(dst):
|
|
u = src[dst == v]
|
|
et = etype_array[dst == v]
|
|
all_u = all_src[all_dst == v]
|
|
all_et = all_etype_array[all_dst == v]
|
|
for etype in set(et):
|
|
u_etype = set(u[et == etype])
|
|
all_u_etype = set(all_u[all_et == etype])
|
|
assert (len(u_etype) == fanouts[etype]) or (u_etype == all_u_etype)
|
|
else:
|
|
for u in set(src):
|
|
v = dst[src == u]
|
|
et = etype_array[src == u]
|
|
all_v = all_dst[all_src == u]
|
|
all_et = all_etype_array[all_src == u]
|
|
for etype in set(et):
|
|
v_etype = set(v[et == etype])
|
|
all_v_etype = set(all_v[all_et == etype])
|
|
assert (len(v_etype) == fanouts[etype]) or (v_etype == all_v_etype)
|
|
|
|
all_src, all_dst = h_g.edges()
|
|
h_g = h_g.formats(format_)
|
|
if (direction, format_) in [('in', 'csr'), ('out', 'csc')]:
|
|
h_g = h_g.formats(['csc', 'csr', 'coo'])
|
|
for _ in range(5):
|
|
subg = dgl.sampling.sample_etype_neighbors(
|
|
h_g, seeds, dgl.ETYPE, fanouts, replace=replace, edge_dir=direction)
|
|
check_num(h_g, all_src, all_dst, subg, replace, fanouts, direction)
|
|
|
|
|
|
@unittest.skipIf(F._default_context_str == 'gpu', reason="GPU sample neighbors not implemented")
|
|
@pytest.mark.parametrize('format_', ['csr', 'csc'])
|
|
@pytest.mark.parametrize('direction', ['in', 'out'])
|
|
def test_sample_neighbors_etype_sorted_homogeneous(format_, direction):
|
|
rare_cnt = 4
|
|
g = create_etype_test_graph(100, 30, rare_cnt)
|
|
h_g = dgl.to_homogeneous(g)
|
|
seed_ntype = g.get_ntype_id("u")
|
|
seeds = F.nonzero_1d(h_g.ndata[dgl.NTYPE] == seed_ntype)
|
|
fanouts = F.tensor([6, 5, 4, 3, 2], dtype=F.int64)
|
|
h_g = h_g.formats(format_)
|
|
if (direction, format_) in [('in', 'csr'), ('out', 'csc')]:
|
|
h_g = h_g.formats(['csc', 'csr', 'coo'])
|
|
orig_etype = F.asnumpy(h_g.edata[dgl.ETYPE])
|
|
h_g.edata[dgl.ETYPE] = F.tensor(
|
|
np.sort(orig_etype)[::-1].tolist(), dtype=F.int64)
|
|
|
|
try:
|
|
dgl.sampling.sample_etype_neighbors(
|
|
h_g, seeds, dgl.ETYPE, fanouts, edge_dir=direction, etype_sorted=True)
|
|
fail = False
|
|
except dgl.DGLError:
|
|
fail = True
|
|
assert fail
|
|
|
|
@pytest.mark.parametrize('dtype', ['int32', 'int64'])
|
|
def test_sample_neighbors_exclude_edges_heteroG(dtype):
|
|
d_i_d_u_nodes = F.zerocopy_from_numpy(np.unique(np.random.randint(300, size=100, dtype=dtype)))
|
|
d_i_d_v_nodes = F.zerocopy_from_numpy(np.random.randint(25, size=d_i_d_u_nodes.shape, dtype=dtype))
|
|
d_i_g_u_nodes = F.zerocopy_from_numpy(np.unique(np.random.randint(300, size=100, dtype=dtype)))
|
|
d_i_g_v_nodes = F.zerocopy_from_numpy(np.random.randint(25, size=d_i_g_u_nodes.shape, dtype=dtype))
|
|
d_t_d_u_nodes = F.zerocopy_from_numpy(np.unique(np.random.randint(300, size=100, dtype=dtype)))
|
|
d_t_d_v_nodes = F.zerocopy_from_numpy(np.random.randint(25, size=d_t_d_u_nodes.shape, dtype=dtype))
|
|
|
|
g = dgl.heterograph({
|
|
('drug', 'interacts', 'drug'): (d_i_d_u_nodes, d_i_d_v_nodes),
|
|
('drug', 'interacts', 'gene'): (d_i_g_u_nodes, d_i_g_v_nodes),
|
|
('drug', 'treats', 'disease'): (d_t_d_u_nodes, d_t_d_v_nodes)
|
|
}).to(F.ctx())
|
|
|
|
(U, V, EID) = (0, 1, 2)
|
|
|
|
nd_b_idx = np.random.randint(low=1, high=24, dtype=dtype)
|
|
nd_e_idx = np.random.randint(low=25, high=49, dtype=dtype)
|
|
did_b_idx = np.random.randint(low=1, high=24, dtype=dtype)
|
|
did_e_idx = np.random.randint(low=25, high=49, dtype=dtype)
|
|
sampled_amount = np.random.randint(low=1, high=10, dtype=dtype)
|
|
|
|
drug_i_drug_edges = g.all_edges(form='all', etype=('drug','interacts','drug'))
|
|
excluded_d_i_d_edges = drug_i_drug_edges[EID][did_b_idx:did_e_idx]
|
|
sampled_drug_node = drug_i_drug_edges[V][nd_b_idx:nd_e_idx]
|
|
did_excluded_nodes_U = drug_i_drug_edges[U][did_b_idx:did_e_idx]
|
|
did_excluded_nodes_V = drug_i_drug_edges[V][did_b_idx:did_e_idx]
|
|
|
|
nd_b_idx = np.random.randint(low=1, high=24, dtype=dtype)
|
|
nd_e_idx = np.random.randint(low=25, high=49, dtype=dtype)
|
|
dig_b_idx = np.random.randint(low=1, high=24, dtype=dtype)
|
|
dig_e_idx = np.random.randint(low=25, high=49, dtype=dtype)
|
|
drug_i_gene_edges = g.all_edges(form='all', etype=('drug','interacts','gene'))
|
|
excluded_d_i_g_edges = drug_i_gene_edges[EID][dig_b_idx:dig_e_idx]
|
|
dig_excluded_nodes_U = drug_i_gene_edges[U][dig_b_idx:dig_e_idx]
|
|
dig_excluded_nodes_V = drug_i_gene_edges[V][dig_b_idx:dig_e_idx]
|
|
sampled_gene_node = drug_i_gene_edges[V][nd_b_idx:nd_e_idx]
|
|
|
|
nd_b_idx = np.random.randint(low=1, high=24, dtype=dtype)
|
|
nd_e_idx = np.random.randint(low=25, high=49, dtype=dtype)
|
|
dtd_b_idx = np.random.randint(low=1, high=24, dtype=dtype)
|
|
dtd_e_idx = np.random.randint(low=25, high=49, dtype=dtype)
|
|
drug_t_dis_edges = g.all_edges(form='all', etype=('drug','treats','disease'))
|
|
excluded_d_t_d_edges = drug_t_dis_edges[EID][dtd_b_idx:dtd_e_idx]
|
|
dtd_excluded_nodes_U = drug_t_dis_edges[U][dtd_b_idx:dtd_e_idx]
|
|
dtd_excluded_nodes_V = drug_t_dis_edges[V][dtd_b_idx:dtd_e_idx]
|
|
sampled_disease_node = drug_t_dis_edges[V][nd_b_idx:nd_e_idx]
|
|
excluded_edges = {('drug', 'interacts', 'drug'): excluded_d_i_d_edges,
|
|
('drug', 'interacts', 'gene'): excluded_d_i_g_edges,
|
|
('drug', 'treats', 'disease'): excluded_d_t_d_edges
|
|
}
|
|
|
|
sg = dgl.sampling.sample_neighbors(g, {'drug': sampled_drug_node,
|
|
'gene': sampled_gene_node,
|
|
'disease': sampled_disease_node},
|
|
sampled_amount, exclude_edges=excluded_edges)
|
|
|
|
assert not np.any(F.asnumpy(sg.has_edges_between(did_excluded_nodes_U,did_excluded_nodes_V,
|
|
etype=('drug','interacts','drug'))))
|
|
assert not np.any(F.asnumpy(sg.has_edges_between(dig_excluded_nodes_U,dig_excluded_nodes_V,
|
|
etype=('drug','interacts','gene'))))
|
|
assert not np.any(F.asnumpy(sg.has_edges_between(dtd_excluded_nodes_U,dtd_excluded_nodes_V,
|
|
etype=('drug','treats','disease'))))
|
|
|
|
@pytest.mark.parametrize('dtype', ['int32', 'int64'])
|
|
def test_sample_neighbors_exclude_edges_homoG(dtype):
|
|
u_nodes = F.zerocopy_from_numpy(np.unique(np.random.randint(300,size=100, dtype=dtype)))
|
|
v_nodes = F.zerocopy_from_numpy(np.random.randint(25, size=u_nodes.shape, dtype=dtype))
|
|
g = dgl.graph((u_nodes, v_nodes)).to(F.ctx())
|
|
|
|
(U, V, EID) = (0, 1, 2)
|
|
|
|
nd_b_idx = np.random.randint(low=1,high=24, dtype=dtype)
|
|
nd_e_idx = np.random.randint(low=25,high=49, dtype=dtype)
|
|
b_idx = np.random.randint(low=1,high=24, dtype=dtype)
|
|
e_idx = np.random.randint(low=25,high=49, dtype=dtype)
|
|
sampled_amount = np.random.randint(low=1,high=10, dtype=dtype)
|
|
|
|
g_edges = g.all_edges(form='all')
|
|
excluded_edges = g_edges[EID][b_idx:e_idx]
|
|
sampled_node = g_edges[V][nd_b_idx:nd_e_idx]
|
|
excluded_nodes_U = g_edges[U][b_idx:e_idx]
|
|
excluded_nodes_V = g_edges[V][b_idx:e_idx]
|
|
|
|
sg = dgl.sampling.sample_neighbors(g, sampled_node,
|
|
sampled_amount, exclude_edges=excluded_edges)
|
|
|
|
assert not np.any(F.asnumpy(sg.has_edges_between(excluded_nodes_U,excluded_nodes_V)))
|
|
|
|
@pytest.mark.parametrize('dtype', ['int32', 'int64'])
|
|
def test_global_uniform_negative_sampling(dtype):
|
|
g = dgl.graph(([], []), num_nodes=1000).to(F.ctx())
|
|
src, dst = dgl.sampling.global_uniform_negative_sampling(g, 2000, False, True)
|
|
assert len(src) == 2000
|
|
assert len(dst) == 2000
|
|
|
|
g = dgl.graph((np.random.randint(0, 20, (300,)), np.random.randint(0, 20, (300,)))).to(F.ctx())
|
|
src, dst = dgl.sampling.global_uniform_negative_sampling(g, 20, False, True)
|
|
assert not F.asnumpy(g.has_edges_between(src, dst)).any()
|
|
|
|
src, dst = dgl.sampling.global_uniform_negative_sampling(g, 20, False, False)
|
|
assert not F.asnumpy(g.has_edges_between(src, dst)).any()
|
|
src = F.asnumpy(src)
|
|
dst = F.asnumpy(dst)
|
|
s = set(zip(src.tolist(), dst.tolist()))
|
|
assert len(s) == len(src)
|
|
|
|
g = dgl.graph(([0], [1])).to(F.ctx())
|
|
src, dst = dgl.sampling.global_uniform_negative_sampling(g, 20, True, False, redundancy=10)
|
|
src = F.asnumpy(src)
|
|
dst = F.asnumpy(dst)
|
|
# should have either no element or (1, 0)
|
|
assert len(src) < 2
|
|
assert len(dst) < 2
|
|
if len(src) == 1:
|
|
assert src[0] == 1
|
|
assert dst[0] == 0
|
|
|
|
g = dgl.heterograph({
|
|
('A', 'AB', 'B'): (np.random.randint(0, 20, (300,)), np.random.randint(0, 40, (300,))),
|
|
('B', 'BA', 'A'): (np.random.randint(0, 40, (200,)), np.random.randint(0, 20, (200,)))}).to(F.ctx())
|
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src, dst = dgl.sampling.global_uniform_negative_sampling(g, 20, False, etype='AB')
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assert not F.asnumpy(g.has_edges_between(src, dst, etype='AB')).any()
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if __name__ == '__main__':
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from itertools import product
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for args in product(['coo', 'csr', 'csc'], ['in', 'out'], [False, True]):
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test_sample_neighbors_etype_homogeneous(*args)
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test_non_uniform_random_walk()
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test_uniform_random_walk(False)
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test_pack_traces()
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test_pinsage_sampling()
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test_sample_neighbors_outedge()
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test_sample_neighbors_topk()
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test_sample_neighbors_topk_outedge()
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test_sample_neighbors_with_0deg()
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test_sample_neighbors_biased_homogeneous()
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test_sample_neighbors_biased_bipartite()
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test_sample_neighbors_exclude_edges_heteroG('int32')
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test_sample_neighbors_exclude_edges_homoG('int32')
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test_global_uniform_negative_sampling('int32')
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test_global_uniform_negative_sampling('int64')
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