def _generate_word_network(self, progress_callback):
if progress_callback:
progress_callback(90.0)
th = self.word_threshold
data = np.array(
[v / 2 for v in self.word_matrix.values() if (v / 2) >= th],
dtype=np.float64)
row_ind = np.array(
[k[0] for k, v in self.word_matrix.items() if (v / 2) >= th],
dtype=np.float64)
col_ind = np.array(
[k[1] for k, v in self.word_matrix.items() if (v / 2) >= th],
dtype=np.float64)
s = len(self.word_freqs)
edges = csr_matrix((data, (row_ind, col_ind)), shape=(s, s))
ind2word = {v: k for k, v in self.word2ind.items()}
words = np.array([ind2word[ind] for ind in range(s)])
freqs = np.array([self.word_freqs[ind2word[ind]] for ind in range(s)],
dtype=np.float64)
network = Network(nodes=words, edges=edges, name='Word Network')
self.word_network = network.subgraph(self.mask)
domain = Domain([ContinuousVariable('word_frequency')], None,
[StringVariable('word')])
self.word_items = Table(domain,
freqs.reshape((-1, 1))[self.mask], None,
words.reshape((-1, 1))[self.mask])
if progress_callback:
progress_callback(100.0)
def setUp(self):
row, col, w = zip(*((1, 2, 1.0), (1, 3, 3.0), (2, 3, 1.0), (2, 6, 0.5), (3, 4, 1.0), (4, 5, 1.0), (4, 7, -1.0),
(5, 6, 0.0), (6, 5, 0.1), (6, 2, 0.1)))
dir_edges = DirectedEdges(sp.csr_matrix((w, (row, col)), shape=(8, 8)))
self.toy_directed = Network(np.arange(8), dir_edges)
row, col, w = zip(*((1, 2, 1.0), (1, 3, 3.0), (2, 3, 1.0), (2, 6, 0.5), (3, 4, 1.0), (4, 5, 1.0), (4, 7, -1.0),
(5, 6, 0.1)))
undir_edges = UndirectedEdges(sp.csr_matrix((w, (row, col)), shape=(8, 8)))
self.toy_undirected = Network(np.arange(8), undir_edges)
def test_call(self):
n2v = Node2Vec(num_walks=10, walk_len=80, emb_size=300)
embeddings = n2v(self.toy_directed)
self.assertEqual(embeddings.X.shape, (self.toy_directed.number_of_nodes(), 300))
# check that domain is extended and that the existing attributes do not change places
empty = np.array([[] for _ in range(8)])
data = Table(Domain([ContinuousVariable("var1")]), np.array([[i] for i in range(8)]), empty, empty)
toy_net_with_data = Network(data, self.toy_directed.edges[0])
extended_data = n2v(toy_net_with_data)
self.assertEqual(extended_data.X.shape, (toy_net_with_data.number_of_nodes(), 1 + 300))
np.testing.assert_array_almost_equal(extended_data.X[:, 0], np.arange(8))
def _create_net(edges, n=None, directed=False):
edge_cons = DirectedEdges if directed else UndirectedEdges
row, col, data = zip(*edges)
if n is None:
n = max(*row, *col) + 1
return Network(np.arange(n),
edge_cons(sp.coo_matrix((data, (row, col)), shape=(n, n))))
def wrapped(*args):
row, col, *n = f(*args)
n = n[0] if n else max(np.max(row), np.max(col)) + 1
edges = sp.csr_matrix((np.ones(len(row)), (row, col)), shape=(n, n))
return Network(
range(n), edges,
name=f"{f.__name__}{args}".replace(",)", ")"))
def geometric(n_nodes, n_edges):
n_pairs = n_nodes * (n_nodes - 1) // 2
if n_edges > n_pairs:
raise ValueError(
f"There are only {n_pairs} (< {n_edges}) possible edges between "
f"{n_nodes} points")
xy = np.random.random((n_nodes, 2))
xx = row_norms(xy, squared=True)[:, np.newaxis]
distances = np.dot(xy, xy.T)
distances *= -2
distances += xx
distances += xx.T
ur = np.triu_indices(n_nodes, k=1)
# skip zeros and repetitions
dist_threshold = np.partition(distances[ur], n_edges)[n_edges]
mask = distances <= dist_threshold
mask[np.tril_indices(n_nodes)] = False
row, col = mask.nonzero()
edges = sp.csr_matrix((np.ones(len(row)), (row, col)),
shape=(n_nodes, n_nodes))
return Network(
range(n_nodes), edges,
name=f"geometric({n_nodes},{n_edges})",
coordinates=xy
)
def test_show_errors(self):
widget = self.widget
model = widget.controls.variable.model()
a, b, c, d = self.a, self.b, self.c, self.d
cb_connector = widget.controls.connector_value
no_data = widget.Error.no_data.is_shown
no_categorical = widget.Error.no_categorical.is_shown
same_values = widget.Error.same_values.is_shown
self._set_graph(Table(Domain([a, b, c, d])))
self.assertSequenceEqual(model, [a, c])
self.assertFalse(no_data())
self.assertFalse(no_categorical())
self.assertFalse(same_values())
self._set_graph(Table(Domain([b, d])))
self.assertSequenceEqual(model, [])
self.assertFalse(no_data())
self.assertTrue(no_categorical())
self.assertFalse(same_values())
self._set_graph(Table(Domain([a, b, c, d])))
self.assertSequenceEqual(model, [a, c])
self.assertFalse(no_data())
self.assertFalse(no_categorical())
self.assertFalse(same_values())
widget.connector_value = widget.connect_value + 1
cb_connector.activated[int].emit(widget.connector_value)
self.assertFalse(no_data())
self.assertFalse(no_categorical())
self.assertTrue(same_values())
net = Network(range(3), sp.csr_matrix([[0, 1], [1, 2]]))
self.send_signal(widget.Inputs.network, net)
self.assertTrue(no_data())
self.assertFalse(no_categorical())
self.assertFalse(same_values())
self._set_graph(Table(Domain([a, b, c, d])))
widget.connector_value = widget.connect_value + 1
self.send_signal(widget.Inputs.network, None)
self.assertFalse(no_data())
self.assertFalse(no_categorical())
self.assertFalse(same_values())
self._set_graph(Table(Domain([a, b, c, d])))
widget.connector_value = widget.connect_value + 1
cb_connector.activated[int].emit(widget.connector_value)
self.assertFalse(no_data())
self.assertFalse(no_categorical())
self.assertTrue(same_values())
self._set_graph(Table(Domain([b, d])))
self.assertFalse(no_data())
self.assertTrue(no_categorical())
self.assertFalse(same_values())
class TestEmbeddings(unittest.TestCase):
def setUp(self):
row, col, w = zip(*((1, 2, 1.0), (1, 3, 3.0), (2, 3, 1.0), (2, 6, 0.5), (3, 4, 1.0), (4, 5, 1.0), (4, 7, -1.0),
(5, 6, 0.0), (6, 5, 0.1), (6, 2, 0.1)))
dir_edges = DirectedEdges(sp.csr_matrix((w, (row, col)), shape=(8, 8)))
self.toy_directed = Network(np.arange(8), dir_edges)
row, col, w = zip(*((1, 2, 1.0), (1, 3, 3.0), (2, 3, 1.0), (2, 6, 0.5), (3, 4, 1.0), (4, 5, 1.0), (4, 7, -1.0),
(5, 6, 0.1)))
undir_edges = UndirectedEdges(sp.csr_matrix((w, (row, col)), shape=(8, 8)))
self.toy_undirected = Network(np.arange(8), undir_edges)
def test_node_probas(self):
""" Test that node probabilities get calculated correctly """
n2v = Node2Vec()
# nowhere to go from isolated node
self.assertEqual(len(n2v.node_probas(self.toy_directed, 0)), 0)
# should not have division by zero when weights of edges to neighbors sum to 0
self.assertDictEqual(n2v.node_probas(self.toy_directed, 5), {6: 1.0})
probas = n2v.node_probas(self.toy_directed, 4)
self.assertAlmostEqual(probas[5], 0.881, places=3)
self.assertAlmostEqual(probas[7], 0.119, places=3)
self.assertDictEqual(n2v.node_probas(self.toy_directed, 1), {2: 0.25, 3: 0.75})
self.assertDictEqual(n2v.node_probas(self.toy_undirected, 3), {1: 0.6, 2: 0.2, 4: 0.2})
def test_edge_probas(self):
""" Test that edge probabilities get calculated appropriately based on shortest distance between previous node
and next node (equations in 'Search bias' section of node2vec paper) """
n2v = Node2Vec(p=0.8, q=0.5)
edge_probas = n2v.edge_probas(self.toy_directed, 3, 4)
self.assertAlmostEqual(edge_probas[(4, 5)], 0.982, places=3) # d_tx = 2
self.assertAlmostEqual(edge_probas[(4, 7)], 0.018, places=3) # d_tx = 2
edge_probas = n2v.edge_probas(self.toy_directed, 1, 2)
self.assertAlmostEqual(edge_probas[(2, 3)], 0.5) # d_tx = 1
edge_probas = n2v.edge_probas(self.toy_directed, 5, 6)
self.assertAlmostEqual(edge_probas[(6, 5)], 0.385, places=3) # d_tx = 0
edge_probas = n2v.edge_probas(self.toy_undirected, 1, 2)
self.assertAlmostEqual(edge_probas[(2, 1)], 0.385, places=3) # d_tx = 0
self.assertAlmostEqual(edge_probas[(2, 3)], 0.308, places=3) # d_tx = 1
self.assertAlmostEqual(edge_probas[(2, 6)], 0.308, places=3) # d_tx = 2
def test_call(self):
n2v = Node2Vec(num_walks=10, walk_len=80, emb_size=300)
embeddings = n2v(self.toy_directed)
self.assertEqual(embeddings.X.shape, (self.toy_directed.number_of_nodes(), 300))
# check that domain is extended and that the existing attributes do not change places
empty = np.array([[] for _ in range(8)])
data = Table(Domain([ContinuousVariable("var1")]), np.array([[i] for i in range(8)]), empty, empty)
toy_net_with_data = Network(data, self.toy_directed.edges[0])
extended_data = n2v(toy_net_with_data)
self.assertEqual(extended_data.X.shape, (toy_net_with_data.number_of_nodes(), 1 + 300))
np.testing.assert_array_almost_equal(extended_data.X[:, 0], np.arange(8))
def _generate_document_network(self, progress_callback):
if progress_callback:
progress_callback(90.0)
edges = self.document_matrix.copy()
edges[edges < self.document_threshold] = 0
self.document_network = Network(nodes=np.array(self.corpus.titles),
edges=csr_matrix(edges),
name='Document Network')
if progress_callback:
progress_callback(100.0)
def _map_network(self):
edges = self.network.edges[0].edges.tocoo()
row, col = edges.row, edges.col
if self.weighting == self.WeightByWeights:
weights = edges.data
else:
weights = None
if self.normalize:
self._normalize_weights(row, col, weights)
row, col = self._map_into_feature_values(row, col)
return Network(self._construct_items(),
self._construct_edges(row, col, weights))
def test_filtered_edges(self):
def assert_edges(actual, expected):
self.assertEqual(len(actual.data), len(expected))
self.assertEqual(actual.data.dtype, float)
self.assertEqual(set(zip(actual.row, actual.col, actual.data)),
set(expected))
net = _create_net(((0, 4, 1.), (4, 1, 5), (1, 5, 3), (2, 4, 4),
(2, 5, 2), (3, 6, 6)))
# All edges
assert_edges(
tm._filtered_edges(net, np.array([True] * 4 + [False] * 3),
np.array([False] * 4 + [True] * 3)),
((0, 4, 1.), (1, 4, 5.), (1, 5, 3.), (2, 4, 4.), (2, 5, 2.),
(3, 6, 6.)))
# All edges, opposite mode roles
assert_edges(
tm._filtered_edges(net, np.array([False] * 4 + [True] * 3),
np.array([True] * 4 + [False] * 3)),
((0, 0, 1.), (0, 1, 5.), (1, 1, 3.), (0, 2, 4.), (1, 2, 2.),
(2, 3, 6.)))
# Not all edges
assert_edges(
tm._filtered_edges(net, np.array([True] * 4 + [False] * 3),
np.array([False] * 5 + [True] * 2)),
((1, 5, 3.), (2, 5, 2.), (3, 6, 6.)))
# One mode is empty
assert_edges(
tm._filtered_edges(net, np.array([True] * 4 + [False] * 3),
np.array([False] * 7)), ())
# The other mode is empty
assert_edges(
tm._filtered_edges(net, np.array([False] * 7),
np.array([False] * 5 + [True] * 2)), ())
# Both modes are empty
assert_edges(
tm._filtered_edges(net, np.array([False] * 7),
np.array([False] * 7)), ())
# Graph is empty
net = Network(range(7), sp.csr_matrix((7, 7)))
assert_edges(
tm._filtered_edges(net, np.array([True] * 4 + [False] * 3),
np.array([False] * 7)), ())
def summarize_(net: Network):
n = net.number_of_nodes()
if len(net.edges) == 1:
nettype = ['Network', 'Directed network'][net.edges[0].directed]
details = f"<nobr>{nettype} with {n} nodes " \
f"and {net.number_of_edges()} edges</nobr>"
else:
details = f"<nobr>Network with {n} nodes"
if net.edges:
details += " and {len(net.edges)} edge types:</nobr><ul>" + "".join(
f"<li>{len(edges)} edges, "
f"{['undirected', 'directed'][edges.directed]}</li>"
for edges in net.edges)
return PartialSummary(n, details)
def to_single_mode(net, mode_mask, conn_mask, weighting):
"""
Convert two-mode network into a single mode
Args:
net: network to convert
mode_mask (boolean array): a mask with nodes to connect
conn_mask (boolean array): a mask with nodes to use for connecting
weighting (int): normalization for edge weigthts
Returns:
single-mode network
"""
mode_edges = _filtered_edges(net, mode_mask, conn_mask)
new_edges = Weighting[weighting].func(mode_edges)
return Network(net.nodes[mode_mask], new_edges)
def test_weights(self):
label_var = DiscreteVariable("label", values=tuple("abcde"))
domain = Domain([label_var], [])
items = Table.from_numpy(domain,
np.array([[0, 0, 1, 3, 4, 0, 1, 2, 4]]).T)
src, dst, weights = np.array([[0, 1, 5], [1, 2, 4], [3, 4,
6], [0, 5, 3],
[1, 6, 1], [2, 7, 2], [3, 8, 8],
[4, 8, 7], [5, 6, 2]]).T
edges = sp.coo_matrix((weights.astype(float), (src, dst)),
shape=(9, 9))
network = Network(items, edges)
expected = np.zeros((5, 5), dtype=float)
widget = self.widget
buttons = widget.controls.weighting.buttons
self.send_signal(widget.Inputs.network, network)
buttons[widget.NoWeights].click()
groups = widget._map_network()
for i, j in [(0, 1), (1, 2), (3, 4)]:
expected[i, j] = 1
np.testing.assert_equal(groups.edges[0].edges.todense(), expected)
buttons[widget.WeightByDegrees].click()
groups = widget._map_network()
expected[0, 1] = 3
expected[1, 2] = 1
expected[3, 4] = 2
np.testing.assert_equal(groups.edges[0].edges.todense(), expected)
buttons[widget.WeightByWeights].click()
widget.normalize = False
groups = widget._map_network()
expected[0, 1] = 7
expected[1, 2] = 2
expected[3, 4] = 14
np.testing.assert_equal(groups.edges[0].edges.todense(), expected)
widget.normalize = True
groups = widget._map_network()
expected[0, 1] = 1 / sqrt(10 * 3) + 4 / sqrt(10 * 6) + 2 / sqrt(5 * 3)
expected[1, 2] = 2 / sqrt(6 * 2)
expected[3, 4] = 6 / sqrt(14 * 13) + 8 / sqrt(14 * 15)
np.testing.assert_equal(groups.edges[0].edges.todense(), expected)
def _set_graph(self, data, edges=None):
net = Network(
data,
sp.csr_matrix((len(data), len(data))) if edges is None else edges)
self.send_signal(self.widget.Inputs.network, net)
def test_empty_network(self):
net = Network([], [])
# should not crash
self.send_signal(self.widget.Inputs.network, net)
def wrapped(*args):
m = f(*args)
return Network(
range(len(m)), sp.csr_matrix(m),
name=f"{f.__name__}{args}".replace(",)", ")"))
def wrapped(*args):
edges = f(*args)
return Network(
range(edges.shape[0]), edges,
name=f"{f.__name__}{args}".replace(",)", ")"))
def _create_net(edges, n=None):
row, col, data = zip(*edges)
if n is None:
n = max(*row, *col) + 1
return Network(np.arange(n),
sp.coo_matrix((data, (row, col)), shape=(n, n)))