def fit(self, X, y):
## build graph of the citation network
ids1 = X[:, 0]
ids2 = X[:, 1]
vertices = list(set(ids1.astype(str)).union(ids2.astype(str)))
edges = [
tuple([str(row[0]), str(row[1])]) for row, link in zip(X, y)
if link == 1
]
self.graph = igraph.Graph()
self.graph.add_vertices(vertices)
self.graph.add_edges(edges)
self.di_network_graph = nx.DiGraph()
self.di_network_graph.add_nodes_from(vertices)
self.di_network_graph.add_edges_from(edges)
self.un_network_graph = nx.Graph()
self.un_network_graph.add_nodes_from(vertices)
self.un_network_graph.add_edges_from(edges)
vs = zip(vertices, range(len(vertices)))
self.hash_vs = {a: b for a, b in vs}
#print 'calculating shortest paths...'
#self.dmatrix = np.array(self.graph.shortest_paths())
#uncomment
# WARNING: cutoff should not be set in our final submission, which is equivalent to set it to infinity
print 'calculating betweenness centrality'
self.di_b_centrality = self.graph.betweenness(directed=True)
self.un_b_centrality = self.graph.betweenness(directed=False)
print 'calculating local edge connectivity'
H = build_auxiliary_edge_connectivity(self.di_network_graph)
R = build_residual_network(H, 'capacity')
self.di_connectivity = dict.fromkeys(self.di_network_graph, dict())
for u, v in itertools.combinations(self.di_network_graph, 2):
k = local_edge_connectivity(self.di_network_graph,
u,
v,
auxiliary=H,
residual=R)
self.di_connectivity[u][v] = k
H = build_auxiliary_edge_connectivity(self.un_network_graph)
R = build_residual_network(H, 'capacity')
self.un_connectivity = dict.fromkeys(self.un_network_graph, dict())
for u, v in itertools.combinations(self.un_network_graph, 2):
k = local_edge_connectivity(self.un_network_graph,
u,
v,
auxiliary=H,
residual=R)
self.un_connectivity[u][v] = k
def test_directed_edge_connectivity():
G = nx.cycle_graph(10, create_using=nx.DiGraph()) # only one direction
D = nx.cycle_graph(10).to_directed() # 2 reciprocal edges
for flow_func in flow_funcs:
errmsg = f"Assertion failed in function: {flow_func.__name__}"
assert 1 == nx.edge_connectivity(G, flow_func=flow_func), errmsg
assert 1 == local_edge_connectivity(G, 1, 4,
flow_func=flow_func), errmsg
assert 1 == nx.edge_connectivity(G, 1, 4, flow_func=flow_func), errmsg
assert 2 == nx.edge_connectivity(D, flow_func=flow_func), errmsg
assert 2 == local_edge_connectivity(D, 1, 4,
flow_func=flow_func), errmsg
assert 2 == nx.edge_connectivity(D, 1, 4, flow_func=flow_func), errmsg
def test_directed_edge_connectivity():
G = nx.cycle_graph(10, create_using=nx.DiGraph()) # only one direction
D = nx.cycle_graph(10).to_directed() # 2 reciprocal edges
for flow_func in flow_funcs:
assert_equal(1, nx.edge_connectivity(G, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(1, local_edge_connectivity(G, 1, 4, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(1, nx.edge_connectivity(G, 1, 4, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.edge_connectivity(D, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(2, local_edge_connectivity(D, 1, 4, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.edge_connectivity(D, 1, 4, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
def test_directed_edge_connectivity():
G = nx.cycle_graph(10, create_using=nx.DiGraph()) # only one direction
D = nx.cycle_graph(10).to_directed() # 2 reciprocal edges
for flow_func in flow_funcs:
assert_equal(1, nx.edge_connectivity(G, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(1, local_edge_connectivity(G, 1, 4, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(1, nx.edge_connectivity(G, 1, 4, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.edge_connectivity(D, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(2, local_edge_connectivity(D, 1, 4, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.edge_connectivity(D, 1, 4, flow_func=flow_func),
msg=msg.format(flow_func.__name__))
def test_brandes_erlebach():
# Figure 1 chapter 7: Connectivity
# http://www.informatik.uni-augsburg.de/thi/personen/kammer/Graph_Connectivity.pdf
G = nx.Graph()
G.add_edges_from([(1, 2), (1, 3), (1, 4), (1, 5), (2, 3), (2, 6), (3, 4),
(3, 6), (4, 6), (4, 7), (5, 7), (6, 8), (6, 9), (7, 8),
(7, 10), (8, 11), (9, 10), (9, 11), (10, 11)])
for flow_func in flow_funcs:
kwargs = dict(flow_func=flow_func)
assert_equal(3,
local_edge_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(3,
nx.edge_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2,
local_node_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2,
nx.node_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(
2,
nx.edge_connectivity(G, **kwargs), # node 5 has degree 2
msg=msg.format(flow_func.__name__))
assert_equal(2,
nx.node_connectivity(G, **kwargs),
msg=msg.format(flow_func.__name__))
def connections(self):
# References taken from NetwrokX documentation
def check_connections(self):
"""
:return: a True/ False value depending on connections
"""
count = 0
DG = Navigation.read_from_csv_get_attribute('edges.csv',
'nodes.csv',
handicap_mode_flag=bool)
H = build_auxiliary_edge_connectivity(DG)
# And the function for building the residual network from the
# flow package
# Note that the auxiliary digraph has an edge attribute named capacity
R = build_residual_network(H, 'capacity')
result = dict.fromkeys(DG, dict())
# Reuse the auxiliary digraph and the residual network by passing them
# as parameters
#print(local_edge_connectivity(DG, 'Indiana1', 'DisneyLandMonoRail'))
for u, v in itertools.combinations(DG, 2):
k = local_edge_connectivity(DG, u, v, auxiliary=H, residual=R)
result[u][v] = k
# print(u,v)
# print(result[u][v])
if result[u][v] == 0:
count = 1
#print(u,v)
if count == 1:
return False
else:
return True
def calc_path_redundancy(graph, node, distances):
"""Determines the path redundancy (number of node/edge disjoint paths)
from one specific node to all other nodes"""
# NOTE: we calculate the minimum number of node independent paths as an approximation (and not
# the maximum)
count_nodes = graph.number_of_nodes()
path_redundancy = np.zeros(count_nodes - 1,
dtype=[('distance', 'float'),
('count_node_disjoint_paths', 'uint'),
('count_edge_disjoint_paths', 'uint')])
iter_veh = 0
for node_iter_veh in graph.nodes():
if node_iter_veh == node:
continue
idx_cond = utils.square_to_condensed(node, node_iter_veh, count_nodes)
path_redundancy[iter_veh]['distance'] = distances[idx_cond]
path_redundancy[iter_veh][
'count_node_disjoint_paths'] = nx_con_approx.local_node_connectivity(
graph, source=node, target=node_iter_veh)
path_redundancy[iter_veh][
'count_edge_disjoint_paths'] = nx_con.local_edge_connectivity(
graph, node, node_iter_veh)
iter_veh += 1
return path_redundancy
def connected_all(st_lst, H):
#print H.edges()
for (u, v) in st_lst:
if local_edge_connectivity(H, u, v) > 0:
continue
else:
return False
return True
def avg_edge_connectivity(G, I, s):
total_connectivity = 0
for t in I:
if t != s:
total_connectivity += local_edge_connectivity(G, s, t)
avg_connectivity = total_connectivity / (len(I) - 1)
# TODO: normalize
return avg_connectivity
def __select_removal_candidate(graph):
"""
:type graph: networkx.classes.graph.Graph
:rtype: tuple
"""
for u, v in graph.edges_iter():
if local_edge_connectivity(graph, u, v) > 1:
return u, v
return None
def connected_all(st_lst, H):
for edge in st_lst:
u = edge[0]
v = edge[1]
if local_edge_connectivity(H, u, v)>0:
continue
else:
return False
return True
def test_brandes_erlebach():
# Figure 1 chapter 7: Connectivity
# http://www.informatik.uni-augsburg.de/thi/personen/kammer/Graph_Connectivity.pdf
G = nx.Graph()
G.add_edges_from([(1, 2), (1, 3), (1, 4), (1, 5), (2, 3), (2, 6), (3, 4),
(3, 6), (4, 6), (4, 7), (5, 7), (6, 8), (6, 9), (7, 8),
(7, 10), (8, 11), (9, 10), (9, 11), (10, 11)])
for flow_func in flow_funcs:
kwargs = dict(flow_func=flow_func)
assert_equal(3, local_edge_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(3, nx.edge_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2, local_node_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.node_connectivity(G, 1, 11, **kwargs),
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.edge_connectivity(G, **kwargs), # node 5 has degree 2
msg=msg.format(flow_func.__name__))
assert_equal(2, nx.node_connectivity(G, **kwargs),
msg=msg.format(flow_func.__name__))
def test_brandes_erlebach():
# Figure 1 chapter 7: Connectivity
# http://www.informatik.uni-augsburg.de/thi/personen/kammer/Graph_Connectivity.pdf
G = nx.Graph()
G.add_edges_from([
(1, 2),
(1, 3),
(1, 4),
(1, 5),
(2, 3),
(2, 6),
(3, 4),
(3, 6),
(4, 6),
(4, 7),
(5, 7),
(6, 8),
(6, 9),
(7, 8),
(7, 10),
(8, 11),
(9, 10),
(9, 11),
(10, 11),
])
for flow_func in flow_funcs:
kwargs = dict(flow_func=flow_func)
errmsg = f"Assertion failed in function: {flow_func.__name__}"
assert 3 == local_edge_connectivity(G, 1, 11, **kwargs), errmsg
assert 3 == nx.edge_connectivity(G, 1, 11, **kwargs), errmsg
assert 2 == local_node_connectivity(G, 1, 11, **kwargs), errmsg
assert 2 == nx.node_connectivity(G, 1, 11, **kwargs), errmsg
assert 2 == nx.edge_connectivity(G, **kwargs), errmsg
assert 2 == nx.node_connectivity(G, **kwargs), errmsg
if flow_func is flow.preflow_push:
assert 3 == nx.edge_connectivity(G, 1, 11, cutoff=2,
**kwargs), errmsg
else:
assert 2 == nx.edge_connectivity(G, 1, 11, cutoff=2,
**kwargs), errmsg
def state_features(self, G, K, T, profile):
f = []
E_0 = self.profile_to_E0[profile]
adjacency_0 = self.profile_to_adjacency0[profile]
if params.use_in_out_matrix:
out_degree = G.out_degree(self.I)
for (i, j) in out_degree:
f.extend(
RP_utils.polynomialize(
RP_utils.safe_div(j, E_0.out_degree(i)),
params.num_polynomial))
in_degree = G.in_degree(self.I)
for (i, j) in in_degree:
f.extend(
RP_utils.polynomialize(
RP_utils.safe_div(j, E_0.in_degree(i)),
params.num_polynomial))
if params.use_total_degree_matrix:
for i in self.I:
i_total = G.out_degree(i) + G.in_degree(i)
i_e0_total = E_0.out_degree(i) + E_0.in_degree(i)
f.extend(
RP_utils.polynomialize(
RP_utils.safe_div(i_total, i_e0_total),
params.num_polynomial))
if params.use_in_out_binary_matrix:
out_degree = G.out_degree(self.I)
for (i, j) in out_degree:
f.append(2 * int(j > 0) - 1)
in_degree = G.in_degree(self.I)
for (i, j) in in_degree:
f.append(2 * int(j > 0) - 1)
if params.use_voting_rules_matrix:
for i in self.profile_to_plurality[profile]:
f.extend(RP_utils.polynomialize(i, params.num_polynomial))
for i in self.profile_to_borda[profile]:
f.extend(RP_utils.polynomialize(i, params.num_polynomial))
for i in self.profile_to_copeland[profile]:
f.extend(RP_utils.polynomialize(i, params.num_polynomial))
for i in self.profile_to_maximin[profile]:
f.extend(RP_utils.polynomialize(i, params.num_polynomial))
if params.use_edge_weight:
f.extend(
RP_utils.polynomialize(
E_0[T[0][0]][T[0][1]]['weight'] /
self.profile_to_max_edge_weight[profile],
params.num_polynomial))
if params.use_vectorized_wmg:
f.extend(self.profile_to_vectorized_wmg[profile])
if params.use_posmat:
f.extend(self.profile_to_posmat[profile])
if params.use_tier_adjacency_matrix:
T_matrix = np.zeros((int(params.m), int(params.m)))
for (c1, c2) in T:
T_matrix[c1, c2] = 1
T_vec = list(T_matrix.flatten())
f.extend(T_vec)
if params.use_connectivity_matrix:
for i in self.I:
for j in self.I:
if i != j:
f.extend(
RP_utils.polynomialize(
local_edge_connectivity(G, i, j) /
(params.m - 2), params.num_polynomial)
) # normalized by m-2 since max edges needed to disconnect i and j is all edges but i -> i and i -> j
all_pairs_node_connectivity = nx.all_pairs_node_connectivity(G)
for i in self.I:
for j in self.I:
if i != j:
f.extend(
RP_utils.polynomialize(
all_pairs_node_connectivity[i][j] /
(params.m - 2), params.num_polynomial)
) # normalized by m-2 since max nodes needed to disconnect i and j is all nodes but i and j
# adjacency matrix
if params.use_adjacency_matrix:
adjacency = nx.adjacency_matrix(G, nodelist=self.I).todense()
adjacency = np.multiply(adjacency, adjacency_0)
adjacency_normalized = np.divide(adjacency, params.n)
f.extend(adjacency_normalized.flatten().tolist()[0])
# K representation
if params.use_K_representation:
K_list = []
for i in self.I:
if i in K:
K_list.append(1)
else:
K_list.append(0)
f.extend(K_list)
return Variable(torch.from_numpy(np.array(f)).float())
def state_features(self):
f = []
legal_actions = self.get_legal_actions()
if params.use_in_out_matrix:
out_degree = self.G.out_degree(self.I)
for (i, j) in out_degree:
f.extend(
RP_utils.polynomialize(j / params.m,
params.num_polynomial))
in_degree = self.G.in_degree(self.I)
for (i, j) in in_degree:
f.extend(
RP_utils.polynomialize(j / params.m,
params.num_polynomial))
if params.use_in_out_relative_matrix:
out_degree = self.G.out_degree(self.I)
for (i, j) in out_degree:
f.extend(
RP_utils.polynomialize(
RP_utils.safe_div(j, self.E_0.out_degree(i)),
params.num_polynomial))
in_degree = self.G.in_degree(self.I)
for (i, j) in in_degree:
f.extend(
RP_utils.polynomialize(
RP_utils.safe_div(j, self.E_0.in_degree(i)),
params.num_polynomial))
if params.use_total_degree_matrix:
for i in self.I:
i_total = self.G.out_degree(i) + self.G.in_degree(i)
i_e0_total = self.E_0.out_degree(i) + self.E_0.in_degree(i)
f.extend(
RP_utils.polynomialize(
RP_utils.safe_div(i_total, i_e0_total),
params.num_polynomial))
if params.use_in_out_binary_matrix:
out_degree = self.G.out_degree(self.I)
for (i, j) in out_degree:
f.append(2 * int(j > 0) - 1)
in_degree = self.G.in_degree(self.I)
for (i, j) in in_degree:
f.append(2 * int(j > 0) - 1)
if params.use_voting_rules_matrix:
for i in self.plurality_scores:
f.extend(RP_utils.polynomialize(i, params.num_polynomial))
for i in self.borda_scores:
f.extend(RP_utils.polynomialize(i, params.num_polynomial))
for i in self.copeland_scores:
f.extend(RP_utils.polynomialize(i, params.num_polynomial))
for i in self.maximin_scores:
f.extend(RP_utils.polynomialize(i, params.num_polynomial))
if params.use_edge_weight:
f.extend(
RP_utils.polynomialize(
self.E_0_really[legal_actions[0][0]][legal_actions[0][1]]
['weight'] / self.max_edge_weight, params.num_polynomial))
if params.use_vectorized_wmg:
f.extend(self.vectorized_wmg)
if params.use_posmat:
f.extend(self.posmat)
if params.use_tier_adjacency_matrix:
T_matrix = np.zeros((int(params.m), int(params.m)))
for (c1, c2) in legal_actions:
T_matrix[c1, c2] = 1
T_vec = list(T_matrix.flatten())
f.extend(T_vec)
if params.use_connectivity_matrix:
for i in self.I:
for j in self.I:
if i != j:
f.extend(
RP_utils.polynomialize(
local_edge_connectivity(self.G, i, j) /
(params.m - 2), params.num_polynomial)
) # normalized by m-2 since max edges needed to disconnect i and j is all edges but i -> i and i -> j
all_pairs_node_connectivity = nx.all_pairs_node_connectivity(
self.G)
for i in self.I:
for j in self.I:
if i != j:
f.extend(
RP_utils.polynomialize(
all_pairs_node_connectivity[i][j] /
(params.m - 2), params.num_polynomial)
) # normalized by m-2 since max nodes needed to disconnect i and j is all nodes but i and j
# adjacency matrix of current state
if params.use_adjacency_matrix:
adjacency = nx.adjacency_matrix(self.G, nodelist=self.I).todense()
adjacency = np.multiply(adjacency, self.adjacency_0)
adjacency_normalized = np.divide(adjacency, params.n)
f.extend(adjacency_normalized.flatten().tolist()[0])
# K representation
if params.use_K_representation:
K_list = []
for i in self.I:
if i in self.K:
K_list.append(1)
else:
K_list.append(0)
f.extend(K_list)
# node2vec every time
# G_with_weights = nx.DiGraph()
# G_with_weights.add_nodes_from(self.I)
# for (cand1, cand2) in self.G.edges():
# G_with_weights.add_edge(cand1, cand2, weight=self.E_0_really[cand1][cand2]['weight'])
# node2vec_G = node2vec.Graph(G_with_weights, True, self.node2vec_args.p, self.node2vec_args.q)
# node2vec_G.preprocess_transition_probs()
# walks = node2vec_G.simulate_walks(self.node2vec_args.num_walks, self.node2vec_args.walk_length)
# self.node2vec_model = node2vecmain.learn_embeddings(walks, self.node2vec_args)
# node2vec features
# node2vec_u = self.node2vec_model.wv[str(u)]
# node2vec_v = self.node2vec_model.wv[str(v)]
# node2vec_uv = np.append(node2vec_u, node2vec_v)
# node2vec_f = np.append(node2vec_uv, np.array(f))
if params.debug_mode >= 3:
print("features", f)
return Variable(torch.from_numpy(np.array(f)).float())