def test_google_matrix(self):
G = self.G
M = networkx.google_matrix(G, alpha=0.9)
e, ev = numpy.linalg.eig(M.T)
p = numpy.array(ev[:, 0] / ev[:, 0].sum())[:, 0]
for (a, b) in zip(p, self.G.pagerank.values()):
assert_almost_equal(a, b)
personalize = dict((n, random.random()) for n in G)
M = networkx.google_matrix(G, alpha=0.9, personalization=personalize)
personalize.pop(1)
assert_raises(networkx.NetworkXError, networkx.google_matrix, G,
personalization=personalize)
def test_google_matrix(self):
G = self.G
M = networkx.google_matrix(G, alpha=0.9, nodelist=sorted(G))
e, ev = numpy.linalg.eig(M.T)
p = numpy.array(ev[:, 0] / ev[:, 0].sum())[:, 0]
for (a, b) in zip(p, self.G.pagerank.values()):
assert_almost_equal(a, b)
def test_google_matrix(self):
G = self.G
M = nx.google_matrix(G, alpha=0.9, nodelist=sorted(G))
e, ev = np.linalg.eig(M.T)
p = np.array(ev[:, 0] / ev[:, 0].sum())[:, 0]
for (a, b) in zip(p, self.G.pagerank.values()):
assert a == pytest.approx(b, abs=1e-7)
def LRW_Index (matrix, graph, n):
P = nx.google_matrix(graph)
trans = np.transpose(P)
pi = []
vector = np.zeros(nodes_num)
vector[0] = 1
new_v = copy.copy(vector)
pi.append(new_v)
for i in range(1, nodes_num):
vector[i-1] = 0
vector[i] = 1
new_v = copy.copy(vector)
pi.append(new_v)
for i in range(0, n):
for x in range(0, nodes_num):
pi[x] = pi[x].dot(trans)
s = (nodes_num, nodes_num)
S_LRW = np.zeros(s)
degree_matrix = nx.laplacian_matrix(graph) + matrix
for x in range(0, nodes_num):
q_x = degree_matrix[x, x] / len(graph.edges)
for y in range(0, nodes_num):
q_y = degree_matrix[y, y] / len(graph.edges)
S_LRW[x, y] = q_x * pi[x].tolist()[0][y] +q_y * pi[y].tolist()[0][x]
return S_LRW
def RWR_Index (graph, nodes_num, c):
# google matrix == transition matrix z papera
P = nx.google_matrix(graph)
idn = np.identity(nodes_num)
trans = np.transpose(P)
core = (1 - c) * LAD.inv((idn - c * trans))
vector = np.zeros(nodes_num)
qs = []
vector[0] = 1
new_v = copy.copy(vector)
# vector <==> "baza" wektora
qs.append(core.dot(new_v))
for i in range(1, nodes_num):
vector[i - 1] = 0
vector[i] = 1
new_v = copy.copy(vector)
qs.append(core.dot(new_v))
s = (nodes_num, nodes_num)
S_RWR = np.zeros(s)
for x in range(0, nodes_num):
for y in range(0, nodes_num):
S_RWR[x, y] = qs[x].tolist()[0][y] + qs[y].tolist()[0][x]
return S_RWR
def page_rank(data):
import pandas as pd
import numpy as np
import networkx as nx
df = pd.DataFrame(data)
graph = nx.DiGraph()
h = nx.path_graph(pd.Series.count(np.unique(df[0])))
graph.add_nodes_from(h)
graph.add_node(h)
for i in range(len(df[0])):
graph.add_edge(df[0][i], df[1][i])
graph[df[0][i]][df[1][i]]['weight'] = df[3][i]
transition_matrix = nx.google_matrix(graph)
n = min(transition_matrix.shape)
p0 = np.repeat(1 / n, n)
pi = np.matmul(p0, transition_matrix)
eps = 0.0000025
i = 1
while np.sum(np.abs(pi - p0)) >= eps:
p0 = pi
pi = np.matmul(pi, transition_matrix)
print(i)
print(pi)
i = i + 1
print('The final rank is :', pi)
def test_google_matrix(self):
G = self.G
M = networkx.google_matrix(G, alpha=0.9, nodelist=sorted(G))
e, ev = numpy.linalg.eig(M.T)
p = numpy.array(ev[:, 0] / ev[:, 0].sum())[:, 0]
for (a, b) in zip(p, self.G.pagerank.values()):
assert_almost_equal(a, b)
def pagerank_numpy(G,
alpha=0.85,
personalization=None,
weight='weight',
dangling=None):
"""Return the PageRank of the nodes in the graph.
"""
if len(G) == 0:
return {}
M = nx.google_matrix(G,
alpha,
personalization=personalization,
weight=weight,
dangling=dangling)
# use numpy LAPACK solver
eigenvalues, eigenvectors = np.linalg.eig(M.T)
ind = eigenvalues.argsort()
# eigenvector of largest eigenvalue at ind[-1], normalized
largest = np.array(eigenvectors[:, ind[-1]]).flatten().real
norm = float(largest.sum())
return dict(zip(G, map(float, largest / norm)))
def test_empty(self):
try:
import numpy
except ImportError:
raise SkipTest('numpy not available.')
G = networkx.Graph()
assert_equal(networkx.pagerank(G), {})
assert_equal(networkx.pagerank_numpy(G), {})
assert_equal(networkx.google_matrix(G).shape, (0, 0))
def test_empty(self):
try:
import numpy
except ImportError:
raise SkipTest("numpy not available.")
G = networkx.Graph()
assert_equal(networkx.pagerank(G), {})
assert_equal(networkx.pagerank_numpy(G), {})
assert_equal(networkx.google_matrix(G).shape, (0, 0))
def test_dangling_matrix(self):
"""
Tests that the google_matrix doesn't change except for the dangling
nodes.
"""
G = self.G
dangling = self.dangling_edges
dangling_sum = float(sum(dangling.values()))
M1 = nx.google_matrix(G, personalization=dangling)
M2 = nx.google_matrix(G, personalization=dangling, dangling=dangling)
for i in range(len(G)):
for j in range(len(G)):
if i == self.dangling_node_index and (j + 1) in dangling:
assert almost_equal(M2[i, j],
dangling[j + 1] / dangling_sum,
places=4)
else:
assert almost_equal(M2[i, j], M1[i, j], places=4)
def test_dangling_matrix(self):
"""
Tests that the google_matrix doesn't change except for the dangling
nodes.
"""
G = self.G
dangling = self.dangling_edges
dangling_sum = float(sum(dangling.values()))
M1 = networkx.google_matrix(G, personalization=dangling)
M2 = networkx.google_matrix(G, personalization=dangling,
dangling=dangling)
for i in range(len(G)):
for j in range(len(G)):
if i == self.dangling_node_index and (j + 1) in dangling:
assert_almost_equal(M2[i, j],
dangling[j + 1] / dangling_sum,
places=4)
else:
assert_almost_equal(M2[i, j], M1[i, j], places=4)
def test_google_matrix(self):
try:
import numpy.linalg
except ImportError:
raise SkipTest('numpy not available.')
G=self.G
M=networkx.google_matrix(G,alpha=0.9)
e,ev=numpy.linalg.eig(M.T)
p=numpy.array(ev[:,0]/ev[:,0].sum())[:,0]
for (a,b) in zip(p,self.G.pagerank.values()):
assert_almost_equal(a,b)
def calc(g,negative,alpha,M,beta=1):
epsilon = 0.000000001
print "start calc pagetrust, epsilon =",epsilon
N = len(g)
x = np.ones(N)
x = x * 1/N
visualize("x",x)
P,tildeP = initialize_P(g,negative)
t = 0
G = nx.google_matrix(g)
pagerank = nx.pagerank(g,alpha=alpha)
visualize("Google matrix",G)
t = 0
while True:
t += 1
#build the transition matrix T
print "***"
print "*** iteration start, time = ",t
print "***"
T = build_transition_matrix(alpha,x,g,G,M)
tildeP = np.dot(T,P)
visualize("P",P)
visualize("tildeP",tildeP)
x2 = np.zeros(N)
for i in range(N):
p = 0
for k in range(N):
p += G[k,i]*x[k]
x2[i] = (1 - tildeP[i][i])**beta*p
for j in range(N):
if (i,j) in negative:
P[i,j] = 1
elif i == j:
P[i,j] = 0
else:
P[i,j] = tildeP[i,j]
#normalization
tmpl = 0
for l in range(N):
tmpl += x2[l]
for o in range(N):
x2[o] = x2[o] / tmpl
visualize("x2",x2)
e = is_converged(x,x2)
print "e:",e
if e < epsilon:
#visualize('pagerank',pagerank)
break
else:
#x <- x(t+1)
for p in range(N):
x[p] = x2[p]
print x2
return x2
def test_google_matrix(self):
try:
import numpy.linalg
except ImportError:
raise SkipTest('numpy not available.')
G = self.G
M = networkx.google_matrix(G, alpha=0.9)
e, ev = numpy.linalg.eig(M.T)
p = numpy.array(ev[:, 0] / ev[:, 0].sum())[:, 0]
for (a, b) in zip(p, self.G.pagerank.values()):
assert_almost_equal(a, b)
def calc(g, negative, alpha, M, beta=1):
epsilon = 0.000000001
print "start calc pagetrust, epsilon =", epsilon
N = len(g)
x = np.ones(N)
x = x * 1 / N
visualize("x", x)
P, tildeP = initialize_P(g, negative)
t = 0
G = nx.google_matrix(g)
pagerank = nx.pagerank(g, alpha=alpha)
visualize("Google matrix", G)
t = 0
while True:
t += 1
#build the transition matrix T
print "***"
print "*** iteration start, time = ", t
print "***"
T = build_transition_matrix(alpha, x, g, G, M)
tildeP = np.dot(T, P)
visualize("P", P)
visualize("tildeP", tildeP)
x2 = np.zeros(N)
for i in range(N):
p = 0
for k in range(N):
p += G[k, i] * x[k]
x2[i] = (1 - tildeP[i][i])**beta * p
for j in range(N):
if (i, j) in negative:
P[i, j] = 1
elif i == j:
P[i, j] = 0
else:
P[i, j] = tildeP[i, j]
#normalization
tmpl = 0
for l in range(N):
tmpl += x2[l]
for o in range(N):
x2[o] = x2[o] / tmpl
visualize("x2", x2)
e = is_converged(x, x2)
print "e:", e
if e < epsilon:
#visualize('pagerank',pagerank)
break
else:
#x <- x(t+1)
for p in range(N):
x[p] = x2[p]
print x2
return x2
def test_google_matrix(self):
G=self.G
try:
import numpy.linalg
M=networkx.google_matrix(G,alpha=0.9)
e,ev=numpy.linalg.eig(M.T)
p=numpy.array(ev[:,0]/ev[:,0].sum())[:,0]
for (a,b) in zip(p,self.G.pagerank):
assert_almost_equal(a,b)
except ImportError:
print "Skipping google_matrix test"
def graph_structure(graph, content_graph, path):
""" Builds interaction graph with structure based weighs
similarity metric, and save it at the given path """
A = scipy.sparse.csr_matrix(
nx.google_matrix(graph, alpha=1, weight='weight'))
W = nx.to_scipy_sparse_matrix(content_graph)
W2 = (W.dot(A) + A.transpose().dot(W)) * 0.5
# rescaling in range 0-1
max_val = W2.max()
W2 = W2.multiply(1.0 / max_val)
save_matrix_to_edgelist(W2, path)
def exhaustive_set(G, query_nodes, target_nodes, n_edges, start_dist):
"""Exaustively searches all the combinations of k links between
a set of query nodes Q and a set of absorbing
target nodes C such that Q \cap C = \emptyset.
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
ac_scores: list
The set of scores of adding the links
"""
query_set_size = len(query_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
P = csc_matrix(nx.google_matrix(G, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum())[0,0]
candidates = list(product(query_nodes, target_nodes))
eligible = [candidates[i] for i in range(len(candidates))
if G.has_edge(candidates[i][0], candidates[i][1]) == False]
ac_scores = [row_sums]
exhaustive_links = []
for L in range(1, n_edges+1):
print '\t Number of edges {}'.format(L)
round_min = -1
best_combination = []
for subset in combinations(eligible, L):
H = G.copy()
F_modified = F.copy()
for links_to_add in subset:
F_updated = update_fundamental_mat(F_modified, H, map_query_to_org, links_to_add[0])
H.add_edge(links_to_add[0], links_to_add[1])
F_modified = F_updated
abs_cen = start_dist.dot( F_updated.sum(axis = 1))[0,0]
if abs_cen < round_min or round_min == -1:
best_combination = subset
round_min = abs_cen
exhaustive_links.append(best_combination)
ac_scores.append(round_min)
return exhaustive_links, ac_scores
def page_rank(graph, jump_probability=.15, weighted=False):
if weighted:
wt = 'weight'
else:
wt = None
alpha = 1 - jump_probability
M = _nx.google_matrix(graph, alpha, weight=wt)
_, v = _eigs(M.T, k=1)
r = v.flatten().real
r /= r.sum()
return _pd.Series(r, index=graph.nodes).sort_index()
def linkrank(G):
c = arange(len(G.nodes()))
goo = nx.google_matrix(G)
goo = array(goo)
m = nx.pagerank_numpy(G)
m = m.items()
m = [i[1] for i in m]
m = array([m])
m = m.T
L = tile(m,[1,len(goo)])*goo
Q = 0
mm = tile(m,[1,len(goo)])*tile(m.T,[len(goo),1])
Qlr = L - mm
return greedyMax(Qlr,c,0)
def _google_matrix(graph, anchors, normalize):
aut = {}
node_to_num = dict((node, i) for i, node in enumerate(graph.nodes()))
num_to_node = dict(enumerate(graph.nodes()))
aut_mat = nx.google_matrix(graph)
for num, node in enumerate(graph.nodes()):
d = []
for anchor in anchors:
a_num = node_to_num[anchor]
d.append(aut_mat[num, a_num])
if normalize:
d = normalized(d)
aut[node] = np.array(d)
return aut
def linkrank(G):
c = arange(len(G.nodes()))
goo = nx.google_matrix(G)
goo = array(goo)
m = nx.pagerank_numpy(G)
m = m.items()
m = [i[1] for i in m]
m = array([m])
m = m.T
L = tile(m, [1, len(goo)]) * goo
Q = 0
mm = tile(m, [1, len(goo)]) * tile(m.T, [len(goo), 1])
Qlr = L - mm
return greedyMax(Qlr, c, 0)
def pagerank(g):
import numpy as np
import networkx as nx
trm = nx.google_matrix(g)
n = min(trm.shape)
p0 = np.repeat(1 / n, n)
pi = np.matmul(p0, trm)
i = 1
eps = 0.00015
while np.sum(np.abs(pi - p0)) >= eps:
p0 = pi
pi = np.matmul(pi, trm)
i = i + 1
if i == 10000:
break
return pi
def pagerank_numpy(G,alpha=0.85,max_iter=100,tol=1.0e-6,nodelist=None):
"""Return a NumPy array of the PageRank of G.
"""
import numpy
import networkx
M=networkx.google_matrix(G,alpha,nodelist)
(n,m)=M.shape # should be square
x=numpy.ones((n))/n
for i in range(max_iter):
xlast=x
x=numpy.dot(x,M)
# check convergence, l1 norm
err=numpy.abs(x-xlast).sum()
if err < n*tol:
return numpy.asarray(x).flatten()
raise NetworkXError("pagerank: power iteration failed to converge in %d iterations."%(i+1))
def random_links(G, query_nodes, target_nodes, n_edges, start_dist):
"""Selects a random set of links between a set of query nodes Q and a set of absorbing
target nodes C such that Q \cap C = \emptyset.
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
ac_scores: list
The set of scores of adding the links
"""
query_set_size = len(query_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
P = csc_matrix(nx.google_matrix(G, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum())[0,0]
candidates = list(product(query_nodes, target_nodes))
eligible = [candidates[i] for i in range(len(candidates))
if G.has_edge(candidates[i][0], candidates[i][1]) == False]
links_to_add = sample(eligible, n_edges)
ac_scores = []
ac_scores.append(row_sums)
i = 0
while i < n_edges:
F_updated = update_fundamental_mat(F, G, map_query_to_org, links_to_add[i][0])
G.add_edge(links_to_add[i][0], links_to_add[i][1])
abs_cen = start_dist.dot(F_updated.sum(axis = 1))[0,0]
F = F_updated
ac_scores.append(abs_cen)
i += 1
return links_to_add, ac_scores
def pagerank_numpy(G, alpha=0.85, max_iter=100, tol=1.0e-6, nodelist=None):
"""Return a NumPy array of the PageRank of G.
"""
import numpy
import networkx
M = networkx.google_matrix(G, alpha, nodelist)
(n, m) = M.shape # should be square
x = numpy.ones((n)) / n
for i in range(max_iter):
xlast = x
x = numpy.dot(x, M)
# check convergence, l1 norm
err = numpy.abs(x - xlast).sum()
if err < n * tol:
return numpy.asarray(x).flatten()
raise NetworkXError(
"pagerank: power iteration failed to converge in %d iterations." %
(i + 1))
def cluster(seed_nodes, graph):
# Compute adjacency matrix
A = nx.adjacency_matrix(graph, weight='weight').todense()
# Compute the initial transition matrix
M = A / A.sum(axis=1)
M[np.isnan(M)] = 0
# Compute the initial google matrix
P = nx.google_matrix(graph, weight='weight')
PF = np.copy(P)
# Compute random walk for t steps
t = 3
for i in range(2, t + 1):
PF += np.linalg.matrix_power(P, i)
P_degree = np.diag(PF)
P_weight = cosine_similarity(PF)
coms = set()
membership = {}
# Sort the nodes array in decreasing value of weights
sorted_P_deg = np.sort(P_degree)[::-1]
sorted_P_deg_indices = np.argsort(P_degree)
nodes_list = list(graph.nodes)
sorted_nodes = [nodes_list[i] for i in sorted_P_deg_indices]
# Take the P-degree of N/4th node as threshold
Pt = sorted_P_deg[graph.number_of_nodes() // 4]
# Loop over the nodes and check if P-degree of node > Pt
# If P-degree of a node > Pt and P-degree is not in a sub region,
# keep the node as a seed node and map the nodes connected to as a
# community
# If P-degree of a node < Pt and P-degree is in a sub-region, skip
for i, node in enumerate(sorted_nodes):
if sorted_P_deg[i] > Pt and node not in coms:
coms |= {node, *graph.neighbors(node)}
membership[node] = [*graph.neighbors(node)]
def M(path, graph, a, personal):
if path is None and graph is None:
return
g = nx.read_gpickle(path) if path is not None else graph
P = nx.google_matrix(g, alpha=1, dangling=personal) # Transition matrix (per row). Returns NumPy array that is different from
# ndarray!
P_transp = np.transpose(P)
I = np.identity(len(g.nodes()))
m = np.subtract(I,np.dot(a,P_transp))
m_inv = linalg.inv(m)
p_array = np.array(P_transp)
return (m_inv,p_array)
def sim(n=4, m=15):
I_graph = nx.DiGraph()
nodes = ["FB", "Amazon", "HCP", "LinkedIn"]
# nodes = range(n)
edges = np.random.choice(nodes,2*m).reshape(m,2)
# I_graph.add_edges_from(edges)
I_graph.add_edge("FB", "HCP")
I_graph.add_edge("Amazon", "HCP")
I_graph.add_edge("LinkedIn", "HCP")
# visualize
graphVizWrapper.graph(I_graph.edges(), 'di')
# google transition matrix
G = nx.google_matrix(I_graph, alpha=1.0)
# make indexing consistent
G = np.array(G)
surfer = Markov_process(I_graph.nodes(), G)
print(surfer.sample_game(stop=10))
print(G)
print(I_graph.node)
surfer.sim_distribution()
walk[0] = i
elements = np.arange(a.shape[0]) # for our graph [0,1,2,3]
c_index = i # current index for this iteration
for k in range(iters):
count = 0 # count of transitions
probs = a[c_index].reshape((-1,)) # probability of transitions
# sample from probs
sample = np.random.choice(elements,p=probs) # sample a target using probs
index = sample # go to target
walk[k+1] = index
c_index = index
return walk
# print(pd.DataFrame(nx.adj_matrix(G).todense()))
walk_length = 1000000
markov_matrix = np.array(nx.google_matrix(G, alpha=1))
nodes = G.nodes()
vocab = {f"node_{node}":node for node in nodes}
n2voc = {node:name for name, node in vocab.items()}
starting_point = np.random.choice(nodes)
walk = random_walk(markov_matrix, starting_point, walk_length)
walk
# %%
sliding_windows = np.vstack((walk,np.roll(walk, -1), np.roll(walk, -2), np.roll(walk, -3), np.roll(walk, -4))).astype(np.int)
sliding_windows
# %%
cooccurence_matrix = np.zeros_like(markov_matrix)
center_node_pos = int(sliding_windows.shape[0]/2)
for position in range(walk_length):
def get_d_erH(self, alpha = 1, gamma = 1, N = 100): p_mtx = nx.google_matrix(self.graph, alpha = alpha) r_mtx = -1 * np.eye(self.graph.order()) + p_mtx d_erH = (np.eye(self.graph.order()) + (float(gamma) / N ) * r_mtx) ** N return(d_erH)
def get_trans_matrix(graph):
P = nx.google_matrix(graph, alpha=1)
return P.T
def test_empty(self):
G = networkx.Graph()
assert_equal(networkx.pagerank(G), {})
assert_equal(networkx.pagerank_numpy(G), {})
assert_equal(networkx.google_matrix(G).shape, (0, 0))
def test_empty(self):
G = networkx.Graph()
assert networkx.pagerank(G) == {}
assert networkx.pagerank_numpy(G) == {}
assert networkx.google_matrix(G).shape == (0, 0)
def greedy_navigation(G, query_nodes, target_nodes, n_edges, start_dist):
"""Selects a set of links with a greedy descent algorithm that reduce the
absorbing RW centrality between a set of query nodes Q and a set of absorbing
target nodes C such that Q \cap C = \emptyset. The query and target set
must be a 'viable' partition of the graph.
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
P : Scipy matrix
The transition matrix of the graph G
F : Scipy matrix
The fundamental matrix for the graph G with the given set of absorbing
random walk nodes
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
"""
H = G.copy()
prng = RandomState()
query_set_size = len(query_nodes)
target_set_size = len(target_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
P = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum(axis=1))[0,0]
best_F = zeros(F.shape)
optimal_set = []
ac_scores = []
ac_scores.append(row_sums)
while n_edges > 0:
round_min = -1
best_node = -1
for i in query_nodes:
abs_neighbours = [l for l in H.neighbors(i) if l in target_nodes]
if len(abs_neighbours) == target_set_size:
continue
F_updated = update_fundamental_mat(F, H, map_query_to_org, i)
abs_cen = start_dist.dot( F_updated.sum(axis = 1))[0,0]
if abs_cen < round_min or round_min == -1:
best_node = i
round_min = abs_cen
best_F = F_updated
F = best_F
ac_scores.append(round_min)
optimal_candidate_edges = [(best_node, k, round_min)
for k in target_nodes
if H.has_edge(best_node, k) == False ]
try:
edge_idx = prng.randint(0, len(optimal_candidate_edges))
except ValueError:
print(H.neighbors(best_node))
print([l for l in H.neighbors(best_node) if l in target_nodes])
print(best_node)
print(optimal_candidate_edges)
print(target_nodes)
H.add_edge(optimal_candidate_edges[edge_idx][0],
optimal_candidate_edges[edge_idx][1])
optimal_set.append(optimal_candidate_edges[edge_idx])
n_edges -= 1
return optimal_set, ac_scores
def compute_security(star_dict, edge_dict, num_seeds, num_iterations):
#build up a nx graph
galaxy = networkx.Graph()
for v, vertex in star_dict.iteritems():
galaxy.add_node(v)
for v, neighbors in edge_dict.iteritems():
for n in neighbors:
galaxy.add_edge(v,n)
#use the centrality measures already computed to find seeds
#find the top 25% vertices of each centrality measure
betweenness_limit = int(len(star_dict)* 0.4)
sorted_betweenness = sorted((v['betweenness'], k) for k, v in star_dict.iteritems())
top_betweenness = {k for (value, k) in sorted_betweenness[-betweenness_limit:]}
closeness_limit = int(len(star_dict)* 0.15)
sorted_closeness = sorted((v['closeness'], k) for k, v in star_dict.iteritems())
top_closeness = {k for (value, k) in sorted_closeness[-closeness_limit:]}
pagerank_limit = int(len(star_dict)* 0.4)
sorted_pagerank = sorted((v['pagerank'], k) for k, v in star_dict.iteritems())
top_pagerank = {k for (value, k) in sorted_pagerank[-pagerank_limit:]}
#take the intersection of all the top measures. this will be our pool to choose seeds from
seed_pool = top_betweenness & top_closeness & top_pagerank
print len(seed_pool)
seeds = set()
#loop until we have num_seeds or the seed pool is exhausted
while(len(seed_pool) > 0 and len(seeds) < num_seeds):
#pick a random vertex and remove it from the seed pool
current_seed = random.choice(list(seed_pool))
seed_pool.remove(current_seed)
#find all vertices within 10 jumps
close_vertices = networkx.single_source_shortest_path(galaxy, source=current_seed, cutoff=15)
#if none of the current seeds were found within 10 jumps, add this as a seed
if(len(seeds.intersection(close_vertices.iterkeys())) == 0):
seeds.add(current_seed)
print len(seeds)
#apply the random walk algorithm, aka pagerank with alpha=1
personalization_dict = {k: v['closeness']**10 for k,v in star_dict.iteritems()}
mat = networkx.google_matrix(galaxy, alpha=1, personalization=personalization_dict, nodelist=star_dict.keys())
mat = csr_matrix(mat)
#for the initial array, set the seeds to 1 and everything else to 0
weight_array = numpy.empty(len(star_dict), dtype=mat.dtype)
weight_array.fill(0.0001)
for i,k in enumerate(star_dict.iterkeys()):
if(k in seeds):
weight_array[i] = 1
#iterate that shit
for i in xrange(num_iterations):
weight_array = weight_array * mat
#create a security dict to normalize
security_dict = {k:weight_array[i] for i, k in enumerate(star_dict.iterkeys())}
security_dict = normalize(security_dict)
#apply some data transformations - the square root will create more hisec, and the subtraction will create nullsec
for key,value in security_dict.iteritems():
security_dict[key] = value ** 0.025 - 0.94
security_dict = normalize(security_dict)
#copy the result into the security field
for k,v in star_dict.iteritems():
v['security'] = security_dict[k]
import networkx as nx
import numpy as np
import sys
sys.path.append('./src')
from dataset import createFromDataset
from stationary import statDist
G = createFromDataset()
# Especifique a matriz P_ (P_barra) referente ao modelo Pagerank considerando alpha = 0.1.
P_ = nx.google_matrix(G, alpha=0.1)
print(P_)
#Considerando k = 100, aplique o Power method e compare o resultado com o obtido no item b).
# As distribuições estacionárias obtidas em b) e c) são iguais ou diferentes?
# distribuição estacionaria item C
wdict = nx.pagerank(G, alpha=0.1, max_iter=100)
witemC = [0. for i in range(len(P_))]
for key in wdict:
witemC[key - 1] = wdict[key]
# distribuição estacionária item B
witemB = statDist(G, 100)
# Comparar vetores:
isDif = False # booleana para diferentes
contDif = 0 # contador para os diferentes
for i in range(len(witemB)):
help='pagerank algorithm type. naive for pagerank(), numpy for pagerank_numpy(), scipy for pagerank_scipy(), google for google_matrix()')
arg = parser.parse_args()
print("pagerank begins!")
begintime = time.time()
G = nx.DiGraph()
G = buildGFromFile(G)
print("building Graph elapsed time: ", time.time() - begintime)
if arg.type == 'naive':
beginTime = time.time()
PageRankResult = nx.pagerank(G, alpha=1 - arg.rate, max_iter=int(arg.num_iter), tol=arg.eps)
print("PageRank elapsed time: ", time.time() - beginTime)
elif arg.type == 'numpy':
beginTime = time.time()
PageRankResult = nx.pagerank_numpy(G, alpha=1 - arg.rate, max_iter=int(arg.num_iter), tol=arg.eps)
print("pagerank_numpy elapsed time: ", time.time() - beginTime)
elif arg.type == 'scipy':
beginTime = time.time()
PageRankResult = nx.pagerank_scipy(G, alpha=1 - arg.rate)
print("PageRank_scipy elapsed time: ", time.time() - beginTime)
elif arg.type == 'google':
beginTime = time.time()
PageRankResult = nx.google_matrix(G, alpha=1 - arg.rate)
print("Google Matrix elapsed time: ", time.time() - beginTime)
pr_res = json.dumps(PageRankResult)
f = open('rank_save.tsv', 'w')
f.write(pr_res)
f.close()
def getTransMatrix(graph):
P = nx.google_matrix(graph, alpha=1)
# P /= P.sum(axis=1)
P = P.T
return P
def test_empty(self):
G = nx.Graph()
assert nx.pagerank(G) == {}
assert _pagerank_python(G) == {}
assert nx.pagerank_numpy(G) == {}
assert nx.google_matrix(G).shape == (0, 0)
def link_prediction(G, query_nodes, target_nodes, n_edges, start_dist, alg = "ra"):
"""Selects a random set of links between based on the scores calculated by
a standard link-prediction algorithm from networkx library
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
alg: string
A string describing the link-prediction algorithm to be used
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
ac_scores: list
The set of scores of adding the links
"""
assert alg in ["ra", "pa", "jaccard", "aa"], "alg must be one of [\"ra\", \"pa\", \"jaccard\", \"aa\"]."
H = G.copy()
query_set_size = len(query_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
P = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum())[0,0]
candidates = list(product(query_nodes, target_nodes))
eligible = [candidates[i] for i in range(len(candidates))
if H.has_edge(candidates[i][0], candidates[i][1]) == False]
links_to_add = []
if alg == 'ra':
preds = nx.resource_allocation_index(H, eligible)
elif alg == 'jaccard':
preds = nx.jaccard_coefficient(H, eligible)
elif alg == 'aa':
preds = nx.adamic_adar_index(H, eligible)
elif alg == 'pa':
preds = nx.preferential_attachment(H, eligible)
for u,v,p in preds:
links_to_add.append((u,v,p))
links_to_add.sort(key=lambda x: x[2], reverse = True)
ac_scores = []
ac_scores.append(row_sums)
i = 0
while i < n_edges:
F_updated = update_fundamental_mat(F, H, map_query_to_org, links_to_add[i][0])
H.add_edge(links_to_add[i][0], links_to_add[i][1])
abs_cen = start_dist.dot(F_updated.sum(axis = 1))[0,0]
F = F_updated
ac_scores.append(abs_cen)
i += 1
return links_to_add, ac_scores
def googleMatrix(self):
fname = self.DIR + '/googleMatricx.txt'
google_matrix = nx.google_matrix(self.graph)
numpy.savetxt(fname, google_matrix)
print(fname)
def get_approx_boundary(G, query_nodes, target_nodes, n_edges, start_dist):
"""
Used to calculate an approximation guarantee for greedy algorithm
"""
H = G.copy() # GET A COPY OF THE GRAPH
query_set_size = len(query_nodes)
target_set_size = len(target_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
candidates = list(product(query_nodes, target_nodes))
# ALL minus exitsting in G
eligible = [candidates[i] for i in range(len(candidates))
if H.has_edge(candidates[i][0], candidates[i][1]) == False]
# CALCULATE MARGINAL GAIN TO EMPTY SET FOR ALL NODES IN STEEPNESS FUNCTION
P = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums_empty = start_dist.dot(F.sum(axis=1))[0,0] # F(\emptyset)
# candidates = list(product(query_nodes, target_nodes))
ac_marginal_empty = []
ac_marginal_full = []
source_idx_empty = []
node_processed = -1
for out_edge in eligible:
abs_cen = -1
source_node = out_edge[0]
if(node_processed == source_node):
# skip updating matrix because this updates the F matrix in the same way
continue
node_processed = source_node
F_updated = update_fundamental_mat(F, H, map_query_to_org, source_node)
abs_cen = start_dist.dot(F_updated.sum(axis = 1))[0,0]
ac_marginal_empty.append(abs_cen)
source_idx_empty.append(source_node)
sorted_indexes_empty = [i[0] for i in sorted(enumerate(source_idx_empty), key=lambda x:x[1])]
ac_marginal_empty = [ac_marginal_empty[i] for i in sorted_indexes_empty]
# CALCULATE MARGINAL GAIN FOR FULL SET
H.add_edges_from(eligible)
P_all = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs_all = P_all[list(query_nodes),:][:,list(query_nodes)]
F_all = compute_fundamental(P_abs_all)
row_sums_all = start_dist.dot(F_all.sum(axis=1))[0,0]
node_prcessed = -1
source_idx = []
for out_edge in eligible:
abs_cen = -1
source_node = out_edge[0]
if(node_prcessed == source_node):
# skip updating matrix because this updates the F matrix in the same way
continue
node_prcessed = source_node
F_all_updated = update_rev_fundamental_mat(F_all, H, map_query_to_org, source_node)
abs_cen = start_dist.dot(F_all_updated.sum(axis = 1))[0,0]
ac_marginal_full.append(abs_cen)
source_idx.append(source_node)
sorted_indexes = [i[0] for i in sorted(enumerate(source_idx), key=lambda x:x[1])]
ac_marginal_full = [ac_marginal_full[i] for i in sorted_indexes]
assert sorted_indexes == sorted_indexes_empty , "Something is wrong with the way scores are appended"
all_steepness = (asarray(ac_marginal_full) - row_sums_all) / (row_sums_empty-asarray(ac_marginal_empty))
s = min(all_steepness)
node_max = argmin(all_steepness)
return 1-s, sorted_indexes[node_max]
def localPartitioningAttempt(alpha, beta, node):
gamma = alpha + beta - alpha * beta
global nodeIntDict
nodeIntDict = getNodeIntDict(DG)
#This returns the transition matrix, which I think is the random walk matrix
M = nx.google_matrix(DG)
print "M"
print M
print "about to page rank"
# Compute the two global page rank vectors
prBeta = nx.pagerank(DG, alpha=beta)
prGamma = nx.pagerank(DG, alpha=gamma)
#starting vector for local page rank with all probability on node
localDict = dict.fromkeys(DG.nodes(), 0)
localDict[node] = 1
localPR = nx.pagerank(DG, alpha=gamma, nstart=localDict, personalization=localDict)
#linear combination
#this would maybe be faster if I used actual arrays instead of dictionaries
p = {}
for key in localPR.keys():
p[key] = (alpha/gamma)*localPR[key] + (((1-alpha)*beta)/gamma)*prGamma[key]
p[key] = p[key]/prBeta[key]
#create a list of tuples sorted in non-increasing order by value
sortedP = sorted(p.iteritems(), key = operator.itemgetter(1), reverse=True)
sortedLocalPR = sorted(localPR.iteritems(), key = operator.itemgetter(1), reverse=True)
print "node is " + str(node)
print "sortedLocalPR is "
print sortedLocalPR[0:20]
print "sortedP"
print sortedP[0:20]
print "Conductance Loop"
S = []
notS = DG.nodes()
j = 0
S.append(sortedP[j][0])
notS.remove(sortedP[j][0])
minConducance = calculateConductance(S, notS)
minJ = j
for j in range(2,len(sortedP)):
S.append(sortedP[j][0])
notS.remove(sortedP[j][0])
tempConductance = calculateConductance(S, notS)
#print "cond " + str(tempConductance)
if tempConductance < minConducance:
minConducance = tempConductance
minJ = j
print minJ
print minConducance
minSet = sortedP[0:j]
print "minset"
print minSet
print "length of minset " + str(len(minSet))
return minSet
"""
def test_empty(self):
G = networkx.Graph()
assert_equal(networkx.pagerank(G), {})
assert_equal(networkx.pagerank_numpy(G), {})
assert_equal(networkx.google_matrix(G).shape, (0, 0))
'''
n3graph = nx.read_edgelist('../3node2SPs1direct.csv',
create_using=nx.DiGraph())
'''
Simplest Pagerank, use defaults (but print google matrix first)
'''
n3res = pagerank(n3graph,
alpha=0.85,
personalization=None,
dangling=None,
max_iter=1000,
nstart=None,
weight=None)
print("Pagerank, NO teleport set:")
print(google_matrix(n3graph, alpha=0.85, weight=None))
print(n3res)
print("Numpy version:")
n3res = pagerank_numpy(n3graph, alpha=0.85)
print(n3res)
print("Scipy version:")
n3res = pagerank_scipy(n3graph, alpha=0.85)
print(n3res)
print("\n=============================\n")
'''
We only need to provide values for the nodes we want considered (rather than all nodes)
Personalization values are normalized automatically
'''
pValues = {'A': 1}
n3res = pagerank(n3graph,
alpha=0.85,
N = M.shape[1]
v = np.random.rand(N, 1)
v = v / np.linalg.norm(v, 1)
M_hat = (d * M + (1 - d) / N)
start = time.process_time()
for i in range(iters):
v = M_hat @ v
end = time.process_time()
return v
# experiment parameters
N = 10000
iters = 25
# prepare pagerank matrix
print("constructing pagerank matrix...")
# use nx to create representation of a web graph
d = 0.85
G = nx.scale_free_graph(N, alpha=0.41, beta=0.49, gamma=0.1, delta_in=0)
M = nx.google_matrix(G, alpha=1).T
start = time.process_time()
v = pagerank(M, 25, 0.85)
end = time.process_time()
print("numpy:")
print(end - start)
print(v[1], v[2], v[3])
def reverse_greedy(G, query_nodes, target_nodes, n_edges, start_dist):
"""Selects a set of links with a reverse greedy descent algorithm that reduce the
absorbing RW centrality between a set of query nodes Q and a set of absorbing
target nodes C such that Q \cap C = \emptyset. The query and target set
must be a 'viable' partition of the graph.
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
P : Scipy matrix
The transition matrix of the graph G
F : Scipy matrix
The fundamental matrix for the graph G with the given set of absorbing
random walk nodes
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
"""
H = G.copy()
query_set_size = len(query_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
candidates = list(product(query_nodes, target_nodes))
eligible = [candidates[i] for i in range(len(candidates))
if H.has_edge(candidates[i][0], candidates[i][1]) == False]
H.add_edges_from(eligible)
P = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum(axis=1))[0,0]
# candidates = list(product(query_nodes, target_nodes))
worst_F = zeros(F.shape)
worst_set = []
optimal_set = []
ac_scores = []
# ac_scores.append(row_sums)
while len(eligible) > 0:
round_min = -1
worst_link = (-1,-1)
node_prcessed = -1
for out_edge in eligible:
source_node = out_edge[0]
if(node_prcessed == source_node):
# skip updating matrix because this updates the F matrix in the same way
continue
node_prcessed = source_node
F_updated = update_rev_fundamental_mat(F, H, map_query_to_org, source_node)
abs_cen = start_dist.dot(F_updated.sum(axis = 1))[0,0]
if abs_cen < round_min or round_min == -1:
worst_link = out_edge
round_min = abs_cen
worst_F = F_updated
F = worst_F
H.remove_edge(*worst_link)
worst_set.append(worst_link)
eligible.remove(worst_link)
if (len(eligible) <= n_edges):
ac_scores.append(round_min)
optimal_set.append(worst_link)
return list(reversed(optimal_set)), list(reversed(ac_scores))