def _fit(self, parameters):
global _current_clusters
self.graph = _filter_graph(
_base_graph[0].copy(),
node_weight_threshold=self.node_weight_threshold,
edge_weight_threshold=self.edge_weight_threshold,
sem_weight_threshold=self.sem_weight_threshold)
if self.communities == 0:
self.potential_clusters = [
sorted(clq) for clq in nx.find_cliques(self.graph)
if len(clq) >= 3
]
else:
if _current_clusters[1][1:] == parameters[1:]:
self.potential_clusters = [
sorted(clq) for clq in nx.k_clique_communities(
self.graph, 3, cliques=_current_clusters[0])
]
else:
self.potential_clusters = [
sorted(clq)
for clq in nx.k_clique_communities(self.graph, 3)
]
_current_clusters[0] = self.potential_clusters
_current_clusters[1] = parameters
def test_zachary():
z = nx.karate_club_graph()
# clique percolation with k=2 is just connected components
zachary_k2_ground_truth = set([frozenset(z.nodes())])
zachary_k3_ground_truth = set([
frozenset([
0, 1, 2, 3, 7, 8, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 26,
27, 28, 29, 30, 31, 32, 33
]),
frozenset([0, 4, 5, 6, 10, 16]),
frozenset([24, 25, 31])
])
zachary_k4_ground_truth = set([
frozenset([0, 1, 2, 3, 7, 13]),
frozenset([8, 32, 30, 33]),
frozenset([32, 33, 29, 23])
])
zachary_k5_ground_truth = set([frozenset([0, 1, 2, 3, 7, 13])])
zachary_k6_ground_truth = set([])
assert set(k_clique_communities(z, 2)) == zachary_k2_ground_truth
assert set(k_clique_communities(z, 3)) == zachary_k3_ground_truth
assert set(k_clique_communities(z, 4)) == zachary_k4_ground_truth
assert set(k_clique_communities(z, 5)) == zachary_k5_ground_truth
assert set(k_clique_communities(z, 6)) == zachary_k6_ground_truth
def test_overlaping_K5():
G = nx.Graph()
G.add_edges_from(combinations(range(5), 2)) # Add a five clique
G.add_edges_from(combinations(range(2,7), 2)) # Add another five clique
c = list(nx.k_clique_communities(G, 4))
assert_equal(c,[frozenset([0, 1, 2, 3, 4, 5, 6])])
c= list(nx.k_clique_communities(G, 5))
assert_equal(c,[])
def findClaimID(self, cliqueSize, density, mean=0.1, std=0.05):
# STEP1: allocate subnets for fraud rings
if self.subset is None:
c = nx.k_clique_communities(self.G, cliqueSize)
N = len(self.G)
nodeList = None
for count, n in enumerate(list(c)):
print 'Community = ', count, ' Size = ', len(n)
if nodeList is None:
nodeList = n
elif len(n) > (mean - std) * N and len(n) < (mean + std) * N:
nodeList = n
self.subset = list(nodeList)
if self.subset:
self.fraudRingModifier(density=density)
# STEP2: calculate network KPIs
c = nx.k_clique_communities(self.G, cliqueSize)
maximum = 0.0
for count, n in enumerate(list(c)):
N_claim = 0.
N_part = 0.
for NI in n:
if self.G.node[NI]['label'].split('_')[0] == 'ClaimID':
N_claim += 1.0
else:
N_part += 1.0
for NI in n:
ratio = N_claim / N_part
self.G.node[NI]['modularityClass'] = count + 1
self.G.node[NI]['fraudScore'] = ratio
if maximum < ratio:
maximum = ratio
# STEP3: assign fraud scores
c = nx.k_clique_communities(self.G, cliqueSize)
for count, n in enumerate(list(c)):
for NI in n:
self.G.node[NI]['fraudScore'] /= maximum
self.G.node[NI]['fraudScore'] *= 100
self.G.node[NI]['fraudScore'] = int(
self.G.node[NI]['fraudScore'])
def report_communities(graph: networkx.Graph):
communities = {}
for community_id, community in enumerate(
networkx.k_clique_communities(graph, 3)):
for node in community:
communities[node] = community_id + 1
# Group actors from same communities together
community_to_actors = {}
for key, val in communities.items():
if val not in community_to_actors:
community_to_actors[val] = []
community_to_actors[val].append(key)
# Sort based on the length of the list of actors
community_to_actors_sorted = sorted(community_to_actors.items(),
key=lambda element: len(element[1]),
reverse=True)
print("=" * 80)
print("COMMUNITIES:")
for community in community_to_actors_sorted[:10]:
print("ID {}, {} actors: {}".format(community[0], len(community[1]),
", ".join(community[1])))
print("=" * 80)
# Add as attribute to graph
for actor, community_id in communities.items():
graph.node[actor]['community_id'] = community_id
def output_graph_stats(g):
"""
Clique percolation, along with some other NetworkX statistics
about the generated graph that may be useful.
"""
stat_file = open(OUTPUT_STATS, 'w')
stat_file.write("NOTE: graph is treated as an unweighted graph" + "\n\n")
stat_file.write(str(nx.info(g)) + "\n\n")
stat_file.write("TRANSITIVITY: " + str(nx.transitivity(g)) + "\n\n")
clust_coeffs = nx.clustering(g)
stat_file.write("NODES WITH CLUST COEFF = 1: " + "\n")
for node in clust_coeffs:
if clust_coeffs[node] == 1.0:
stat_file.write(node + " " + str(g.neighbors(node)) + "\n")
stat_file.write("AVG CLUSTERING COEFFICIENT: " +
str(nx.average_clustering(g)) + "\n\n")
stat_file.write("DEGREE HISTOGRAM: " + str(nx.degree_histogram(g)) +
"\n\n")
stat_file.write("NODES WITH HIGHEST DEGREE CENTRALITY: " + "\n")
stat_file.write(
str(
sorted(nx.degree_centrality(g).items(),
key=operator.itemgetter(1),
reverse=True)[:5]) + "\n\n")
stat_file.write("4-CLIQUE COMMUNITIES (clique percolation): " + "\n")
for clique in nx.k_clique_communities(g, 4):
stat_file.write(str(clique) + "\n")
stat_file.write("\nMAXIMAL CLIQUES: " + "\n")
for clique in nx.find_cliques(g):
if len(clique) >= 3:
stat_file.write(str(clique) + "\n")
def all_users_group_evolution(self):
slots = []
for i in range(1,7):
G = self._graph_from_cursor('all_posts_s%d' % i)
communities = nx.k_clique_communities(G, 3)
communities = sorted(communities, key = lambda c: len(c), reverse = True)[:10]
slots.append(communities)
for i in range(5):
comm1 = slots[i]
comm2 = slots[i+1]
# remapped = []
# for c1 in comm1:
# remapped.append(max(comm2, key=lambda c2: len(set(c1) & set(c2))))
# slots[i+1] = remapped
cover = []
for i in range(1,6):
row = []
for j in range(10):
isl = len(set(slots[i-1][j]) & set(slots[i][j]))
n = len(slots[i-1][j])
f = isl*100/n
row.append(f)
cover.append(row)
for i in range(5):
print cover[i]
def user_clique(user):
G = get_graph(user)
c = maxrank(user)
print str(len(G.nodes())) + " nodes for user " + str(user)
if user in [345,0,21869,18844]:
return (user, [[c]])
# do not calculate for large graphs (it takes too long)
if len(G.nodes()) > tooManyNodesThreshold:
return (user, [[c]])
# find comunities using k_clique_communities()
listOfCircles = []
kCliqueComunities = list(nx.k_clique_communities(G,cliqueSize))
for community in kCliqueComunities:
# leave only relativly large communities
if len(community) >= tooLittleFriendsInCircleThreshold:
listOfCircles.append(list(community))
# if no prediction was created, use max pagerank friend
if len(listOfCircles) == 0:
return (user, [[c]])
else:
return (user, listOfCircles)
def plotUnweightedCommunities(G, k_clique, n_nodes, iw):
cls = nx.find_cliques(G)
communities = list(nx.k_clique_communities(G, k_clique, cliques=cls))
print(len(communities))
pos = nx.graphviz_layout(G) # positions for all nodes
plt.figure(figsize=(12, 12))
#colors = ["green","yellow","red","blue","pink","orange","gray","brown","black","white","purple","green","yellow","red","blue","pink","orange","gray","brown","black","white","purple"]
# colors = ["#ff0000","#ff8000","#ffbf00","#ffff00","#bfff00","#80ff00","#40ff00","#00ff00", "#00ff40", "#00ff80", "#00ffbf", "#00ffff", "#00bfff", "#0080ff", "#0040ff", "#0000ff", "#4000ff", "#8000ff", "#bf00ff", "#ff00ff", "#ff00bf", "#ff0080", "#ff0040","#ff0000","#ff8000","#ffbf00","#ffff00","#bfff00","#80ff00","#40ff00","#00ff00", "#00ff40", "#00ff80", "#00ffbf", "#00ffff", "#00bfff", "#0080ff", "#0040ff", "#0000ff", "#4000ff", "#8000ff", "#bf00ff", "#ff00ff", "#ff00bf", "#ff0080", "#ff0040"]
for i in range(len(communities)):
nx.draw_networkx_nodes(G,
pos,
nodelist=list(communities[i]),
node_color=colors[i % len(colors)])
nx.draw_networkx_edges(G, pos, width=0.5)
# labels
#nx.draw_networkx_labels(G,pos,font_size=10,font_family='sans-serif')
plt.axis('off')
plt.savefig("./communities/unweighted_" + "comm_" + "w" + str(iw) + "k" +
str(k_clique) + ".png") # save as png
plt.close()
def plotWeightedCommunities(G, W_lim, k_clique, n_nodes):
for i in range(0, n_nodes):
for j in range(i, n_nodes):
if (i != j):
print(i, j)
if (G[i][j]['weight'] < W_lim):
G.remove_edge(i, j)
cls = nx.find_cliques(G)
communities = list(nx.k_clique_communities(G, k_clique, cliques=cls))
print(len(communities))
pos = nx.graphviz_layout(G) # positions for all nodes
plt.figure(figsize=(12, 12))
#colors = ["green","yellow","red","blue","pink","orange","gray","brown","black","white","purple","green","yellow","red","blue","pink","orange","gray","brown","black","white","purple"]
for i in range(len(communities)):
nx.draw_networkx_nodes(G,
pos,
nodelist=list(communities[i]),
node_color=colors[i])
nx.draw_networkx_edges(G, pos, width=0.5)
# labels
#nx.draw_networkx_labels(G,pos,font_size=10,font_family='sans-serif')
plt.axis('off')
plt.savefig("comm_w_" + str(W_lim) + "k" + str(k_clique) +
".png") # save as png
plt.close()
def singleDetection(twitter_api, group):
#handle a single group
#delete repeated user ids
group=list(set(group))
G=nx.Graph()
#construct graph for the group by finding all the edges
for user_id in group:
friends_ids, followers_ids = get_friends_followers_ids(twitter_api, user_id=user_id)
friends_ids_str=[str(friend_id) for friend_id in friends_ids]
followers_ids_str=[str(follower_id) for follower_id in followers_ids]
vertices = list(set(friends_ids_str) & set(group) & set(followers_ids_str)) #find nodes connected to current node in the group
edges=[(str(user_id), vertex)for vertex in vertices]
G.add_edges_from(edges)
#find communites using CPM
c=[]
k=0
for size in range(3,6):
c_original=list(nx.k_clique_communities(G, size))
if len(c_original)>0:
c_listed=[list(froz) for froz in c_original]
c=c_listed #if find communities using larger k, drop previous ones
k=size
else:
break
return G.nodes(), G.edges(), c
def cliqueData(self, cnumber, data, header, sg, k):
for n in data:
data[n] += [0, 0, 0]
com = list(nx.k_clique_communities(sg, k))
header += [
str(k) + '_clique_size',
str(k) + '_clique_edges',
str(k) + '_clique_density'
]
for c in com:
count = self.edgesCount(list(c))
for n in c:
if len(c) > data[n][-3]:
data[n][-3] = len(c)
data[n][-2] = count
data[n][-1] = count / (data[n][-3] * data[n][-3] -
data[n][-3])
header += [str(k) + '_min_edges', str(k) + '_min_edges_ratio']
for n in data:
if data[n][-1] > 0:
data[n].append(np.ceil(data[n][-3] * cnumber[n] / 2))
data[n].append(data[n][-3] / data[n][-1])
else:
data[n] += [0, 0]
return data, header
def k_comm(Gn):
comm_list_G = list(nx.k_clique_communities(Gn, 3)) # k=3
comm_list = []
for item in comm_list_G:
item = map(int, item)
comm_list.append(list(item))
return comm_list
def plotWeightedCommunities(G, W_lim, k_clique, n_nodes):
for i in range(0,n_nodes):
for j in range(i,n_nodes):
if(i!=j):
if(G[i][j]['weight'] < W_lim):
G.remove_edge(i,j)
cls = nx.find_cliques(G)
communities = list(nx.k_clique_communities(G,k_clique ,cliques = cls))
print(len(communities))
pos=nx.graphviz_layout(G) # positions for all nodes
plt.figure(figsize=(12,12))
#colors = ["green","yellow","red","blue","pink","orange","gray","brown","black","white","purple","green","yellow","red","blue","pink","orange","gray","brown","black","white","purple"]
for i in range(len(communities)):
nx.draw_networkx_nodes(G,pos,nodelist=list(communities[i]),node_color=colors[i])
nx.draw_networkx_edges(G,pos,width=0.5)
# labels
nx.draw_networkx_labels(G,pos,font_size=10,font_family='sans-serif')
plt.axis('off')
plt.savefig("comm_w_"+str(W_lim)+"k"+str(k_clique)+".png") # save as png
plt.close()
def popular_group_centralities():
path = '../sna/all_posts_s5.graphml'
G = nx.read_graphml(path)
cliques = nx.k_clique_communities(G, 3)
cliques = list(cliques)
popular_clique = sorted(cliques, key=lambda x:len(x), reverse=True)[0]
G = G.subgraph(popular_clique)
degree = nx.degree_centrality(G)
pagerank = nx.pagerank(G)
closeness = nx.closeness_centrality(G)
betweeness = nx.betweenness_centrality(G)
sd = pandas.Series(degree)
sp = pandas.Series(pagerank)
sc = pandas.Series(closeness)
sb = pandas.Series(betweeness)
print sd.describe()
print sp.describe()
print sc.describe()
print sb.describe()
sd.plot.hist(bins=100).get_figure().savefig('../sna/pg_degree.png')
sp.plot.hist(bins=100).get_figure().savefig('../sna/pg_pagerank.png')
def plotUnweightedCommunities(G, k_clique, n_nodes,iw):
cls = nx.find_cliques(G)
communities = list(nx.k_clique_communities(G,k_clique ,cliques = cls))
print(len(communities))
pos=nx.graphviz_layout(G) # positions for all nodes
plt.figure(figsize=(12,12))
#colors = ["green","yellow","red","blue","pink","orange","gray","brown","black","white","purple","green","yellow","red","blue","pink","orange","gray","brown","black","white","purple"]
# colors = ["#ff0000","#ff8000","#ffbf00","#ffff00","#bfff00","#80ff00","#40ff00","#00ff00", "#00ff40", "#00ff80", "#00ffbf", "#00ffff", "#00bfff", "#0080ff", "#0040ff", "#0000ff", "#4000ff", "#8000ff", "#bf00ff", "#ff00ff", "#ff00bf", "#ff0080", "#ff0040","#ff0000","#ff8000","#ffbf00","#ffff00","#bfff00","#80ff00","#40ff00","#00ff00", "#00ff40", "#00ff80", "#00ffbf", "#00ffff", "#00bfff", "#0080ff", "#0040ff", "#0000ff", "#4000ff", "#8000ff", "#bf00ff", "#ff00ff", "#ff00bf", "#ff0080", "#ff0040"]
for i in range(len(communities)):
nx.draw_networkx_nodes(G,pos,nodelist=list(communities[i]),node_color=colors[i%len(colors)])
nx.draw_networkx_edges(G,pos,width=0.5)
# labels
nx.draw_networkx_labels(G,pos,font_size=10,font_family='sans-serif')
plt.axis('off')
plt.savefig("./communities/unweighted_"+"comm_"+"w"+str(iw)+"k"+str(k_clique)+".png") # save as png
plt.close()
def test_isolated_K5():
G = nx.Graph()
G.add_edges_from(combinations(range(0, 5), 2)) # Add a five clique
G.add_edges_from(combinations(range(5, 10), 2)) # Add another five clique
c = list(nx.k_clique_communities(G, 5))
assert_equal(set(c),
set([frozenset([0, 1, 2, 3, 4]),
frozenset([5, 6, 7, 8, 9])]))
def graph_communities(self):
communities = nx.k_clique_communities(self.G, 6)
communities_index = {}
for i, group in enumerate(communities):
for member in group:
communities_index[member] = i + 1
return communities_index
def kcliques_to_html(G):
kcliques = list(networkx.k_clique_communities(G, 2))
#pdb.set_trace()
kcliques_colors = [random.randint(0,1000000)*len(l) for l in kcliques]
for clique in kcliques:
color = kcliques_colors[kcliques.index(clique)]
for node in clique:
G.node[node]['kclique'] = color
def clique(gr):
G=g_load(gr)
li=list(list(networkx.k_clique_communities(G,2))[0])
mv=majority_vote.list_majority(li,G)
#print(mv)
#s=sorted(mv.items(),key=operator.itemgetter(1),reverse=True)
return mv
def getCliques(self, G='default', nclique=4):
if G == 'default':
G = self.G
cliques = list(nx.k_clique_communities(G, nclique))
return cliques
def get_coalesced_communities(g, no_overlap=False):
average_clique_size = int(get_average_clique_size(g))
communities = map(lambda c: Community(c), nx.k_clique_communities(g, average_clique_size))
communities = coalesce_communities(communities, .7)
communities2 = map(lambda c: Community(c), nx.k_clique_communities(g, 3))
communities2 = coalesce_communities(communities2, .7)
communities = communities + filter(lambda c: len(c.members) <= 10, communities2)
communities = coalesce_communities(communities, .7)
communities = filter(lambda c: len(c.members) > 1, communities)
if not no_overlap:
return communities
members = set()
overlapping_subs = set()
for c in communities:
for s in c.members:
if s in members:
overlapping_subs.add(s)
else:
members.add(s)
for overlapped in overlapping_subs:
best_weight = 0
best_comm = None
overlapped_comms = filter(lambda c: overlapped in c.members, communities)
for community in overlapped_comms:
source = overlapped
weight = 0
for target in community.members:
if g.has_edge(source, target):
weight += g[source][target]['weight']
if weight > best_weight:
best_weight = weight
best_comm = community
for c in overlapped_comms:
c.members.remove(overlapped)
best_comm.members.add(overlapped)
return communities
def graph_communities(self):
communities = nx.k_clique_communities(self.G, 6)
communities_index = {}
for i, group in enumerate(communities):
for member in group:
communities_index[member] = i + 1
return communities_index
def nxCommunity():
import networkx as nx
import matplotlib.pyplot as plt
G = nx.connected_caveman_graph(6, 4)
#first compute the best partition
c = list(nx.k_clique_communities(G, 5))
print c
nx.draw(G)
plt.show()
def main():
# reads from file and building the LastFm network
artists, net = ma.read_data()
listening = ma.get_node_listening(artists)
print_vectors(artists)
communities = list(nx.k_clique_communities(net, 5))
community_statistics(communities, 'k-clique')
community_listening(communities, listening, artists, 'k-clique')
def report_communities(graph):
communities = {node: cid + 1 for cid, community in enumerate(networkx.k_clique_communities(graph, 3)) for node in
community}
pos = networkx.circular_layout(graph)
networkx.draw(graph, pos, font_size=8,
labels={v: str(v) for v in graph},
cmap=plt.get_cmap("rainbow"),
node_color=[communities[v] if v in communities else 0 for v in graph])
plt.savefig("communities.png")
def find_k_cliques(self, k = 3):
for kc in nx.k_clique_communities(self.G, k):
self.k_cliques.append(set(kc))
self.k_clique_groups = self.find_common_subsets(self.k_cliques)
if self.verbose:
print 'K-CLIQUES'
print 'Found %s k-cliques' %(len(self.k_cliques))
print 'Found %s k-clique groups' %(len(self.k_clique_groups))
return len(self.k_clique_groups)
def test_zachary():
z = nx.karate_club_graph()
# clique percolation with k=2 is just connected components
zachary_k2_ground_truth = set([frozenset(z.nodes())])
zachary_k3_ground_truth = set([frozenset([0, 1, 2, 3, 7, 8, 12, 13, 14,
15, 17, 18, 19, 20, 21, 22, 23,
26, 27, 28, 29, 30, 31, 32, 33]),
frozenset([0, 4, 5, 6, 10, 16]),
frozenset([24, 25, 31])])
zachary_k4_ground_truth = set([frozenset([0, 1, 2, 3, 7, 13]),
frozenset([8, 32, 30, 33]),
frozenset([32, 33, 29, 23])])
zachary_k5_ground_truth = set([frozenset([0, 1, 2, 3, 7, 13])])
zachary_k6_ground_truth = set([])
assert set(k_clique_communities(z, 2)) == zachary_k2_ground_truth
assert set(k_clique_communities(z, 3)) == zachary_k3_ground_truth
assert set(k_clique_communities(z, 4)) == zachary_k4_ground_truth
assert set(k_clique_communities(z, 5)) == zachary_k5_ground_truth
assert set(k_clique_communities(z, 6)) == zachary_k6_ground_truth
def spatial_major(in_folder, cliqueThresh):
for file in os.listdir(in_folder):
if file != '.DS_Store': #weird MAC thing
path = in_folder + file
G = getJsonNet(path)
G = nx.Graph(G) #can't do cliques on directed nets
if G.order() > 0:
n = nx.graph_clique_number(G)
if n > cliqueThresh:
print file
for c in nx.k_clique_communities(G, n):
print list(c)
def k_clique_CD(graph, cut_str, k_range):
print '########\tK-CLIQUE CD WITH K RANGE = ' + str(k_range) + '\t########'
# num_cliques = nx.number_of_cliques(actor_network_cut3)
# print len(num_cliques)
for k in k_range:
print '\n########\t'+str(k)+'-CLIQUE CD '+cut_str+' START\t########'
output = nx.k_clique_communities(graph, k)
output_communities_list = list(map(list, output)) # per covertire tutte le communities in liste
print '########\t'+str(k)+'-CLIQUE CD '+cut_str+' COMPLETE\t########'
output_file = OUTPUT_DIRECTORY_KCLIQUE+"/kclique_actor_"+str(k)+"_"+cut_str+".txt"
print '> numero di community trovate: ' + str(len(output_communities_list))
serialize_communities(output_communities_list, output_file)
def make_modules_multik(graph, k=None):
"""make modules with networkx k-clique communities and annotate network"""
if k is None:
k = [2, 3, 4, 5, 6]
communities = dict()
for k_val in list(k):
cliques = list(nx.k_clique_communities(graph, k_val))
cliques = [list(i) for i in cliques]
communities[k_val] = cliques
for i, clique in enumerate(cliques):
for node in clique:
graph.node[node]['k_' + str(k_val)] = i
return graph, {k: list(v) for k, v in communities.iteritems()}
def k_clique_analysis(G,k_list,out_path):
for k in k_list:
c = list(nx.k_clique_communities(G, k))
print(type(c[0]))
quit()
c = list(map(list,c))
out = open(out_path + str(k) + "_clique.dat","w")
for community in c:
out.write("%d\t[" % c.index(community))
for node in community:
out.write('"%s",' % node)
out.write("]\n")
out.close()
def main():
# reads from file and building the LastFm network
artists, net = ma.read_data()
listening = ma.get_node_listening(artists)
genre_vectors, artist_vector = build_vectors(artists)
communities_kcliques = list(nx.k_clique_communities(net, 5))
community_statistics(communities_kcliques, 'k-clique')
community_listening(communities_kcliques, listening, artists, 'k-clique', genre_vectors, artist_vector)
communities_demon = read_demon()
community_statistics(communities_demon, 'demon')
community_listening(communities_demon, listening, artists, 'demon', genre_vectors, artist_vector)
def findCommunites(threshold=0.5, sector=None, k=5, force=False): th = re.sub(r'([0-9]*)\.([0-9]*)',r'\1\2',str(threshold)) if sector != None: graphInFilename = PROCESSED_FILE_LOC + PREFIX + CRITERIA + "stock_graph_nx_"+sector+"_th"+th+".xml" graphOutFilename = PROCESSED_FILE_LOC + PREFIX + CRITERIA + "stock_communities_nx_"+sector+"_th"+th+"_k"+str(k)+".xml" outFilename = PROCESSED_FILE_LOC + PREFIX + CRITERIA + "stock_communities_nx_"+sector+"_th"+th+"_k"+str(k)+".csv" else: graphInFilename = PROCESSED_FILE_LOC + PREFIX + CRITERIA + "stock_graph_nx_th"+th+".xml" graphOutFilename = PROCESSED_FILE_LOC + PREFIX + CRITERIA + "stock_communities_nx"+"_th"+th+"_k"+str(k)+".xml" outFilename = PROCESSED_FILE_LOC + PREFIX + CRITERIA + "stock_communities_nx"+"_th"+th+"_k"+str(k)+".csv" print "reading graph from file: ", graphInFilename print "writing graph with community info to file: ", outFilename print "writing community details in csv format to file: ", outFilename if force or not isfile(graphOutFilename): g = nx.read_graphml(graphInFilename) #freq = findFreqOfCliquesInGraph(g) #plotHistFromDict(freq) comm = nx.k_clique_communities(g, k) communities = [] for c in comm: communities.append(c) numCommunities = len(communities) print "number of communities found: ", numCommunities colors = range(numCommunities) i = 0 for c in communities: for v in c: g.node[v]['cluster'] = colors[i] + 1 i += 1 nx.write_graphml(g, graphOutFilename) import csv with open(outFilename, "wb") as f: writer = csv.writer(f, delimiter='|', quotechar="'", quoting=csv.QUOTE_MINIMAL) writer.writerow(["sector", "symbol", "name", "cluster"]) for v in g: writer.writerow([g.node[v]['sector'], g.node[v]['symbol'], g.node[v]['name'], g.node[v]['cluster']]) results = PROCESSED_FILE_LOC + "results.csv" with open(results, "a") as f1: f1.write(str(dt.datetime.today()) + "," + outFilename + "," + str(numCommunities) + "," + str(calculateModularity(graphOutFilename)) + "\n") drawGraph(graphOutFilename, "gt")
def predict_user(G,
cliqueSize=5,
tooLittleFriendsInCircleThreshold=10,
#tooManyNodesThreshold=220
):
# find comunities using k_clique_communities()
listOfCircles = []
kCliqueComunities = list(nx.k_clique_communities(G,cliqueSize))
for community in kCliqueComunities:
# leave only relativly large communities
if len(community) >= tooLittleFriendsInCircleThreshold:
listOfCircles.append(list(community))
return listOfCircles
def DetectionComNX(graphe,path):
import networkx as nx
graph=nx.read_edgelist(path+graphe)
kcliques=nx.k_clique_communities(graph,3,nx.find_cliques(graph))
c=list(kcliques)
commClus={}
for indx,val in enumerate(c):
temp=[]
for j in val:
temp.append(int(j.replace("n","")))
commClus[indx]=temp
return commClus
def calculateModularity():
#very slow!, exp(N) complexity
community_growth = []
communities = []
max_cliques = 20
for k in tqdm(range(max_cliques),desc='Running k-clique modularity algorithm'):
communities.append(list(nx.k_clique_communities(G_gn,k+2)))
community_growth = [len(list(x)) for x in communities]
plt.plot([k for k in range(2,max_cliques+2)],community_growth,'*')
plt.xlabel('clique size (k)')
plt.ylabel('Qty Clique Communities')
plt.title('Number of k-clique communities vs clique size via percolation method')
plt.grid()
plt.show()
return [k for k in range(2,max_cliques+2)],communities
def get_comunidades(grafico):
comunidades = list(nx.k_clique_communities(grafico.to_undirected, 3, nx.find_cliques(grafico.to_undirected()))) #si todo salio bien, los sets de miembros son solamente de ids de usuario sin numeros enteros agregados
g = nx.Graph() #ahora volvemos a crear un grafico para visualizar todo
for i in comunidades:
g.add_nodes_from(i)
for i in comunidades:
g.add_edges_from(list(permutations(i,2)))
pos = nx.spring_layout(g)
plt.axis('off')
nx.draw_networkx(g, pos)
plt.show()
return comunidades
def make_modules(graph, k=3, prefix="module"):
"""make modules with networkx k-clique communities and annotate network"""
premodules = list(nx.k_clique_communities(graph, k))
# reverse modules so observations will be added to smallest modules
premodules = list(enumerate(premodules))
premodules.reverse()
modules = dict()
seen = set()
for i, module in premodules:
# process module
module = module-seen
seen = seen | module
modules[prefix+"_"+str(i)] = module
for node in module:
graph.node[node][prefix] = i
return graph, modules
def week4():
path = "D:\Dropbox\PhD\My Work\Algorithms\@Machine Learning\Lectures\Social Network Analysis\Week 4_Community Structure\wikipedia.gml"
wiki = nx.read_gml(path)
wiki = wiki.to_undirected()
# cliques
cid, cls = max(nx.node_clique_number(wiki).iteritems(), key=operator.itemgetter(1))
print 'clique', cid, ' size:', cls
# k-cores
kcs = nx.k_core(wiki)
print 'k-core size:', len(kcs.node)
# community
cs = list(nx.k_clique_communities(wiki, 2))
ratio = (len(cs[0]) + 0.0) / len(wiki.node)
print 'community ratio:', ratio
def get_statistics():
"""
uses data statistics to find the most important papers in the collection.
"""
with open(MAIN_FOLDER + "network.pkl", "r") as f:
network = pickle.load(f)
betweenness_dict = networkx.betweenness_centrality(network.to_undirected())
sorted_betweenness = sorted(betweenness_dict.items(), key=operator.itemgetter(1), reverse=True)
betweenness = [x[0] for x in sorted_betweenness[:5]]
pagerank_dict = networkx.pagerank(network.to_undirected())
sorted_pagerank = sorted(pagerank_dict.items(), key=operator.itemgetter(1), reverse=True)
pagerank = [x[0] for x in sorted_pagerank[:5]]
hits_dict = networkx.hits(network.to_undirected())
sorted_hits = sorted(hits_dict[0].items(), key=operator.itemgetter(1), reverse=True)
hits = [x[0] for x in sorted_hits[:5]]
in_degree_dict = network.in_degree()
sorted_in_degree = sorted(in_degree_dict.items(), key=operator.itemgetter(1), reverse=True)
in_degree = [x[0] for x in sorted_in_degree[:5]]
community_dict = []
for k in xrange(20):
community_dict += list(networkx.k_clique_communities(network.to_undirected(), 21 - k))
if community_dict:
break
modules = []
for index, community in enumerate(community_dict):
modules.append([])
for p in community:
modules[index].append(p)
statistics = {'in_degree': in_degree, 'betweenness': betweenness, 'hits': hits, 'pagerank': pagerank,
'modules': modules}
with open(MAIN_FOLDER + "statistics.pkl", "wa") as f:
pickle.dump(statistics, f)
def main():
"""docstring for main"""
g = build_graph(sys.argv[1])
global nodes_
global nrows_, ncols_
cliques = nx.k_clique_communities(g_, 5)
img = np.zeros(shape=(nrows_, ncols_), dtype=np.uint16)
for i, c in enumerate(cliques):
pos = [nodes_[x] for x in c]
# pos = np.array( pos )
print(pos)
if len(pos) < 4:
continue
for p in pos:
cv2.circle(img, p, 1, 10 * i)
# cv2.putText( img, str(i), p, cv2.FONT_HERSHEY_COMPLEX, 0.1, i )
# cv2.polylines( img, np.int32( [ pos ] ), False, i )
plt.imshow(img, cmap='gray', interpolation='none', aspect='auto')
plt.colorbar()
plt.savefig('corr.png')
def main():
"""docstring for main"""
g = build_graph( sys.argv[1] )
global nodes_
global nrows_, ncols_
cliques = nx.k_clique_communities( g_, 5 )
img = np.zeros( shape=(nrows_,ncols_), dtype=np.uint16 )
for i, c in enumerate(cliques):
pos = [ nodes_[x] for x in c ]
# pos = np.array( pos )
print( pos )
if len(pos) < 4:
continue
for p in pos:
cv2.circle( img, p, 1, 10*i )
# cv2.putText( img, str(i), p, cv2.FONT_HERSHEY_COMPLEX, 0.1, i )
# cv2.polylines( img, np.int32( [ pos ] ), False, i )
plt.imshow( img, cmap='gray', interpolation = 'none', aspect = 'auto' )
plt.colorbar( )
plt.savefig( 'corr.png' )
def clusterGraph(G):
print("Clustering and Colorizing Graph")
c = list(nx.k_clique_communities(G, COMMUNITY_SIZE=10))
usedColors = list()
for cluster in c:
goldenRatio = 0.618033988749895
h = random.random()
color = "0"
while color in usedColors or color == "0":
h += goldenRatio
h %= 1
rgb = colorsys.hsv_to_rgb(h, 0.5, 0.95)
color = "#{0:02x}{1:02x}{2:02x}".format(int(rgb[0] * 255),
int(rgb[1] * 255),
int(rgb[2] * 255))
usedColors.append(color)
for nodeID in cluster:
print("Giving", nodeID, "Color", color)
G.node[nodeID]['color'] = color
print("Used Colors:", usedColors)
return G
def printCommunities(graph):
communities = {}
for community_id, community in enumerate(nx.k_clique_communities(graph, 3)):
for node in community:
communities[node] = community_id + 1
community_actors = {}
for key, val in communities.items():
if val not in community_actors:
community_actors[val] = []
community_actors[val].append(key)
print("\nCommunities:")
print("\t5 biggest communities size: ", end="")
for comm in sorted(community_actors.items(), key= lambda item: len(item[1]), reverse=True)[:5]:
print(len(comm[1]), end=",")
print("\n\tMembers of biggest community:")
for comm in sorted(community_actors.items(), key=lambda item: len(item[1]), reverse=True)[:1]:
print("\t{}".format(comm[1]))
for actor, community_id in communities.items():
graph.node[actor]['community_id'] = community_id
def get_ego_kclique_communities(ego):
if ego in [5881, 12800]:
print 'In get_ego_kclique_communities, skipping ego', ego
return {}
ego_kcc_dmp = join(DATA_DIR, 'cliques', 'kcc_%s.zip'%ego)
if os.path.exists(ego_kcc_dmp):
with zipfile.ZipFile(ego_kcc_dmp, mode='r') as zf:
ccs = json.loads(zf.read('files1.json'))
else:
ego_cliques = get_ego_cliques(ego)
print 'Processing k-clique communities: nx.find_cliques, ego:', ego
G = load_ego_graph(ego)
ccs = [list(cc) for cc in nx.k_clique_communities(G, 6, cliques=ego_cliques)]
try:
import zlib
compression = zipfile.ZIP_DEFLATED
except:
compression = zipfile.ZIP_STORED
json_rslt = json.dumps(ccs, ensure_ascii=False, indent=True)
with zipfile.ZipFile(ego_kcc_dmp, mode='w') as zf:
zf.writestr('files1.json', json_rslt, compress_type=compression)
return ccs
def all_users_timeslots(self):
stats = []
for i in range(1,7):
G = self._graph_from_cursor('all_posts_s%d' % i)
for nd in G.nodes():
G.node[nd]['color'] = 0
j = 1
cl = []
for clique in nx.k_clique_communities(G, 3):
cl.append(clique)
for nd in clique:
G.node[nd]['color'] = j
j += 1
n = len(G.nodes())
e = len(G.edges())
d = pandas.Series(nx.degree_centrality(G)).mean()
eg = pandas.Series(nx.eigenvector_centrality(G, max_iter=1000)).mean()
closeness = {}
for node in random.sample(G.nodes(),100):
closeness[node] = nx.closeness_centrality(G, node)
c = pandas.Series(closeness).mean()
b = pandas.Series(nx.betweenness_centrality(G, k=20)).mean()
stats.append((n,e,d,eg,c,b,cl))
nx.write_graphml(G, '../sna/all_posts_s%d.graphml'%i)
print 'nodes, edges, m. degree, m. eigenvector, m. closeness, m. betweeness'
for s in stats:
print '%s, %s, %s, %s, %s, %s' % (s[0], s[1], s[2], s[3], s[4], s[5])
def calculateSimilarities(self): """ TODO: Break up graph into communities, if a user A belongs to a community C, similarities[A] = list of (all other nodes in C, score=1) tuples """ min_community_size = 5 # Calculate similarities and populate similarities dict here print "Finding CommunitySimilarity! Yay!" communities = list(nx.k_clique_communities(self.yelpGraph, min_community_size)) print "Number of test communities: %d" % len(communities) total_size = 0 for c in communities: #print len(c) total_size += len(c) print "Total size: %d" % total_size # for each community count = 0 for community in communities: print "We've entered a new community!" # for every node in the community for user in community: count += 1 self.similarities[user] = list() # make a list of all other tuples that are in the community (skip self) for friend in community: if friend != user: self.similarities[user].append((friend, 1)) print "The count is %d" % count print "Number of pairs: %d .... should be equal to 2995" % len(self.similarities) # Write similarity map to file pickle.dump(self.similarities, open( "communitySim.p", "wb" ) )
if not G.has_edge(terms[i],
terms[j]): # add edge if it is not there already
G.add_edge(terms[i], terms[j])
G.edge[terms[i]][terms[j]]['freq'] = 1 # the count is 1
else:
G.edge[terms[i]][terms[j]][
'freq'] += 1 # existing edge, increment the count
f.close()
#remove all edges with a freq less than 3
remove = []
for N1, N2 in G.edges(): # for each edge
if G.edge[N1][N2]['freq'] < 3:
remove.append((N1, N2)) # add it to the 'remove' list
G.remove_edges_from(remove) # filter
#find all maximal cliques
cliques = list(nx.find_cliques(G))
sorted_cliques = sorted(cliques, key=len, reverse=True) # sort cliques by size
print(sorted_cliques[0])
#find all k-cliques communities
kcliques = list(nx.k_clique_communities(G, 3))
sorted_cliques = sorted(kcliques, key=len,
reverse=True) # sort cliques by size
print(sorted_cliques[0])
tupl = sorted_Pr[ii]
print tupl
#Hits and Authorities
h, a = nx.hits(G_hybrid)
number = 5
print "hubs nodes"
sorted_h = sorted(h.items(), key=operator.itemgetter(1), reverse=True)
for ii in range(number):
tupl = sorted_h[ii]
print tupl
number = 5
print "authority nodes"
sorted_a = sorted(a.items(), key=operator.itemgetter(1), reverse=True)
for ii in range(number):
tupl = sorted_a[ii]
print tupl
#Cliques
ratioDenominator = 1000
smallestSize = nx.number_of_nodes(G_hybrid) / ratioDenominator
communities = list(nx.k_clique_communities(G_hybrid, smallestSize))
for community in communities:
print list(community)
for userId in list(submission['UserId']):
# read graph
filename = str(userId) + '.egonet'
G = read_nodeadjlist(egonetFolderName + filename)
# do not calculate for large graphs (it takes too long)
if len(G.nodes()) > tooManyNodesThreshold:
print('skipping user ' + str(userId))
continue
else:
print('predicting for user ' + str(userId))
# find comunities using k_clique_communities()
listOfCircles = []
kCliqueComunities = list(nx.k_clique_communities(G,cliqueSize))
for community in kCliqueComunities:
# leave only relativly large communities
if len(community) >= tooLittleFriendsInCircleThreshold:
listOfCircles.append(list(community))
# populate prediction string
predictionString = ''
for circle in listOfCircles:
for node in circle:
predictionString = predictionString + str(node) + ' '
predictionString = predictionString[:-1] + ';'
predictionString = predictionString[:-1]
# if no prediction was created, use 'all friends in one circle'
if len(listOfCircles) > 0:
for c in communities:
if name in c:
nodes.append({
'name':name,
'group':g
})
g = g + 1
return nodes
G = nx.Graph()
topAuthorNames = [a[0] for a in authorsCounter.most_common(50)] # top 40 authors
G.add_nodes_from(topAuthorNames) # assign nodes, edges are assigned in cooccurrence_links()
collaborators = collaborators_matrix(authors)
cooccurrences = {'nodes':[], 'links':[]}
cooccurrences['links'] = cooccurrence_links(authorsCounter, collaborators)
communities=list(nx.k_clique_communities(G,3)) # detect communities and than assign groups
cooccurrences['nodes'] = cooccurrence_nodes(authorsCounter, 50, communities)
# dest = '/Users/asif/Sites/scholars/neuromodulation/cooccurrences.json'
# f = open(dest, 'w+')
# f.write(json.dumps(cooccurrences))
# f.close()
###########################################################
# Edge-bindings collaborators
###########################################################
# Edge bindings
def collaborators_bindings(groupCounters, collaborators):
mostfreq = [x[0] for x in groupCounters.most_common(50)]
collaborators_bindings = []
def calculate_k_clique(G, K):
communities = nx.k_clique_communities(G, K)
if verbose:
print "k-cliques " + str(K)
write_csv_groups('./data/results/kClique' + str(K) + '.csv', communities)
#g.remove_bridges("/home/kazem/weakc/out",0,",")
g.export_G_to_csv(1)
#diam_ = nx.algorithms.distance_measures.diameter(g.G)
#print "diameter of G: %d" %diam_
if(0):
g = WCG(100)
edge_thr = 1800
#let's read the contact duration between pairs
reader = csv.reader(open("/Users/kazemjahanbakhsh/Downloads/graph_cd.txt"), delimiter=',')
for line in reader:
if float(line[2]) > edge_thr:
g.G.add_edge(int(line[0]),int(line[1]),weight=float(line[2]))
#plot G
#g.plot_graph(g.G)
c = list(nx.k_clique_communities(g.G, 4))
print c
if(0):
g = WCG(100)
g.build_csv("/home/kazem/data/FB/facebook-links.txt", 0, "\t")
#g.findWhiskers("/home/kazem/weakc/out","/home/kazem/weakc/export.csv",0,",")
#H = g.G.subgraph([60512, 60513, 60514, 60515, 60516, 60517, 60518, 60519, 60520, 60508, 60509, 60510, 60511])
#H = g.G.subgraph([63008, 63687, 54988, 54989, 54990, 54991, 55065, 55066, 63356, 63357, 63007])
#H = g.G.subgraph([54380, 54381, 54382, 54383, 54384, 54385, 54386, 54387, 54388, 35581])
#H = g.G.subgraph([62496, 60099, 60100, 45811, 45812, 45813, 50652, 61054, 61055])
#H = g.G.subgraph([48870, 48871, 48872, 49773, 49774, 50609, 50610, 50611, 50612])
H = g.G.subgraph([45958, 45959, 45960, 45961, 45962, 45963, 49551, 49082, 49083, 49084, 49085, 49086, 59970, 59971, 51115, 51116, 62238, 62239, 61477, 55530, 61143, 59418, 59419, 59583, 59055, 59052, 59053, 59054, 41127, 47426, 47427, 47428, 47429, 57631, 49120, 49121, 49122, 54528, 49119, 63321, 59490, 52851, 52852, 63483, 52888, 52889, 52890, 59523, 59522, 54816, 60288, 62493, 62437, 60287, 59792, 59793, 59794, 59790, 59791, 37891, 37892, 15773, 36262, 59569, 60724, 60614, 28727, 61408, 55076, 55075, 29972, 48870, 48871, 48872, 49773, 49774, 50609, 50610, 50611, 50612, 62496, 60099, 60100, 45811, 45812, 45813, 50652, 61054, 61055, 54380, 54381, 54382, 54383, 54384, 54385, 54386, 54387, 54388, 35581, 63008, 63687, 54988, 54989, 54990, 54991, 55065, 55066, 63356, 63357, 63007, 60512, 60513, 60514, 60515, 60516, 60517, 60518, 60519, 60520, 60508, 60509, 60510, 60511, 57953, 57801, 57802, 57946, 53501, 53502, 53503])
if(0):
g = WCG(2048)
g.build_csv("/Users/kazemjahanbakhsh/Downloads/facebook-links.txt", 0, "\t")
def community(G,number):
c = list(nx.k_clique_communities(G,number))
return c