def local_search(graph,
part_init=None,
weight='weight',
resolution=1.,
randomize=None):
if type(graph) != nx.Graph:
raise TypeError("Bad graph type, use only non directed graph")
# special case, when there is no link
# the best partition is everyone in its community
if graph.number_of_edges() == 0:
part = dict([])
for node in graph.nodes():
part[node] = node
return [part]
current_graph = graph.copy()
status = Status()
status.init(current_graph, weight, part_init)
__one_level(current_graph, status, weight, resolution, randomize)
partition = __renumber(status.node2com)
return partition
def contribution_nodeneighbor(partition, graph, weight='weight'):
contribution = dict([])
participation = dict([])
node_neighbor = dict([])
newstatus = Status()
newstatus.init(graph, weight, partition)
links = newstatus.total_weight
if links == 0:
raise ValueError("A graph without link has an undefined modularity")
for node in graph:
com_node = newstatus.node2com[node]
deg_node = newstatus.gdegrees.get(node, 0.)
deg_com = newstatus.degrees.get(com_node, 0.)
neigh_communities = __neighcom(node,
graph,
newstatus,
weight_key=weight)
if neigh_communities:
contribution[node] = round(
neigh_communities.get(com_node, 0) -
(0.5 * deg_node * deg_com) / links, 4)
for com, dnc in neigh_communities.items():
participation[node] = participation.get(
node, 1) - (dnc / deg_node)**2
if com != com_node:
if node_neighbor.has_key(node):
node_neighbor[node].append(com)
else:
node_neighbor[node] = [com]
if node_neighbor.has_key(node):
pass
else:
node_neighbor[node] = [com_node]
return contribution, participation, node_neighbor
def node_contribution(partition, graph, weight='weight'):
indegree = dict([])
contribution = dict([])
links = graph.size(weight=weight)
newstatus = Status()
newstatus.init(graph, weight, partition)
if links == 0:
raise ValueError("A graph without link has an undefined modularity")
for node in graph:
com = partition[node]
for neighbor, datas in graph[node].items():
edge_weight = datas.get(weight, 1)
if partition[neighbor] == com:
if neighbor != node:
indegree[node] = indegree.get(node,
0.) + float(edge_weight)
contribution[node] = round(
indegree[node] -
(0.5 * newstatus.gdegrees[node] * newstatus.degrees[com]) / links,
4)
return contribution
def generate_dendrogram(graph,
inc_fnc,
part_init=None,
weight='weight',
randomize=False):
"""Find communities in the graph and return the associated dendrogram
A dendrogram is a tree and each level is a partition of the graph nodes.
Level 0 is the first partition, which contains the smallest communities,
and the best is len(dendrogram) - 1. The higher the level is, the bigger
are the communities
"""
# special case, when there is no link
# the best partition is everyone in its community
if graph.number_of_edges() == 0:
part = dict([])
for node in list(graph.nodes()):
part[node] = node
return [part]
current_graph = graph.copy()
status = Status()
status.init(current_graph, weight, part_init)
status_list = list()
changed = one_level(current_graph, inc_fnc, status, weight, randomize)
partition = renumber(status.node2com)
status_list.append(partition)
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
while False:
changed = one_level(current_graph, inc_fnc, status, weight, randomize)
if not changed:
break
partition = renumber(status.node2com)
status_list.append(partition)
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
return status_list[:]
def generate_dendrogram(graph,
part_init=None,
weight='weight',
resolution=1.,
randomize=None):
"""Find communities in the graph and return the associated dendrogram
A dendrogram is a tree and each level is a partition of the graph nodes.
Level 0 is the first partition, which contains the smallest communities,
and the best is len(dendrogram) - 1. The higher the level is, the bigger
are the communities
Parameters
----------
graph : networkx.Graph
the networkx graph which will be decomposed
part_init : dict, optional
the algorithm will start using this partition of the nodes. It's a
dictionary where keys are their nodes and values the communities
weight : str, optional
the key in graph to use as weight. Default to 'weight'
resolution : double, optional
Will change the size of the communities, default to 1.
represents the time described in
"Laplacian Dynamics and Multiscale Modular Structure in Networks",
R. Lambiotte, J.-C. Delvenne, M. Barahona
Returns
-------
dendrogram : list of dictionaries
a list of partitions, ie dictionnaries where keys of the i+1 are the
values of the i. and where keys of the first are the nodes of graph
Raises
------
TypeError
If the graph is not a networkx.Graph
See Also
--------
best_partition
Notes
-----
Uses Louvain algorithm
References
----------
.. 1. Blondel, V.D. et al. Fast unfolding of communities in large
networks. J. Stat. Mech 10008, 1-12(2008).
Examples
--------
>>> G=nx.erdos_renyi_graph(100, 0.01)
>>> dendo = generate_dendrogram(G)
>>> for level in range(len(dendo) - 1) :
>>> print("partition at level", level,
>>> "is", partition_at_level(dendo, level))
:param weight:
:type weight:
"""
if type(graph) != nx.Graph:
raise TypeError("Bad graph type, use only non directed graph")
# special case, when there is no link
# the best partition is everyone in its community
if graph.number_of_edges() == 0:
part = dict([])
for node in graph.nodes():
part[node] = node
return [part]
current_graph = graph.copy()
status = Status()
status.init(current_graph, weight, part_init)
status_list = list()
__one_level(current_graph, status, weight, resolution, randomize)
new_mod = __modularity(status)
partition = __renumber(status.node2com)
status_list.append(partition)
mod = new_mod
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
while True:
__one_level(current_graph, status, weight, resolution)
new_mod = __modularity(status)
if new_mod - mod < __MIN:
break
partition = __renumber(status.node2com)
status_list.append(partition)
mod = new_mod
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
return status_list[:]
def generate_dendrogram(graph, part_init=None, weight='weight', resolution=1.):
"""Find communities in the graph and return the associated dendrogram
A dendrogram is a tree and each level is a partition of the graph nodes.
Level 0 is the first partition, which contains the smallest communities,
and the best is len(dendrogram) - 1. The higher the level is, the bigger
are the communities
Parameters
----------
graph : networkx.Graph
the networkx graph which will be decomposed
part_init : dict, optional
the algorithm will start using this partition of the nodes. It's a
dictionary where keys are their nodes and values the communities
weight : str, optional
the key in graph to use as weight. Default to 'weight'
resolution : double, optional
Will change the size of the communities, default to 1.
represents the time described in
"Laplacian Dynamics and Multiscale Modular Structure in Networks",
R. Lambiotte, J.-C. Delvenne, M. Barahona
Returns
-------
dendrogram : list of dictionaries
a list of partitions, ie dictionnaries where keys of the i+1 are the
values of the i. and where keys of the first are the nodes of graph
Raises
------
TypeError
If the graph is not a networkx.Graph
See Also
--------
best_partition
Notes
-----
Uses Louvain algorithm
References
----------
.. 1. Blondel, V.D. et al. Fast unfolding of communities in large
networks. J. Stat. Mech 10008, 1-12(2008).
Examples
--------
>>> G=nx.erdos_renyi_graph(100, 0.01)
>>> dendo = generate_dendrogram(G)
>>> for level in range(len(dendo) - 1) :
>>> print("partition at level", level,
>>> "is", partition_at_level(dendo, level))
:param weight:
:type weight:
"""
if type(graph) != nx.Graph:
raise TypeError("Bad graph type, use only non directed graph")
# special case, when there is no link
# the best partition is everyone in its community
if graph.number_of_edges() == 0:
part = dict([])
for node in graph.nodes():
part[node] = node
return [part]
current_graph = graph.copy()
status = Status()
status.init(current_graph, weight, part_init)
status_list = list()
__one_level(current_graph, status, weight, resolution)
new_mod = __modularity(status)
partition = __renumber(status.node2com)
status_list.append(partition)
mod = new_mod
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
while True:
__one_level(current_graph, status, weight, resolution)
new_mod = __modularity(status)
if new_mod - mod < __MIN:
break
partition = __renumber(status.node2com)
status_list.append(partition)
mod = new_mod
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
return status_list[:]
def generate_dendrogram(graph,
part_init=None,
weight='weight',
resolution=1.,
randomize=None,
random_state=None):
"""Find communities in the graph and return the associated dendrogram
A dendrogram is a tree and each level is a partition of the graph nodes.
Level 0 is the first partition, which contains the smallest communities,
and the best is len(dendrogram) - 1. The higher the level is, the bigger
are the communities
Parameters
----------
graph : networkx.Graph
the networkx graph which will be decomposed
part_init : dict, optional
the algorithm will start using this partition of the nodes. It's a
dictionary where keys are their nodes and values the communities
weight : str, optional
the key in graph to use as weight. Default to 'weight'
resolution : double, optional
Will change the size of the communities, default to 1.
represents the time described in
"Laplacian Dynamics and Multiscale Modular Structure in Networks",
R. Lambiotte, J.-C. Delvenne, M. Barahona
Returns
-------
dendrogram : list of dictionaries
a list of partitions, ie dictionnaries where keys of the i+1 are the
values of the i. and where keys of the first are the nodes of graph
Raises
------
TypeError
If the graph is not a networkx.Graph
See Also
--------
best_partition
Notes
-----
Uses Louvain algorithm
References
----------
.. 1. Blondel, V.D. et al. Fast unfolding of communities in large
networks. J. Stat. Mech 10008, 1-12(2008).
Examples
--------
>>> G=nx.erdos_renyi_graph(100, 0.01)
>>> dendo = generate_dendrogram(G)
>>> for level in range(len(dendo) - 1) :
>>> print("partition at level", level,
>>> "is", partition_at_level(dendo, level))
:param weight:
:type weight:
"""
if graph.is_directed():
raise TypeError("Bad graph type, use only non directed graph")
# Properly handle random state, eventually remove old `randomize` parameter
# NOTE: when `randomize` is removed, delete code up to random_state = ...
if randomize is not None:
warnings.warn(
"The `randomize` parameter will be deprecated in future "
"versions. Use `random_state` instead.", DeprecationWarning)
# If shouldn't randomize, we set a fixed seed to get determinisitc results
if randomize is False:
random_state = 0
# We don't know what to do if both `randomize` and `random_state` are defined
if randomize and random_state is not None:
raise ValueError(
"`randomize` and `random_state` cannot be used at the "
"same time")
random_state = check_random_state(random_state)
# special case, when there is no link
# the best partition is everyone in its community
if graph.number_of_edges() == 0:
part = dict([])
for i, node in enumerate(graph.nodes()):
part[node] = i
return [part]
current_graph = graph.copy()
status = Status()
status.init(current_graph, weight, part_init)
status_list = list()
__one_level(current_graph, status, weight, resolution, random_state)
new_mod = __modularity(status)
partition = __renumber(status.node2com)
status_list.append(partition)
mod = new_mod
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
while True:
__one_level(current_graph, status, weight, resolution, random_state)
new_mod = __modularity(status)
if new_mod - mod < __MIN:
break
partition = __renumber(status.node2com)
status_list.append(partition)
mod = new_mod
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
return status_list[:]
def generate_dendrogram(graph,
part_init=None,
weight='weight',
resolution=1.,
randomize=None,
random_state=None):
"""Finds communities in the graph and return the associated dendrogram
A dendrogram is a tree and each level is a partition of the graph nodes.
Level 0 is the first partition, which contains the smallest communities,
and the best is len(dendrogram) - 1. The higher the level is, the bigger
are the communities.
"""
random_state = check_random_state(random_state)
# special case, when there is no link
# the best partition is everyone in its community
if graph.number_of_edges() == 0:
part = dict([])
for i, node in enumerate(graph.nodes()):
part[node] = i
return [part]
current_graph = graph.copy()
status = Status()
status.init(current_graph, weight, part_init)
status_list = list()
__one_level(current_graph, status, weight, resolution, random_state)
# runs the investigation multiple times until the improvement is smaller than the predefined threshold
new_mod = __modularity(status)
# computes the modularity of the graph, based on discovered communities
partition = __renumber(status.node2com)
# resets the community indices such that they start with 0 and goes up one by one (instead of random list of numbers between 1 and n that we had)
status_list.append(partition)
# appends a set of assigned communities at a certain level of detection to $status_list
mod = new_mod
# computes the modularity after the first change in community assignment but on the same graph (not induced graph)
current_graph = induced_graph(partition, current_graph, weight)
# createsa new graph based on the former one such that each community becomes a node in this new one.
status.init(current_graph, weight)
# updates the $status such that obliterates the former one.
while True:
__one_level(current_graph, status, weight, resolution, random_state)
# runs the investigation multiple times until the improvement is smaller than the predefined threshold
new_mod = __modularity(status)
if new_mod - mod < __MIN:
# check if the new modularity after creating a new graph and assign new communities is improved more than threshold in comparison with the former graph or not
# this if statement checks the modularity value for two different graphs but the stop condition for $__one_level is for one graph with new community assignment
break
partition = __renumber(status.node2com)
status_list.append(partition)
mod = new_mod
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
# while loop ends when the new induced graph (with more convoluted and merged communities) is no better than the former step.
return status_list[:]
def generate_dendrogram(graph, IncFnc, part_init=None, weight='weight'):
"""Find communities in the graph and return the associated dendrogram
A dendrogram is a tree and each level is a partition of the graph nodes.
Level 0 is the first partition, which contains the smallest communities,
and the best is len(dendrogram) - 1. The higher the level is, the bigger
are the communities
Parameters
----------
graph : networkx.Graph
the networkx graph which will be decomposed
part_init : dict, optional
the algorithm will start using this partition of the nodes. It's a
dictionary where keys are their nodes and values the communities
weight : str, optional
the key in graph to use as weight. Default to 'weight'
Returns
-------
dendrogram : list of dictionaries
a list of partitions, ie dictionnaries where keys of the i+1 are the
values of the i. and where keys of the first are the nodes of graph
Raises
------
TypeError
If the graph is not a networkx.Graph
See Also
--------
best_partition
Notes
-----
Uses Louvain's optimization algorithm
References
----------
.. 1. Blondel, V.D. et al. Fast unfolding of communities in large
networks. J. Stat. Mech 10008, 1-12(2008).
.. 2. reference to SIWO paper TODO
Examples
--------
>>> G=nx.erdos_renyi_graph(100, 0.01)
>>> dendo = generate_dendrogram(G)
>>> for level in range(len(dendo) - 1) :
>>> print("partition at level", level,
>>> "is", partition_at_level(dendo, level))
:param weight:
:type weight:
"""
if type(graph) != nx.Graph:
raise TypeError("Bad graph type, use only non directed graph")
# special case, when there is no link
# the best partition is everyone in its community
if graph.number_of_edges() == 0:
part = dict([])
for node in graph.nodes():
part[node] = node
return [part]
current_graph = graph.copy()
status = Status()
status.init(current_graph, weight, part_init)
status_list = list()
changed = __one_level(current_graph, IncFnc, status, weight)
partition = __renumber(status.node2com)
status_list.append(partition)
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
while True:
changed = __one_level(current_graph, IncFnc, status, weight)
if not changed:
break
partition = __renumber(status.node2com)
status_list.append(partition)
current_graph = induced_graph(partition, current_graph, weight)
status.init(current_graph, weight)
return status_list[:]
def generate_dendrogram(graph,
part_init=None,
weight='weight',
resolution=1.,
randomize=False):
"""Find communities in the graph and return the associated dendrogram
A dendrogram is a tree and each level is a partition of the graph nodes.
Level 0 is the first partition, which contains the smallest communities,
and the best is len(dendrogram) - 1. The higher the level is, the bigger
are the communities
Parameters
----------
graph : networkx.Graph
the networkx graph which will be decomposed
part_init : dict, optional
the algorithm will start using this partition of the nodes. It's a
dictionary where keys are their nodes and values the communities
weight : str, optional
the key in graph to use as weight. Default to 'weight'
resolution : double, optional
Will change the size of the communities, default to 1.
represents the time described in
"Laplacian Dynamics and Multiscale Modular Structure in Networks",
R. Lambiotte, J.-C. Delvenne, M. Barahona
Returns
-------
dendrogram : list of dictionaries
a list of partitions, ie dictionnaries where keys of the i+1 are the
values of the i. and where keys of the first are the nodes of graph
Raises
------
TypeError
If the graph is not a networkx.Graph
See Also
--------
best_partition
Notes
-----
Uses Louvain algorithm
References
----------
.. 1. Blondel, V.D. et al. Fast unfolding of communities in large
networks. J. Stat. Mech 10008, 1-12(2008).
Examples
--------
>>> G=nx.erdos_renyi_graph(100, 0.01)
>>> dendo = generate_dendrogram(G)
>>> for level in range(len(dendo) - 1) :
>>> print("partition at level", level,
>>> "is", partition_at_level(dendo, level))
:param weight:
:type weight:
"""
if graph.is_directed():
raise TypeError("Bad graph type, use only non directed graph")
# special case, when there is no link
# the best partition is everyone in its community
if graph.number_of_edges() == 0:
part = dict([])
for node in graph.nodes():
part[node] = node
return [part]
current_graph = graph.copy()
#status = Status()
#status.init(current_graph, weight, part_init)
status_list = list()
posStatus = Status()
posGraph = nx.Graph()
posGraph.add_nodes_from(current_graph.nodes)
posGraph.add_edges_from([(a, b, {
'weight': c
}) for (a, b, c) in current_graph.edges.data('weight', default=1)
if c > 0])
posStatus.init(posGraph, weight, part_init)
#posStatus.list=list()
negStatus = Status()
negGraph = nx.Graph()
negGraph.add_nodes_from(current_graph.nodes)
negGraph.add_edges_from([(a, b, {
'weight': -c
}) for (a, b, c) in current_graph.edges.data('weight', default=-1)
if c < 0])
negStatus.init(negGraph, weight, part_init)
#negStatus.list = list()
print(posStatus.total_weight)
print(negStatus.total_weight)
print(len(negGraph.nodes()), len(posGraph.nodes()))
print(len(negGraph.edges()), len(posGraph.edges()))
#print(negGraph.nodes(),negGraph.edges())
#print(current_graph.edges.data('weight', default=-1))
#print(current_graph.edges.data('weight', default=0))
__one_level(posGraph, negGraph, posStatus, negStatus, weight, resolution,
randomize)
#TODO Edit one_levl function
posMul = float(posStatus.total_weight /
(posStatus.total_weight +
negStatus.total_weight)) #Multip by 2 is impactless
negMul = float(negStatus.total_weight /
(posStatus.total_weight +
negStatus.total_weight)) #Multip by 2 is impactless
new_mod = posMul * __modularity(posStatus) - negMul * __modularity(
negStatus)
#TODO check modularity works correct
partition = __renumber(posStatus.node2com)
status_list.append(partition)
mod = new_mod
#current_graph = induced_graph(partition, current_graph, weight)
#status.init(current_graph, weight)
posGraph = induced_graph(partition, posGraph, weight)
posStatus.init(posGraph, weight, part_init)
negGraph = induced_graph(partition, negGraph, weight)
negStatus.init(negGraph, weight, part_init)
print(" WHile ")
while True:
print(" WHile ")
__one_level(posGraph, negGraph, posStatus, negStatus, weight,
resolution, randomize)
#__one_level(current_graph, status, weight, resolution, randomize)
#new_mod = __modularity(status)
pos_mod = __modularity(posStatus)
neg_mod = __modularity(negStatus)
new_mod = posMul * pos_mod - negMul * neg_mod
#TODO Sth is not double
if new_mod - mod < __MIN:
break
partition = __renumber(posStatus.node2com)
status_list.append(partition)
mod = new_mod
posGraph = induced_graph(partition, posGraph, weight)
negGraph = induced_graph(partition, negGraph, weight)
posStatus.init(posGraph, weight)
negStatus.init(negGraph, weight)
print("\n\n\n our modularity: ", mod)
print("eow WHile ")
return status_list[:]