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Commit 07a2d099 authored by Tiago Peixoto's avatar Tiago Peixoto
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Docstrings and small fixes in centrality algorithms 

This fully documents the centrality module.
parent 95405617
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src/graph/centrality/graph_eigentrust.cc
View file @ 07a2d099
......@@ -28,21 +28,24 @@ using namespace std;
using namespace boost;
using namespace graph_tool;
void eigentrust(GraphInterface& g, boost::any c, boost::any t,
double epslon, size_t max_iter)
size_t eigentrust(GraphInterface& g, boost::any c, boost::any t,
double epslon, size_t max_iter)
{
if (!belongs<writable_edge_scalar_properties>()(c))
throw GraphException("edge property must be writable");
if (!belongs<vertex_floating_vector_properties>()(t))
throw GraphException("vertex property must be of floating point value type");
if (!belongs<vertex_floating_properties>()(t))
throw GraphException("vertex property must be of floating point"
" value type");
size_t iter = 0;
run_action<>()
(g, bind<void>
(get_eigentrust(),
_1, g.GetVertexIndex(), g.GetEdgeIndex(), _2,
_3, epslon, max_iter),
_3, epslon, max_iter, ref(iter)),
writable_edge_scalar_properties(),
vertex_floating_properties())(c,t);
return iter;
}
void export_eigentrust()
......
src/graph/centrality/graph_eigentrust.hh
View file @ 07a2d099
......@@ -33,7 +33,7 @@ struct get_eigentrust
class InferredTrustMap>
void operator()(Graph& g, VertexIndex vertex_index,
EdgeIndex edge_index, TrustMap c, InferredTrustMap t,
double epslon, size_t max_iter) const
double epslon, size_t max_iter, size_t& iter) const
{
typedef typename property_traits<TrustMap>::value_type c_type;
typedef typename property_traits<InferredTrustMap>::value_type t_type;
......@@ -88,7 +88,7 @@ struct get_eigentrust
}
// init inferred trust t
int i, N = num_vertices(g);
int i, N = num_vertices(g), V = HardNumVertices()(g);
#pragma omp parallel for default(shared) private(i) \
schedule(dynamic)
for (i = 0; i < N; ++i)
......@@ -96,11 +96,11 @@ struct get_eigentrust
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, g);
if (v == graph_traits<Graph>::null_vertex())
continue;
t[v] = 1.0/N;
t[v] = 1.0/V;
}
t_type delta = 2*epslon;
size_t iter = 0;
t_type delta = epslon + 1;
iter = 0;
while (delta >= epslon)
{
delta = 0;
......@@ -129,6 +129,7 @@ struct get_eigentrust
delta += abs(t_temp[v] - t[v]);
}
swap(t_temp, t);
++iter;
if (max_iter > 0 && iter== max_iter)
break;
......
src/graph/centrality/graph_pagerank.cc
View file @ 07a2d099
......@@ -33,7 +33,7 @@ size_t pagerank(GraphInterface& g, boost::any rank, double d, double epslon,
size_t max_iter)
{
if (!belongs<writable_vertex_scalar_properties>()(rank))
throw GraphException("vertex property must be of writable");
throw GraphException("vertex property must be writable");
size_t iter;
run_action<>()
......
src/graph_tool/centrality/__init__.py
View file @ 07a2d099
......@@ -16,6 +16,13 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
Centrality
==========
This module includes centrality-related algorithms.
"""
from .. dl_import import dl_import
dl_import("import libgraph_tool_centrality")
......@@ -25,8 +32,89 @@ import numpy
__all__ = ["pagerank", "betweenness", "central_point_dominance", "eigentrust",
"absolute_trust"]
def pagerank(g, damping=0.8, prop=None, epslon=1e-6, max_iter=0,
def pagerank(g, damping=0.8, prop=None, epslon=1e-6, max_iter=None,
ret_iter=False):
r"""
Calculate the PageRank of each vertex.
Parameters
----------
g : Graph
Graph to be used.
damping : float, optional (default: 0.8)
Damping factor.
prop : ProperyMap, optional (default: None)
Vertex property map to store the PageRank values.
epslon : float, optional (default: 1e-6)
Convergence condition. The iteration will stop if the total delta of all
vertices are below this value.
max_iter : int, optional (default: None)
If supplied, this will limit the total number of iterations.
ret_iter : bool, optional (default: False)
If true, the total number of iterations is also returned.
Returns
-------
A vertex property map containing the PageRank values.
See Also
--------
betweenness: betweenness centrality
eigentrust: eigentrust centrality
absolute_trust: absolute trust centrality
Notes
-----
The value of PageRank of vertex v :math:`PR(v)` is given interactively by
the relation:
.. math:
PR(v) = \frac{1-d}{N} + d \sum_{w \in \Gamma^{-}(v)}
\frac{PR (w)}{d^{+}(w)}</math>
where :math:`\Gamma^{-}(v)` are the in-neighbours of v, :math:`d^{+}(w)` is
the out-degree of w, and d is a damping factor.
The implemented algorithm progressively iterates the above condition, until
it no longer changes, according to the parameter epslon. It has a
topology-dependent running time.
If enabled during compilation, this algorithm runs in parallel.
Examples
--------
>>> from numpy.random import poisson
>>> g = gt.random_graph(100, lambda: (poisson(3), poisson(3)), seed=42)
>>> pr = gt.pagerank(g)
>>> print pr.get_array()
[ 1.23631405 1.26200483 1.96751522 0.64733031 0.70919769 0.30955985
1.52538634 0.61243582 0.53488703 0.5495016 0.63962998 0.45806361
1.67723278 0.26623242 0.32215029 0.53362967 0.32231378 0.33050213
0.5356975 0.37390974 0.93677559 0.38228945 0.36843877 0.84068062
1.06194997 0.53691497 1.13629299 1.16796209 0.55409311 0.75573135
0.58224114 0.40017455 0.35638757 1.16638209 0.74002981 0.47176731
0.42552094 1.73280634 0.57785889 1.5858852 0.49093732 0.46508149
0.71090896 1.31162119 0.6081533 0.795906 0.66140379 1.45468664
0.87347307 0.35982942 0.75867436 0.29503668 0.2 0.42730891
0.39734128 0.68474907 0.27070849 1.09135253 0.99528067 0.62147738
0.45554969 0.60866561 0.3757151 0.76052526 0.24 1.96136727
0.45867667 1.69554306 0.5334554 0.33116212 0.58532863 0.59491545
0.45311729 0.64750618 0.46664234 0.77742232 0.59982206 0.4484523
0.2 0.67184777 1.4206807 0.31958008 0.45240096 0.9407526
0.24 0.94460064 0.97453039 0.60548406 0.44192809 0.35467411
0.32231378 0.93392279 1.12016048 1.21238 0.34737551 0.39613672
0.95560285 0.623376 0.2 0.59657029]
References
----------
.. [pagerank_wikipedia] http://en.wikipedia.org/wiki/Pagerank
.. [lawrence_pagerank_1998] P. Lawrence, B. Sergey, M. Rajeev, W. Terry,
"The pagerank citation ranking: Bringing order to the web", Technical
report, Stanford University, 1998
"""
if max_iter == None:
max_iter = 0
if prop == None:
prop = g.new_vertex_property("double")
ic = libgraph_tool_centrality.\
......@@ -37,7 +125,85 @@ def pagerank(g, damping=0.8, prop=None, epslon=1e-6, max_iter=0,
else:
return prop
def betweenness(g, eprop=None, vprop=None, weight=None, norm=True):
def betweenness(g, vprop=None, eprop=None, weight=None, norm=True):
r"""
Calculate the betweenness centrality for each vertex and edge.
Parameters
----------
g : Graph
Graph to be used.
vprop : ProperyMap, optional (default: None)
Vertex property map to store the vertex betweenness values.
eprop : ProperyMap, optional (default: None)
Edge property map to store the edge betweenness values.
weight : ProperyMap, optional (default: None)
Edge property map corresponding to the weight value of each edge.
norm : bool, optional (default: True)
Whether or not the betweenness values should be normalized.
Returns
-------
A tuple containing a vertex property map and an edge property map with the
respective betweenness values.
See Also
--------
central_point_dominance: central point dominance of the graph
pagerank: PageRank centrality
eigentrust: eigentrust centrality
absolute_trust: absolute trust centrality
Notes
-----
Betweenness centrality of a vertex :math:`C_B(v)` is defined as,
.. math:
C_B(v)= \sum_{s \neq v \neq t \in V \atop s \neq t}
\frac{\sigma_{st}(v)}{\sigma_{st}}
where :math:`\sigma_{st}` is the number of shortest geodesic paths from s to
t, and :math:`\sigma_{st}(v)` is the number of shortest geodesic paths from
s to t that pass through a vertex v. This may be normalised by dividing
through the number of pairs of vertices not including v, which is
:math:`(n-1)(n-2)/2`.
The algorithm used here is defined in _[brandes_faster_2001], and has a
complexity of :math:`O(VE)` for unweighted graphs and :math:`O(VE + V(V+E)
\log V)` for weighted graphs. The space complexity is :math:`O(VE)`.
If enabled during compilation, this algorithm runs in parallel.
Examples
--------
>>> from numpy.random import poisson
>>> g = gt.random_graph(100, lambda: (poisson(3), poisson(3)), seed=42)
>>> vb, eb = gt.betweenness(g)
>>> print vb.get_array()
[ 0.04156663 0.04437293 0.05111713 0.04426975 0.05518562 0.01015239
0. 0.02696981 0.00849224 0.01177936 0.03467101 0.01958941
0.05491377 0.00140963 0.00810379 0.0061649 0.01325843 0.
0.00388506 0. 0.07004857 0.01540617 0.02101045 0.03078003
0.02823591 0.01752393 0. 0.0487721 0.04102476 0.02308081
0.00320094 0.01265714 0.0168692 0.06652112 0.02913082 0.
0.01509914 0.08867136 0.01399966 0.09695112 0.01803752 0.
0.01628919 0.10413395 0.00860251 0. 0. 0.06342465
0.07319201 0.01197855 0.01750122 0.00393044 0. 0.01697703
0.01301164 0.04819859 0. 0.0284821 0.03074227 0.02090606
0.02107045 0.03068094 0.01983066 0.02918679 0.00164227 0.06705493
0.02547069 0.10370115 0.02012076 0.02351567 0.01136589 0.01367043
0.01392008 0.00634258 0. 0.0530404 0.02245571 0.01590784
0. 0.03704311 0.05519485 0.00966124 0.0130797 0.01528993
0.00145159 0.00298564 0.02297654 0.03740528 0.02934682 0.0101206 0.
0.02320795 0.04883052 0.0322225 0.01573123 0. 0.04031835
0.05886674 0. 0.01637893]
References
----------
.. [betweenness_wikipedia] http://en.wikipedia.org/wiki/Centrality#Betweenness_centrality
.. [brandes_faster_2001] U. Brandes, "A faster algorithm for betweenness
centrality", Journal of Mathematical Sociology, 2001
"""
if vprop == None:
vprop = g.new_vertex_property("double")
if eprop == None:
......@@ -52,21 +218,249 @@ def betweenness(g, eprop=None, vprop=None, weight=None, norm=True):
return vprop, eprop
def central_point_dominance(g, betweenness):
r"""
Calculate the central point dominance of the graph, given the betweenness
centrality of each vertex.
Parameters
----------
g : Graph
Graph to be used.
betweenness : ProperyMap
Vertex property map with the betweenness centrality values. The values
must be normalized.
Returns
-------
The central point dominance (float).
See Also
--------
betweenness: betweenness centrality
Notes
-----
Let :math:`v^*` be the vertex with the largest relative betweenness
centrality; then, the central point dominance _[freeman_set_1977] is defined
as:
.. math:
C'_B = \frac{1}{|V|-1} \sum_{v} C_B(v^*) - C_B(v)
where :math:`C_B(v)` is the normalized betweenness centrality of vertex
v. The value of :math:`C_B` lies in the range [0,1].
The algorithm has a complexity of :math:`O(V)`.
Examples
--------
>>> from numpy.random import poisson
>>> g = gt.random_graph(100, lambda: (poisson(3), poisson(3)), seed=42)
>>> vb, eb = gt.betweenness(g)
>>> print gt.central_point_dominance(g, vb)
0.138990020139
References
----------
.. [freeman_set_1977] Linton C. Freeman, "A Set of Measures of Centrality
Based on Betweenness", Sociometry, Vol. 40, No. 1, pp. 35-41 (1977)
"""
return libgraph_tool_centrality.\
central_point_dominance(g._Graph__graph,
get_central_point_dominance(g._Graph__graph,
_prop("v", g, betweenness))
def eigentrust(g, trust_map, vprop=None, epslon=1e-6, max_iter=0,
def eigentrust(g, trust_map, vprop=None, norm=False, epslon=1e-6, max_iter=0,
ret_iter=False):
r"""
Calculate the eigentrust centrality of each vertex in the graph.
Parameters
----------
g : Graphs
Graph to be used.
trust_map : ProperyMap
Edge property map with the values of trust associated with each
edge. The values must not lie in the range [0,1].
vprop : PropertyMap, optional (default: None)
Vertex property map where the values of eigentrust must be stored.
norm : bool, optional (default: false)
Norm eigentrust values so that the total sum equals 1.
epslon : float, optional (default: 1e-6)
Convergence condition. The iteration will stop if the total delta of all
vertices are below this value.
max_iter : int, optional (default: None)
If supplied, this will limit the total number of iterations.
ret_iter : bool, optional (default: False)
If true, the total number of iterations is also returned.
Returns
-------
A vertex property map containing the eigentrust values.
See Also
--------
betweenness: betweenness centrality
pagerank: PageRank centrality
absolute_trust: absolute trust centrality
Notes
-----
The eigentrust _[kamvar_eigentrust_2003] values :math:`t_i` correspond the
following limit
.. math:
\mathbf{t} = \lim_{n\to\infty} \left(C^T\right)^n \mathbf{c}
where :math:`c_i = 1/|V|` and the elements of the matrix :math:`C` are the
normalized trust values:
.. math:
c_{ij} = \frac{\max(s_{ij},0)}{\sum_{j} \max(s_{ij}, 0)}
The algorithm has a topology-dependent complexity.
If enabled during compilation, this algorithm runs in parallel.
Examples
--------
>>> from numpy.random import poisson, random, seed
>>> seed(42)
>>> g = gt.random_graph(100, lambda: (poisson(3), poisson(3)), seed=42)
>>> trust = g.new_edge_property("double")
>>> trust.get_array()[:] = random(g.num_edges())*42
>>> t = eigentrust(g, trust, norm=True)
>>> print t.get_array()
[ 9.48423789e-04 1.66078086e-02 3.24301008e-02 2.51269077e-02
4.58889062e-03 6.32886469e-03 3.95308763e-03 4.87246882e-03
5.53852192e-03 9.37363084e-03 1.17843106e-02 2.65124314e-03
4.47045232e-03 2.51950468e-03 1.59255295e-02 6.03159113e-03
6.72140367e-03 1.71280616e-03 1.24012407e-02 1.14231095e-02
9.85151282e-03 5.56192871e-03 6.74797491e-03 2.63245538e-03
9.21152238e-03 8.16728082e-03 3.98587427e-03 1.70045178e-02
8.37146815e-03 1.29174460e-02 3.19556744e-03 2.67554442e-03
1.24085488e-02 1.17337267e-02 3.13424443e-03 1.66366342e-02
1.25374784e-02 2.65548170e-02 2.17676368e-02 1.73783204e-02
9.20641085e-03 2.11744591e-02 6.25110430e-03 2.05212010e-03
1.43759959e-02 1.63283789e-02 3.17898495e-03 8.86981181e-03
4.94416312e-03 1.24896279e-03 1.07967554e-03 3.54578850e-04
3.86590892e-04 4.21633271e-02 2.52101241e-03 2.32337004e-02
1.69840276e-02 1.61722366e-02 7.24752207e-03 1.03185292e-02
2.04849646e-02 1.94466303e-02 2.01785230e-03 9.31938244e-05
1.67364460e-02 9.37317475e-03 2.06112300e-03 3.78202160e-03
9.33152939e-03 5.00810967e-03 6.95505313e-03 2.49521643e-03
4.53346948e-02 3.74770290e-03 6.78252167e-03 2.55396413e-02
0.00000000e+00 6.66150362e-03 0.00000000e+00 8.30734676e-03
9.81158582e-03 1.36569726e-03 1.27503978e-02 1.07028771e-02
7.91984678e-03 1.81615021e-02 8.05566933e-03 6.71131661e-03
2.69021984e-02 3.20556792e-03 3.44845723e-03 2.28971468e-04
1.76318611e-02 1.25007850e-02 1.06310753e-02 1.33265004e-02
1.10624438e-02 0.00000000e+00 2.00750355e-02 5.37349566e-03]
References
----------
.. [kamvar_eigentrust_2003] S. D. Kamvar, M. T. Schlosser, H. Garcia-Molina
"The eigentrust algorithm for reputation management in p2p networks",
Proceedings of the 12th international conference on World Wide Web,
Pages: 640 - 651, 2003
"""
if vprop == None:
vprop = g.new_vertex_property("double")
libgraph_tool_centrality.\
get_eigentrust(g._Graph__graph, _prop("e", g, trust_map),
_prop("v", g, vprop), epslon, max_iter)
return vprop
i = libgraph_tool_centrality.\
get_eigentrust(g._Graph__graph, _prop("e", g, trust_map),
_prop("v", g, vprop), epslon, max_iter)
if norm:
vprop.get_array()[:] /= sum(vprop.get_array())
if ret_iter:
return vprop, i
else:
return vprop
def absolute_trust(g, trust_map, vprop=None, epslon=0.1, max_iter=None,
seed=None, ret_iter=False)
r"""
Samples the absolute trust centrality of each vertex in the graph.
Parameters
----------
g : Graphs
Graph to be used.
trust_map : ProperyMap
Edge property map with the values of trust associated with each
edge. The values must lie in the range [0,1].
vprop : PropertyMap, optional (default: None)
Vertex property map where the values of eigentrust must be stored.
epslon : float, optional (default: 0.1)
Convergence condition. The iteration will stop if the total delta of all
vertices are below this value.
max_iter : int, optional (default: None)
If supplied, this will limit the total number of iterations.
seed : int, optional (default: None)
The initializing seed for the random number generator. If not supplied
a different random value will be chosen each time.
ret_iter : bool, optional (default: False)
If true, the total number of iterations is also returned.
Returns
-------
A vertex property map containing the absolute trust vector from the
corresponding vertex to the rest of the network. Each element i of the
vector is the trust value of the vertex with index i, from the given vertex.
See Also
--------
eigentrust: eigentrust centrality
betweenness: betweenness centrality
pagerank: PageRank centrality
Notes
-----
The absolute trust between vertices i and j is defined as
.. math:
t_{ij} = \frac{1}{|\{i\to j\}|}\sum_{\{i\to j\}}
\prod_{e\in \{i\to j\}}
\frac{c_e^2}{\sum_{w\in\Gamma^+(s(e))}c_{s(e),w}}}
where the sum is taken over all paths from i to j (without loops), and
:math:`c_e` is the direct trust value associated with edge e.
The algorithm progressively samples all possible paths, until the trust
values converge, and has a topology-dependent complexity.
If enabled during compilation, this algorithm runs in parallel.
Examples
--------
>>> from numpy.random import poisson, random, seed
>>> seed(42)
>>> g = gt.random_graph(100, lambda: (poisson(3), poisson(3)), seed=42)
>>> trust = g.new_edge_property("double")
>>> trust.get_array()[:] = random(g.num_edges())
>>> t = absolute_trust(g, trust)
>>> print array(t[g.vertex(10)])
[ 0.00452395 0.00358993 0.00520913 0.00151395 0.09479413 0.00431631
0.09957709 0.00722076 0.02488298 0.02720262 0. 0.02958085
0.05583483 0.00525581 0.02112018 0.00157646 0.02070552 0.01317581
0.01565533 0.00568109 0.04568674 0.00202402 0.0024926 0.14040174
0.0093484 0.00124116 0.009818 0.039403 0.00787983 0.0130681
0.02046159 0.02044219 0.00625258 0.00253353 0.00992648 0.00658357
0.00328796 0.05730617 0.00752433 0.00289023 0. 0.01610246
0.03151005 0.05449376 0.0195204 0.00296101 0.0187164 0.19553864
0.01089019 0.01516855 0.01621888 0.29711525 0.00164373 0.02045437
0.01388174 0.00109321 0.03034565 0.00289681 0.06903929 0.02392237
0.01491933 0.02128263 0.03091464 0.03457097 0.14454613 0.01821371
0.00943718 0.0247563 0.00495901 0.03532278 0.00053465 0.
0.00142457 0.03393286 0.0058909 0.01881276 0.00156345 0.00878983
0.00832669 0.08389869 0.43991565 0.04075081 0.00323008 0.02823037
0.03224312 0.00430044 0.0331929 0.00268128 0.01462425 0.00720545
0.06730403 0.02771813 0.03289217 0.01326689 0.06876157 0.02382899
0.1502834 0.00980331 0.0086688 0.00495706]
"""
def absolute_trust(g, trust_map, vprop=None, epslon=0.1, max_iter=0,
seed=0):
if seed != 0:
seed = numpy.random.randint(0, sys.maxint)
if vprop == None:
......@@ -74,5 +468,8 @@ def absolute_trust(g, trust_map, vprop=None, epslon=0.1, max_iter=0,
ic = libgraph_tool_centrality.\
get_absolute_trust(g._Graph__graph, _prop("e", g, trust_map),
_prop("v", g, vprop), epslon, max_iter, seed)
return vprop
if ret_iter:
return vprop, ic
else:
return vprop
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