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Commit 24a2a628 authored by Tiago Peixoto's avatar Tiago Peixoto
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Implement HITS centrality (aka hubs and authorities)

parent 7d08675e
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src/graph/centrality/Makefile.am
View file @ 24a2a628
......@@ -19,6 +19,7 @@ libgraph_tool_centrality_la_SOURCES = \
graph_centrality_bind.cc \
graph_eigentrust.cc \
graph_eigenvector.cc \
graph_hits.cc \
graph_pagerank.cc \
graph_trust_transitivity.cc
......@@ -26,5 +27,6 @@ libgraph_tool_centrality_la_include_HEADERS = \
graph_eigentrust.hh \
graph_eigenvector.hh \
graph_pagerank.hh \
graph_hits.hh \
graph_trust_transitivity.hh \
minmax.hh
src/graph/centrality/graph_centrality_bind.cc
View file @ 24a2a628
......@@ -22,6 +22,7 @@ using namespace boost;
void export_betweenness();
void export_eigentrust();
void export_eigenvector();
void export_hits();
void export_trust_transitivity();
void export_pagerank();
......@@ -30,6 +31,7 @@ BOOST_PYTHON_MODULE(libgraph_tool_centrality)
export_betweenness();
export_eigentrust();
export_eigenvector();
export_hits();
export_trust_transitivity();
export_pagerank();
}
src/graph/centrality/graph_hits.cc 0 → 100644
View file @ 24a2a628
// graph-tool -- a general graph modification and manipulation thingy
//
// Copyright (C) 2007-2012 Tiago de Paula Peixoto <tiago@skewed.de>
//
// This program is free software; you can redistribute it and/or
// modify it under the terms of the GNU General Public License
// as published by the Free Software Foundation; either version 3
// of the License, or (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
#include "graph_filtering.hh"
#include <boost/python.hpp>
#include "graph.hh"
#include "graph_selectors.hh"
#include "graph_hits.hh"
using namespace std;
using namespace boost;
using namespace graph_tool;
struct get_hits_dispatch
{
template <class Graph, class VertexIndex, class WeightMap,
class CentralityMap>
void operator()(Graph& g, VertexIndex vertex_index, WeightMap w,
CentralityMap x, boost::any ay, double epsilon,
size_t max_iter, long double& eig) const
{
try
{
typename CentralityMap::checked_t y = any_cast<typename CentralityMap::checked_t>(ay);
get_hits()(g, vertex_index, w, x,
y.get_unchecked(num_vertices(g)), epsilon, max_iter,
eig);
}
catch (bad_any_cast&)
{
throw GraphException("x and y vertex properties must be of the same type.");
}
}
};
long double hits(GraphInterface& g, boost::any w, boost::any x, boost::any y,
double epsilon, size_t max_iter)
{
if (!w.empty() && !belongs<writable_edge_scalar_properties>()(w))
throw ValueException("edge property must be writable");
if (!belongs<vertex_floating_properties>()(x))
throw ValueException("vertex property must be of floating point"
" value type");
typedef ConstantPropertyMap<int, GraphInterface::edge_t> weight_map_t;
typedef mpl::push_back<writable_edge_scalar_properties, weight_map_t>::type
weight_props_t;
if(w.empty())
w = weight_map_t(1);
long double eig = 0;
run_action<>()
(g, bind<void>
(get_hits_dispatch(), _1, g.GetVertexIndex(), _2,
_3, y, epsilon, max_iter, ref(eig)),
weight_props_t(),
vertex_floating_properties())(w, x);
return eig;
}
void export_hits()
{
using namespace boost::python;
def("get_hits", &hits);
}
src/graph/centrality/graph_hits.hh 0 → 100644
View file @ 24a2a628
// graph-tool -- a general graph modification and manipulation thingy
//
// Copyright (C) 2007-2012 Tiago de Paula Peixoto <tiago@skewed.de>
//
// This program is free software; you can redistribute it and/or
// modify it under the terms of the GNU General Public License
// as published by the Free Software Foundation; either version 3
// of the License, or (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
#ifndef GRAPH_EIGENVECTOR_HH
#define GRAPH_EIGENVECTOR_HH
#include "graph.hh"
#include "graph_filtering.hh"
#include "graph_util.hh"
#include <ext/numeric>
using __gnu_cxx::power;
namespace graph_tool
{
using namespace std;
using namespace boost;
struct get_hits
{
template <class Graph, class VertexIndex, class WeightMap,
class CentralityMap>
void operator()(Graph& g, VertexIndex vertex_index, WeightMap w,
CentralityMap x, CentralityMap y, double epsilon,
size_t max_iter, long double& eig) const
{
typedef typename property_traits<WeightMap>::value_type c_type;
typedef typename property_traits<CentralityMap>::value_type t_type;
CentralityMap x_temp(vertex_index, num_vertices(g));
CentralityMap y_temp(vertex_index, num_vertices(g));
// init centrality
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)
{
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, g);
if (v == graph_traits<Graph>::null_vertex())
continue;
x[v] = 1.0 / V;
y[v] = 1.0 / V;
}
t_type x_norm = 0;
t_type delta = epsilon + 1;
size_t iter = 0;
while (delta >= epsilon)
{
x_norm = 0;
#pragma omp parallel for default(shared) private(i) \
schedule(dynamic) reduction(+:norm)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v =
vertex(i, g);
if (v == graph_traits<Graph>::null_vertex())
continue;
x_temp[v] = 0;
typename in_or_out_edge_iteratorS<Graph>::type ie, ie_end;
for (tie(ie, ie_end) = in_or_out_edge_iteratorS<Graph>::get_edges(v, g);
ie != ie_end; ++ie)
{
typename graph_traits<Graph>::vertex_descriptor s =
source(*ie, g);
if (is_directed::apply<Graph>::type::value)
s = source(*ie, g);
else
s = target(*ie,g);
x_temp[v] += get(w, *ie) * y[s];
}
x_norm += power(x_temp[v], 2);
y_temp[v] = 0;
typename graph_traits<Graph>::out_edge_iterator e, e_end;
for (tie(e, e_end) = out_edges(v, g); e != e_end; ++e)
{
typename graph_traits<Graph>::vertex_descriptor s = target(*e, g);
y_temp[v] += get(w, *e) * x[s];
}
}
x_norm = sqrt(x_norm);
delta = 0;
#pragma omp parallel for default(shared) private(i) \
schedule(dynamic) reduction(+:delta)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v =
vertex(i, g);
if (v == graph_traits<Graph>::null_vertex())
continue;
x_temp[v] /= x_norm;
delta += abs(x_temp[v] - x[v]);
delta += abs(y_temp[v] - y[v]);
}
swap(x_temp, x);
swap(y_temp, y);
++iter;
if (max_iter > 0 && iter== max_iter)
break;
}
if (iter % 2 != 0)
{
#pragma omp parallel for default(shared) private(i) \
schedule(dynamic)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v =
vertex(i, g);
if (v == graph_traits<Graph>::null_vertex())
continue;
x[v] = x_temp[v];
y[v] = y_temp[v];
}
}
eig = x_norm;
}
};
}
#endif
src/graph_tool/centrality/__init__.py
View file @ 24a2a628
......@@ -34,6 +34,7 @@ Summary
betweenness
central_point_dominance
eigenvector
hits
eigentrust
trust_transitivity
......@@ -51,7 +52,7 @@ import sys
import numpy
__all__ = ["pagerank", "betweenness", "central_point_dominance", "eigentrust",
"eigenvector", "trust_transitivity"]
"eigenvector", "hits", "trust_transitivity"]
def pagerank(g, damping=0.85, pers=None, weight=None, prop=None, epsilon=1e-6,
......@@ -89,6 +90,8 @@ def pagerank(g, damping=0.85, pers=None, weight=None, prop=None, epsilon=1e-6,
--------
betweenness: betweenness centrality
eigentrust: eigentrust centrality
eigenvector: eigenvector centrality
hits: hubs and authority centralities
trust_transitivity: pervasive trust transitivity
Notes
......@@ -231,6 +234,8 @@ def betweenness(g, vprop=None, eprop=None, weight=None, norm=True):
central_point_dominance: central point dominance of the graph
pagerank: PageRank centrality
eigentrust: eigentrust centrality
eigenvector: eigenvector centrality
hits: hubs and authority centralities
trust_transitivity: pervasive trust transitivity
Notes
......@@ -387,6 +392,7 @@ def eigenvector(g, weight=None, vprop=None, epsilon=1e-6, max_iter=None):
--------
betweenness: betweenness centrality
pagerank: PageRank centrality
hits: hubs and authority centralities
trust_transitivity: pervasive trust transitivity
Notes
......@@ -463,6 +469,155 @@ def eigenvector(g, weight=None, vprop=None, epsilon=1e-6, max_iter=None):
return ee, vprop
def hits(g, weight=None, xprop=None, yprop=None, epsilon=1e-6, max_iter=None):
r"""
Calculate the authority and hub centralities of each vertex in the graph.
Parameters
----------
g : :class:`~graph_tool.Graph`
Graph to be used.
weight : :class:`~graph_tool.PropertyMap` (optional, default: ``None``)
Edge property map with the edge weights.
xprop : :class:`~graph_tool.PropertyMap`, optional (default: ``None``)
Vertex property map where the authority centrality must be stored.
yprop : :class:`~graph_tool.PropertyMap`, optional (default: ``None``)
Vertex property map where the hub centrality must be stored.
epsilon : 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.
Returns
-------
eig : `float`
The largest eigenvalue of the cocitation matrix.
x : :class:`~graph_tool.PropertyMap`
A vertex property map containing the authority centrality values.
y : :class:`~graph_tool.PropertyMap`
A vertex property map containing the hub centrality values.
See Also
--------
betweenness: betweenness centrality
eigenvector: eigenvector centrality
pagerank: PageRank centrality
trust_transitivity: pervasive trust transitivity
Notes
-----
The Hyperlink-Induced Topic Search (HITS) centrality assigns hub
(:math:`\mathbf{y}`) and authority (:math:`\mathbf{x}`) centralities to the
vertices, following:
.. math::
\begin{align}
\mathbf{x} &= \alpha\mathbf{A}\mathbf{y} \\
\mathbf{y} &= \beta\mathbf{A}^T\mathbf{x}
\end{align}
where :math:`\mathbf{A}` is the (weighted) adjacency matrix and
:math:`\lambda = 1/(\alpha\beta)` is the largest eigenvalue of the
cocitation matrix, :math:`\mathbf{A}\mathbf{A}^T`. (Without loss of
generality, we set :math:`\beta=1` in the algorithm.)
The algorithm uses the power method which has a topology-dependent complexity of
:math:`O\left(N\times\frac{-\log\epsilon}{\log|\lambda_1/\lambda_2|}\right)`,
where :math:`N` is the number of vertices, :math:`\epsilon` is the ``epsilon``
parameter, and :math:`\lambda_1` and :math:`\lambda_2` are the largest and
second largest eigenvalues of the (weighted) cocitation matrix, respectively.
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)))
>>> w = g.new_edge_property("double")
>>> w.a = random(g.num_edges()) * 42
>>> l, x, y = gt.hits(g, w)
>>> print(l)
8.1281860004e-05
>>> print(x.a)
[ 3.24207627e-02 9.86207526e-02 1.35737601e-03 2.81221883e-03
0.00000000e+00 3.50637929e-02 6.07494974e-03 1.73442186e-02
7.70292609e-02 3.16281170e-02 6.23685289e-03 5.33251236e-03
3.90261094e-03 1.39799492e-01 3.32727532e-03 2.75600277e-02
4.17864911e-03 1.35434601e-01 1.12371826e-01 3.14487794e-02
1.56239625e-03 1.53154844e-02 0.00000000e+00 9.76595823e-03
6.84470944e-02 3.99230637e-03 1.61380128e-02 6.30396302e-03
6.03036275e-02 1.32849969e-02 3.04151276e-02 5.42617854e-02
2.08833632e-02 2.28460202e-02 7.57731579e-02 1.83496779e-02
4.73479252e-01 9.24456456e-02 6.05629566e-04 6.52238551e-02
0.00000000e+00 8.29910892e-03 1.13757465e-02 4.83645107e-02
2.71118703e-02 5.49281707e-02 1.26313788e-03 1.55217802e-01
1.19145685e-02 5.68602825e-02 4.09272093e-02 6.21803861e-02
2.79433626e-03 6.33529895e-03 1.74347486e-02 4.77049040e-02
2.29321775e-01 9.82639314e-05 1.33196598e-01 1.07649933e-03
2.24082303e-02 2.90035582e-03 4.40055377e-03 1.81697665e-01
7.04846456e-03 0.00000000e+00 7.86454159e-03 7.11419961e-02
2.56300819e-02 2.56393002e-03 1.38263616e-01 0.00000000e+00
2.97294623e-01 3.87958584e-01 1.57869881e-02 1.78305749e-02
4.25241895e-02 8.25617611e-04 9.42672676e-03 1.12595761e-01
5.96375228e-02 3.60860657e-01 2.13119143e-02 0.00000000e+00
1.17954701e-04 2.64968422e-03 5.35828471e-65 1.82261998e-01
2.23512354e-01 1.18366359e-01 5.23661102e-02 1.33577328e-04
1.38032617e-02 5.00359873e-02 7.12945214e-03 4.82585969e-03
8.28225880e-02 2.45545154e-02 3.93940652e-02 2.36085882e-02]
>>> print(y.a)
[ 1.19518911e+01 4.24393415e+01 1.99799643e+00 2.21936973e+00
4.05229016e+00 1.96921433e+00 5.28773128e+01 3.07583159e+00
3.84349214e+00 1.43864706e-01 1.15485811e+01 3.88897379e+01
1.25350058e+01 8.23442356e-01 5.16533892e+00 5.82076701e-01
0.00000000e+00 2.49809577e+01 3.01041295e+00 1.62691697e-01
2.07143530e+00 3.04855423e-01 4.29357896e+00 6.67497836e-01
6.87288592e-01 4.79338810e+00 1.91391421e+00 9.79201735e-01
5.05465736e+00 6.14454206e+00 1.74858481e+00 0.00000000e+00
3.73904255e+00 5.60767290e-01 1.09558455e+01 8.41912714e+00
1.43428505e+00 2.08906862e+01 2.95186438e+00 1.21143763e+00
1.57869686e+01 3.59363866e+00 1.64801081e-03 2.99040323e+00
7.22166777e-02 3.08057330e+00 0.00000000e+00 6.03006855e-63
0.00000000e+00 2.52297825e+01 3.54764499e+00 8.31117522e-01
1.79062457e+00 1.33432369e+01 8.55091617e-04 6.34751541e+00
2.59640589e+00 6.62572431e+00 8.55178204e-02 5.27425893e-01
4.33163271e+00 1.12133638e+00 1.34099527e+00 1.71416121e+01
1.24989675e+01 2.76622179e+00 2.88210334e-01 8.36393997e+00
2.93852144e-01 9.31043745e-01 9.47642397e-02 7.38290147e+00
5.91868714e+00 4.66993445e-01 1.98366671e+00 9.30041719e+00
4.53580404e-01 1.45961552e+00 1.07607675e+01 0.00000000e+00
1.50664001e+01 3.05884574e+00 0.00000000e+00 7.37716446e-01
8.67607706e-01 3.96919920e-01 6.28437918e-01 4.05469431e+01
1.05754629e+00 7.36234170e+00 7.89914973e+00 9.30338044e-02
5.47835232e+00 7.54663318e+00 2.48594880e+00 5.16658324e-01
0.00000000e+00 6.17005885e+00 9.42499389e+00 1.45784289e+00]
References
----------
.. [hits-algorithm] http://en.wikipedia.org/wiki/HITS_algorithm
.. [kleinberg-authoritative] J. Kleinberg, "Authoritative sources in a
hyperlinked environment", Journal of the ACM 46 (5): 604–632, 1999,
:DOI:`10.1145/324133.324140`.
.. [power-method] http://en.wikipedia.org/wiki/Power_iteration
"""
if xprop is None:
xprop = g.new_vertex_property("double")
if yprop is None:
yprop = g.new_vertex_property("double")
if max_iter is None:
max_iter = 0
l = libgraph_tool_centrality.\
get_hits(g._Graph__graph, _prop("e", g, weight), _prop("v", g, xprop),
_prop("v", g, yprop), epsilon, max_iter)
return 1. / l, xprop, yprop
def eigentrust(g, trust_map, vprop=None, norm=False, epsilon=1e-6, max_iter=0,
ret_iter=False):
r"""
......
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