Network reconstruction
----------------------
An important application of generative models is to be able to
generalize from observations and make predictions that go beyond what is
seen in the data. This is particularly useful when the network we
observe is incomplete, or contains errors, i.e. some of the edges are
either missing or are outcomes of mistakes in measurement, or is not
even observed at all. In this situation, we can use statistical
inference to reconstruct the original network. Following
[peixoto-reconstructing-2018]_, if :math:`\boldsymbol{\mathcal{D}}` is
the observed data, the network can be reconstructed according to the
posterior distribution,
.. math::
P(\boldsymbol A, \boldsymbol b | \boldsymbol{\mathcal{D}}) =
\frac{P(\boldsymbol{\mathcal{D}} | \boldsymbol A)P(\boldsymbol A, \boldsymbol b)}{P(\boldsymbol{\mathcal{D}})}
where the likelihood :math:`P(\boldsymbol{\mathcal{D}}|\boldsymbol A)`
models the measurement process, and for the prior :math:`P(\boldsymbol
A, \boldsymbol b)` we use the SBM as before. This means that when
performing reconstruction, we sample both the community structure
:math:`\boldsymbol b` and the network :math:`\boldsymbol A` itself from
the posterior distribution. From it, we can obtain the marginal probability
of each edge,
.. math::
\pi_{ij} = \sum_{\boldsymbol A, \boldsymbol b}A_{ij}P(\boldsymbol A, \boldsymbol b | \boldsymbol{\mathcal{D}}).
Based on the marginal posterior probabilities, the best estimate for the
whole underlying network :math:`\boldsymbol{\hat{A}}` is given by the
maximum of this distribution,
.. math::
\hat A_{ij} =
\begin{cases}
1 & \text{ if } \pi_{ij} > \frac{1}{2},\\
0 & \text{ if } \pi_{ij} < \frac{1}{2}.\\
\end{cases}
We can also make estimates :math:`\hat y` of arbitrary scalar network
properties :math:`y(\boldsymbol A)` via posterior averages,
.. math::
\begin{align}
\hat y &= \sum_{\boldsymbol A, \boldsymbol b}y(\boldsymbol A)P(\boldsymbol A, \boldsymbol b | \boldsymbol{\mathcal{D}}),\\
\sigma^2_y &= \sum_{\boldsymbol A, \boldsymbol b}(y(\boldsymbol A)-\hat y)^2P(\boldsymbol A, \boldsymbol b | \boldsymbol{\mathcal{D}})
\end{align}
with uncertainty given by :math:`\sigma_y`. This is gives us a complete
probabilistic reconstruction framework that fully reflects both the
information and the uncertainty in the measurement data. Furthermore,
the use of the SBM means that the reconstruction can take advantage of
the *correlations* observed in the data to further inform it, which
generally can lead to substantial improvements
[peixoto-reconstructing-2018]_ [peixoto-network-2019]_.
In graph-tool there is support for reconstruction with the above
framework for three measurement processes: 1. Repeated measurements with
uniform errors (via
:class:`~graph_tool.inference.uncertain_blockmodel.MeasuredBlockState`), 2. Repeated
measurements with heterogeneous errors (via
:class:`~graph_tool.inference.uncertain_blockmodel.MixedMeasuredBlockState`),
and 3. Extraneously obtained edge probabilities (via
:class:`~graph_tool.inference.uncertain_blockmodel.UncertainBlockState`),
which we describe in the following.
In addition, it is also possible to reconstruct networks from observed
dynamical, as described in :ref:`reconstruction_dynamics`.
Measured networks
+++++++++++++++++
This model assumes that the node pairs :math:`(i,j)` were measured
:math:`n_{ij}` times, and an edge has been recorded :math:`x_{ij}`
times, where a missing edge occurs with probability :math:`p` and a
spurious edge occurs with probability :math:`q`, uniformly for all node
pairs, yielding a likelihood
.. math::
P(\boldsymbol x | \boldsymbol n, \boldsymbol A, p, q) =
\prod_{i`__, which
specify the amount of prior knowledge we have on the noise
parameters. An important special case, which is the default unless
otherwise specified, is when we are completely agnostic *a priori* about
the noise magnitudes, and all hyperparameters are unity,
.. math::
P(\boldsymbol x | \boldsymbol n, \boldsymbol A) \equiv
P(\boldsymbol x | \boldsymbol n, \boldsymbol A, \alpha=1,\beta=1,\mu=1,\nu=1).
In this situation the priors :math:`P(p|\alpha=1,\beta=1)` and
:math:`P(q|\mu=1,\nu=1)` are uniform distribution in the interval :math:`[0,1]`.
.. note::
It is important to emphasize that since this approach makes use of
the *correlations* between edges to inform the reconstruction, as
described by the inferred SBM, this means it can also be used when
only single measurements have been performed, :math:`n_{ij}=1`, and
the error magnitudes :math:`p` and :math:`q` are unknown. Since every
arbitrary adjacency matrix can be cast in this setting, this method
can be used to reconstruct networks for which no error assessments of
any kind have been provided.
Below, we illustrate how the reconstruction can be performed with a
simple example, using
:class:`~graph_tool.inference.uncertain_blockmodel.MeasuredBlockState`:
.. testsetup:: measured
import os
try:
os.chdir("demos/inference")
except FileNotFoundError:
pass
np.random.seed(42)
gt.seed_rng(44)
.. testcode:: measured
g = gt.collection.data["lesmis"].copy()
# pretend we have measured and observed each edge twice
n = g.new_ep("int", 2) # number of measurements
x = g.new_ep("int", 2) # number of observations
e = g.edge(11, 36)
x[e] = 1 # pretend we have observed edge (11, 36) only once
e = g.add_edge(15, 73)
n[e] = 2 # pretend we have measured non-edge (15, 73) twice,
x[e] = 1 # but observed it as an edge once.
bs = [g.get_vertices()] + [zeros(1)] * 5 # initial hierarchical partition
# We inititialize MeasuredBlockState, assuming that each non-edge has
# been measured only once (as opposed to twice for the observed
# edges), as specified by the 'n_default' and 'x_default' parameters.
state = gt.MeasuredBlockState(g, n=n, n_default=1, x=x, x_default=0,
state_args=dict(bs=bs))
# We will first equilibrate the Markov chain
gt.mcmc_equilibrate(state, wait=1000, mcmc_args=dict(niter=10))
# Now we collect the marginals for exactly 100,000 sweeps, at
# intervals of 10 sweeps:
u = None # marginal posterior edge probabilities
pv = None # marginal posterior group membership probabilities
cs = [] # average local clustering coefficient
def collect_marginals(s):
global pv, u, cs
u = s.collect_marginal(u)
bstate = s.get_block_state()
pv = bstate.levels[0].collect_vertex_marginals(pv)
cs.append(gt.local_clustering(s.get_graph()).fa.mean())
gt.mcmc_equilibrate(state, force_niter=10000, mcmc_args=dict(niter=10),
callback=collect_marginals)
eprob = u.ep.eprob
print("Posterior probability of edge (11, 36):", eprob[u.edge(11, 36)])
print("Posterior probability of non-edge (15, 73):", eprob[u.edge(15, 73)])
print("Estimated average local clustering: %g ± %g" % (np.mean(cs), np.std(cs)))
Which yields the following output:
.. testoutput:: measured
Posterior probability of edge (11, 36): 0.890889...
Posterior probability of non-edge (15, 73): 0.056005...
Estimated average local clustering: 0.572758 ± 0.003998...
We have a successful reconstruction, where both ambiguous adjacency
matrix entries are correctly recovered. The value for the average
clustering coefficient is also correctly estimated, and is compatible
with the true value :math:`0.57313675`, within the estimated error.
Below we visualize the maximum marginal posterior estimate of the
reconstructed network:
.. testcode:: measured
# The maximum marginal posterior estimator can be obtained by
# filtering the edges with probability larger than .5
u = gt.GraphView(u, efilt=u.ep.eprob.fa > .5)
# Mark the recovered true edges as red, and the removed spurious edges as green
ecolor = u.new_ep("vector", val=[0, 0, 0, .6])
for e in u.edges():
if g.edge(e.source(), e.target()) is None or (e.source(), e.target()) == (11, 36):
ecolor[e] = [1, 0, 0, .6]
for e in g.edges():
if u.edge(e.source(), e.target()) is None:
ne = u.add_edge(e.source(), e.target())
ecolor[ne] = [0, 1, 0, .6]
# Duplicate the internal block state with the reconstructed network
# u, for visualization purposes.
bstate = state.get_block_state()
bstate = bstate.levels[0].copy(g=u)
pv = u.own_property(pv)
edash = u.new_ep("vector")
edash[u.edge(15, 73)] = [.1, .1, 0]
bstate.draw(pos=u.own_property(g.vp.pos), vertex_shape="pie", vertex_pie_fractions=pv,
edge_color=ecolor, edge_dash_style=edash, edge_gradient=None,
output="lesmis-reconstruction-marginals.svg")
.. figure:: lesmis-reconstruction-marginals.*
:align: center
:width: 450px
Reconstructed network of characters in the novel Les Misérables,
assuming that each edge has been measured and recorded twice, and
each non-edge has been measured only once, with the exception of edge
(11, 36), shown in red, and non-edge (15, 73), shown in green, which
have been measured twice and recorded as an edge once. Despite the
ambiguity, both errors are successfully corrected by the
reconstruction. The pie fractions on the nodes correspond to the
probability of being in group associated with the respective color.
Heterogeneous errors
^^^^^^^^^^^^^^^^^^^^
In a more general scenario the measurement errors can be different for
each node pair, i.e. :math:`p_{ij}` and :math:`q_{ij}` are the missing
and spurious edge probabilities for node pair :math:`(i,j)`. The
measurement likelihood then becomes
.. math::
P(\boldsymbol x | \boldsymbol n, \boldsymbol A, \boldsymbol p, \boldsymbol q) =
\prod_{i`__, like
before. Instead of pre-specifying the hyperparameters, we include them
from the posterior distribution
.. math::
P(\boldsymbol A, \boldsymbol b, \alpha,\beta,\mu,\nu | \boldsymbol x, \boldsymbol n) =
\frac{P(\boldsymbol x | \boldsymbol n, \boldsymbol A, \alpha,\beta,\mu,\nu)P(\boldsymbol A, \boldsymbol b)P(\alpha,\beta,\mu,\nu)}{P(\boldsymbol x| \boldsymbol n)},
where :math:`P(\alpha,\beta,\mu,\nu)\propto 1` is a uniform hyperprior.
Operationally, the inference with this model works similarly to the one
with uniform error rates, as we see with the same example:
.. testcode:: measured
state = gt.MixedMeasuredBlockState(g, n=n, n_default=1, x=x, x_default=0,
state_args=dict(bs=bs))
# We will first equilibrate the Markov chain
gt.mcmc_equilibrate(state, wait=1000, mcmc_args=dict(niter=10))
# Now we collect the marginals for exactly 100,000 sweeps, at
# intervals of 10 sweeps:
u = None # marginal posterior edge probabilities
pv = None # marginal posterior group membership probabilities
cs = [] # average local clustering coefficient
gt.mcmc_equilibrate(state, force_niter=10000, mcmc_args=dict(niter=10),
callback=collect_marginals)
eprob = u.ep.eprob
print("Posterior probability of edge (11, 36):", eprob[u.edge(11, 36)])
print("Posterior probability of non-edge (15, 73):", eprob[u.edge(15, 73)])
print("Estimated average local clustering: %g ± %g" % (np.mean(cs), np.std(cs)))
Which yields:
.. testoutput:: measured
Posterior probability of edge (11, 36): 0.515651...
Posterior probability of non-edge (15, 73): 0.009000...
Estimated average local clustering: 0.571673 ± 0.003228...
The results are very similar to the ones obtained with the uniform model
in this case, but can be quite different in situations where a large
number of measurements has been performed (see
[peixoto-reconstructing-2018]_ for details).
Extraneous error estimates
++++++++++++++++++++++++++
In some situations the edge uncertainties are estimated by means other
than repeated measurements, using domain-specific models. Here we
consider the general case where the error estimates are extraneously
provided as independent edge probabilities :math:`\boldsymbol Q`,
.. math::
P_Q(\boldsymbol A | \boldsymbol Q) = \prod_{i .5)
# Mark the recovered true edges as red, and the removed spurious edges as green
ecolor = u.new_ep("vector", val=[0, 0, 0, .6])
edash = u.new_ep("vector")
for e in u.edges():
if g.edge(e.source(), e.target()) is None or (e.source(), e.target()) == (11, 36):
ecolor[e] = [1, 0, 0, .6]
for e in g.edges():
if u.edge(e.source(), e.target()) is None:
ne = u.add_edge(e.source(), e.target())
ecolor[ne] = [0, 1, 0, .6]
if (e.source(), e.target()) == (15, 73):
edash[ne] = [.1, .1, 0]
bstate = state.get_block_state()
bstate = bstate.levels[0].copy(g=u)
pv = u.own_property(pv)
bstate.draw(pos=u.own_property(g.vp.pos), vertex_shape="pie", vertex_pie_fractions=pv,
edge_color=ecolor, edge_dash_style=edash, edge_gradient=None,
output="lesmis-uncertain-reconstruction-marginals.svg")
.. figure:: lesmis-uncertain-reconstruction-marginals.*
:align: center
:width: 450px
Reconstructed network of characters in the novel Les Misérables,
assuming that each edge as a measurement probability of
:math:`.98`. Edge (11, 36), shown in red, and non-edge (15, 73),
shown in green, both have probability :math:`0.5`. Despite the
ambiguity, both errors are successfully corrected by the
reconstruction. The pie fractions on the nodes correspond to the
probability of being in group associated with the respective color.
.. include:: _reconstruction_dynamics.rst