5,303 research outputs found
Graphs in machine learning: an introduction
Graphs are commonly used to characterise interactions between objects of
interest. Because they are based on a straightforward formalism, they are used
in many scientific fields from computer science to historical sciences. In this
paper, we give an introduction to some methods relying on graphs for learning.
This includes both unsupervised and supervised methods. Unsupervised learning
algorithms usually aim at visualising graphs in latent spaces and/or clustering
the nodes. Both focus on extracting knowledge from graph topologies. While most
existing techniques are only applicable to static graphs, where edges do not
evolve through time, recent developments have shown that they could be extended
to deal with evolving networks. In a supervised context, one generally aims at
inferring labels or numerical values attached to nodes using both the graph
and, when they are available, node characteristics. Balancing the two sources
of information can be challenging, especially as they can disagree locally or
globally. In both contexts, supervised and un-supervised, data can be
relational (augmented with one or several global graphs) as described above, or
graph valued. In this latter case, each object of interest is given as a full
graph (possibly completed by other characteristics). In this context, natural
tasks include graph clustering (as in producing clusters of graphs rather than
clusters of nodes in a single graph), graph classification, etc. 1 Real
networks One of the first practical studies on graphs can be dated back to the
original work of Moreno [51] in the 30s. Since then, there has been a growing
interest in graph analysis associated with strong developments in the modelling
and the processing of these data. Graphs are now used in many scientific
fields. In Biology [54, 2, 7], for instance, metabolic networks can describe
pathways of biochemical reactions [41], while in social sciences networks are
used to represent relation ties between actors [66, 56, 36, 34]. Other examples
include powergrids [71] and the web [75]. Recently, networks have also been
considered in other areas such as geography [22] and history [59, 39]. In
machine learning, networks are seen as powerful tools to model problems in
order to extract information from data and for prediction purposes. This is the
object of this paper. For more complete surveys, we refer to [28, 62, 49, 45].
In this section, we introduce notations and highlight properties shared by most
real networks. In Section 2, we then consider methods aiming at extracting
information from a unique network. We will particularly focus on clustering
methods where the goal is to find clusters of vertices. Finally, in Section 3,
techniques that take a series of networks into account, where each network i
Uncovering latent structure in valued graphs: A variational approach
As more and more network-structured data sets are available, the statistical
analysis of valued graphs has become common place. Looking for a latent
structure is one of the many strategies used to better understand the behavior
of a network. Several methods already exist for the binary case. We present a
model-based strategy to uncover groups of nodes in valued graphs. This
framework can be used for a wide span of parametric random graphs models and
allows to include covariates. Variational tools allow us to achieve approximate
maximum likelihood estimation of the parameters of these models. We provide a
simulation study showing that our estimation method performs well over a broad
range of situations. We apply this method to analyze host--parasite interaction
networks in forest ecosystems.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS361 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Strategies for online inference of model-based clustering in large and growing networks
In this paper we adapt online estimation strategies to perform model-based
clustering on large networks. Our work focuses on two algorithms, the first
based on the SAEM algorithm, and the second on variational methods. These two
strategies are compared with existing approaches on simulated and real data. We
use the method to decipher the connexion structure of the political websphere
during the US political campaign in 2008. We show that our online EM-based
algorithms offer a good trade-off between precision and speed, when estimating
parameters for mixture distributions in the context of random graphs.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS359 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
The random subgraph model for the analysis of an ecclesiastical network in Merovingian Gaul
In the last two decades many random graph models have been proposed to
extract knowledge from networks. Most of them look for communities or, more
generally, clusters of vertices with homogeneous connection profiles. While the
first models focused on networks with binary edges only, extensions now allow
to deal with valued networks. Recently, new models were also introduced in
order to characterize connection patterns in networks through mixed
memberships. This work was motivated by the need of analyzing a historical
network where a partition of the vertices is given and where edges are typed. A
known partition is seen as a decomposition of a network into subgraphs that we
propose to model using a stochastic model with unknown latent clusters. Each
subgraph has its own mixing vector and sees its vertices associated to the
clusters. The vertices then connect with a probability depending on the
subgraphs only, while the types of edges are assumed to be sampled from the
latent clusters. A variational Bayes expectation-maximization algorithm is
proposed for inference as well as a model selection criterion for the
estimation of the cluster number. Experiments are carried out on simulated data
to assess the approach. The proposed methodology is then applied to an
ecclesiastical network in Merovingian Gaul. An R code, called Rambo,
implementing the inference algorithm is available from the authors upon
request.Comment: Published in at http://dx.doi.org/10.1214/13-AOAS691 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Non-parametric Bayesian modeling of complex networks
Modeling structure in complex networks using Bayesian non-parametrics makes
it possible to specify flexible model structures and infer the adequate model
complexity from the observed data. This paper provides a gentle introduction to
non-parametric Bayesian modeling of complex networks: Using an infinite mixture
model as running example we go through the steps of deriving the model as an
infinite limit of a finite parametric model, inferring the model parameters by
Markov chain Monte Carlo, and checking the model's fit and predictive
performance. We explain how advanced non-parametric models for complex networks
can be derived and point out relevant literature
Model Selection in Overlapping Stochastic Block Models
Networks are a commonly used mathematical model to describe the rich set of
interactions between objects of interest. Many clustering methods have been
developed in order to partition such structures, among which several rely on
underlying probabilistic models, typically mixture models. The relevant hidden
structure may however show overlapping groups in several applications. The
Overlapping Stochastic Block Model (2011) has been developed to take this
phenomenon into account. Nevertheless, the problem of the choice of the number
of classes in the inference step is still open. To tackle this issue, we
consider the proposed model in a Bayesian framework and develop a new criterion
based on a non asymptotic approximation of the marginal log-likelihood. We
describe how the criterion can be computed through a variational Bayes EM
algorithm, and demonstrate its efficiency by running it on both simulated and
real data.Comment: articl
Mixed membership stochastic blockmodels
Observations consisting of measurements on relationships for pairs of objects
arise in many settings, such as protein interaction and gene regulatory
networks, collections of author-recipient email, and social networks. Analyzing
such data with probabilisic models can be delicate because the simple
exchangeability assumptions underlying many boilerplate models no longer hold.
In this paper, we describe a latent variable model of such data called the
mixed membership stochastic blockmodel. This model extends blockmodels for
relational data to ones which capture mixed membership latent relational
structure, thus providing an object-specific low-dimensional representation. We
develop a general variational inference algorithm for fast approximate
posterior inference. We explore applications to social and protein interaction
networks.Comment: 46 pages, 14 figures, 3 table
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