Learning tractable multidimensional Bayesian network classifiers

Multidimensional classification has become one of the most relevant topics in view of the many domains that require a vector of class values to be assigned to a vector of given features. The popularity of multidimensional Bayesian network classifiers has increased in the last few years due to their expressive power and the existence of methods for learning different families of these models. The problem with this approach is that the computational cost of using the learned models is usually high, especially if there are a lot of class variables. Class-bridge decomposability means that the multidimensional classification problem can be divided into multiple subproblems for these models. In this paper, we prove that class-bridge decomposability can also be used to guarantee the tractability of the models. We also propose a strategy for efficiently bounding their inference complexity, providing a simple learning method with an order-based search that obtains tractable multidimensional Bayesian network classifiers. Experimental results show that our approach is competitive with other methods in the state of the art and ensures the tractability of the learned models

Molecular Network Control Through Boolean Canalization

Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of network modeling where each layer of canalization adds a degree of stability in the dynamics of the network. Recently, dynamic network control approaches have been used for the design of new therapeutic interventions and for other applications such as stem cell reprogramming. This work studies the role of canalization in the control of Boolean molecular networks. It provides a method for identifying the potential edges to control in the wiring diagram of a network for avoiding undesirable state transitions. The method is based on identifying appropriate input-output combinations on undesirable transitions that can be modified using the edges in the wiring diagram of the network. Moreover, a method for estimating the number of changed transitions in the state space of the system as a result of an edge deletion in the wiring diagram is presented. The control methods of this paper were applied to a mutated cell-cycle model and to a p53-mdm2 model to identify potential control targets

Containing epidemic outbreaks by message-passing techniques

The problem of targeted network immunization can be defined as the one of finding a subset of nodes in a network to immunize or vaccinate in order to minimize a tradeoff between the cost of vaccination and the final (stationary) expected infection under a given epidemic model. Although computing the expected infection is a hard computational problem, simple and efficient mean-field approximations have been put forward in the literature in recent years. The optimization problem can be recast into a constrained one in which the constraints enforce local mean-field equations describing the average stationary state of the epidemic process. For a wide class of epidemic models, including the susceptible-infected-removed and the susceptible-infected-susceptible models, we define a message-passing approach to network immunization that allows us to study the statistical properties of epidemic outbreaks in the presence of immunized nodes as well as to find (nearly) optimal immunization sets for a given choice of parameters and costs. The algorithm scales linearly with the size of the graph and it can be made efficient even on large networks. We compare its performance with topologically based heuristics, greedy methods, and simulated annealing

Coarse graining methods for spin net and spin foam models

We undertake first steps in making a class of discrete models of quantum gravity, spin foams, accessible to a large scale analysis by numerical and computational methods. In particular, we apply Migdal-Kadanoff and Tensor Network Renormalization schemes to spin net and spin foam models based on finite Abelian groups and introduce `cutoff models' to probe the fate of gauge symmetries under various such approximated renormalization group flows. For the Tensor Network Renormalization analysis, a new Gauss constraint preserving algorithm is introduced to improve numerical stability and aid physical interpretation. We also describe the fixed point structure and establish an equivalence of certain models.Comment: 39 pages, 13 figures, 1 tabl

Maximum likelihood estimation based on the Laplace approximation for p2 network regression models

The class of p2 models is suitable for modeling binary relation data in social network analysis. A p2 model is essentially a regression model for bivariate binary responses, featuring within‐dyad dependence and correlated crossed random effects to represent heterogeneity of actors. Despite some desirable properties, these models are used less frequently in empirical applications than other models for network data. A possible reason for this is due to the limited possibilities for this model for accounting for (and explicitly modeling) structural dependence beyond the dyad as can be done in exponential random graph models. Another motive, however, may lie in the computational difficulties existing to estimate such models by means of the methods proposed in the literature, such as joint maximization methods and Bayesian methods. The aim of this article is to investigate maximum likelihood estimation based on the Laplace approximation approach, that can be refined by importance sampling. Practical implementation of such methods can be performed in an efficient manner, and the article provides details on a software implementation using R. Numerical examples and simulation studies illustrate the methodology