Cycle-based Cluster Variational Method for Direct and Inverse Inference

We elaborate on the idea that loop corrections to belief propagation could be dealt with in a systematic way on pairwise Markov random fields, by using the elements of a cycle basis to define region in a generalized belief propagation setting. The region graph is specified in such a way as to avoid dual loops as much as possible, by discarding redundant Lagrange multipliers, in order to facilitate the convergence, while avoiding instabilities associated to minimal factor graph construction. We end up with a two-level algorithm, where a belief propagation algorithm is run alternatively at the level of each cycle and at the inter-region level. The inverse problem of finding the couplings of a Markov random field from empirical covariances can be addressed region wise. It turns out that this can be done efficiently in particular in the Ising context, where fixed point equations can be derived along with a one-parameter log likelihood function to minimize. Numerical experiments confirm the effectiveness of these considerations both for the direct and inverse MRF inference.Comment: 47 pages, 16 figure

Truncating the loop series expansion for Belief Propagation

Recently, M. Chertkov and V.Y. Chernyak derived an exact expression for the partition sum (normalization constant) corresponding to a graphical model, which is an expansion around the Belief Propagation solution. By adding correction terms to the BP free energy, one for each "generalized loop" in the factor graph, the exact partition sum is obtained. However, the usually enormous number of generalized loops generally prohibits summation over all correction terms. In this article we introduce Truncated Loop Series BP (TLSBP), a particular way of truncating the loop series of M. Chertkov and V.Y. Chernyak by considering generalized loops as compositions of simple loops. We analyze the performance of TLSBP in different scenarios, including the Ising model, regular random graphs and on Promedas, a large probabilistic medical diagnostic system. We show that TLSBP often improves upon the accuracy of the BP solution, at the expense of increased computation time. We also show that the performance of TLSBP strongly depends on the degree of interaction between the variables. For weak interactions, truncating the series leads to significant improvements, whereas for strong interactions it can be ineffective, even if a high number of terms is considered.Comment: 31 pages, 12 figures, submitted to Journal of Machine Learning Researc

Factored expectation propagation for input-output FHMM models in systems biology

We consider the problem of joint modelling of metabolic signals and gene expression in systems biology applications. We propose an approach based on input-output factorial hidden Markov models and propose a structured variational inference approach to infer the structure and states of the model. We start from the classical free form structured variational mean field approach and use a expectation propagation to approximate the expectations needed in the variational loop. We show that this corresponds to a factored expectation constrained approximate inference. We validate our model through extensive simulations and demonstrate its applicability on a real world bacterial data set

Quantifying the tension between the Higgs mass and (g-2)_mu in the CMSSM

Supersymmetry has been often invoqued as the new physics that might reconcile the experimental muon magnetic anomaly, a_mu, with the theoretical prediction (basing the computation of the hadronic contribution on e^+ e^- data). However, in the context of the CMSSM, the required supersymmetric contributions (which grow with decreasing supersymmetric masses) are in potential tension with a possibly large Higgs mass (which requires large stop masses). In the limit of very large m_h supersymmetry gets decoupled, and the CMSSM must show the same discrepancy as the SM with a_mu . But it is much less clear for which size of m_h does the tension start to be unbearable. In this paper, we quantify this tension with the help of Bayesian techniques. We find that for m_h > 125 GeV the maximum level of discrepancy given current data (~ 3.3 sigma) is already achieved. Requiring less than 3 sigma discrepancy, implies m_h < 120 GeV. For a larger Higgs mass we should give up either the CMSSM model or the computation of a_mu based on e^+ e^-; or accept living with such inconsistency

Loop corrections in spin models through density consistency

Computing marginal distributions of discrete or semidiscrete Markov random fields (MRFs) is a fundamental, generally intractable problem with a vast number of applications in virtually all fields of science. We present a new family of computational schemes to approximately calculate the marginals of discrete MRFs. This method shares some desirable properties with belief propagation, in particular, providing exact marginals on acyclic graphs, but it differs with the latter in that it includes some loop corrections; i.e., it takes into account correlations coming from all cycles in the factor graph. It is also similar to the adaptive Thouless-Anderson-Palmer method, but it differs with the latter in that the consistency is not on the first two moments of the distribution but rather on the value of its density on a subset of values. The results on finite-dimensional Isinglike models show a significant improvement with respect to the Bethe-Peierls (tree) approximation in all cases and with respect to the plaquette cluster variational method approximation in many cases. In particular, for the critical inverse temperature $\beta_{c}$ of the homogeneous hypercubic lattice, the expansion of $\left(d\beta_{c}\right)^{-1}$ around $d=\infty$ of the proposed scheme is exact up to the $d^{-4}$ order, whereas the two latter are exact only up to the $d^{-2}$ order.Comment: 12 pages, 3 figures, 1 tabl

Loop series for discrete statistical models on graphs

In this paper we present derivation details, logic, and motivation for the loop calculus introduced in \cite{06CCa}. Generating functions for three inter-related discrete statistical models are each expressed in terms of a finite series. The first term in the series corresponds to the Bethe-Peierls (Belief Propagation)-BP contribution, the other terms are labeled by loops on the factor graph. All loop contributions are simple rational functions of spin correlation functions calculated within the BP approach. We discuss two alternative derivations of the loop series. One approach implements a set of local auxiliary integrations over continuous fields with the BP contribution corresponding to an integrand saddle-point value. The integrals are replaced by sums in the complimentary approach, briefly explained in \cite{06CCa}. A local gauge symmetry transformation that clarifies an important invariant feature of the BP solution, is revealed in both approaches. The partition function remains invariant while individual terms change under the gauge transformation. The requirement for all individual terms to be non-zero only for closed loops in the factor graph (as opposed to paths with loose ends) is equivalent to fixing the first term in the series to be exactly equal to the BP contribution. Further applications of the loop calculus to problems in statistical physics, computer and information sciences are discussed.Comment: 20 pages, 3 figure