text: It has recently been observed that the permanent of a nonnegative square matrix, i.e., of a square matrix containing only nonnegative real entries, can very well be approximated by solving a certain Bethe free energy function minimization problem with the help of the sum-product algorithm. We call the resulting approximation of the permanent the Bethe permanent. In this paper, we give reasons why this approach to approximating the permanent works well. Namely, we show that the Bethe free energy function is convex and that the sum-product algorithm finds its minimum efficiently. We then discuss the fact that the permanent is lower bounded by the Bethe permanent, and we comment on potential upper bounds on the permanent based on the Bethe permanent. We also present a combinatorial characterization of the Bethe permanent in terms of permanents of so-called lifted versions of the matrix under consideration. Moreover, we comment on possibilities to modify the Bethe permanent so that it approximates the permanent even better, and we conclude the paper with some observations and conjectures about permanent-based pseudocodewords and permanent-based kernels.
  @cite_48: We discuss schemes for exact and approximate computations of permanents, and compare them with each other. Specifically, we analyze and generalize the Belief Propagation (BP) approach to computing the permanent of a non-negative matrix. Known bounds and conjectures are verified in experiments, and some new theoretical relations, bounds and conjectures are proposed. We introduce a fractional free energy functional parameterized by a scalar parameter @math , where @math corresponds to the BP limit and @math corresponds to the exclusion principle Mean-Field (MF) limit, and show monotonicity and continuity of the functional with @math . We observe that the optimal value of @math , where the @math -parameterized functional is equal to the exact free energy (defined as the minus log of the permanent), lies in the @math range, with the low and high values from the range producing provable low and upper bounds for the permanent. Our experimental analysis suggests that the optimal @math varies for different ensembles considered but it always lies in the @math interval. Besides, for all ensembles considered the behavior of the optimal @math is highly distinctive, thus offering a lot of practical potential for estimating permanents of non-negative matrices via the fractional free energy functional approach.
  @cite_65: 
  @cite_83: 
  @cite_23: Methods to extract information from the tracking of mobile objects particles have broad interest in biological and physical sciences. Techniques based on simple criteria of proximity in time-consecutive snapshots are useful to identify the trajectories of the particles. However, they become problematic as the motility and or the density of the particles increases due to uncertainties on the trajectories that particles followed during the images’ acquisition time. Here, we report an efficient method for learning parameters of the dynamics of the particles from their positions in time-consecutive images. Our algorithm belongs to the class of message-passing algorithms, known in computer science, information theory, and statistical physics as belief propagation (BP). The algorithm is distributed, thus allowing parallel implementation suitable for computations on multiple machines without significant intermachine overhead. We test our method on the model example of particle tracking in turbulent flows, which is particularly challenging due to the strong transport that those flows produce. Our numerical experiments show that the BP algorithm compares in quality with exact Markov Chain Monte Carlo algorithms, yet BP is far superior in speed. We also suggest and analyze a random distance model that provides theoretical justification for BP accuracy. Methods developed here systematically formulate the problem of particle tracking and provide fast and reliable tools for the model’s extensive range of applications.
  @cite_76: In this paper we present the derivation details, logic, and motivation for the three loop calculus introduced in Chertkov and Chernyak (2006 Phys. Rev. E 73 065102(R)). Generating functions for each of the three interrelated discrete statistical models are 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 labelled 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 complementary approach, briefly explained in Chertkov and Chernyak (2006 Phys. Rev. E 73 065102(R)). Local gauge symmetry transformations that clarify an important invariant feature of the BP solution are revealed in both approaches. The individual terms change under the gauge transformation while the partition function remains invariant. The requirement for all individual terms to be nonzero 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.
  @cite_11: We consider computation of the permanent of a positive (N × N) non-negative matrix, P = (Pji|i, j = 1, ..., N), or equivalently the problem of weighted counting of the perfect matchings over the complete bipartite graph KN, N. The problem is known to be of likely exponential complexity. Stated as the partition function Z of a graphical model, the problem allows for exact loop calculus representation (Chertkov M and Chernyak V 2006 Phys. Rev. E 72 065102) in terms of an interior minimum of the Bethe free energy functional over non-integer doubly stochastic matrix of marginal beliefs, β = (βji|i, j = 1, ..., N), also correspondent to a fixed point of the iterative message-passing algorithm of the belief propagation (BP) type. Our main result is an explicit expression of the exact partition function (permanent) in terms of the matrix of BP marginals, β, as Z = Perm(P) = ZBP Perm(βji(1 − βji)) ∏i, j(1 − βji), where ZBP is the BP expression for the permanent stated explicitly in terms of β. We give two derivations of the formula, a direct one based on the Bethe free energy and an alternative one combining the Ihara graph-ζ function and the loop calculus approaches. Assuming that the matrix β of the BP marginals is calculated, we provide two lower bounds and one upper bound to estimate the multiplicative term. Two complementary lower bounds are based on the Gurvits–van der Waerden theorem and on a relation between the modified permanent and determinant, respectively.
summary: Besides the already cited papers @cite_65 @cite_83 on Bethe-approximation-based methods to the permanent of a non-negative matrix, some aspects of the Bethe free energy function were analyzed by Watanabe and Chertkov in @cite_11 and by Chertkov, Kroc, Krzakala, Vergassola, and Zdeborov 'a in @cite_23 . (In particular, the paper @cite_11 applied the loop calculus technique by Chertkov and Chernyak @cite_76 .) Very recent work in that line of research is presented in a paper by A. B. Yedidia and Chertkov @cite_48 that studies so-called fractional free energy functionals, and resulting lower and upper bounds on the permanent of a non-negative matrix.