Searching for network modules

When analyzing complex networks a key target is to uncover their modular structure, which means searching for a family of modules, namely node subsets spanning each a subnetwork more densely connected than the average. This work proposes a novel type of objective function for graph clustering, in the form of a multilinear polynomial whose coefficients are determined by network topology. It may be thought of as a potential function, to be maximized, taking its values on fuzzy clusterings or families of fuzzy subsets of nodes over which every node distributes a unit membership. When suitably parametrized, this potential is shown to attain its maximum when every node concentrates its all unit membership on some module. The output thus is a partition, while the original discrete optimization problem is turned into a continuous version allowing to conceive alternative search strategies. The instance of the problem being a pseudo-Boolean function assigning real-valued cluster scores to node subsets, modularity maximization is employed to exemplify a so-called quadratic form, in that the scores of singletons and pairs also fully determine the scores of larger clusters, while the resulting multilinear polynomial potential function has degree 2. After considering further quadratic instances, different from modularity and obtained by interpreting network topology in alternative manners, a greedy local-search strategy for the continuous framework is analytically compared with an existing greedy agglomerative procedure for the discrete case. Overlapping is finally discussed in terms of multiple runs, i.e. several local searches with different initializations.Comment: 10 page

Pairwise MRF Calibration by Perturbation of the Bethe Reference Point

We investigate different ways of generating approximate solutions to the pairwise Markov random field (MRF) selection problem. We focus mainly on the inverse Ising problem, but discuss also the somewhat related inverse Gaussian problem because both types of MRF are suitable for inference tasks with the belief propagation algorithm (BP) under certain conditions. Our approach consists in to take a Bethe mean-field solution obtained with a maximum spanning tree (MST) of pairwise mutual information, referred to as the \emph{Bethe reference point}, for further perturbation procedures. We consider three different ways following this idea: in the first one, we select and calibrate iteratively the optimal links to be added starting from the Bethe reference point; the second one is based on the observation that the natural gradient can be computed analytically at the Bethe point; in the third one, assuming no local field and using low temperature expansion we develop a dual loop joint model based on a well chosen fundamental cycle basis. We indeed identify a subclass of planar models, which we refer to as \emph{Bethe-dual graph models}, having possibly many loops, but characterized by a singly connected dual factor graph, for which the partition function and the linear response can be computed exactly in respectively O(N) and $O(N^2)$ operations, thanks to a dual weight propagation (DWP) message passing procedure that we set up. When restricted to this subclass of models, the inverse Ising problem being convex, becomes tractable at any temperature. Experimental tests on various datasets with refined $L_0$ or $L_1$ regularization procedures indicate that these approaches may be competitive and useful alternatives to existing ones.Comment: 54 pages, 8 figure. section 5 and refs added in V

General Bounds for Incremental Maximization

We propose a theoretical framework to capture incremental solutions to cardinality constrained maximization problems. The defining characteristic of our framework is that the cardinality/support of the solution is bounded by a value $k\in\mathbb{N}$ that grows over time, and we allow the solution to be extended one element at a time. We investigate the best-possible competitive ratio of such an incremental solution, i.e., the worst ratio over all $k$ between the incremental solution after $k$ steps and an optimum solution of cardinality $k$. We define a large class of problems that contains many important cardinality constrained maximization problems like maximum matching, knapsack, and packing/covering problems. We provide a general $2.618$-competitive incremental algorithm for this class of problems, and show that no algorithm can have competitive ratio below $2.18$ in general. In the second part of the paper, we focus on the inherently incremental greedy algorithm that increases the objective value as much as possible in each step. This algorithm is known to be $1.58$-competitive for submodular objective functions, but it has unbounded competitive ratio for the class of incremental problems mentioned above. We define a relaxed submodularity condition for the objective function, capturing problems like maximum (weighted) ($b$-)matching and a variant of the maximum flow problem. We show that the greedy algorithm has competitive ratio (exactly) $2.313$ for the class of problems that satisfy this relaxed submodularity condition. Note that our upper bounds on the competitive ratios translate to approximation ratios for the underlying cardinality constrained problems.Comment: fixed typo