Convex Relaxations for Permutation Problems

Seriation seeks to reconstruct a linear order between variables using unsorted, pairwise similarity information. It has direct applications in archeology and shotgun gene sequencing for example. We write seriation as an optimization problem by proving the equivalence between the seriation and combinatorial 2-SUM problems on similarity matrices (2-SUM is a quadratic minimization problem over permutations). The seriation problem can be solved exactly by a spectral algorithm in the noiseless case and we derive several convex relaxations for 2-SUM to improve the robustness of seriation solutions in noisy settings. These convex relaxations also allow us to impose structural constraints on the solution, hence solve semi-supervised seriation problems. We derive new approximation bounds for some of these relaxations and present numerical experiments on archeological data, Markov chains and DNA assembly from shotgun gene sequencing data.Comment: Final journal version, a few typos and references fixe

Coding Theory and Algebraic Combinatorics

This chapter introduces and elaborates on the fruitful interplay of coding theory and algebraic combinatorics, with most of the focus on the interaction of codes with combinatorial designs, finite geometries, simple groups, sphere packings, kissing numbers, lattices, and association schemes. In particular, special interest is devoted to the relationship between codes and combinatorial designs. We describe and recapitulate important results in the development of the state of the art. In addition, we give illustrative examples and constructions, and highlight recent advances. Finally, we provide a collection of significant open problems and challenges concerning future research.Comment: 33 pages; handbook chapter, to appear in: "Selected Topics in Information and Coding Theory", ed. by I. Woungang et al., World Scientific, Singapore, 201

Efficient Semidefinite Branch-and-Cut for MAP-MRF Inference

We propose a Branch-and-Cut (B&C) method for solving general MAP-MRF inference problems. The core of our method is a very efficient bounding procedure, which combines scalable semidefinite programming (SDP) and a cutting-plane method for seeking violated constraints. In order to further speed up the computation, several strategies have been exploited, including model reduction, warm start and removal of inactive constraints. We analyze the performance of the proposed method under different settings, and demonstrate that our method either outperforms or performs on par with state-of-the-art approaches. Especially when the connectivities are dense or when the relative magnitudes of the unary costs are low, we achieve the best reported results. Experiments show that the proposed algorithm achieves better approximation than the state-of-the-art methods within a variety of time budgets on challenging non-submodular MAP-MRF inference problems.Comment: 21 page

Mathematical Programming Decoding of Binary Linear Codes: Theory and Algorithms

Mathematical programming is a branch of applied mathematics and has recently been used to derive new decoding approaches, challenging established but often heuristic algorithms based on iterative message passing. Concepts from mathematical programming used in the context of decoding include linear, integer, and nonlinear programming, network flows, notions of duality as well as matroid and polyhedral theory. This survey article reviews and categorizes decoding methods based on mathematical programming approaches for binary linear codes over binary-input memoryless symmetric channels.Comment: 17 pages, submitted to the IEEE Transactions on Information Theory. Published July 201