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

On bounding the bandwidth of graphs with symmetry

We derive a new lower bound for the bandwidth of a graph that is based on a new lower bound for the minimum cut problem. Our new semidefinite programming relaxation of the minimum cut problem is obtained by strengthening the known semidefinite programming relaxation for the quadratic assignment problem (or for the graph partition problem) by fixing two vertices in the graph; one on each side of the cut. This fixing results in several smaller subproblems that need to be solved to obtain the new bound. In order to efficiently solve these subproblems we exploit symmetry in the data; that is, both symmetry in the min-cut problem and symmetry in the graphs. To obtain upper bounds for the bandwidth of graphs with symmetry, we develop a heuristic approach based on the well-known reverse Cuthill-McKee algorithm, and that improves significantly its performance on the tested graphs. Our approaches result in the best known lower and upper bounds for the bandwidth of all graphs under consideration, i.e., Hamming graphs, 3-dimensional generalized Hamming graphs, Johnson graphs, and Kneser graphs, with up to 216 vertices

Reduced-Dimension Linear Transform Coding of Correlated Signals in Networks

A model, called the linear transform network (LTN), is proposed to analyze the compression and estimation of correlated signals transmitted over directed acyclic graphs (DAGs). An LTN is a DAG network with multiple source and receiver nodes. Source nodes transmit subspace projections of random correlated signals by applying reduced-dimension linear transforms. The subspace projections are linearly processed by multiple relays and routed to intended receivers. Each receiver applies a linear estimator to approximate a subset of the sources with minimum mean squared error (MSE) distortion. The model is extended to include noisy networks with power constraints on transmitters. A key task is to compute all local compression matrices and linear estimators in the network to minimize end-to-end distortion. The non-convex problem is solved iteratively within an optimization framework using constrained quadratic programs (QPs). The proposed algorithm recovers as special cases the regular and distributed Karhunen-Loeve transforms (KLTs). Cut-set lower bounds on the distortion region of multi-source, multi-receiver networks are given for linear coding based on convex relaxations. Cut-set lower bounds are also given for any coding strategy based on information theory. The distortion region and compression-estimation tradeoffs are illustrated for different communication demands (e.g. multiple unicast), and graph structures.Comment: 33 pages, 7 figures, To appear in IEEE Transactions on Signal Processin

Retracting Graphs to Cycles

We initiate the algorithmic study of retracting a graph into a cycle in the graph, which seeks a mapping of the graph vertices to the cycle vertices so as to minimize the maximum stretch of any edge, subject to the constraint that the restriction of the mapping to the cycle is the identity map. This problem has its roots in the rich theory of retraction of topological spaces, and has strong ties to well-studied metric embedding problems such as minimum bandwidth and 0-extension. Our first result is an O(min{k, sqrt{n}})-approximation for retracting any graph on n nodes to a cycle with k nodes. We also show a surprising connection to Sperner\u27s Lemma that rules out the possibility of improving this result using certain natural convex relaxations of the problem. Nevertheless, if the problem is restricted to planar graphs, we show that we can overcome these integrality gaps by giving an optimal combinatorial algorithm, which is the technical centerpiece of the paper. Building on our planar graph algorithm, we also obtain a constant-factor approximation algorithm for retraction of points in the Euclidean plane to a uniform cycle

Optimization bounds from the branching dual

We present a general method for obtaining strong bounds for discrete optimization problems that is based on a concept of branching duality. It can be applied when no useful integer programming model is available, and we illustrate this with the minimum bandwidth problem. The method strengthens a known bound for a given problem by formulating a dual problem whose feasible solutions are partial branching trees. It solves the dual problem with a “worst-bound” local search heuristic that explores neighboring partial trees. After proving some optimality properties of the heuristic, we show that it substantially improves known combinatorial bounds for the minimum bandwidth problem with a modest amount of computation. It also obtains significantly tighter bounds than depth-first and breadth-first branching, demonstrating that the dual perspective can lead to better branching strategies when the object is to find valid bounds.Accepted manuscrip

Arrangement Problems Parameterized by Neighbourhood Diversity

We show that the arrangement problems BANDWIDTH, DISTORTION and IMBALANCE is FPT when parameterized by neighbourhood diversity, and establish some structural results for CUTWIDTH parameterized by neighbourhood diversity.Masteroppgave i informatikkINF39

Parallelization of Reordering Algorithms for Bandwidth and Wavefront Reduction

Abstract—Many sparse matrix computations can be speeded up if the matrix is first reordered. Reordering was originally developed for direct methods but it has recently become popular for improving the cache locality of parallel iterative solvers since reordering the matrix to reduce bandwidth and wavefront can improve the locality of reference of sparse matrix-vector multiplication (SpMV), the key kernel in iterative solvers. In this paper, we present the first parallel implementations of two widely used reordering algorithms: Reverse Cuthill-McKee (RCM) and Sloan. On 16 cores of the Stampede supercomputer, our parallel RCM is 5.56 times faster on the average than a state-of-the-art sequential implementation of RCM in the HSL library. Sloan is significantly more constrained than RCM, but our parallel implementation achieves a speedup of 2.88X on the average over sequential HSL-Sloan. Reordering the matrix using our parallel RCM and then performing 100 SpMV iterations is twice as fast as using HSL-RCM and then performing the SpMV iterations; it is also 1.5 times faster than performing the SpMV iterations without reordering the matrix. I

Algorithms for string and graph layout

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.Includes bibliographical references (p. 121-125).Many graph optimization problems can be viewed as graph layout problems. A layout of a graph is a geometric arrangement of the vertices subject to given constraints. For example, the vertices of a graph can be arranged on a line or a circle, on a two- or three-dimensional lattice, etc. The goal is usually to place all the vertices so as to optimize some specified objective function. We develop combinatorial methods as well as models based on linear and semidefinite programming for graph layout problems. We apply these techniques to some well-known optimization problems. In particular, we give improved approximation algorithms for the string folding problem on the two- and three-dimensional square lattices. This combinatorial graph problem is motivated by the protein folding problem, which is central in computational biology. We then present a new semidefinite programming formulation for the linear ordering problem (also known as the maximum acyclic subgraph problem) and show that it provides an improved bound on the value of an optimal solution for random graphs. This is the first relaxation that improves on the trivial "all edges" bound for random graphs.by Alantha Newman.Ph.D