Typical solution time for a vertex-covering algorithm on finite-connectivity random graphs

In this letter, we analytically describe the typical solution time needed by a backtracking algorithm to solve the vertex-cover problem on finite-connectivity random graphs. We find two different transitions: The first one is algorithm-dependent and marks the dynamical transition from linear to exponential solution times. The second one gives the maximum computational complexity, and is found exactly at the threshold where the system undergoes an algorithm-independent phase transition in its solvability. Analytical results are corroborated by numerical simulations.Comment: 4 pages, 2 figures, to appear in Phys. Rev. Let

Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index

Finding approximate occurrences of a pattern in a text using a full-text index is a central problem in bioinformatics and has been extensively researched. Bidirectional indices have opened new possibilities in this regard allowing the search to start from anywhere within the pattern and extend in both directions. In particular, use of search schemes (partitioning the pattern and searching the pieces in certain orders with given bounds on errors) can yield significant speed-ups. However, finding optimal search schemes is a difficult combinatorial optimization problem. Here for the first time, we propose a mixed integer program (MIP) capable to solve this optimization problem for Hamming distance with given number of pieces. Our experiments show that the optimal search schemes found by our MIP significantly improve the performance of search in bidirectional FM-index upon previous ad-hoc solutions. For example, approximate matching of 101-bp Illumina reads (with two errors) becomes 35 times faster than standard backtracking. Moreover, despite being performed purely in the index, the running time of search using our optimal schemes (for up to two errors) is comparable to the best state-of-the-art aligners, which benefit from combining search in index with in-text verification using dynamic programming. As a result, we anticipate a full-fledged aligner that employs an intelligent combination of search in the bidirectional FM-index using our optimal search schemes and in-text verification using dynamic programming outperforms today's best aligners. The development of such an aligner, called FAMOUS (Fast Approximate string Matching using OptimUm search Schemes), is ongoing as our future work

A New Look at the Easy-Hard-Easy Pattern of Combinatorial Search Difficulty

The easy-hard-easy pattern in the difficulty of combinatorial search problems as constraints are added has been explained as due to a competition between the decrease in number of solutions and increased pruning. We test the generality of this explanation by examining one of its predictions: if the number of solutions is held fixed by the choice of problems, then increased pruning should lead to a monotonic decrease in search cost. Instead, we find the easy-hard-easy pattern in median search cost even when the number of solutions is held constant, for some search methods. This generalizes previous observations of this pattern and shows that the existing theory does not explain the full range of the peak in search cost. In these cases the pattern appears to be due to changes in the size of the minimal unsolvable subproblems, rather than changing numbers of solutions.Comment: See http://www.jair.org/ for any accompanying file

A Tutorial on Clique Problems in Communications and Signal Processing

Since its first use by Euler on the problem of the seven bridges of K\"onigsberg, graph theory has shown excellent abilities in solving and unveiling the properties of multiple discrete optimization problems. The study of the structure of some integer programs reveals equivalence with graph theory problems making a large body of the literature readily available for solving and characterizing the complexity of these problems. This tutorial presents a framework for utilizing a particular graph theory problem, known as the clique problem, for solving communications and signal processing problems. In particular, the paper aims to illustrate the structural properties of integer programs that can be formulated as clique problems through multiple examples in communications and signal processing. To that end, the first part of the tutorial provides various optimal and heuristic solutions for the maximum clique, maximum weight clique, and $k$-clique problems. The tutorial, further, illustrates the use of the clique formulation through numerous contemporary examples in communications and signal processing, mainly in maximum access for non-orthogonal multiple access networks, throughput maximization using index and instantly decodable network coding, collision-free radio frequency identification networks, and resource allocation in cloud-radio access networks. Finally, the tutorial sheds light on the recent advances of such applications, and provides technical insights on ways of dealing with mixed discrete-continuous optimization problems

Statistical mechanics of the vertex-cover problem

We review recent progress in the study of the vertex-cover problem (VC). VC belongs to the class of NP-complete graph theoretical problems, which plays a central role in theoretical computer science. On ensembles of random graphs, VC exhibits an coverable-uncoverable phase transition. Very close to this transition, depending on the solution algorithm, easy-hard transitions in the typical running time of the algorithms occur. We explain a statistical mechanics approach, which works by mapping VC to a hard-core lattice gas, and then applying techniques like the replica trick or the cavity approach. Using these methods, the phase diagram of VC could be obtained exactly for connectivities $c<e$, where VC is replica symmetric. Recently, this result could be confirmed using traditional mathematical techniques. For $c>e$, the solution of VC exhibits full replica symmetry breaking. The statistical mechanics approach can also be used to study analytically the typical running time of simple complete and incomplete algorithms for VC. Finally, we describe recent results for VC when studied on other ensembles of finite- and infinite-dimensional graphs.Comment: review article, 26 pages, 9 figures, to appear in J. Phys. A: Math. Ge

Minimizing energy below the glass thresholds

Focusing on the optimization version of the random K-satisfiability problem, the MAX-K-SAT problem, we study the performance of the finite energy version of the Survey Propagation (SP) algorithm. We show that a simple (linear time) backtrack decimation strategy is sufficient to reach configurations well below the lower bound for the dynamic threshold energy and very close to the analytic prediction for the optimal ground states. A comparative numerical study on one of the most efficient local search procedures is also given.Comment: 12 pages, submitted to Phys. Rev. E, accepted for publicatio