Construct, Merge, Solve and Adapt: Application to the repetition-free longest common subsequence problem

In this paper we present the application of a recently proposed, general, algorithm for combinatorial optimization to the repetition-free longest common subsequence problem. The applied algorithm, which is labelled Construct, Merge, Solve & Adapt, generates sub-instances based on merging the solution components found in randomly constructed solutions. These sub-instances are subsequently solved by means of an exact solver. Moreover, the considered sub-instances are dynamically changing due to adding new solution components at each iteration, and removing existing solution components on the basis of indicators about their usefulness. The results of applying this algorithm to the repetition-free longest common subsequence problem show that the algorithm generally outperforms competing approaches from the literature. Moreover, they show that the algorithm is competitive with CPLEX for small and medium size problem instances, whereas it outperforms CPLEX for larger problem instances.Peer ReviewedPostprint (author's final draft

Exact Solution Methods for the kk-item Quadratic Knapsack Problem

The purpose of this paper is to solve the 0-1 $k$-item quadratic knapsack problem $(kQKP)$, a problem of maximizing a quadratic function subject to two linear constraints. We propose an exact method based on semidefinite optimization. The semidefinite relaxation used in our approach includes simple rank one constraints, which can be handled efficiently by interior point methods. Furthermore, we strengthen the relaxation by polyhedral constraints and obtain approximate solutions to this semidefinite problem by applying a bundle method. We review other exact solution methods and compare all these approaches by experimenting with instances of various sizes and densities.Comment: 12 page

Orbital Shrinking: A New Tool for Hybrid MIP/CP Methods

Abstract. Orbital shrinking is a newly developed technique in the MIP community to deal with symmetry issues, which is based on aggregation rather than on symmetry breaking. In a recent work, a hybrid MIP/CP scheme based on orbital shrinking was developed for the multi-activity shift scheduling problem, showing significant improvements over previ-ous pure MIP approaches. In the present paper we show that the scheme above can be extended to a general framework for solving arbitrary sym-metric MIP instances. This framework naturally provides a new way for devising hybrid MIP/CP decompositions. Finally, we specialize the above framework to the multiple knapsack problem. Computational re-sults show that the resulting method can be orders of magnitude faster than pure MIP approaches on hard symmetric instances.

Brownian dynamics simulation of DNA condensation.

DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA

Solving Medium-Density Subset Sum Problems in Expected Polynomial Time: An Enumeration Approach

The subset sum problem (SSP) can be briefly stated as: given a target integer $E$ and a set $A$ containing $n$ positive integer $a_j$, find a subset of $A$ summing to $E$. The \textit{density} $d$ of an SSP instance is defined by the ratio of $n$ to $m$, where $m$ is the logarithm of the largest integer within $A$. Based on the structural and statistical properties of subset sums, we present an improved enumeration scheme for SSP, and implement it as a complete and exact algorithm (EnumPlus). The algorithm always equivalently reduces an instance to be low-density, and then solve it by enumeration. Through this approach, we show the possibility to design a sole algorithm that can efficiently solve arbitrary density instance in a uniform way. Furthermore, our algorithm has considerable performance advantage over previous algorithms. Firstly, it extends the density scope, in which SSP can be solved in expected polynomial time. Specifically, It solves SSP in expected $O(n\log{n})$ time when density $d \geq c\cdot \sqrt{n}/\log{n}$, while the previously best density scope is $d \geq c\cdot n/(\log{n})^{2}$. In addition, the overall expected time and space requirement in the average case are proven to be $O(n^5\log n)$ and $O(n^5)$ respectively. Secondly, in the worst case, it slightly improves the previously best time complexity of exact algorithms for SSP. Specifically, the worst-case time complexity of our algorithm is proved to be $O((n-6)2^{n/2}+n)$, while the previously best result is $O(n2^{n/2})$.Comment: 11 pages, 1 figur

Exact Cover with light

We suggest a new optical solution for solving the YES/NO version of the Exact Cover problem by using the massive parallelism of light. The idea is to build an optical device which can generate all possible solutions of the problem and then to pick the correct one. In our case the device has a graph-like representation and the light is traversing it by following the routes given by the connections between nodes. The nodes are connected by arcs in a special way which lets us to generate all possible covers (exact or not) of the given set. For selecting the correct solution we assign to each item, from the set to be covered, a special integer number. These numbers will actually represent delays induced to light when it passes through arcs. The solution is represented as a subray arriving at a certain moment in the destination node. This will tell us if an exact cover does exist or not.Comment: 20 pages, 4 figures, New Generation Computing, accepted, 200