Computational Performance Evaluation of Two Integer Linear Programming Models for the Minimum Common String Partition Problem

In the minimum common string partition (MCSP) problem two related input strings are given. "Related" refers to the property that both strings consist of the same set of letters appearing the same number of times in each of the two strings. The MCSP seeks a minimum cardinality partitioning of one string into non-overlapping substrings that is also a valid partitioning for the second string. This problem has applications in bioinformatics e.g. in analyzing related DNA or protein sequences. For strings with lengths less than about 1000 letters, a previously published integer linear programming (ILP) formulation yields, when solved with a state-of-the-art solver such as CPLEX, satisfactory results. In this work, we propose a new, alternative ILP model that is compared to the former one. While a polyhedral study shows the linear programming relaxations of the two models to be equally strong, a comprehensive experimental comparison using real-world as well as artificially created benchmark instances indicates substantial computational advantages of the new formulation.Comment: arXiv admin note: text overlap with arXiv:1405.5646 This paper version replaces the one submitted on January 10, 2015, due to detected error in the calculation of the variables involved in the ILP model

Shape predicates allow unbounded verification of linearizability using canonical abstraction

Canonical abstraction is a static analysis technique that represents states as 3-valued logical structures, and is able to construct finite representations of systems with infinite statespaces for verification. The granularity of the abstraction can be altered by the definition of instrumentation predicates, which derive their meaning from other predicates. We introduce shape predicates for preserving certain structures of the state during abstraction. We show that shape predicates allow linearizability to be verified for concurrent data structures using canonical abstraction alone, and use the approach to verify a stack and two queue algorithms. This contrasts with previous efforts to verify linearizability with canonical abstraction, which have had to employ other techniques as well

Practical applications of probabilistic model checking to communication protocols

Probabilistic model checking is a formal verification technique for the analysis of systems that exhibit stochastic behaviour. It has been successfully employed in an extremely wide array of application domains including, for example, communication and multimedia protocols, security and power management. In this chapter we focus on the applicability of these techniques to the analysis of communication protocols. An analysis of the performance of such systems must successfully incorporate several crucial aspects, including concurrency between multiple components, real-time constraints and randomisation. Probabilistic model checking, in particular using probabilistic timed automata, is well suited to such an analysis. We provide an overview of this area, with emphasis on an industrially relevant case study: the IEEE 802.3 (CSMA/CD) protocol. We also discuss two contrasting approaches to the implementation of probabilistic model checking, namely those based on numerical computation and those based on discrete-event simulation. Using results from the two tools PRISM and APMC, we summarise the advantages, disadvantages and trade-offs associated with these techniques

Mobility: a double-edged sword for HSPA networks

This paper presents an empirical study on the performance of mobile High Speed Packet Access (HSPA, a 3.5G cellular standard) networks in Hong Kong via extensive field tests. Our study, from the viewpoint of end users, covers virtually all possible mobile scenarios in urban areas, including subways, trains, off-shore ferries and city buses. We have confirmed that mobility has largely negative impacts on the performance of HSPA networks, as fast-changing wireless environment causes serious service deterioration or even interruption. Meanwhile our field experiment results have shown unexpected new findings and thereby exposed new features of the mobile HSPA networks, which contradict commonly held views. We surprisingly find out that mobility can improve fairness of bandwidth sharing among users and traffic flows. Also the triggering and final results of handoffs in mobile HSPA networks are unpredictable and often inappropriate, thus calling for fast reacting fallover mechanisms. We have conducted in-depth research to furnish detailed analysis and explanations to what we have observed. We conclude that mobility is a double-edged sword for HSPA networks. To the best of our knowledge, this is the first public report on a large scale empirical study on the performance of commercial mobile HSPA networks

A micro/macro parallel-in-time (parareal) algorithm applied to a climate model with discontinuous non-monotone coefficients and oscillatory forcing

We present the application of a micro/macro parareal algorithm for a 1-D energy balance climate model with discontinuous and non-monotone coefficients and forcing terms. The micro/macro parareal method uses a coarse propagator, based on a (macroscopic) 0-D approximation of the underlying (microscopic) 1-D model. We compare the performance of the method using different versions of the macro model, as well as different numerical schemes for the micro propagator, namely an explicit Euler method with constant stepsize and an adaptive library routine. We study convergence of the method and the theoretical gain in computational time in a realization on parallel processors. We show that, in this example and for all settings, the micro/macro parareal method converges in fewer iterations than the number of used parareal subintervals, and that a theoretical gain in performance of up to 10 is possible

Molecular Dynamics Simulation Study of Nonconcatenated Ring Polymers in a Melt: I. Statics

Molecular dynamics simulations were conducted to investigate the structural properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N=1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. For the rings, the radius of gyration squared was found to scale as N to the 4/5 power for an intermediate regime and N to the 2/3 power for the larger rings indicating an overall conformation of a crumpled globule. However, almost all beads of the rings are "surface beads" interacting with beads of other rings, a result also in agreement with a primitive path analysis performed in the following paper (DOI: 10.1063/1.3587138). Details of the internal conformational properties of the ring and linear polymers as well as their packing are analyzed and compared to current theoretical models.Comment: 15 pages, 14 figure