A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees

Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work and are publicly available. We also apply our methods to real data

Better Practical Algorithms for rSPR Distance and Hybridization Number

The problem of computing the rSPR distance of two phylogenetic trees (denoted by RDC) is NP-hard and so is the problem of computing the hybridization number of two phylogenetic trees (denoted by HNC). Since they are important problems in phylogenetics, they have been studied extensively in the literature. Indeed, quite a number of exact or approximation algorithms have been designed and implemented for them. In this paper, we design and implement one exact algorithm for HNC and several approximation algorithms for RDC and HNC. Our experimental results show that the resulting exact program is much faster (namely, more than 80 times faster for the easiest dataset used in the experiments) than the previous best and its superiority in speed becomes even more significant for more difficult instances. Moreover, the resulting approximation programs output much better results than the previous bests; indeed, the outputs are always nearly optimal and often optimal. Of particular interest is the usage of the Monte Carlo tree search (MCTS) method in the design of our approximation algorithms. Our experimental results show that with MCTS, we can often solve HNC exactly within short time

On unrooted and root-uncertain variants of several well-known phylogenetic network problems

The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an \emph{unrooted} phylogenetic network displays (i.e. embeds) an \emph{unrooted} phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the Tree Bisection and Reconnect (TBR) distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.Comment: 28 pages, 8 Figure

Submodular memetic approximation for multiobjective parallel test paper generation

Parallel test paper generation is a biobjective distributed resource optimization problem, which aims to generate multiple similarly optimal test papers automatically according to multiple user-specified assessment criteria. Generating high-quality parallel test papers is challenging due to its NP-hardness in both of the collective objective functions. In this paper, we propose a submodular memetic approximation algorithm for solving this problem. The proposed algorithm is an adaptive memetic algorithm (MA), which exploits the submodular property of the collective objective functions to design greedy-based approximation algorithms for enhancing steps of the multiobjective MA. Synergizing the intensification of submodular local search mechanism with the diversification of the population-based submodular crossover operator, our algorithm can jointly optimize the total quality maximization objective and the fairness quality maximization objective. Our MA can achieve provable near-optimal solutions in a huge search space of large datasets in efficient polynomial runtime. Performance results on various datasets have shown that our algorithm has drastically outperformed the current techniques in terms of paper quality and runtime efficiency

A Survey of League Championship Algorithm: Prospects and Challenges

The League Championship Algorithm (LCA) is sport-inspired optimization algorithm that was introduced by Ali Husseinzadeh Kashan in the year 2009. It has since drawn enormous interest among the researchers because of its potential efficiency in solving many optimization problems and real-world applications. The LCA has also shown great potentials in solving non-deterministic polynomial time (NP-complete) problems. This survey presents a brief synopsis of the LCA literatures in peer-reviewed journals, conferences and book chapters. These research articles are then categorized according to indexing in the major academic databases (Web of Science, Scopus, IEEE Xplore and the Google Scholar). The analysis was also done to explore the prospects and the challenges of the algorithm and its acceptability among researchers. This systematic categorization can be used as a basis for future studies.Comment: 10 pages, 2 figures, 2 tables, Indian Journal of Science and Technology, 201

Hybrid algorithms for independent batch scheduling in grids

Grid computing has emerged as a wide area distributed paradigm for solving large-scale problems in science, engineering, etc. and is known as the family of eScience grid-enabled applications. Computing planning of incoming jobs efficiently with available machines in the grid system is the main requirement for optimised system performance. One version of the problem is that of independent batch scheduling, in which jobs are assumed to be independent and are scheduled in batches aimed at minimising the makespan and flowtime. Given the hardness of the problem, heuristics are used to find high quality solutions for practical purposes of designing efficient grid schedulers. Recently, considerable efforts were spent in implementing and evaluating not only stand-alone heuristics and meta-heuristics, but also their hybridisation into even higher level algorithms. In this paper, we present a study on the performance of two popular algorithms for the problem, namely Genetic Algorithms (GAs) and Tabu Search (TS) and two hybridisations involving them, namely, the GA (TS) and GA-TS, which differ in the way the main control and cooperation among GA and TS are implemented. The hierarchic and simultaneous optimisation modes are considered for the bi-objective scheduling problem. Evaluation is done using different grid scenarios generated by a grid simulator. The computational results showed that the hybrid algorithm outperforms both the GA and TS for the makespan parameter, but not for the flowtime parameter.Peer ReviewedPostprint (author's final draft

A survey on financial applications of metaheuristics

Modern heuristics or metaheuristics are optimization algorithms that have been increasingly used during the last decades to support complex decision-making in a number of fields, such as logistics and transportation, telecommunication networks, bioinformatics, finance, and the like. The continuous increase in computing power, together with advancements in metaheuristics frameworks and parallelization strategies, are empowering these types of algorithms as one of the best alternatives to solve rich and real-life combinatorial optimization problems that arise in a number of financial and banking activities. This article reviews some of the works related to the use of metaheuristics in solving both classical and emergent problems in the finance arena. A non-exhaustive list of examples includes rich portfolio optimization, index tracking, enhanced indexation, credit risk, stock investments, financial project scheduling, option pricing, feature selection, bankruptcy and financial distress prediction, and credit risk assessment. This article also discusses some open opportunities for researchers in the field, and forecast the evolution of metaheuristics to include real-life uncertainty conditions into the optimization problems being considered.This work has been partially supported by the Spanish Ministry of Economy and Competitiveness (TRA2013-48180-C3-P, TRA2015-71883-REDT), FEDER, and the Universitat Jaume I mobility program (E-2015-36)