On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

Transferring Interactive Search-Based Software Testing to Industry

Search-Based Software Testing (SBST) is the application of optimization algorithms to problems in software testing. In previous work, we have implemented and evaluated Interactive Search-Based Software Testing (ISBST) tool prototypes, with a goal to successfully transfer the technique to industry. While SBSE solutions are often validated on benchmark problems, there is a need to validate them in an operational setting. The present paper discusses the development and deployment of SBST tools for use in industry and reflects on the transfer of these techniques to industry. In addition to previous work discussing the development and validation of an ISBST prototype, a new version of the prototype ISBST system was evaluated in the laboratory and in industry. This evaluation is based on an industrial System under Test (SUT) and was carried out with industrial practitioners. The Technology Transfer Model is used as a framework to describe the progression of the development and evaluation of the ISBST system. The paper presents a synthesis of previous work developing and evaluating the ISBST prototype, as well as presenting an evaluation, in both academia and industry, of that prototype's latest version. This paper presents an overview of the development and deployment of the ISBST system in an industrial setting, using the framework of the Technology Transfer Model. We conclude that the ISBST system is capable of evolving useful test cases for that setting, though improvements in the means the system uses to communicate that information to the user are still required. In addition, a set of lessons learned from the project are listed and discussed. Our objective is to help other researchers that wish to validate search-based systems in industry and provide more information about the benefits and drawbacks of these systems.Comment: 40 pages, 5 figure

An Optimized Soft Computing Based Passage Retrieval System

In this paper we propose and evaluate a soft computing-based passage retrieval system for Question Answering Systems (QAS). Fuzzy PR, our base-line passage retrieval system, employs a similarity measure that attempts to model accurately the question reformulation intuition. The similarity measure includes fuzzy logic-based models that evaluate efficiently the proximity of question terms and detect term variations occurring within a passage. Our experimental results using FuzzyPR on the TREC and CLEF corpora show that our novel passage retrieval system achieves better performance compared to other similar systems. Finally, we describe the performance results of OptFuzzyPR, an optimized version of FuzzyPR, created by optimizing the values of FuzzyPR system parameters using genetic algorithms

Preventing premature convergence and proving the optimality in evolutionary algorithms

http://ea2013.inria.fr//proceedings.pdfInternational audienceEvolutionary Algorithms (EA) usually carry out an efficient exploration of the search-space, but get often trapped in local minima and do not prove the optimality of the solution. Interval-based techniques, on the other hand, yield a numerical proof of optimality of the solution. However, they may fail to converge within a reasonable time due to their inability to quickly compute a good approximation of the global minimum and their exponential complexity. The contribution of this paper is a hybrid algorithm called Charibde in which a particular EA, Differential Evolution, cooperates with a Branch and Bound algorithm endowed with interval propagation techniques. It prevents premature convergence toward local optima and outperforms both deterministic and stochastic existing approaches. We demonstrate its efficiency on a benchmark of highly multimodal problems, for which we provide previously unknown global minima and certification of optimality

Multivariate Fine-Grained Complexity of Longest Common Subsequence

We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent, no $O(n^{2-\varepsilon})$-time algorithm is known. Recent work indeed shows that such an algorithm would refute the Strong Exponential Time Hypothesis (SETH) [Abboud, Backurs, Vassilevska Williams + Bringmann, K\"unnemann FOCS'15]. Despite the quadratic-time barrier, for over 40 years an enduring scientific interest continued to produce fast algorithms for LCS and its variations. Particular attention was put into identifying and exploiting input parameters that yield strongly subquadratic time algorithms for special cases of interest, e.g., differential file comparison. This line of research was successfully pursued until 1990, at which time significant improvements came to a halt. In this paper, using the lens of fine-grained complexity, our goal is to (1) justify the lack of further improvements and (2) determine whether some special cases of LCS admit faster algorithms than currently known. To this end, we provide a systematic study of the multivariate complexity of LCS, taking into account all parameters previously discussed in the literature: the input size $n:=\max\{|x|,|y|\}$, the length of the shorter string $m:=\min\{|x|,|y|\}$, the length $L$ of an LCS of $x$ and $y$, the numbers of deletions $\delta := m-L$ and $\Delta := n-L$, the alphabet size, as well as the numbers of matching pairs $M$ and dominant pairs $d$. For any class of instances defined by fixing each parameter individually to a polynomial in terms of the input size, we prove a SETH-based lower bound matching one of three known algorithms. Specifically, we determine the optimal running time for LCS under SETH as $(n+\min\{d, \delta \Delta, \delta m\})^{1\pm o(1)}$. [...]Comment: Presented at SODA'18. Full Version. 66 page

Optimal and efficient time series classification with burrows-wheeler transform and spectral window based transformation

With the progressing amount of data every day, Time series classification acts as a vital role in the real life environment. Raised data volume for the time periods will make hard for the researchers to examine as well as assess the data. Therefore time series classification is taken as a significant research problem for the examining as well as identifying the time series dataset. On the other hand the previous research might carry out low in case of existence of weak classifiers. It is solved by introducing the Weak Classifier aware Time Series Data Classification Algorithm (WCTSD). In this proposed technique, with the help of the Burrows-Wheeler Transform (BWT), primarily frequency domain based data transformation is carried out. After that, by means of presenting the technique called spectral window based transformation, time series based data transformation is performed. With the help of the Hybrid K Nearest Neighbour, Hybrid decision tree algorithm, Linear Multiclass Support Vector Machine, these transformed data is classified. Here, to enhance the classification accuracy, the weak classifier is eliminated by utilizing hybrid particle swarm with firefly algorithm. In the MATLAB simulation environment, the total implementation of the presented research technique is carried out and it is confirmed that the presented research technique WCTSD results in providing the best possible outcome compared to the previous research methods

A Dual Scheduling Model for Optimizing Robustness and Energy Consumption in Manufacturing Systems

[EN] Manufacturing systems involve a huge number of combinatorial problems that must be optimized in an efficient way. One of these problems is related to task scheduling problems. These problems are NP-hard, so most of the complete techniques are not able to obtain an optimal solution in an efficient way. Furthermore, most of real manufacturing problems are dynamic, so the main objective is not only to obtain an optimized solution in terms of makespan, tardiness, and so on but also to obtain a solution able to absorb minor incidences/disruptions presented in any daily process. Most of these industries are also focused on improving the energy efficiency of their industrial processes. In this article, we propose a knowledge-based model to analyse previous incidences occurred in the machines with the aim of modelling the problem to obtain robust and energy-aware solutions. The resultant model (called dual model) will protect the more dynamic and disrupted tasks by assigning buffer times. These buffers will be used to absorb incidences during execution and to reduce the machine rate to minimize energy consumption. This model is solved by a memetic algorithm which combines a genetic algorithm with a local search to obtain robust and energy-aware solutions able to absorb further disruptions. The proposed dual model has been proven to be efficient in terms of energy consumption, robustness and stability in different and well-known benchmarks.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This research has been supported by the Spanish Government under research project TIN2013-46511-C2-1 for the Spanish government and the TETRACOM EU project FP7-ICT-2013-10-No 609491.Escamilla Fuster, J.; Salido Gregorio, MA. (2016). A Dual Scheduling Model for Optimizing Robustness and Energy Consumption in Manufacturing Systems. Proceedings of the Institution of Mechanical Engineers, Part B: Journal of Engineering Manufacture. 1(1):1-12. https://doi.org/10.1177/0954405415625915S1121

Lateness minimization with Tabu search for job shop scheduling problem with sequence dependent setup times

We tackle the job shop scheduling problem with sequence dependent setup times and maximum lateness minimization by means of a tabu search algorithm. We start by defining a disjunctive model for this problem, which allows us to study some properties of the problem. Using these properties we define a new local search neighborhood structure, which is then incorporated into the proposed tabu search algorithm. To assess the performance of this algorithm, we present the results of an extensive experimental study, including an analysis of the tabu search algorithm under different running conditions and a comparison with the state-of-the-art algorithms. The experiments are performed across two sets of conventional benchmarks with 960 and 17 instances respectively. The results demonstrate that the proposed tabu search algorithm is superior to the state-of-the-art methods both in quality and stability. In particular, our algorithm establishes new best solutions for 817 of the 960 instances of the first set and reaches the best known solutions in 16 of the 17 instances of the second se