Measuring the similarity of protein structures by means of the universal similarity metric

Motivation: As an increasing number of protein structures become available, the need for algorithms that can quantify the similarity between protein structures increases as well. Thus, the comparison of proteins’ structures, and their clustering accordingly to a given similarity measure, is at the core of today’s biomedical research. In this paper, we show how an algorithmic information theory inspired Universal Similarity Metric (USM) can be used to calculate similarities between protein pairs.The method, besides being theoretically supported, is surprisingly simple to implement and computationally efficient. Results: Structural similarity between proteins in four different datasets was measured using the USM.The sample employed represented alpha, beta, alpha–beta, tim–barrel, globins and serpine protein types. The use of the proposed metric allows for a correct measurement of similarity and classification of the proteins in the four datasets. Availability: All the scripts and programs used for the preparation of this paper are available at http://www.cs.nott.ac.uk/ ~nxk/USM/protocol.html. In that web-page the reader will find a brief description on how to use the various scripts and programs.TIC2002-04242-C03-0

Algorithm portfolio based scheme for dynamic optimization problems

Since their first appearance in 1997 in the prestigious journal Science, algorithm portfolios have become a popular approach to solve static problems. Nevertheless and despite that success, they have not received much attention in Dynamic Optimization Problems (DOPs). In this work, we aim at showing these methods as a powerful tool to solve combinatorial DOPs. To this end, we propose a new algorithm portfolio for this type of problems that incorporates a learning scheme to select, among the metaheuristics that compose it, the most appropriate solver or solvers for each problem, configuration and search stage. This method was tested over 5 binary-coded problems (dynamic variants of OneMax, Plateau, RoyalRoad, Deceptive and Knapsack) and compared versus two reference algorithms for these problems (Adaptive Hill Climbing Memetic Algorithm and Self Organized Random Immigrants Genetic Algorithm). The results showed the importance of a good design of the learning scheme, the superiority of the algorithm portfolio against the isolated version of the metaheuristics that integrate it, and the competitiveness of its performance versus the reference algorithms.Spanish Government TIN2011-27696-C02-01 TEC2013-45585-C2-2-RAndalusian Government P11-TIC-8001European CommissionBasque Government PC2013-71AIbero-American University Association for Post Graduate Studies (AUIP

PRoA: An intelligent multi-criteria Personalized Route Assistant

Personalization of pedestrian routes becomes a necessity due to the wide variety of user profiles that may differ on preferences or requirements to choose a route. Several software applications offer routes usually based on single criterion like distance or time; however, these criteria do not often fit the pedestrian needs. Here, we will first focus on the Personalized Routes Problem and then we will approach the specific case of designing accessible and green pedestrian routes. The proposal is implemented as a freely available Android application (named as PRoA, by intelligent multi-criteria Personalized Route Assistant), which automatically obtains geographical data and information for the decision criteria from open datasets. The proposal is evaluated using real cases at the city of Granada, Spain.Research supported in part by projects TIN2014-55024-P (Spanish Ministry of Economy and Competitiveness) and P11-TIC-8001 (Consejería de Economía, Innovación y Ciencia, Junta de Andalucía). Both projects include FEDER funds from the European Union. M. Torres enjoys a Ph.D. research training staff grant associated with the project TIN2014-55024-P and co-funded by the European Social Fund

Optimisation problems as decision problems: The case of fuzzy optimisation problems

The importance that decision-making problems and optimisation problems have today in all aspects of life is beyond all doubt. Despite that importance, both problems tend to be thought of as following different routes, when they have, in fact, a “symbiotic” relation. Here, we consider the different decision problems that arise when different kinds of information and framework of behaviour are considered, and we explore the corresponding optimisation problems that can be derived for searching the best possible decision. We explore the case where Fuzzy Mathematical Programming problems are obtained as well as other new ones in the fuzzy context.Research supported by the project TIN2014-55024-P from the Spanish Govern as well as by the project TIC-8001 from the Andalusian Govern (both financed with FEDER funds)

The Role of Metaheuristics as Solutions Generators

Optimization problems are ubiquitous nowadays. Many times, their corresponding computational models necessarily leave out of consideration several characteristics and features of the real world, so trying to obtain the optimum solution can not be enough for a problem solving point of view. The aim of this paper is to illustrate the role of metaheuristics as solutions’ generators in a basic problem solving framework. Metaheuristics become relevant in two modes: firstly because every run (in the case of population based techniques) allows to obtain a set of potentially good solutions, and secondly, if a reference solution is available, one can set up a new optimization problem that allows to obtain solutions with similar quality in the objectives space but maximally different structure in the design space. Once a set of solutions is obtained, an example of an a posteriori analysis to rank them according with decision maker’s preferences is shown. All the problem solving framework steps, emphasizing the role of metaheuristics are illustrated with a dynamic version of the tourist trip design problem (for the first mode), and with a perishable food distribution problem (for the second one). These examples clearly show the benefits of the problem solving framework proposed. The potential role of the symmetry concept is also exploredProject PID2020-112754GB-I00 from MCINAEI/10.13039/ 501100011033

A Metaheuristic Based Approach for the Customer-Centric Perishable Food Distribution Problem

The CNRST has awarded H. El Raoui an excellence scholarship. D. Pelta acknowledges support from projects TIN2017-86647-P (Spanish Ministry of Economy, Industry, and Competitiveness. Including FEDER funds) and PID2020-112754GB-I00 (Spanish Ministry of Science and Innovation).High transportation costs and poor quality of service are common vulnerabilities in various logistics networks, especially in food distribution. Here we propose a many-objective Customercentric Perishable Food Distribution Problem that focuses on the cost, the quality of the product, and the service level improvement by considering not only time windows but also the customers’ target time and their priority. Recognizing the difficulty of solving such model, we propose a General Variable Neighborhood Search (GVNS) metaheuristic based approach that allows to efficiently solve a subproblem while allowing us to obtain a set of solutions. These solutions are evaluated over some non-optimized criteria and then ranked using an a posteriori approach that requires minimal information about decision maker preferences. The computational results show (a) GVNS achieved same quality solutions as an exact solver (CPLEX) in the subproblem; (b) GVNS can generate a wide number of candidate solutions, and (c) the use of the a posteriori approach makes easy to generate different decision maker profiles which in turn allows to obtain different rankings of the solutions.CNRSTSpanish Ministry of Economy, Industry, and Competitiveness TIN2017-86647-PEuropean Commission TIN2017-86647-PSpanish Government PID2020-112754GB-I0

A Critical Analysis of a Tourist Trip Design Problem with Time-Dependent Recommendation Factors and Waiting Times

Data Availability Statement: Publicly available datasets were analyzed in this study. This data can be found here: http://github.com/cporrasn/TTDP_TDRF_WT_NWT.git.Acknowledgments: C.P. has been supported by a scholarship from AUIP Association coordinated with the Universidad de Granada. B.P.-C. was supported by the Erasmus+ programme of the European Union. The authors are grateful to the editors and the anonymous reviewers for their constructive comments and suggestions.The tourist trip design problem (TTDP) is a well-known extension of the orienteering problem, where the objective is to obtain an itinerary of points of interest for a tourist that maximizes his/her level of interest. In several situations, the interest of a point depends on when the point is visited, and the tourist may delay the arrival to a point in order to get a higher interest. In this paper, we present and discuss two variants of the TTDP with time-dependent recommendation factors (TTDP-TDRF), which may or may not take into account waiting times in order to have a better recommendation value. Using a mixed-integer linear programming solver, we provide solutions to 27 real-world instances. Although reasonable at first sight, we observed that including waiting times is not justified: in both cases (allowing or not waiting times) the quality of the solutions is almost the same, and the use of waiting times led to a model with higher solving times. This fact highlights the need to properly evaluate the benefits of making the problem model more complex than is actually needed.Projects PID2020-112754GB-I0, MCIN/AEI/10.13039/501100011033FEDER/Junta de Andalucía, Consejería de Transformación Económica, Industria, Conocimiento y Universidades/ Proyecto (B-TIC-640-UGR20

A methodology for the analysis of In-Core fuel management configurations in BWR’s

A configuration for the integral problem of in-core fuel management consists of a fuel lattice and a fuel assembly designs, as well as a fuel reload and a control rod pattern design, so that the different criteria for the proper operation of a BWR reactor are met. Such a configuration or solution is not unique. There is an universe of potential candidate solutions that solve the problem in different ways. Departing from a database of candidate configurations, we describe and show the application of a multicriteria analysis methodology based on intervals and possibility function. The nuclear engineer must define his/her preferences in terms of the relevance assigned to the configurations’ features and next, using the methodology, those configurations are ranked. Besides this, the methodology can help us to identify the role that play some fuel lattice variables into the in-core fuel problem performance.D. Pelta and P. Novoa acknowledge support from projects PID2020-112 754 GB-I0, MCIN/AEI /10.13039/501100011033 and FEDER/Junta de Andalucía - Consejería de Transformaci´on Econ´omica, Industria, Conocimiento y Universidades / Proyecto (B-TIC-640-UGR20

El método TOPSIS relativo vs. absoluto

Los métodos de decisión multicriterio constituyen una herramienta básica para la toma de decisiones en el mundo empresarial. En este trabajo nos vamos a centrar en la aplicación del método TOPSIS analizando el impacto que tiene en los resultados, la utilización de diferentes formas de la matriz de decisión. En primer lugar se utiliza el modo tradicional o relativo y, en segundo lugar, el modo absoluto que tiene en cuenta el rango del correspondiente criterio. Concretamente se pretende realizar un estudio de la repercusión que tiene en el resultado final la elección de un modo u otro realizando las pruebas pertinentes sobre un problema de localización asociado a las energías renovables.Multicriteria decision making methods are essential tools to make decisions in the corporate world. We focus here in the TOPSIS method to analyze the impact that, the way the decision matrix is constructed affects the final results. Two different ways are analized: firstly, the original matrix is considered, and secondly, a variant including two novel alternatives is used. These alternatives are constructed taking into account the range of the corresponding criteria. We made comparisons using a location problem derived from the renewable energy field

Digital Justice. Guide for the dialogue on the efficient, quality and ethical design and use of technological tools in civil justice.

Esta Guía tiene por objeto promover el diálogo sobre un diseño eficiente, de calidad y ético de herramientas tecnológicas para ser utilizadas en la resolución de litigios con un foco en la seguridad y protección de derechos. El objetivo es identificar las claves éticas fundamentales que deben condicionar las reformas legales y dar comienzo a la evaluación de las diferentes alternativas de regulación bajo un enfoque interdisciplinar, con el objetivo de orientar las políticas públicas en este ámbito.The Guide aims to promote the dialogue on an efficient, quality and ethical design of technological tools to be used in the resolution of disputes with a focus on security and protection of rights. The objective is to identify the fundamental ethical keys that should condition legal reforms and to begin the evaluation of the different regulatory alternatives under an interdisciplinary approach, with the aim of guiding public policies in this field.Fundación Cotec para la Innovación - Universidad de Granada - Unidad de Excelencia de Investigación Sociedad Digital: Seguridad y protección de Derechos