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A new heuristic with a multi-threaded implementation of a modified Firefly Algorithm

2018 , Murillo-Suárez, Alfonso , Martínez Ríos, Félix Orlando

In this article, we present a modified version of the Firefly Algorithm implemented in a multi-threaded model to improve the results obtained by the original algorithm significantly. This multi-threaded algorithm allows the threads to obtain different results by the independent execution of the heuristic method in each of them, although for keeping all the threads with significant executions, the algorithm performs some crossover techniques, explained in detail in this article, for the threads to learn between them while maintaining its independence. For testing the new algorithm, we use the six benchmark functions used in the literature for testing the original Firefly Algorithm, and to prove that the improved results are significant, we perform the Wilcoxon test to the results obtained. The results obtained with this new heuristic proved to be significantly better while taking advantage of today's commercial processors. © 2020 Alfonso Murillo-Suarez et al., licensed to EAI.

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New Particle Swarm Optimizer Algorithm with Chaotic Maps for Combinatorial Global Optimization Problems. An Application to the Deconvolution of Mössbauer Spectra

2024-01-01 , Martínez Ríos, Félix Orlando , Jiménez-López, Omar , Alvarez Guillen, Luis Alejandro

In this chapter, we present a novel method for addressing global optimization problems inspired by evolutionary algorithms found in nature. We integrate the Comprehensive Learning Particle Swarm Optimization (CLPSO) algorithm with random value generation based on chaotic maps. The resulting algorithm is applied to the computationally complex task of deconvoluting Mossbauer spectra. We implement ten chaotic maps to generate random values and compare their performance with traditional random number generators. Through experiments, we demonstrate that the developed algorithm excels in exploring the search space and exhibits fast intensification in finding the global minimum. In addition, we perform a comprehensive review of existing solutions to the Mossbauer spectrum deconvolution problem, highlighting the scarce availability of developments in this area. We also present a user-friendly program designed with an intuitive interface to facilitate the deconvolution process by Spector Mossbauer. This program will be freely distributed without operational restrictions. Experimental validation is performed on Mossbauer spectra generated using the developed program and those obtained by experimental means, affirming the efficiency of the new algorithm conceived. ©Springer.

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StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks

2023 , Aguilera-Mendoza, Longendri , Ayala-Ruano, Sebastián , Martínez Ríos, Félix Orlando , Chávez, Edgar , García-Jacas, César R. , Brizuela, Carlos A. , Marrero-Ponce, Yovani

Motivation: Antimicrobial peptides (AMPs) are promising molecules to treat infectious diseases caused by multi-drug resistance pathogens, some types of cancer, and other conditions. Computer-aided strategies are efficient tools for the high-throughput screening of AMPs. Copyright © 2024 Oxford University Press

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Golden Ratio Annealing for Satisfiability Problems Using Dynamically Cooling Schemes

2008 , Frausto-Solís, Juan , Martínez Ríos, Félix Orlando

Abstract Satisfiability (SAT) Problem is an NP-Complete problem which means no deterministic algorithm is able to solve it in a polynomial time. Simulated Annealing (SA) can find very good solutions of SAT instances if its control parameters are correctly tuned. SA can be tuned experimentally or by using a Markov approach; the latter has been shown to be the most efficient one. Moreover Golden Ratio (GR) is an unconventional technique used to solve many problems. In this paper a new algorithm named Golden Ratio for Simulated Annealing (GRSA) is presented; it is tuned for three different cooling schemes. GRSA uses GR to dynamically decrease the SA temperature and a Markov Model to tune its parameters. Two SA tuned versions are compared in this paper: GRSA and a classical SA. Experimentation shows that the former is much more efficient than the latter. © Springer Nature

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A first-year design experience based on SAE Aero Design contest to support ABET learning outcomes and engineering vocation in freshmen student

2017 , Martínez Ríos, Félix Orlando

The a-k outcomes established by Accreditation Board for Engineering and Technology (ABET) for Engineering students in their self-assessment framework, should be reflected in the different subjects that taught to the students of the first two years of the various engineering programs. On the other hand, in those first semesters, the vocation of the students about the different Engineering is not very well defined. This experiment shows a proposal that links the results of ABET with an international student competition such as Society of Automotive Engineers (SAE) Aero Design, to reinforce and guide the new students in their future choice of specialization in the School of Engineering. We also show the relationship between the challenges and problems in the SAE Aero Design competition for new students and ABET's a-k outcomes. We show the results obtained with nineteen students over three years. It is important to mention that none of the students involved in this experiment comes from Aeronautical Engineering (or similar to it).

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Correction to: Data Analysis and Optimization for Engineering and Computing Problems

2020 , Vasant, Pandian , Litvinchev, Igor , Marmolejo Saucedo, José Antonio , Rodríguez Aguilar, Román , Martínez Ríos, Félix Orlando

This book was inadvertently published without updating the following (or with the following error) © Springer Nature Switzerland AG 2020

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A new swarm algorithm for global optimization of multimodal functions over multi-threading architecture hybridized with simulating annealing

2018 , Martínez Ríos, Félix Orlando , Murillo-Suarez, Alfonso

This paper presents a new algorithm, PCLPSO, based on particle swarm optimization, which uses comprehensive learning particle swarm optimizer. Our algorithm executes C parallel CLPSO algorithms. We adopted as a criterion of completion a maximum value of evaluations of the objective function. During the execution of the CLPSO algorithms, when a certain evaluation value of the functions is reached, the best k are selected, and different initialization criteria are applied to continue the execution of the CLPSO algorithms: restarting the worst ones for the best solution or restores the worst ones to a random solution. For this restart, we use the Boltzmann criterion in a similar way as Simulating Annealing (SA) does. In this work, the experimental results obtained for the search of the minimum of 16 multimodal test functions such as Rosenbrock, Griewank, Rastrigin, Brannin, Schwefel, and others. Our algorithm proved to be more efficient than the traditional CLPSO in its experimental results, and the nonparametric Wilcoxon test confirmed this.

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A New method to optimize BGP routes using SDN and reducing latency

2018 , Elguea, Lorenzo M. , Martínez Ríos, Félix Orlando

Latency on Internet mainly depends on the distance that packets travel in WAN networks1. This latency can be reduced if the hops between autonomous systems are reduced. This is the main function of the BGP protocol that is used by default in all the ISPs, but the lack of announcement of some network segments causes some routes to increase. This paper proposes a simple method to detect the routes that can be optimized and also a method using SDN to correct them. The first step is to determine which routes can be optimized, that is, those that are sent to a neighbor when they travel the greater distance, although this can not be determined by the router since it does not analyze all the routes that BGP receives in context. The second step is to add the new routes to the router, also by BGP, so that the router uses them. © 2018 The Authors. Published by Elsevier Ltd.

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A Novel Network Science and Similarity-Searching-Based Approach for Discovering Potential Tumor-Homing Peptides from Antimicrobials

2022 , Romero, Maylin , Marrero-Ponce, Yovani , Rodríguez, Hortensia , Agüero-Chapin, Guillermin , Antunes, Agostinho , Aguilera-Mendoza, Longendri , Martínez Ríos, Félix Orlando

Peptide-based drugs are promising anticancer candidates due to their biocompatibility and low toxicity. In particular, tumor-homing peptides (THPs) have the ability to bind specifically to cancer cell receptors and tumor vasculature. Despite their potential to develop antitumor drugs, there are few available prediction tools to assist the discovery of new THPs. Two webservers based on machine learning models are currently active, the TumorHPD and the THPep, and more recently the SCMTHP. Herein, a novel method based on network science and similarity searching implemented in the starPep toolbox is presented for THP discovery. The approach leverages from exploring the structural space of THPs with Chemical Space Networks (CSNs) and from applying centrality measures to identify the most relevant and non-redundant THP sequences within the CSN. Such THPs were considered as queries (Qs) for multi-query similarity searches that apply a group fusion (MAX-SIM rule) model. The resulting multi-query similarity searching models (SSMs) were validated with three benchmarking datasets of THPs/non-THPs. The predictions achieved accuracies that ranged from 92.64 to 99.18% and Matthews Correlation Coefficients between 0.894–0.98, outperforming state-of-the-art predictors. The best model was applied to repurpose AMPs from the starPep database as THPs, which were subsequently optimized for the TH activity. Finally, 54 promising THP leads were discovered, and their sequences were analyzed to encounter novel motifs. These results demonstrate the potential of CSNs and multi-query similarity searching for the rapid and accurate identification of THPs.

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A new approach of the rain-fall optimization algorithm using parallelization

2020 , Guerrero-Valadez, Juan Manuel , Martínez Ríos, Félix Orlando

This chapter introduces a new implementation of the Rain-Fall Optimization Algorithm (RFO) proposed by Kaboli, Sevbaraj, and Rahim in “Rain-Fall Optimization Algorithm. A Population-Based Algorithm for Solving Constrained Optimization Problems” by Kaboli et al. (J Comput Sci 19:31–42, 2017). RFO is a nature-inspired algorithm, which is based on the behavior of the water drops produced by a rainfall going down through a mountain to find the minimum values of specific functions. The algorithm was tested on four multidimensional benchmark functions: Ackley, Griewank, Rosenbrock, and Sphere functions. It was also tested in a four-dimensional function, the Kowalik function. The first step was to match the results of the rewritten algorithm with the results obtained by the original authors. Then the algorithm had to be modified to make some efficiency improvements and to get better results. The main modifications were a new equation to modify the step size for a function called explosion process and a parallel execution of the algorithm with two different restarting techniques: restart to the best and genetic restart to the best. © Springer Nature Switzerland AG 2020.