A bi-objective turning restriction design problem in urban road networks

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An Enhanced Flower Pollination Algorithm For Multiple Sequence Alignment

Multiple sequence alignment (MSA) is an alignment of three or more sequences. Studies show that MSA exhibits a challenge, that is, how to find the MSA that maximises the Quality (Q) score and Total Column (TC) score. This problem is an NP-complete problem. Hence, numerous researchers have devoted their efforts to tackle the MSA problem, yet, there is still a shortcoming in the accuracy

Protein multiple sequence alignment by hybrid bio-inspired algorithms

This article presents an immune inspired algorithm to tackle the Multiple Sequence Alignment (MSA) problem. MSA is one of the most important tasks in biological sequence analysis. Although this paper focuses on protein alignments, most of the discussion and methodology may also be applied to DNA alignments. The problem of finding the multiple alignment was investigated in the study by Bonizzoni and Vedova and Wang and Jiang, and proved to be a NP-hard (non-deterministic polynomial-time hard) problem. The presented algorithm, called Immunological Multiple Sequence Alignment Algorithm (IMSA), incorporates two new strategies to create the initial population and specific ad hoc mutation operators. It is based on the ‘weighted sum of pairs’ as objective function, to evaluate a given candidate alignment. IMSA was tested using both classical benchmarks of BAliBASE (versions 1.0, 2.0 and 3.0), and experimental results indicate that it is comparable with state-of-the-art multiple alignment algorithms, in terms of quality of alignments, weighted Sums-of-Pairs (SP) and Column Score (CS) values. The main novelty of IMSA is its ability to generate more than a single suboptimal alignment, for every MSA instance; this behaviour is due to the stochastic nature of the algorithm and of the populations evolved during the convergence process. This feature will help the decision maker to assess and select a biologically relevant multiple sequence alignment. Finally, the designed algorithm can be used as a local search procedure to properly explore promising alignments of the search space

Multiobjective characteristic-based framework for very-large multiple sequence alignment

Rubio-Largo, Á., Vanneschi, L., Castelli, M., & Vega-Rodríguez, M. A. (2018). Multiobjective characteristic-based framework for very-large multiple sequence alignment. Applied Soft Computing Journal, 69, 719-736. [Advanced online publication on 27 June 2017]DOI: 10.1016/j.asoc.2017.06.022In the literature, we can find several heuristics for solving the multiple sequence alignment problem. The vast majority of them makes use of flags in order to modify certain alignment parameters; however, if no flags are used, the aligner will run with the default parameter configuration, which, often, is not the optimal one. In this work, we propose a framework that, depending on the biological characteristics of the input dataset, runs the aligner with the best parameter configuration found for another dataset that has similar biological characteristics, improving the accuracy and conservation of the obtained alignment. To train the framework, we use three well-known multiobjective evolutionary algorithms: NSGA-II, IBEA, and MOEA/D. Then, we perform a comparative study between several aligners proposed in the literature and the characteristic-based version of Kalign, MAFFT, and MUSCLE, when solving widely-used benchmarks (PREFAB v4.0 and SABmark v1.65) and very-large benchmarks with thousands of unaligned sequences (HomFam).authorsversionpublishe

Hybrid nature-inspired computation methods for optimization

The focus of this work is on the exploration of the hybrid Nature-Inspired Computation (NIC) methods with application in optimization. In the dissertation, we first study various types of the NIC algorithms including the Clonal Selection Algorithm (CSA), Particle Swarm Optimization (PSO), Ant Colony Optimization (ACO), Simulated Annealing (SA), Harmony Search (HS), Differential Evolution (DE), and Mind Evolution Computing (MEC), and propose several new fusions of the NIC techniques, such as CSA-DE, HS-DE, and CSA-SA. Their working principles, structures, and algorithms are analyzed and discussed in details. We next investigate the performances of our hybrid NIC methods in handling nonlinear, multi-modal, and dynamical optimization problems, e.g., nonlinear function optimization, optimal LC passive power filter design, and optimization of neural networks and fuzzy classification systems. The hybridization of these NIC methods can overcome the shortcomings of standalone algorithms while still retaining all the advantages. It has been demonstrated using computer simulations that the proposed hybrid NIC approaches are capable of yielding superior optimization performances over the individual NIC methods as well as conventional methodologies with regard to the search efficiency, convergence speed, and quantity and quality of the optimal solutions achieved

The Dynamic Multi-objective Multi-vehicle Covering Tour Problem

This work introduces a new routing problem called the Dynamic Multi-Objective Multi-vehicle Covering Tour Problem (DMOMCTP). The DMOMCTPs is a combinatorial optimization problem that represents the problem of routing multiple vehicles to survey an area in which unpredictable target nodes may appear during execution. The formulation includes multiple objectives that include minimizing the cost of the combined tour cost, minimizing the longest tour cost, minimizing the distance to nodes to be covered and maximizing the distance to hazardous nodes. This study adapts several existing algorithms to the problem with several operator and solution encoding variations. The efficacy of this set of solvers is measured against six problem instances created from existing Traveling Salesman Problem instances which represent several real countries. The results indicate that repair operators, variable length solution encodings and variable-length operators obtain a better approximation of the true Pareto front

New evolutionary approaches to protein structure prediction

Programa de doctorado en Biotecnología y Tecnología QuímicaThe problem of Protein Structure Prediction (PSP) is one of the principal topics in Bioinformatics. Multiple approaches have been developed in order to predict the protein structure of a protein. Determining the three dimensional structure of proteins is necessary to understand the functions of molecular protein level. An useful, and commonly used, representation for protein 3D structure is the protein contact map, which represents binary proximities (contact or non-contact) between each pair of amino acids of a protein. This thesis work, includes a compilation of the soft computing techniques for the protein structure prediction problem (secondary and tertiary structures). A novel evolutionary secondary structure predictor is also widely described in this work. Results obtained confirm the validity of our proposal. Furthermore, we also propose a multi-objective evolutionary approach for contact map prediction based on physico-chemical properties of amino acids. The evolutionary algorithm produces a set of decision rules that identifies contacts between amino acids. The rules obtained by the algorithm impose a set of conditions based on amino acid properties in order to predict contacts. Results obtained by our approach on four different protein data sets are also presented. Finally, a statistical study was performed to extract valid conclusions from the set of prediction rules generated by our algorithm.Universidad Pablo de Olavide. Centro de Estudios de Postgrad