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

Identification of Protein Alignment for Elder Health Care

Over many years protein sequence alignment problem has grabbed attention of biologists as it implicates, more than two biological sequences. It states all the important aspects of big data and how medical and health informatics, translational bioinformatics will benefit personalized health care both structured and unstructured, covering genomics, proteomics, metabolism. The system develop approach for biological sequence alignment to increase efficiency of analysis operation that speed up the calculation of alignment for huge real time sequences, to develop distributed scan approach in Smith-waterman algorithm for presenting fast solution and optimize the Smith Waterman(SW) alignment algorithm using Distributed approach

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

A novel approach based on multiobjective variable mesh optimization to Phylogenetics

One of the most relevant problems in Bioinformaticsand Computational Biology is the search and reconstruction ofthe most accurate phylogenetic tree that explains, as exactly aspossible, the evolutionary relationships among species from agiven dataset. Different criteria have been employed to evaluatethe accuracy of evolutionary hypothesis in order to guide a searchalgorithm towards the best tree. However, these criteria may leadto distinct phylogenies, which are often conflicting among them.Therefore, a multi-objective approach can be useful. In this work,we present a phylogenetic adaptation of a multiobjective variablemesh optimization algorithm for inferring phylogenies, to tacklethe phylogenetic inference problem according to two optimalitycriteria: maximum parsimony and maximum likelihood. Theaim of this approach is to propose a complementary view ofphylogenetics in order to generate a set of trade-off phylogenetictopologies that represent a consensus between both criteria.Experiments on four real nucleotide datasets show that ourproposal can achieve promising results, under both multiobjectiveand biological approaches, with regard to other classical andrecent multiobjective metaheuristics from the state-of-the-art. &nbsp

Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.This work is jointly supported by the FundaciónSéneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants 15290/PI/2010 and 18946/JLI/13, by the Spanish MEC and European Commission FEDER under grant with reference TEC2012-37945-C02-02 and TIN2012-31345, by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). We also thank NVIDIA for hardware donation within UCAM GPU educational and research centers.Ingeniería, Industria y Construcció

Solving multiple sequence alignment problems by using a swarm intelligent optimization based approach

In this article, the alignment of multiple sequences is examined through swarm intelligence based an improved particle swarm optimization (PSO). A random heuristic technique for solving discrete optimization problems and realistic estimation was recently discovered in PSO. The PSO approach is a nature-inspired technique based on intelligence and swarm movement. Thus, each solution is encoded as “chromosomes” in the genetic algorithm (GA). Based on the optimization of the objective function, the fitness function is designed to maximize the suitable components of the sequence and reduce the unsuitable components of the sequence. The availability of a public benchmark data set such as the Bali base is seen as an assessment of the proposed system performance, with the potential for PSO to reveal problems in adapting to better performance. This proposed system is compared with few existing approaches such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) alignment (DIALIGN), PILEUP8, hidden Markov model training (HMMT), rubber band technique-genetic algorithm (RBT-GA) and ML-PIMA. In many cases, the experimental results are well implemented in the proposed system compared to other existing approaches

A Survey of Search-Based Refactoring for Software Maintenance

Abstract This survey reviews published materials related to the specific area of Search-Based Software Engineering that concerns software maintenance and, in particular, refactoring. The survey aims to give a comprehensive review of the use of search-based refactoring to maintain software. Fifty different papers have been selected from online databases to analyze and review the use of search-based refactoring in software engineering. The current state of the research is analyzed and patterns in the studies are investigated in order to assess gaps in the area and suggest opportunities for future research. The papers reviewed are tabulated in order to aid researchers in quickly referencing studies. The literature addresses different methods using search-based refactoring for software maintenance, as well as studies that investigate the optimization process and discuss components of the search. There are studies that analyze different software metrics, experiment with multi-objective techniques and propose refactoring tools for use. Analysis of the literature has indicated some opportunities for future research in the area. More experimentation of the techniques in an industrial environment and feedback from software developers is needed to support the approaches. Also, recent work with multi-objective techniques has shown that there are exciting possibilities for future research using these techniques with refactoring. This survey is beneficial as an introduction for any researchers aiming to work in the area of Search-Based Software Engineering with respect to software maintenance and will allow them to gain an understanding of the current landscape of the research and the insights gathered