3,404 research outputs found

    Significance Relations for the Benchmarking of Meta-Heuristic Algorithms

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    The experimental analysis of meta-heuristic algorithm performance is usually based on comparing average performance metric values over a set of algorithm instances. When algorithms getting tight in performance gains, the additional consideration of significance of a metric improvement comes into play. However, from this moment the comparison changes from an absolute to a relative mode. Here the implications of this paradigm shift are investigated. Significance relations are formally established. Based on this, a trade-off between increasing cycle-freeness of the relation and small maximum sets can be identified, allowing for the selection of a proper significance level and resulting ranking of a set of algorithms. The procedure is exemplified on the CEC'05 benchmark of real parameter single objective optimization problems. The significance relation here is based on awarding ranking points for relative performance gains, similar to the Borda count voting method or the Wilcoxon signed rank test. In the particular CEC'05 case, five ranks for algorithm performance can be clearly identified.Comment: 6 pages, 2 figures, 1 tabl

    Benchmarking for Metaheuristic Black-Box Optimization: Perspectives and Open Challenges

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    Research on new optimization algorithms is often funded based on the motivation that such algorithms might improve the capabilities to deal with real-world and industrially relevant optimization challenges. Besides a huge variety of different evolutionary and metaheuristic optimization algorithms, also a large number of test problems and benchmark suites have been developed and used for comparative assessments of algorithms, in the context of global, continuous, and black-box optimization. For many of the commonly used synthetic benchmark problems or artificial fitness landscapes, there are however, no methods available, to relate the resulting algorithm performance assessments to technologically relevant real-world optimization problems, or vice versa. Also, from a theoretical perspective, many of the commonly used benchmark problems and approaches have little to no generalization value. Based on a mini-review of publications with critical comments, advice, and new approaches, this communication aims to give a constructive perspective on several open challenges and prospective research directions related to systematic and generalizable benchmarking for black-box optimization

    Metaheuristic optimization of power and energy systems: underlying principles and main issues of the 'rush to heuristics'

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    In the power and energy systems area, a progressive increase of literature contributions containing applications of metaheuristic algorithms is occurring. In many cases, these applications are merely aimed at proposing the testing of an existing metaheuristic algorithm on a specific problem, claiming that the proposed method is better than other methods based on weak comparisons. This 'rush to heuristics' does not happen in the evolutionary computation domain, where the rules for setting up rigorous comparisons are stricter, but are typical of the domains of application of the metaheuristics. This paper considers the applications to power and energy systems, and aims at providing a comprehensive view of the main issues concerning the use of metaheuristics for global optimization problems. A set of underlying principles that characterize the metaheuristic algorithms is presented. The customization of metaheuristic algorithms to fit the constraints of specific problems is discussed. Some weaknesses and pitfalls found in literature contributions are identified, and specific guidelines are provided on how to prepare sound contributions on the application of metaheuristic algorithms to specific problems

    Identification of metabolic pathways using pathfinding approaches: A systematic review

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    Metabolic pathways have become increasingly available for variousmicroorganisms. Such pathways have spurred the development of a wide array of computational tools, in particular, mathematical pathfinding approaches. This article can facilitate the understanding of computational analysis ofmetabolic pathways in genomics. Moreover, stoichiometric and pathfinding approaches inmetabolic pathway analysis are discussed. Threemajor types of studies are elaborated: stoichiometric identification models, pathway-based graph analysis and pathfinding approaches in cellular metabolism. Furthermore, evaluation of the outcomes of the pathways withmathematical benchmarkingmetrics is provided. This review would lead to better comprehension ofmetabolismbehaviors in living cells, in terms of computed pathfinding approaches. © The Author 2016

    Benchmarking in cluster analysis: A white paper

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    To achieve scientific progress in terms of building a cumulative body of knowledge, careful attention to benchmarking is of the utmost importance. This means that proposals of new methods of data pre-processing, new data-analytic techniques, and new methods of output post-processing, should be extensively and carefully compared with existing alternatives, and that existing methods should be subjected to neutral comparison studies. To date, benchmarking and recommendations for benchmarking have been frequently seen in the context of supervised learning. Unfortunately, there has been a dearth of guidelines for benchmarking in an unsupervised setting, with the area of clustering as an important subdomain. To address this problem, discussion is given to the theoretical conceptual underpinnings of benchmarking in the field of cluster analysis by means of simulated as well as empirical data. Subsequently, the practicalities of how to address benchmarking questions in clustering are dealt with, and foundational recommendations are made

    New error measures and methods for realizing protein graphs from distance data

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    The interval Distance Geometry Problem (iDGP) consists in finding a realization in RK\mathbb{R}^K of a simple undirected graph G=(V,E)G=(V,E) with nonnegative intervals assigned to the edges in such a way that, for each edge, the Euclidean distance between the realization of the adjacent vertices is within the edge interval bounds. In this paper, we focus on the application to the conformation of proteins in space, which is a basic step in determining protein function: given interval estimations of some of the inter-atomic distances, find their shape. Among different families of methods for accomplishing this task, we look at mathematical programming based methods, which are well suited for dealing with intervals. The basic question we want to answer is: what is the best such method for the problem? The most meaningful error measure for evaluating solution quality is the coordinate root mean square deviation. We first introduce a new error measure which addresses a particular feature of protein backbones, i.e. many partial reflections also yield acceptable backbones. We then present a set of new and existing quadratic and semidefinite programming formulations of this problem, and a set of new and existing methods for solving these formulations. Finally, we perform a computational evaluation of all the feasible solver++formulation combinations according to new and existing error measures, finding that the best methodology is a new heuristic method based on multiplicative weights updates

    Metaheuristic Optimization of Power and Energy Systems: Underlying Principles and Main Issues of the `Rush to Heuristics'

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    In the power and energy systems area, a progressive increase of literature contributions that contain applications of metaheuristic algorithms is occurring. In many cases, these applications are merely aimed at proposing the testing of an existing metaheuristic algorithm on a specific problem, claiming that the proposed method is better than other methods that are based on weak comparisons. This ‘rush to heuristics’ does not happen in the evolutionary computation domain, where the rules for setting up rigorous comparisons are stricter but are typical of the domains of application of the metaheuristics. This paper considers the applications to power and energy systems and aims at providing a comprehensive view of the main issues that concern the use of metaheuristics for global optimization problems. A set of underlying principles that characterize the metaheuristic algorithms is presented. The customization of metaheuristic algorithms to fit the constraints of specific problems is discussed. Some weaknesses and pitfalls that are found in literature contributions are identified, and specific guidelines are provided regarding how to prepare sound contributions on the application of metaheuristic algorithms to specific problems

    Inferring Hierarchical Orthologous Groups

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    The reconstruction of ancestral evolutionary histories is the cornerstone of most phylogenetic analyses. Many applications are possible once the evolutionary history is unveiled, such as identifying taxonomically restricted genes (genome barcoding), predicting the function of unknown genes based on their evolutionary related genes gene ontologies, identifying gene losses and gene gains among gene families, or pinpointing the time in evolution where particular gene families emerge (sometimes referred to as “phylostratigraphy”). Typically, the reconstruction of the evolutionary histories is limited to the inference of evolutionary relationships (homology, orthology, paralogy) and basic clustering of these orthologs. In this thesis, we adopted the concept of Hierarchical Orthology Groups (HOGs), introduced a decade ago, and proposed several improvements both to improve their inference and to use them in biological analyses such as the aforementioned applications. In addition, HOGs are a powerful framework to investigate ancestral genomes since HOGs convey information regarding gene family evolution (gene losses, gene duplications or gene gains). In this thesis, an ancestral genome at a given taxonomic level denotes the last common ancestor genome for the related taxon and its hypothetical ancestral gene composition and gene order (synteny). The ancestral genes composition and ancestral synteny for a given ancestral genome provides valuable information to study the genome evolution in terms of genomic rearrangement (duplication, translocation, deletion, inversion) or of gene family evolution (variation of the gene function, accelerate gene evolution, duplication rich clade). This thesis identifies three major open challenges that composed my three research arcs. First, inferring HOGs is complex and computationally demanding meaning that robust and scalable algorithms are mandatory to generate good quality HOGs in a reasonable time. Second, benchmarking orthology clustering without knowing the true evolutionary history is a difficult task, which requires appropriate benchmark strategies. And third, the lack of tools to handle HOGs limits their applications. In the first arc of the thesis, I proposed two new algorithm refinements to improve orthology inference in order to produce orthologs less sensitive to gene fragmentations and imbalances in the rate of evolution among paralogous copies. In addition, I introduced version 2.0 of the GETHOGs 2.0 algorithm, which infers HOGs in a bottom up fashion, and which has been shown to be both faster and more accurate. In the second arc, I proposed new strategies to benchmark the reconstruction of gene families using detailed cases studies based on evidence from multiple sequence alignments along with reconstructed gene trees, and to benchmark orthology using a simulation framework that provides full control of the evolutionary genomic setup. This work highlights the main challenges in current methods. Third, I created pyHam (python HOG analysis method), iHam (interactive HOG analysis method) and GTM (Graph - Tree - Multiple sequence alignment)—a collection of tools to process, manipulate and visualise HOGs. pyHam offers an easy way to handle and work with HOGs using simple python coding. Embedded at its heart are two visualisation tools to synthesise HOG-derived information: iHam that allow interactive browsing of HOG structure and a tree based visualisation called tree profile that pinpoints evolutionary events induced by the HOGs on a species tree. In addition, I develop GTM an interactive web based visualisation tool that combine for a given gene family (or set of genes) the related sequences, gene tree and orthology graph. In this thesis, I show that HOGs are a useful framework for phylogenetics, with considerable work done to produce robust and scalable inferences. Another important aspect is that our inferences are benchmarked using manual case studies and automated verification using simulation or reference Quest for Orthologs Benchmarks. Lastly, one of the major advances was the conception and implementation of tools to manipulate and visualise HOG. Such tools have already proven useful when investigating HOGs for developmental reasons or for downstream analysis. Ultimately, the HOG framework is amenable to integration of all aspects which can reasonably be expected to have evolved along the history of genes and ancestral genome reconstruction. -- La reconstruction de l'histoire évolutive ancestrale est la pierre angulaire de la majorité des analyses phylogénétiques. Nombreuses sont les applications possibles une fois que l'histoire évolutive est révélée, comme l'identification de gènes restreints taxonomiquement (barcoding de génome), la prédiction de fonction pour les gènes inconnus en se basant sur les ontologies des gènes relatifs evolutionnairement, l'identification de la perte ou de l'apparition de gènes au sein de familles de gènes ou encore pour dater au cours de l'évolution l'apparition de famille de gènes (phylostratigraphie). Généralement, la reconstruction de l'histoire évolutive se limite à l'inférence des relations évolutives (homologie, orthologie, paralogie) ainsi qu'à la construction de groupes d’orthologues simples. Dans cette thèse, nous adoptons le concept des groupes hiérarchiques d’orthologues (HOGs en anglais pour Hierarchical Orthology Groups), introduit il y a plus de 10 ans, et proposons plusieurs améliorations tant bien au niveau de leurs inférences que de leurs utilisations dans les analyses biologiques susmentionnées. Cette thèse a pour but d'identifier les trois problématiques majeures qui composent mes trois axes de recherches. Premièrement, l'inférence des HOGs est complexe et nécessite une puissance computationnelle importante ce qui rend obligatoire la création d'algorithmes robustes et efficients dans l'espace temps afin de maintenir une génération de résultats de qualité rigoureuse dans un temps raisonnable. Deuxièmement, le contrôle de la qualité du groupement des orthologues est une tâche difficile si on ne connaît l'histoire évolutive réelle ce qui nécessite la mise en place de stratégies de contrôle de qualité adaptées. Tertio, le manque d'outils pour manipuler les HOGs limite leur utilisation ainsi que leurs applications. Dans le premier axe de ma thèse, je propose deux nouvelles améliorations de l'algorithme pour l'inférence des orthologues afin de pallier à la sensibilité de l'inférence vis à vis de la fragmentation des gènes et de l'asymétrie du taux d'évolution au sein de paralogues. De plus, j'introduis la version 2.0 de l'algorithme GETHOGs qui utilise une nouvelle approche de type 'bottom-up' afin de produire des résultats plus rapides et plus précis. Dans le second axe, je propose de nouvelles stratégies pour contrôler la qualité de la reconstruction des familles de gènes en réalisant des études de cas manuels fondés sur des preuves apportées par des alignement multiples de séquences et des reconstructions d'arbres géniques, et aussi pour contrôler la qualité de l'orthologie en simulant l'évolution de génomes afin de pouvoir contrôler totalement le matériel génétique produit. Ce travail met en avant les principales problématiques des méthodes actuelles. Dans le dernier axe, je montre pyHam, iHam et GTM - une panoplie d'outils que j’ai créée afin de faciliter la manipulation et la visualisation des HOGs en utilisant un programmation simple en python. Deux outils de visualisation sont directement intégrés au sein de pyHam afin de pouvoir synthétiser l'information véhiculée par les HOGs: iHam permet d’interactivement naviguer dans les HOGs ainsi qu’une autre visualisation appelée “tree profile” utilisant un arbre d'espèces où sont localisés les événements révolutionnaires contenus dans les HOGs. En sus, j'ai développé GTM un outil interactif web qui combine pour une famille de gènes donnée (ou un ensemble de gènes) leurs séquences alignées, leur arbre de gène ainsi que le graphe d'orthologie en relation. Dans cette thèse, je montre que le concept des HOGs est utile à la phylogénétique et qu'un travail considérable a été réalisé dans le but d'améliorer leur inférences de façon robuste et rapide. Un autre point important est que la qualité de nos inférences soit contrôlée en réalisant des études de cas manuellement ou en utilisant le Quest for Orthologs Benchmark qui est une référence dans le contrôle de la qualité de l’orthologie. Dernièrement, une des avancée majeure proposée est la conception et l'implémentation d'outils pour visualiser et manipuler les HOGs. Ces outils s'avèrent déjà utilisés tant pour l'étude des HOGs dans un but d'amélioration de leur qualité que pour leur utilisation dans des analyses biologiques. Pour conclure, on peut noter que tous les aspects qui semblent avoir évolué en relation avec l'histoire évolutive des gènes ou des génomes ancestraux peuvent être intégrés au concept des HOGs

    GOOSE Algorithm: A Powerful Optimization Tool for Real-World Engineering Challenges and Beyond

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    This study proposes the GOOSE algorithm as a novel metaheuristic algorithm based on the goose's behavior during rest and foraging. The goose stands on one leg and keeps his balance to guard and protect other individuals in the flock. The GOOSE algorithm is benchmarked on 19 well-known benchmark test functions, and the results are verified by a comparative study with genetic algorithm (GA), particle swarm optimization (PSO), dragonfly algorithm (DA), and fitness dependent optimizer (FDO). In addition, the proposed algorithm is tested on 10 modern benchmark functions, and the gained results are compared with three recent algorithms, such as the dragonfly algorithm, whale optimization algorithm (WOA), and salp swarm algorithm (SSA). Moreover, the GOOSE algorithm is tested on 5 classical benchmark functions, and the obtained results are evaluated with six algorithms, such as fitness dependent optimizer (FDO), FOX optimizer, butterfly optimization algorithm (BOA), whale optimization algorithm, dragonfly algorithm, and chimp optimization algorithm (ChOA). The achieved findings attest to the proposed algorithm's superior performance compared to the other algorithms that were utilized in the current study. The technique is then used to optimize Welded beam design and Economic Load Dispatch Problem, three renowned real-world engineering challenges, and the Pathological IgG Fraction in the Nervous System. The outcomes of the engineering case studies illustrate how well the suggested approach can optimize issues that arise in the real-world

    Birnbaum Importance Patterns and Their Applications in the Component Assignment Problem

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    The Birnbaum importance (BI) is a well-known measure that evaluates the relative contribution of components to system reliability. It has been successfully applied to tackling some reliability problems. This dissertation investigates two topics related to the BI in the reliability field: the patterns of component BIs and the BI-based heuristics and meta-heuristics for solving the component assignment problem (CAP).There exist certain patterns of component BIs (i.e., the relative order of the BI values to the individual components) for linear consecutive-k-out-of-n (Lin/Con/k/n) systems when all components have the same reliability p. This study summarizes and annotates the existing BI patterns for Lin/Con/k/n systems, proves new BI patterns conditioned on the value of p, disproves some patterns that were conjectured or claimed in the literature, and makes new conjectures based on comprehensive computational tests and analysis. More importantly, this study defines a concept of segment in Lin/Con/k/n systems for analyzing the BI patterns, and investigates the relationship between the BI and the common component reliability p and the relationship between the BI and the system size n. One can then use these relationships to further understand the proved, disproved, and conjectured BI patterns.The CAP is to find the optimal assignment of n available components to n positions in a system such that the system reliability is maximized. The ordering of component BIs has been successfully used to design heuristics for the CAP. This study proposes five new BI-based heuristics and discusses their corresponding properties. Based on comprehensive numerical experiments, a BI-based two-stage approach (BITA) is proposed for solving the CAP with each stage using different BI-based heuristics. The two-stage approach is much more efficient and capable to generate solutions of higher quality than the GAMS/CoinBonmin solver and a randomization method.This dissertation then presents a meta-heuristic, i.e., a BI-based genetic local search (BIGLS) algorithm, for the CAP in which a BI-based local search is embedded into the genetic algorithm. Comprehensive numerical experiments show the robustness and effectiveness of the BIGLS algorithm and especially its advantages over the BITA in terms of solution quality
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