MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods

An investigation of messy genetic algorithms

Genetic algorithms (GAs) are search procedures based on the mechanics of natural selection and natural genetics. They combine the use of string codings or artificial chromosomes and populations with the selective and juxtapositional power of reproduction and recombination to motivate a surprisingly powerful search heuristic in many problems. Despite their empirical success, there has been a long standing objection to the use of GAs in arbitrarily difficult problems. A new approach was launched. Results to a 30-bit, order-three-deception problem were obtained using a new type of genetic algorithm called a messy genetic algorithm (mGAs). Messy genetic algorithms combine the use of variable-length strings, a two-phase selection scheme, and messy genetic operators to effect a solution to the fixed-coding problem of standard simple GAs. The results of the study of mGAs in problems with nonuniform subfunction scale and size are presented. The mGA approach is summarized, both its operation and the theory of its use. Experiments on problems of varying scale, varying building-block size, and combined varying scale and size are presented

A similarity-based cooperative co-evolutionary algorithm for dynamic interval multi-objective optimization problems

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Dynamic interval multi-objective optimization problems (DI-MOPs) are very common in real-world applications. However, there are few evolutionary algorithms that are suitable for tackling DI-MOPs up to date. A framework of dynamic interval multi-objective cooperative co-evolutionary optimization based on the interval similarity is presented in this paper to handle DI-MOPs. In the framework, a strategy for decomposing decision variables is first proposed, through which all the decision variables are divided into two groups according to the interval similarity between each decision variable and interval parameters. Following that, two sub-populations are utilized to cooperatively optimize decision variables in the two groups. Furthermore, two response strategies, rgb0.00,0.00,0.00i.e., a strategy based on the change intensity and a random mutation strategy, are employed to rapidly track the changing Pareto front of the optimization problem. The proposed algorithm is applied to eight benchmark optimization instances rgb0.00,0.00,0.00as well as a multi-period portfolio selection problem and compared with five state-of-the-art evolutionary algorithms. The experimental results reveal that the proposed algorithm is very competitive on most optimization instances

Metaheuristic Design Patterns: New Perspectives for Larger-Scale Search Architectures

Design patterns capture the essentials of recurring best practice in an abstract form. Their merits are well established in domains as diverse as architecture and software development. They offer significant benefits, not least a common conceptual vocabulary for designers, enabling greater communication of high-level concerns and increased software reuse. Inspired by the success of software design patterns, this chapter seeks to promote the merits of a pattern-based method to the development of metaheuristic search software components. To achieve this, a catalog of patterns is presented, organized into the families of structural, behavioral, methodological and component-based patterns. As an alternative to the increasing specialization associated with individual metaheuristic search components, the authors encourage computer scientists to embrace the ‘cross cutting' benefits of a pattern-based perspective to optimization algorithms. Some ways in which the patterns might form the basis of further larger-scale metaheuristic component design automation are also discussed

From holism to compositionality: memes and the evolution of segmentation, syntax, and signification in music and language

Steven Mithen argues that language evolved from an antecedent he terms “Hmmmmm, [meaning it was] Holistic, manipulative, multi-modal, musical and mimetic”. Owing to certain innate and learned factors, a capacity for segmentation and cross-stream mapping in early Homo sapiens broke the continuous line of Hmmmmm, creating discrete replicated units which, with the initial support of Hmmmmm, eventually became the semantically freighted words of modern language. That which remained after what was a bifurcation of Hmmmmm arguably survived as music, existing as a sound stream segmented into discrete units, although one without the explicit and relatively fixed semantic content of language. All three types of utterance – the parent Hmmmmm, language, and music – are amenable to a memetic interpretation which applies Universal Darwinism to what are understood as language and musical memes. On the basis of Peter Carruthers’ distinction between ‘cognitivism’ and ‘communicativism’ in language, and William Calvin’s theories of cortical information encoding, a framework is hypothesized for the semantic and syntactic associations between, on the one hand, the sonic patterns of language memes (‘lexemes’) and of musical memes (‘musemes’) and, on the other hand, ‘mentalese’ conceptual structures, in Chomsky’s ‘Logical Form’ (LF)

Evolutionary Computation and QSAR Research

[Abstract] The successful high throughput screening of molecule libraries for a specific biological property is one of the main improvements in drug discovery. The virtual molecular filtering and screening relies greatly on quantitative structure-activity relationship (QSAR) analysis, a mathematical model that correlates the activity of a molecule with molecular descriptors. QSAR models have the potential to reduce the costly failure of drug candidates in advanced (clinical) stages by filtering combinatorial libraries, eliminating candidates with a predicted toxic effect and poor pharmacokinetic profiles, and reducing the number of experiments. To obtain a predictive and reliable QSAR model, scientists use methods from various fields such as molecular modeling, pattern recognition, machine learning or artificial intelligence. QSAR modeling relies on three main steps: molecular structure codification into molecular descriptors, selection of relevant variables in the context of the analyzed activity, and search of the optimal mathematical model that correlates the molecular descriptors with a specific activity. Since a variety of techniques from statistics and artificial intelligence can aid variable selection and model building steps, this review focuses on the evolutionary computation methods supporting these tasks. Thus, this review explains the basic of the genetic algorithms and genetic programming as evolutionary computation approaches, the selection methods for high-dimensional data in QSAR, the methods to build QSAR models, the current evolutionary feature selection methods and applications in QSAR and the future trend on the joint or multi-task feature selection methods.Instituto de Salud Carlos III, PIO52048Instituto de Salud Carlos III, RD07/0067/0005Ministerio de Industria, Comercio y Turismo; TSI-020110-2009-53)Galicia. Consellería de Economía e Industria; 10SIN105004P