1,234 research outputs found
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
Evolutionary Algorithms
Evolutionary algorithms (EAs) are population-based metaheuristics, originally
inspired by aspects of natural evolution. Modern varieties incorporate a broad
mixture of search mechanisms, and tend to blend inspiration from nature with
pragmatic engineering concerns; however, all EAs essentially operate by
maintaining a population of potential solutions and in some way artificially
'evolving' that population over time. Particularly well-known categories of EAs
include genetic algorithms (GAs), Genetic Programming (GP), and Evolution
Strategies (ES). EAs have proven very successful in practical applications,
particularly those requiring solutions to combinatorial problems. EAs are
highly flexible and can be configured to address any optimization task, without
the requirements for reformulation and/or simplification that would be needed
for other techniques. However, this flexibility goes hand in hand with a cost:
the tailoring of an EA's configuration and parameters, so as to provide robust
performance for a given class of tasks, is often a complex and time-consuming
process. This tailoring process is one of the many ongoing research areas
associated with EAs.Comment: To appear in R. Marti, P. Pardalos, and M. Resende, eds., Handbook of
Heuristics, Springe
Implementing metaheuristic optimization algorithms with JECoLi
This work proposes JECoLi - a novel Java-based library
for the implementation of metaheuristic optimization
algorithms with a focus on Genetic and Evolutionary
Computation based methods. The library was developed
based on the principles of flexibility, usability, adaptability,
modularity, extensibility, transparency, scalability, robustness
and computational efficiency. The project is opensource,
so JECoLi is made available under the GPL license,
together with extensive documentation and examples,
all included in a community Wiki-based web site
(http://darwin.di.uminho.pt/jecoli). JECoLi has been/is being
used in several research projects that helped to shape
its evolution, ranging application fields from Bioinformatics,
to Data Mining and Computer Network optimization
Multiobjective evolutionary optimization of water distribution systems : exploiting diversity with infeasible solutions
This article investigates the computational efficiency of constraint handling in multi-objective evolutionary optimization algorithms for water distribution systems. The methodology investigated here encourages the co-existence and simultaneous development including crossbreeding of subpopulations of cost-effective feasible and infeasible solutions based on Pareto dominance. This yields a boundary search approach that also promotes diversity in the gene pool throughout the progress of the optimization by exploiting the full spectrum of non-dominated infeasible solutions. The relative effectiveness of small and moderate population sizes with respect to the number of decision variables is investigated also. The results reveal the optimization algorithm to be efficient, stable and robust. It found optimal and near-optimal solutions reliably and efficiently. The real-world system based optimisation problem involved multiple variable head supply nodes, 29 fire-fighting flows, extended period simulation and multiple demand categories including water loss. The least cost solutions found satisfied the flow and pressure requirements consistently. The cheapest feasible solutions achieved represent savings of 48.1% and 48.2%, for populations of 200 and 1000, respectively, and the population of 1000 achieved slightly better results overall
Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis
26 páginas, 10 figuras, 1 tabla.-- This is an
open access article distributed under the terms of
the Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are creditedFrom cyanobacteria to human, sustained oscillations coordinate important biological functions. Although much has been learned concerning the sophisticated molecular mechanisms underlying biological oscillators, design principles linking structure and functional behavior are not yet fully understood. Here we explore design principles of biological oscillators from a multiobjective optimization perspective, taking into account the trade-offs between conflicting performance goals or demands. We develop a comprehensive tool for automated design of oscillators, based on multicriteria global optimization that allows two modes: (i) the automatic design (forward problem) and (ii) the inference of design principles (reverse analysis problem). From the perspective of synthetic biology, the forward mode allows the solution of design problems that mimic some of the desirable properties appearing in natural oscillators. The reverse analysis mode facilitates a systematic exploration of the design space based on Pareto optimality concepts. The method is illustrated with two case studies: the automatic design of synthetic oscillators from a library of biological parts, and the exploration of design principles in 3-gene oscillatory systemsThis work was supported by MINECO
(and the European Regional Development Fund)
project ªSYNBIOFACTORYº (grant number
DPI2014-55276-C5-2-R).Peer reviewe
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
A Multiobjective Approach Applied to the Protein Structure Prediction Problem
Interest in discovering a methodology for solving the Protein Structure Prediction problem extends into many fields of study including biochemistry, medicine, biology, and numerous engineering and science disciplines. Experimental approaches, such as, x-ray crystallographic studies or solution Nuclear Magnetic Resonance Spectroscopy, to mathematical modeling, such as minimum energy models are used to solve this problem. Recently, Evolutionary Algorithm studies at the Air Force Institute of Technology include the following: Simple Genetic Algorithm (GA), messy GA, fast messy GA, and Linkage Learning GA, as approaches for potential protein energy minimization. Prepackaged software like GENOCOP, GENESIS, and mGA are in use to facilitate experimentation of these techniques. In addition to this software, a parallelized version of the fmGA, the so-called parallel fast messy GA, is found to be good at finding semi-optimal answers in reasonable wall clock time. The aim of this work is to apply a Multiobjective approach to solving this problem using a modified fast messy GA. By dividing the CHARMm energy model into separate objectives, it should be possible to find structural configurations of a protein that yield lower energy values and ultimately more correct conformations
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