Scatter search is a population-based method that has recently been shown to yield promising outcomes for solving combinatorial and nonlinear optimization problems. Based on formulations originally proposed in the 1960s for combining decision rules and problem constraints such as the surrogate constraint method, scatter search uses strategies for combining solution vectors that have proved effective in a variety of problem settings. In this paper, we develop a general purpose heuristic for a class of nonlinear optimization problems. The procedure is based on the scatter search methodology and treats the objective function evaluation as a black box, making the search algorithm context-independent.Most optimization problems in the chemical and bio-chemical industries are highly nonlinear in either the objective function or the constraints. Moreover, they usually present differential-algebraic systems of constraints. In this type of problem, the evaluation of a solution or even the feasibility test of a set of values for the decision variables is a time-consuming operation. In this context, the solution method is limited to a reduced number of solution examinations. We have implemented a scatter search procedure in Matlab for this special class of difficult optimization problems. Our development goes beyond a simple exercise of applying scatter search to this class of problem, but presents innovative mechanisms to obtain a good balance between intensification and diversification in a short-term search horizon. Computational comparisons with other recent methods over a set of benchmark problems favor the proposed procedure.

Background: We consider the problem of parameter estimation (model calibration) in nonlinear dynamic models of biological systems. Due to the frequent ill-conditioning and multi-modality of many of these problems, traditional local methods usually fail (unless initialized with very good guesses of the parameter vector). In order to surmount these difficulties, global optimization (GO) methods have been suggested as robust alternatives. Currently, deterministic GO methods can not solve problems of realistic size within this class in reasonable computation times. In contrast, certain types of stochastic GO methods have shown promising results, although the computational cost remains large. Rodriguez-Fernandez and coworkers have presented hybrid stochasticdeterministic GO methods which could reduce computation time by one order of magnitude while guaranteeing robustness. Our goal here was to further reduce the computational effort without loosing robustness.

BackgroundOptimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools.ResultsWe present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods.ConclusionsMEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods.

Two novel extensions for the well known Ant Colony Optimization (ACO) framework are introduced here, which allow the solution of Mixed Integer Nonlinear Programs (MINLP). Furthermore, a hybrid implementation (ACOmi) based on this extended ACO framework, specially developed for complex non-convex MINLPs, is presented together with numerical results.These extensions on the ACO framework have been developed to serve the needs of practitioners who face highly non-convex and computationally costly MINLPs. The performance of this new method is evaluated considering several non-convex MINLP benchmark problems and one real-world application. The results obtained by our implementation substantiate the success of this new approach.

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An enhanced scatter search method for the global dynamic optimization of nonlinear processes using the control vector parametrization (CVP) approach is presented. Sharing some features of the scatter search metaheuristic, this new method presents a simpler but more effective design which helps to overcome typical difficulties of nonlinear dynamic systems optimization such as noise, flat areas, nonsmoothness, and/or discontinuities. This new algorithm provides a good balance between robustness and efficiency in the global phase, and couples a local search procedure to accelerate the convergence to optimal solutions. Its application to four multimodal dynamic optimization problems, compared with other state-of-the-art global optimization algorithms, including an advanced scatter search design, proves its efficiency and robustness, showing a very good scalability.

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BackgroundThe development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic models. Global optimization methods can be used to solve this type of problems but the associated computational cost is very large. Moreover, many of these methods need the tuning of a number of adjustable search parameters, requiring a number of initial exploratory runs and therefore further increasing the computation times.Here we present a novel parallel method, self-adaptive cooperative enhanced scatter search (saCeSS), to accelerate the solution of this class of problems. The method is based on the scatter search optimization metaheuristic and incorporates several key new mechanisms: (i) asynchronous cooperation between parallel processes, (ii) coarse and fine-grained parallelism, and (iii) self-tuning strategies.ResultsThe performance and robustness of saCeSS is illustrated by solving a set of challenging parameter estimation problems, including medium and large-scale kinetic models of the bacterium E. coli, bakerés yeast S. cerevisiae, the vinegar fly D. melanogaster, Chinese Hamster Ovary cells, and a generic signal transduction network.The results consistently show that saCeSS is a robust and efficient method, allowing very significant reduction of computation times with respect to several previous state of the art methods (from days to minutes, in several cases) even when only a small number of processors is used.ConclusionsThe new parallel cooperative method presented here allows the solution of medium and large scale parameter estimation problems in reasonable computation times and with small hardware requirements. Further, the method includes self-tuning mechanisms which facilitate its use by non-experts. We believe that this new method can play a key role in the development of large-scale and even whole-cell dynamic models.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1452-4) contains supplementary material, which is available to authorized users.