A fuzzy multiobjective algorithm for multiproduct batch plant: Application to protein production

This paper addresses the problem of the optimal design of batch plants with imprecise demands and proposes an alternative treatment of the imprecision by using fuzzy concepts. For this purpose, we extended a multiobjective genetic algorithm (MOGA) developed in previousworks, taking into account simultaneously maximization of the net present value (NPV) and two other performance criteria, i.e. the production delay/advance and a flexibility criterion. The former is computed by comparing the fuzzy computed production time to a given fuzzy production time horizon and the latter is based on the additional fuzzy demand that the plant is able to produce. The methodology provides a set of scenarios that are helpful to the decision’s maker and constitutes a very promising framework for taken imprecision into account in new product development stage

Branch-and-lift algorithm for deterministic global optimization in nonlinear optimal control

This paper presents a branch-and-lift algorithm for solving optimal control problems with smooth nonlinear dynamics and potentially nonconvex objective and constraint functionals to guaranteed global optimality. This algorithm features a direct sequential method and builds upon a generic, spatial branch-and-bound algorithm. A new operation, called lifting, is introduced, which refines the control parameterization via a Gram-Schmidt orthogonalization process, while simultaneously eliminating control subregions that are either infeasible or that provably cannot contain any global optima. Conditions are given under which the image of the control parameterization error in the state space contracts exponentially as the parameterization order is increased, thereby making the lifting operation efficient. A computational technique based on ellipsoidal calculus is also developed that satisfies these conditions. The practical applicability of branch-and-lift is illustrated in a numerical example. © 2013 Springer Science+Business Media New York

Transciptome Analysis Illuminates the Nature of the Intracellular Interaction in a Vertebrate-Algal Symbiosis

During embryonic development, cells of the green alga Oophila amblystomatis enter cells of the salamander Ambystoma maculatum forming an endosymbiosis. Here, using de novo dual-RNA seq, we compared the host salamander cells that harbored intracellular algae to those without algae and the algae inside the animal cells to those in the egg capsule. This two-by-two-way analysis revealed that intracellular algae exhibit hallmarks of cellular stress and undergo a striking metabolic shift from oxidative metabolism to fermentation. Culturing experiments with the alga showed that host glutamine may be utilized by the algal endosymbiont as a primary nitrogen source. Transcriptional changes in salamander cells suggest an innate immune response to the alga, with potential attenuation of NF-κB, and metabolic alterations indicative of modulation of insulin sensitivity. In stark contrast to its algal endosymbiont, the salamander cells did not exhibit major stress responses, suggesting that the host cell experience is neutral or beneficial

Modelling and parameter identification for a two-stage fractional dynamical system in microbial batch process

In this paper, we consider mathematical modelling and parameter identification problem in bioconversion of glycerol to 1,3-propanediol by Klebsiella pneumoniae. In view of the dynamic behavior with memory and heredity and experimental results in batch culture, a two-stage fractional dynamical system with unknown fractional orders and unknown kinetic parameters is proposed to describe the fermentation process. For this system, some important properties of the solution are discussed. Then, taking the weighted least-squares error between the computational values and the experimental data as the performance index, a parameter identification model subject to continuous state inequality constraints is presented. An exact penalty method is introduced to transform the parameter identification problem into the one only with box constraints. On this basis, we develop a parallel Particle Swarm Optimization algorithm to find the optimal fractional orders and kinetic parameters. Finally, numerical results show that the model can reasonably describe the batch fermentation process, as well as the effectiveness of the developed algorithm. Keywords: fractional dynamical system, parameter identification, parallel optimization

An update on statistical boosting in biomedicine

Statistical boosting algorithms have triggered a lot of research during the last decade. They combine a powerful machine-learning approach with classical statistical modelling, offering various practical advantages like automated variable selection and implicit regularization of effect estimates. They are extremely flexible, as the underlying base-learners (regression functions defining the type of effect for the explanatory variables) can be combined with any kind of loss function (target function to be optimized, defining the type of regression setting). In this review article, we highlight the most recent methodological developments on statistical boosting regarding variable selection, functional regression and advanced time-to-event modelling. Additionally, we provide a short overview on relevant applications of statistical boosting in biomedicine

A comparison of algorithms for the optimization of fermentation processes

The optimization of biotechnological processes is a complex problem that has been intensively studied in the past few years due to the economic impact of the products obtained from fermentations. In fed-batch processes, the goal is to find the optimal feeding trajectory that maximizes the final productivity. Several methods, including Evolutionary Algorithms (EAs) have been applied to this task in a number of different fermentation processes. This paper performs an experimental comparison between Particle Swarm Optimization, Differential Evolution and a real-valued EA in three distinct case studies, taken from previous work by the authors and literature, all considering the optimization of fed-batch fermentation processes.Portuguese Foundation for Science and Technology - Project POSC/EIA/59899/2004; Project SeARCH (Services and Advanced Research Computing with HTC/HPC clusters)/Contract CONCREEQ/443/2001

Optimal Biocompatible Solvent Design by Mixed-integer Hybrid Differential Evolution

In this study, a flexible optimization approach is introduced to design an optimal biocompatible solvent for an extractive fermentation process with cell-recycling. The optimal process/solvent design problem is formulated as a mixed-integer nonlinear programming model in which performance requirements of the compounds are reflected in the objectives and the constraints. A flexible or fuzzy optimization approach is applied to soften the rigid requirement for maximization of the production rate, extraction efficiency and to consider the solvent utilization rate as the softened inequality constraint to the process/solvent design problem. Such a trade-off problem is then converted to the goal attainment problem, which is described as the constrained mixed-integer nonlinear programming (MINLP) problem. Mixed-integer hybrid differential evolution with multiplier updating method is introduced to solve the constrained MINLP problem. The adaptive penalty updating scheme is more efficient to achieve a global design

Optimization of fed-batch fermentation processes with bio-inspired algorithms

The optimization of the feeding trajectories in fed-batch fermentation processes is a complex problem that has gained attention given its significant economical impact. A number of bio-inspired algorithms have approached this task with considerable success, but systematic and statistically significant comparisons of the different alternatives are still lacking. In this paper, the performance of different metaheuristics, such as Evolutionary Algorithms (EAs), Differential Evolution (DE) and Particle Swarm Optimization (PSO) is compared, resorting to several case studies taken from literature and conducting a thorough statistical validation of the results. DE obtains the best overall performance, showing a consistent ability to find good solutions and presenting a good convergence speed, with the DE/rand variants being the ones with the best performance. A freely available computational application, OptFerm, is described that provides an interface allowing users to apply the proposed methods to their own models and data.The work is partially funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT (Portuguese Foundation for Science and Technology) within projects Ref. COMPETE FCOMP-01-0124-FEDER-015079 and PEst-OE/ES/UI0752/2011

A software platform for evolutionary computation with pluggable parallelism and quality assurance

This paper proposes the Java Evolutionary Computation Library (JECoLi), an adaptable, flexible, extensible and reliable software framework implementing metaheuristic optimization algorithms, using the Java programming language. JECoLi aims to offer a solution suited for the integration of Evolutionary Computation (EC)-based approaches in larger applications, and for the rapid and efficient benchmarking of EC algorithms in specific problems. Its main contributions are (i) the implementation of pluggable parallelization modules, independent from the EC algorithms, allowing the programs to adapt to the available hardware resources in a transparent way, without changing the base code; (ii) a flexible platform for software quality assurance that allows creating tests for the implemented features and for user-defined extensions. The library is freely available as an open-source project.Fundação para a Ciência e a Tecnologia (FCT) - PTDC/EIA-EIA/115176/2009, Programa COMPET