Regulatory motif discovery using a population clustering evolutionary algorithm

This paper describes a novel evolutionary algorithm for regulatory motif discovery in DNA promoter sequences. The algorithm uses data clustering to logically distribute the evolving population across the search space. Mating then takes place within local regions of the population, promoting overall solution diversity and encouraging discovery of multiple solutions. Experiments using synthetic data sets have demonstrated the algorithm's capacity to find position frequency matrix models of known regulatory motifs in relatively long promoter sequences. These experiments have also shown the algorithm's ability to maintain diversity during search and discover multiple motifs within a single population. The utility of the algorithm for discovering motifs in real biological data is demonstrated by its ability to find meaningful motifs within muscle-specific regulatory sequences

Evolutionary-based sparse regression for the experimental identification of duffing oscillator

In this paper, an evolutionary-based sparse regression algorithm is proposed and applied onto experimental data collected from a Duffing oscillator setup and numerical simulation data. Our purpose is to identify the Coulomb friction terms as part of the ordinary differential equation of the system. Correct identification of this nonlinear system using sparse identification is hugely dependent on selecting the correct form of nonlinearity included in the function library. Consequently, in this work, the evolutionary-based sparse identification is replacing the need for user knowledge when constructing the library in sparse identification. Constructing the library based on the data-driven evolutionary approach is an effective way to extend the space of nonlinear functions, allowing for the sparse regression to be applied on an extensive space of functions. The results show that the method provides an effective algorithm for the purpose of unveiling the physical nature of the Duffing oscillator. In addition, the robustness of the identification algorithm is investigated for various levels of noise in simulation. The proposed method has possible applications to other nonlinear dynamic systems in mechatronics, robotics, and electronics

Evolutionary Synthesis of Fractional Capacitor Using Simulated Annealing Method

Synthesis of fractional capacitor using classical analog circuit synthesis method was described in [6]. The work presented in this paper is focused on synthesis of the same problem by means of evolutionary method simulated annealing. Based on given desired characteristic function as input impedance or transfer function, the proposed method is able to synthesize topology and values of the components of the desired analog circuit. Comparison of the results given in [6] and results obtained by the proposed method will be given and discussed

Evolutionary Synthesis of Analog Electronic Circuits Using EDA Algorithms

Disertační práce je zaměřena na návrh analogových elektronických obvodů pomocí algoritmů s pravěpodobnostními modely (algoritmy EDA). Prezentované metody jsou na základě požadovaných charakteristik cílových obvodů schopny navrhnout jak parametry použitých komponent tak také jejich topologii zapojení. Tři různé metody využití EDA algoritmů jsou navrženy a otestovány na příkladech skutečných problémů z oblasti analogových elektronických obvodů. První metoda je určena pro návrh pasivních analogových obvodů a využívá algoritmus UMDA pro návrh jak topologie zapojení tak také hodnot parametrů použitých komponent. Metoda je použita pro návrh admitanční sítě s požadovanou vstupní impedancí pro účely chaotického oscilátoru. Druhá metoda je také určena pro návrh pasivních analogových obvodů a využívá hybridní přístup - UMDA pro návrh topologie a metodu lokální optimalizace pro návrh parametrů komponent. Třetí metoda umožňuje návrh analogových obvodů obsahujících také tranzistory. Metoda využívá hybridní přístup - EDA algoritmus pro syntézu topologie a metoda lokální optimalizace pro určení parametrů použitých komponent. Informace o topologii je v jednotlivých jedincích populace vyjádřena pomocí grafů a hypergrafů.Dissertation thesis is focused on design of analog electronic circuits using Estimation of Distribution Algorithms (EDA). Based on the desired characteristics of the target circuits the proposed methods are able to design the parameters of the used components and theirs topology of connection as well. Three different methods employing EDA algorithms are proposed and verified on examples of real problems from the area of analog circuits design. The first method is capable to design passive analog circuits. The method employs UMDA algorithm which is used for determination of the parameters of the used components and synthesis of the topology of their connection as well. The method is verified on the problem of design of admittance network with desired input impedance function which is used as a part of chaotic oscillator circuit. The second method is also capable to design passive analog circuits. The method employs hybrid approach - UMDA for synthesis of the topology and local optimization method for determination of the parameters of the components. The third method is capable to design analog circuits which include also ac- tive components such as transistors. Hybrid approach is used. The topology is synthesized using EDA algorithm and the parameters are determined using a local optimization method. In the individuals of the population information about the topology is represented using graphs and hypergraphs.

Open-ended evolution to discover analogue circuits for beyond conventional applications

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s10710-012-9163-8. Copyright @ Springer 2012.Analogue circuits synthesised by means of open-ended evolutionary algorithms often have unconventional designs. However, these circuits are typically highly compact, and the general nature of the evolutionary search methodology allows such designs to be used in many applications. Previous work on the evolutionary design of analogue circuits has focused on circuits that lie well within analogue application domain. In contrast, our paper considers the evolution of analogue circuits that are usually synthesised in digital logic. We have developed four computational circuits, two voltage distributor circuits and a time interval metre circuit. The approach, despite its simplicity, succeeds over the design tasks owing to the employment of substructure reuse and incremental evolution. Our findings expand the range of applications that are considered suitable for evolutionary electronics

Grey-box model identification via evolutionary computing

This paper presents an evolutionary grey-box model identification methodology that makes the best use of a priori knowledge on a clear-box model with a global structural representation of the physical system under study, whilst incorporating accurate blackbox models for immeasurable and local nonlinearities of a practical system. The evolutionary technique is applied to building dominant structural identification with local parametric tuning without the need of a differentiable performance index in the presence of noisy data. It is shown that the evolutionary technique provides an excellent fitting performance and is capable of accommodating multiple objectives such as to examine the relationships between model complexity and fitting accuracy during the model building process. Validation results show that the proposed method offers robust, uncluttered and accurate models for two practical systems. It is expected that this type of grey-box models will accommodate many practical engineering systems for a better modelling accuracy

Review of Face Detection Systems Based Artificial Neural Networks Algorithms

Face detection is one of the most relevant applications of image processing and biometric systems. Artificial neural networks (ANN) have been used in the field of image processing and pattern recognition. There is lack of literature surveys which give overview about the studies and researches related to the using of ANN in face detection. Therefore, this research includes a general review of face detection studies and systems which based on different ANN approaches and algorithms. The strengths and limitations of these literature studies and systems were included also.Comment: 16 pages, 12 figures, 1 table, IJMA Journa