61,052 research outputs found

    First-principles molecular structure search with a genetic algorithm

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    The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment of the conformation space of molecules. The algorithm is designed to work with first-principles methods, facilitated by the incorporation of local optimization and blacklisting conformers to prevent repeated evaluations of very similar solutions. The aim of the search is not only to find the global minimum, but to predict all conformers within an energy window above the global minimum. The performance of the search strategy is: (i) evaluated for a reference data set extracted from a database with amino acid dipeptide conformers obtained by an extensive combined force field and first-principles search and (ii) compared to the performance of a systematic search and a random conformer generator for the example of a drug-like ligand with 43 atoms, 8 rotatable bonds and 1 cis/trans bond

    Flexible protein folding by ant colony optimization

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    Protein structure prediction is one of the most challenging topics in bioinformatics. As the protein structure is found to be closely related to its functions, predicting the folding structure of a protein to judge its functions is meaningful to the humanity. This chapter proposes a flexible ant colony (FAC) algorithm for solving protein folding problems (PFPs) based on the hydrophobic-polar (HP) square lattice model. Different from the previous ant algorithms for PFPs, the pheromones in the proposed algorithm are placed on the arcs connecting adjacent squares in the lattice. Such pheromone placement model is similar to the one used in the traveling salesmen problems (TSPs), where pheromones are released on the arcs connecting the cities. Moreover, the collaboration of effective heuristic and pheromone strategies greatly enhances the performance of the algorithm so that the algorithm can achieve good results without local search methods. By testing some benchmark two-dimensional hydrophobic-polar (2D-HP) protein sequences, the performance shows that the proposed algorithm is quite competitive compared with some other well-known methods for solving the same protein folding problems

    Metaheuristic design of feedforward neural networks: a review of two decades of research

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    Over the past two decades, the feedforward neural network (FNN) optimization has been a key interest among the researchers and practitioners of multiple disciplines. The FNN optimization is often viewed from the various perspectives: the optimization of weights, network architecture, activation nodes, learning parameters, learning environment, etc. Researchers adopted such different viewpoints mainly to improve the FNN's generalization ability. The gradient-descent algorithm such as backpropagation has been widely applied to optimize the FNNs. Its success is evident from the FNN's application to numerous real-world problems. However, due to the limitations of the gradient-based optimization methods, the metaheuristic algorithms including the evolutionary algorithms, swarm intelligence, etc., are still being widely explored by the researchers aiming to obtain generalized FNN for a given problem. This article attempts to summarize a broad spectrum of FNN optimization methodologies including conventional and metaheuristic approaches. This article also tries to connect various research directions emerged out of the FNN optimization practices, such as evolving neural network (NN), cooperative coevolution NN, complex-valued NN, deep learning, extreme learning machine, quantum NN, etc. Additionally, it provides interesting research challenges for future research to cope-up with the present information processing era

    High-Level Object Oriented Genetic Programming in Logistic Warehouse Optimization

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    Disertační práce je zaměřena na optimalizaci průběhu pracovních operací v logistických skladech a distribučních centrech. Hlavním cílem je optimalizovat procesy plánování, rozvrhování a odbavování. Jelikož jde o problém patřící do třídy složitosti NP-težký, je výpočetně velmi náročné nalézt optimální řešení. Motivací pro řešení této práce je vyplnění pomyslné mezery mezi metodami zkoumanými na vědecké a akademické půdě a metodami používanými v produkčních komerčních prostředích. Jádro optimalizačního algoritmu je založeno na základě genetického programování řízeného bezkontextovou gramatikou. Hlavním přínosem této práce je a) navrhnout nový optimalizační algoritmus, který respektuje následující optimalizační podmínky: celkový čas zpracování, využití zdrojů, a zahlcení skladových uliček, které může nastat během zpracování úkolů, b) analyzovat historická data z provozu skladu a vyvinout sadu testovacích příkladů, které mohou sloužit jako referenční výsledky pro další výzkum, a dále c) pokusit se předčit stanovené referenční výsledky dosažené kvalifikovaným a trénovaným operačním manažerem jednoho z největších skladů ve střední Evropě.This work is focused on the work-flow optimization in logistic warehouses and distribution centers. The main aim is to optimize process planning, scheduling, and dispatching. The problem is quite accented in recent years. The problem is of NP hard class of problems and where is very computationally demanding to find an optimal solution. The main motivation for solving this problem is to fill the gap between the new optimization methods developed by researchers in academic world and the methods used in business world. The core of the optimization algorithm is built on the genetic programming driven by the context-free grammar. The main contribution of the thesis is a) to propose a new optimization algorithm which respects the makespan, the utilization, and the congestions of aisles which may occur, b) to analyze historical operational data from warehouse and to develop the set of benchmarks which could serve as the reference baseline results for further research, and c) to try outperform the baseline results set by the skilled and trained operational manager of the one of the biggest warehouses in the middle Europe.

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

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    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

    Predictive modeling of die filling of the pharmaceutical granules using the flexible neural tree

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    In this work, a computational intelligence (CI) technique named flexible neural tree (FNT) was developed to predict die filling performance of pharmaceutical granules and to identify significant die filling process variables. FNT resembles feedforward neural network, which creates a tree-like structure by using genetic programming. To improve accuracy, FNT parameters were optimized by using differential evolution algorithm. The performance of the FNT-based CI model was evaluated and compared with other CI techniques: multilayer perceptron, Gaussian process regression, and reduced error pruning tree. The accuracy of the CI model was evaluated experimentally using die filling as a case study. The die filling experiments were performed using a model shoe system and three different grades of microcrystalline cellulose (MCC) powders (MCC PH 101, MCC PH 102, and MCC DG). The feed powders were roll-compacted and milled into granules. The granules were then sieved into samples of various size classes. The mass of granules deposited into the die at different shoe speeds was measured. From these experiments, a dataset consisting true density, mean diameter (d50), granule size, and shoe speed as the inputs and the deposited mass as the output was generated. Cross-validation (CV) methods such as 10FCV and 5x2FCV were applied to develop and to validate the predictive models. It was found that the FNT-based CI model (for both CV methods) performed much better than other CI models. Additionally, it was observed that process variables such as the granule size and the shoe speed had a higher impact on the predictability than that of the powder property such as d50. Furthermore, validation of model prediction with experimental data showed that the die filling behavior of coarse granules could be better predicted than that of fine granules
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