14,594 research outputs found

    Biology of Applied Digital Ecosystems

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    A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex, dynamic problems. However, the biological processes that contribute to these properties have not been made explicit in Digital Ecosystems research. Here, we discuss how biological properties contribute to the self-organising features of biological ecosystems, including population dynamics, evolution, a complex dynamic environment, and spatial distributions for generating local interactions. The potential for exploiting these properties in artificial systems is then considered. We suggest that several key features of biological ecosystems have not been fully explored in existing digital ecosystems, and discuss how mimicking these features may assist in developing robust, scalable self-organising architectures. An example architecture, the Digital Ecosystem, is considered in detail. The Digital Ecosystem is then measured experimentally through simulations, with measures originating from theoretical ecology, to confirm its likeness to a biological ecosystem. Including the responsiveness to requests for applications from the user base, as a measure of the 'ecological succession' (development).Comment: 9 pages, 4 figure, conferenc

    Evolutionary Dynamics in a Simple Model of Self-Assembly

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    We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model's rule set and its resulting self-assembled structure can be viewed as a genotype-phenotype map and incorporated into a genetic algorithm. The rule sets evolve under selection for specified target structures. The corresponding, complex fitness landscape generates rich evolutionary dynamics as a function of parameters such as the population size, search space size, mutation rate, and method of recombination. Furthermore, these systems are simple enough that in some cases the associated model genome space can be completely characterised, shedding light on how the evolutionary dynamics depends on the detailed structure of the fitness landscape. Finally, we apply the model to study the emergence of the preference for dihedral over cyclic symmetry observed for homomeric protein tetramers

    On the evolutionary optimisation of many conflicting objectives

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    This inquiry explores the effectiveness of a class of modern evolutionary algorithms, represented by Non-dominated Sorting Genetic Algorithm (NSGA) components, for solving optimisation tasks with many conflicting objectives. Optimiser behaviour is assessed for a grid of mutation and recombination operator configurations. Performance maps are obtained for the dual aims of proximity to, and distribution across, the optimal trade-off surface. Performance sweet-spots for both variation operators are observed to contract as the number of objectives is increased. Classical settings for recombination are shown to be suitable for small numbers of objectives but correspond to very poor performance for higher numbers of objectives, even when large population sizes are used. Explanations for this behaviour are offered via the concepts of dominance resistance and active diversity promotion

    Machine learning-guided directed evolution for protein engineering

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    Machine learning (ML)-guided directed evolution is a new paradigm for biological design that enables optimization of complex functions. ML methods use data to predict how sequence maps to function without requiring a detailed model of the underlying physics or biological pathways. To demonstrate ML-guided directed evolution, we introduce the steps required to build ML sequence-function models and use them to guide engineering, making recommendations at each stage. This review covers basic concepts relevant to using ML for protein engineering as well as the current literature and applications of this new engineering paradigm. ML methods accelerate directed evolution by learning from information contained in all measured variants and using that information to select sequences that are likely to be improved. We then provide two case studies that demonstrate the ML-guided directed evolution process. We also look to future opportunities where ML will enable discovery of new protein functions and uncover the relationship between protein sequence and function.Comment: Made significant revisions to focus on aspects most relevant to applying machine learning to speed up directed evolutio

    Visualising Basins of Attraction for the Cross-Entropy and the Squared Error Neural Network Loss Functions

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    Quantification of the stationary points and the associated basins of attraction of neural network loss surfaces is an important step towards a better understanding of neural network loss surfaces at large. This work proposes a novel method to visualise basins of attraction together with the associated stationary points via gradient-based random sampling. The proposed technique is used to perform an empirical study of the loss surfaces generated by two different error metrics: quadratic loss and entropic loss. The empirical observations confirm the theoretical hypothesis regarding the nature of neural network attraction basins. Entropic loss is shown to exhibit stronger gradients and fewer stationary points than quadratic loss, indicating that entropic loss has a more searchable landscape. Quadratic loss is shown to be more resilient to overfitting than entropic loss. Both losses are shown to exhibit local minima, but the number of local minima is shown to decrease with an increase in dimensionality. Thus, the proposed visualisation technique successfully captures the local minima properties exhibited by the neural network loss surfaces, and can be used for the purpose of fitness landscape analysis of neural networks.Comment: Preprint submitted to the Neural Networks journa

    The True Destination of EGO is Multi-local Optimization

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    Efficient global optimization is a popular algorithm for the optimization of expensive multimodal black-box functions. One important reason for its popularity is its theoretical foundation of global convergence. However, as the budgets in expensive optimization are very small, the asymptotic properties only play a minor role and the algorithm sometimes comes off badly in experimental comparisons. Many alternative variants have therefore been proposed over the years. In this work, we show experimentally that the algorithm instead has its strength in a setting where multiple optima are to be identified

    Single temperature for Monte Carlo optimization on complex landscapes

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    We propose a new strategy for Monte Carlo (MC) optimization on rugged multidimensional landscapes. The strategy is based on querying the statistical properties of the landscape in order to find the temperature at which the mean first passage time across the current region of the landscape is minimized. Thus, in contrast to other algorithms such as simulated annealing (SA), we explicitly match the temperature schedule to the statistics of landscape irregularities. In cases where this statistics is approximately the same over the entire landscape, or where non-local moves couple distant parts of the landscape, single-temperature MC will outperform any other MC algorithm with the same move set. We also find that in strongly anisotropic Coulomb spin glass and traveling salesman problems, the only relevant statistics (which we use to assign a single MC temperature) is that of irregularities in low-energy funnels. Our results may explain why protein folding in nature is efficient at room temperatures.Comment: 5 pages, 3 figure
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