14,594 research outputs found
Biology of Applied Digital Ecosystems
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
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
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
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
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
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
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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