6,609 research outputs found
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
Computational models for inferring biochemical networks
Biochemical networks are of great practical importance. The interaction of biological compounds in cells has been enforced to a proper understanding by the numerous bioinformatics projects, which contributed to a vast amount of biological information. The construction of biochemical systems (systems of chemical reactions), which include both topology and kinetic constants of the chemical reactions, is NP-hard and is a well-studied system biology problem. In this paper, we propose a hybrid architecture, which combines genetic programming and simulated annealing in order to generate and optimize both the topology (the network) and the reaction rates of a biochemical system. Simulations and analysis of an artificial model and three real models (two models and the noisy version of one of them) show promising results for the proposed method.The Romanian National Authority for Scientific Research, CNDI–UEFISCDI,
Project No. PN-II-PT-PCCA-2011-3.2-0917
Development of a Multi-Objective Evolutionary Algorithm for Strain-Enhanced Quantum Cascade Lasers
An automated design approach using an evolutionary algorithm for the development of quantum cascade lasers (QCLs) is presented. Our algorithmic approach merges computational intelligence techniques with the physics of device structures, representing a design methodology that reduces experimental effort and costs. The algorithm was developed to produce QCLs with a three-well, diagonal-transition active region and a five-well injector region. Specifically, we applied this technique to AlxGa1xAs/InyGa1yAs strained active region designs. The algorithmic approach is a non-dominated sorting method using four aggregate objectives: target wavelength, population inversion via longitudinal-optical (LO) phonon extraction, injector level coupling, and an optical gain metric. Analysis indicates that the most plausible device candidates are a result of the optical gain metric and a total aggregate of all objectives. However, design limitations exist in many of the resulting candidates, indicating need for additional objective criteria and parameter limits to improve the application of this and other evolutionary algorithm methods
Towards 'smart lasers': self-optimisation of an ultrafast pulse source using a genetic algorithm
Short-pulse fibre lasers are a complex dynamical system possessing a broad
space of operating states that can be accessed through control of cavity
parameters. Determination of target regimes is a multi-parameter global
optimisation problem. Here, we report the implementation of a genetic algorithm
to intelligently locate optimum parameters for stable single-pulse mode-locking
in a Figure-8 fibre laser, and fully automate the system turn-on procedure.
Stable ultrashort pulses are repeatably achieved by employing a compound
fitness function that monitors both temporal and spectral output properties of
the laser. Our method of encoding photonics expertise into an algorithm and
applying machine-learning principles paves the way to self-optimising `smart'
optical technologies
A Framework for Genetic Algorithms Based on Hadoop
Genetic Algorithms (GAs) are powerful metaheuristic techniques mostly used in
many real-world applications. The sequential execution of GAs requires
considerable computational power both in time and resources. Nevertheless, GAs
are naturally parallel and accessing a parallel platform such as Cloud is easy
and cheap. Apache Hadoop is one of the common services that can be used for
parallel applications. However, using Hadoop to develop a parallel version of
GAs is not simple without facing its inner workings. Even though some
sequential frameworks for GAs already exist, there is no framework supporting
the development of GA applications that can be executed in parallel. In this
paper is described a framework for parallel GAs on the Hadoop platform,
following the paradigm of MapReduce. The main purpose of this framework is to
allow the user to focus on the aspects of GA that are specific to the problem
to be addressed, being sure that this task is going to be correctly executed on
the Cloud with a good performance. The framework has been also exploited to
develop an application for Feature Subset Selection problem. A preliminary
analysis of the performance of the developed GA application has been performed
using three datasets and shown very promising performance
Genetic Algorithm Modeling with GPU Parallel Computing Technology
We present a multi-purpose genetic algorithm, designed and implemented with
GPGPU / CUDA parallel computing technology. The model was derived from a
multi-core CPU serial implementation, named GAME, already scientifically
successfully tested and validated on astrophysical massive data classification
problems, through a web application resource (DAMEWARE), specialized in data
mining based on Machine Learning paradigms. Since genetic algorithms are
inherently parallel, the GPGPU computing paradigm has provided an exploit of
the internal training features of the model, permitting a strong optimization
in terms of processing performances and scalability.Comment: 11 pages, 2 figures, refereed proceedings; Neural Nets and
Surroundings, Proceedings of 22nd Italian Workshop on Neural Nets, WIRN 2012;
Smart Innovation, Systems and Technologies, Vol. 19, Springe
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Learning short multivariate time series models through evolutionary and sparse matrix computation
Multivariate time series (MTS) data are widely available in different fields including medicine, finance, bioinformatics, science and engineering. Modelling MTS data accurately is important for many decision making activities. One area that has been largely overlooked so far is the particular type of time series where the data set consists of a large number of variables but with a small number of observations. In this paper we describe the development of a novel computational method based on Natural Computation and sparse matrices that bypasses the size restrictions of traditional statistical MTS methods, makes no distribution assumptions, and also locates the associated parameters. Extensive results are presented, where the proposed method is compared with both traditional statistical and heuristic search techniques and evaluated on a number of criteria. The results have implications for a wide range of applications involving the learning of short MTS models
High-speed detection of emergent market clustering via an unsupervised parallel genetic algorithm
We implement a master-slave parallel genetic algorithm (PGA) with a bespoke
log-likelihood fitness function to identify emergent clusters within price
evolutions. We use graphics processing units (GPUs) to implement a PGA and
visualise the results using disjoint minimal spanning trees (MSTs). We
demonstrate that our GPU PGA, implemented on a commercially available general
purpose GPU, is able to recover stock clusters in sub-second speed, based on a
subset of stocks in the South African market. This represents a pragmatic
choice for low-cost, scalable parallel computing and is significantly faster
than a prototype serial implementation in an optimised C-based
fourth-generation programming language, although the results are not directly
comparable due to compiler differences. Combined with fast online intraday
correlation matrix estimation from high frequency data for cluster
identification, the proposed implementation offers cost-effective,
near-real-time risk assessment for financial practitioners.Comment: 10 pages, 5 figures, 4 tables, More thorough discussion of
implementatio
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