Formation of modules in a computational model of embryogeny

An investigation is conducted into the effects of a complex mapping between genotype and phenotype upon a simulated evolutionary process. A model of embryogeny is utilised to grow simple French flag like patterns. The system is shown to display a phenotypic robustness to damage and it is argued that this is a result of a modularity forming within the mapping process which causes a functional grouping of sections of the genotype

A multi-agent based evolutionary algorithm in non-stationary environments

This article is posted here with permission of IEEE - Copyright @ 2008 IEEEIn this paper, a multi-agent based evolutionary algorithm (MAEA) is introduced to solve dynamic optimization problems. The agents simulate living organism features and co-evolve to find optimum. All agents live in a lattice like environment, where each agent is fixed on a lattice point. In order to increase the energy, agents can compete with their neighbors and can also acquire knowledge based on statistic information. In order to maintain the diversity of the population, the random immigrants and adaptive primal dual mapping schemes are used. Simulation experiments on a set of dynamic benchmark problems show that MAEA can obtain a better performance in non-stationary environments in comparison with several peer genetic algorithms.This work was suported by the Key Program of National Natural Science Foundation of China under Grant No. 70431003, the Science Fund for Creative Research Group of the National Natural Science Foundation of China under Grant No. 60521003, the National Science and Technology Support Plan of China under Grant No. 2006BAH02A09, and the Engineering and Physical Sciences Research Council of the United Kingdom under Grant No. EP/E060722/1

Digital Ecosystems: Ecosystem-Oriented Architectures

We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve high-level software applications. Therefore, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. The Digital Ecosystem was then measured experimentally through simulations, with measures originating from theoretical ecology, evaluating its likeness to biological ecosystems. This included its responsiveness to requests for applications from the user base, as a measure of the ecological succession (ecosystem maturity). Overall, we have advanced the understanding of Digital Ecosystems, creating Ecosystem-Oriented Architectures where the word ecosystem is more than just a metaphor.Comment: 39 pages, 26 figures, journa

A computational framework to emulate the human perspective in flow cytometric data analysis

Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. <p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. <p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics

Learning behavior in abstract memory schemes for dynamic optimization problems

This is the post-print version of this article. The official article can be accessed from the link below - Copyright @ 2009 Springer VerlagIntegrating memory into evolutionary algorithms is one major approach to enhance their performance in dynamic environments. An abstract memory scheme has been recently developed for evolutionary algorithms in dynamic environments, where the abstraction of good solutions is stored in the memory instead of good solutions themselves to improve future problem solving. This paper further investigates this abstract memory with a focus on understanding the relationship between learning and memory, which is an important but poorly studied issue for evolutionary algorithms in dynamic environments. The experimental study shows that the abstract memory scheme enables learning processes and hence efficiently improves the performance of evolutionary algorithms in dynamic environments.The work by S. Yang was supported by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/1