Neutral Evolution of Mutational Robustness

We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population's limit distribution on the neutral network is solely determined by the network topology and given by the principal eigenvector of the network's adjacency matrix. Moreover, the average number of neutral mutant neighbors per individual is given by the matrix spectral radius. This quantifies the extent to which populations evolve mutational robustness: the insensitivity of the phenotype to mutations. Since the average neutrality is independent of evolutionary parameters---such as, mutation rate, population size, and selective advantage---one can infer global statistics of neutral network topology using simple population data available from {\it in vitro} or {\it in vivo} evolution. Populations evolving on neutral networks of RNA secondary structures show excellent agreement with our theoretical predictions.Comment: 7 pages, 3 figure

New insights on neutral binary representations for evolutionary optimization

This paper studies a family of redundant binary representations NNg(l, k), which are based on the mathematical formulation of error control codes, in particular, on linear block codes, which are used to add redundancy and neutrality to the representations. The analysis of the properties of uniformity, connectivity, synonymity, locality and topology of the NNg(l, k) representations is presented, as well as the way an (1+1)-ES can be modeled using Markov chains and applied to NK fitness landscapes with adjacent neighborhood.The results show that it is possible to design synonymously redundant representations that allow an increase of the connectivity between phenotypes. For easy problems, synonymously NNg(l, k) representations, with high locality, and where it is not necessary to present high values of connectivity are the most suitable for an efficient evolutionary search. On the contrary, for difficult problems, NNg(l, k) representations with low locality, which present connectivity between intermediate to high and with intermediate values of synonymity are the best ones. These results allow to conclude that NNg(l, k) representations with better performance in NK fitness landscapes with adjacent neighborhood do not exhibit extreme values of any of the properties commonly considered in the literature of evolutionary computation. This conclusion is contrary to what one would expect when taking into account the literature recommendations. This may help understand the current difficulty to formulate redundant representations, which are proven to be successful in evolutionary computation. (C) 2016 Elsevier B.V. All rights reserved

Robust Multi-Cellular Developmental Design

This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as well as the differentiation value of the cell in the phenotype, are controlled by a Neural Network (the genotype) that takes as inputs the chemicals produced by the neighboring cells at the previous time step. In the proposed model, the number of iterations of the growth process is not pre-determined, but emerges during evolution: only organisms for which the growth process stabilizes give a phenotype (the stable state), others are declared nonviable. The optimization of the controller is done using the NEAT algorithm, that optimizes both the topology and the weights of the Neural Networks. Though each cell only receives local information from its neighbors, the experimental results of the proposed approach on the 'flags' problems (the phenotype must match a given 2D pattern) are almost as good as those of a direct regression approach using the same model with global information. Moreover, the resulting multi-cellular organisms exhibit almost perfect self-healing characteristics

Towards the Evolution of Multi-Layered Neural Networks: A Dynamic Structured Grammatical Evolution Approach

Current grammar-based NeuroEvolution approaches have several shortcomings. On the one hand, they do not allow the generation of Artificial Neural Networks (ANNs composed of more than one hidden-layer. On the other, there is no way to evolve networks with more than one output neuron. To properly evolve ANNs with more than one hidden-layer and multiple output nodes there is the need to know the number of neurons available in previous layers. In this paper we introduce Dynamic Structured Grammatical Evolution (DSGE): a new genotypic representation that overcomes the aforementioned limitations. By enabling the creation of dynamic rules that specify the connection possibilities of each neuron, the methodology enables the evolution of multi-layered ANNs with more than one output neuron. Results in different classification problems show that DSGE evolves effective single and multi-layered ANNs, with a varying number of output neurons

Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions

During development, signaling networks control the formation of multicellular patterns. To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear. Here, we describe a computational approach to predict and analyze the phenotypic diversity that is accessible to a developmental signaling network. Applying this framework to vulval development in C. elegans, we demonstrate that quantitative changes in the regulatory network can render ~500 multicellular phenotypes. This phenotypic capacity is an order-of-magnitude below the theoretical upper limit for this system but yet is large enough to demonstrate that the system is not restricted to a select few outcomes. Using metrics to gauge the robustness of these phenotypes to parameter perturbations, we identify a select subset of novel phenotypes that are the most promising for experimental validation. In addition, our model calculations provide a layout of these phenotypes in network parameter space. Analyzing this landscape of multicellular phenotypes yielded two significant insights. First, we show that experimentally well-established mutant phenotypes may be rendered using non-canonical network perturbations. Second, we show that the predicted multicellular patterns include not only those observed in C. elegans, but also those occurring exclusively in other species of the Caenorhabditis genus. This result demonstrates that quantitative diversification of a common regulatory network is indeed demonstrably sufficient to generate the phenotypic differences observed across three major species within the Caenorhabditis genus. Using our computational framework, we systematically identify the quantitative changes that may have occurred in the regulatory network during the evolution of these species. Our model predictions show that significant phenotypic diversity may be sampled through quantitative variations in the regulatory network without overhauling the core network architecture. Furthermore, by comparing the predicted landscape of phenotypes to multicellular patterns that have been experimentally observed across multiple species, we systematically trace the quantitative regulatory changes that may have occurred during the evolution of the Caenorhabditis genus

Dysfunctions of highly parallel real-time machines as 'developmental disorders': Security concerns and a Caveat Emptor

A cognitive paradigm for gene expression in developmental biology that is based on rigorous application of the asymptotic limit theorems of information theory can be adapted to highly parallel real-time computing. The coming Brave New World of massively parallel 'autonomic' and 'Self-X' machines driven by the explosion of multiple core and molecular computing technologies will not be spared patterns of canonical and idiosyncratic failure analogous to the developmental disorders affecting organisms that have had the relentless benefit of a billion years of evolutionary pruning. This paper provides a warning both to potential users of these machines and, given that many such disorders can be induced by external agents, to those concerned with larger scale matters of homeland security

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