Evidence of coevolution in multi-objective evolutionary algorithms

This paper demonstrates that simple yet important characteristics of coevolution can occur in evolutionary algorithms when only a few conditions are met. We find that interaction-based fitness measurements such as fitness (linear) ranking allow for a form of coevolutionary dynamics that is observed when 1) changes are made in what solutions are able to interact during the ranking process and 2) evolution takes place in a multi-objective environment. This research contributes to the study of simulated evolution in a at least two ways. First, it establishes a broader relationship between coevolution and multi-objective optimization than has been previously considered in the literature. Second, it demonstrates that the preconditions for coevolutionary behavior are weaker than previously thought. In particular, our model indicates that direct cooperation or competition between species is not required for coevolution to take place. Moreover, our experiments provide evidence that environmental perturbations can drive coevolutionary processes; a conclusion that mirrors arguments put forth in dual phase evolution theory. In the discussion, we briefly consider how our results may shed light onto this and other recent theories of evolution

Evolving artificial cell signaling networks using molecular classifier systems

Nature is a source of inspiration for computational techniques which have been successfully applied to a wide variety of complex application domains. In keeping with this we examine Cell Signaling Networks (CSN) which are chemical networks responsible for coordinating cell activities within their environment. Through evolution they have become highly efficient for governing critical control processes such as immunological responses, cell cycle control or homeostasis. Realising (and evolving) Artificial Cell Signaling Networks (ACSNs) may provide new computational paradigms for a variety of application areas. Our abstraction of Cell Signaling Networks focuses on four characteristic properties distinguished as follows: Computation, Evolution, Crosstalk and Robustness. These properties are also desirable for potential applications in the control systems, computation and signal processing field. These characteristics are used as a guide for the development of an ACSN evolutionary simulation platform. In this paper we present a novel evolutionary approach named Molecular Classifier System (MCS) to simulate such ACSNs. The MCS that we have designed is derived from Holland's Learning Classifier System. The research we are currently involved in is part of the multi disciplinary European funded project, ESIGNET, with the central question of the study of the computational properties of CSNs by evolving them using methods from evolutionary computation, and to re-apply this understanding in developing new ways to model and predict real CSNs

Chance and Necessity in Evolution: Lessons from RNA

The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are realized much more frequently than others), (2) the notion of shape space covering (that all typical shapes are realized in a small neighborhood of any random sequence), and (3) the notion of a neutral network (that sequences folding into the same typical shape form networks that percolate through sequence space). Neutral networks loosen the requirements on the mutation rate for selection to remain effective. The original (genotypic) error threshold has to be reformulated in terms of a phenotypic error threshold. With regard to adaptation, neutrality has two seemingly contradictory effects: It acts as a buffer against mutations ensuring that a phenotype is preserved. Yet it is deeply enabling, because it permits evolutionary change to occur by allowing the sequence context to vary silently until a single point mutation can become phenotypically consequential. Neutrality also influences predictability of adaptive trajectories in seemingly contradictory ways. On the one hand it increases the uncertainty of their genotypic trace. At the same time neutrality structures the access from one shape to another, thereby inducing a topology among RNA shapes which permits a distinction between continuous and discontinuous shape transformations. To the extent that adaptive trajectories must undergo such transformations, their phenotypic trace becomes more predictable.Comment: 37 pages, 14 figures; 1998 CNLS conference; high quality figures at http://www.santafe.edu/~walte

Prescriptive formalism for constructing domain-specific evolutionary algorithms

It has been widely recognised in the computational intelligence and machine learning communities that the key to understanding the behaviour of learning algorithms is to understand what representation is employed to capture and manipulate knowledge acquired during the learning process. However, traditional evolutionary algorithms have tended to employ a fixed representation space (binary strings), in order to allow the use of standardised genetic operators. This approach leads to complications for many problem domains, as it forces a somewhat artificial mapping between the problem variables and the canonical binary representation, especially when there are dependencies between problem variables (e.g. problems naturally defined over permutations). This often obscures the relationship between genetic structure and problem features, making it difficult to understand the actions of the standard genetic operators with reference to problem-specific structures. This thesis instead advocates m..

Multi-agent collaborative search : an agent-based memetic multi-objective optimization algorithm applied to space trajectory design

This article presents an algorithm for multi-objective optimization that blends together a number of heuristics. A population of agents combines heuristics that aim at exploring the search space both globally and in a neighbourhood of each agent. These heuristics are complemented with a combination of a local and global archive. The novel agent-based algorithm is tested at first on a set of standard problems and then on three specific problems in space trajectory design. Its performance is compared against a number of state-of-the-art multi-objective optimization algorithms that use the Pareto dominance as selection criterion: non-dominated sorting genetic algorithm (NSGA-II), Pareto archived evolution strategy (PAES), multiple objective particle swarm optimization (MOPSO), and multiple trajectory search (MTS). The results demonstrate that the agent-based search can identify parts of the Pareto set that the other algorithms were not able to capture. Furthermore, convergence is statistically better although the variance of the results is in some cases higher

Sequence homolog-based molecular engineering for shifting the enzymatic pH optimum

AbstractCell-free synthetic biology system organizes multiple enzymes (parts) from different sources to implement unnatural catalytic functions. Highly adaption between the catalytic parts is crucial for building up efficient artificial biosynthetic systems. Protein engineering is a powerful technology to tailor various enzymatic properties including catalytic efficiency, substrate specificity, temperature adaptation and even achieve new catalytic functions. However, altering enzymatic pH optimum still remains a challenging task. In this study, we proposed a novel sequence homolog-based protein engineering strategy for shifting the enzymatic pH optimum based on statistical analyses of sequence-function relationship data of enzyme family. By two statistical procedures, artificial neural networks (ANNs) and least absolute shrinkage and selection operator (Lasso), five amino acids in GH11 xylanase family were identified to be related to the evolution of enzymatic pH optimum. Site-directed mutagenesis of a thermophilic xylanase from Caldicellulosiruptor bescii revealed that four out of five mutations could alter the enzymatic pH optima toward acidic condition without compromising the catalytic activity and thermostability. Combination of the positive mutants resulted in the best mutant M31 that decreased its pH optimum for 1.5 units and showed increased catalytic activity at pH < 5.0 compared to the wild-type enzyme. Structure analysis revealed that all the mutations are distant from the active center, which may be difficult to be identified by conventional rational design strategy. Interestingly, the four mutation sites are clustered at a certain region of the enzyme, suggesting a potential “hot zone” for regulating the pH optima of xylanases. This study provides an efficient method of modulating enzymatic pH optima based on statistical sequence analyses, which can facilitate the design and optimization of suitable catalytic parts for the construction of complicated cell-free synthetic biology systems

Analysis of group evolution prediction in complex networks

In the world, in which acceptance and the identification with social communities are highly desired, the ability to predict evolution of groups over time appears to be a vital but very complex research problem. Therefore, we propose a new, adaptable, generic and mutli-stage method for Group Evolution Prediction (GEP) in complex networks, that facilitates reasoning about the future states of the recently discovered groups. The precise GEP modularity enabled us to carry out extensive and versatile empirical studies on many real-world complex / social networks to analyze the impact of numerous setups and parameters like time window type and size, group detection method, evolution chain length, prediction models, etc. Additionally, many new predictive features reflecting the group state at a given time have been identified and tested. Some other research problems like enriching learning evolution chains with external data have been analyzed as well