Genetic Regulatory Networks (GRNs) in biological organisms are primary engines for cells to enact their engagements with environments, via incessant, continually active coupling. In differentiated multicellular organisms, tremendous complexity has arisen in the course of evolution of life on earth. Engineering and science have so far achieved no working system that can compare with this complexity, depth and scope of organization. Abstracting the dynamics of genetic regulatory control to a computational framework in which artificial GRNs in artificial simulated cells differentiate while connected in a changing topology, it is possible to apply Darwinian evolution in silico to study the capacity of such developmental/differentiated GRNs to evolve. In this volume an evolutionary GRN paradigm is investigated for its evolvability and robustness in models of biological clocks, in simple differentiated multicellularity, and in evolving artificial developing 'organisms' which grow and express an ontogeny starting from a single cell interacting with its environment, eventually including a changing local neighbourhood of other cells. These methods may help us understand the genesis, organization, adaptive plasticity, and evolvability of differentiated biological systems, and may also provide a paradigm for transferring these principles of biology's success to computational and engineering challenges at a scale not previously conceivable.

Genetic Regulatory Networks (GRNs) in biological organisms are primary engines for cells to enact their engagements with environments, via incessant, continually active coupling. In differentiated multicellular organisms, tremendous complexity has arisen in the course of evolution of life on earth. Engineering and science have so far achieved no working system that can compare with this complexity, depth and scope of organization. Abstracting the dynamics of genetic regulatory control to a computational framework in which artificial GRNs in artificial simulated cells differentiate while connected in a changing topology, it is possible to apply Darwinian evolution in silico to study the capacity of such developmental/differentiated GRNs to evolve. In this volume an evolutionary GRN paradigm is investigated for its evolvability and robustness in models of biological clocks, in simple differentiated multicellularity, and in evolving artificial developing 'organisms' which grow and express an ontogeny starting from a single cell interacting with its environment, eventually including a changing local neighbourhood of other cells. These methods may help us understand the genesis, organization, adaptive plasticity, and evolvability of differentiated biological systems, and may also provide a paradigm for transferring these principles of biology's success to computational and engineering challenges at a scale not previously conceivable.

Evolutionary Computation (EC) techniques are e?cient, nature-inspired me- ods based on the principles of natural evolution and genetics. Due to their - ciency and simple underlying principles, these methods can be used for a diverse rangeofactivitiesincludingproblemsolving,optimization,machinelearningand pattern recognition. A large and continuously increasing number of researchers and professionals make use of EC techniques in various application domains. This volume presents a careful selection of relevant EC examples combined with a thorough examination of the techniques used in EC. The papers in the volume illustrate the current state of the art in the application of EC and should help and inspire researchers and professionals to develop e?cient EC methods for design and problem solving. All papers in this book were presented during EvoApplications 2010, which included a range of events on application-oriented aspects of EC. Since 1998, EvoApplications — formerly known as EvoWorkshops— has provided a unique opportunity for EC researchers to meet and discuss application aspects of EC and has been an important link between EC research and its application in a variety of domains. During these 12 years, new events have arisen, some have disappeared,whileothershavematuredtobecomeconferencesoftheirown,such as EuroGP in 2000, EvoCOP in 2004, and EvoBIO in 2007. And from this year, EvoApplications has become a conference as well.

Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well-known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC approaches for analysis and reconstruction of GRN from gene expression data. The third part of this book covers the contemporary advancements in the automatic construction of gene regulatory and reaction networks and gives direction and guidelines for future research. Finally, the last part of this book focuses on applications of GRNs with EC in other fields, such as design, engineering and robotics. • Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary computation (EC) • Covers sub-domains of GRN research using EC, such as expression profile analysis, reverse engineering, GRN evolution, applications • Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology • Delivers state-of-the-art research in genetic algorithms, genetic programming, and swarm intelligence Evolutionary Computation in Gene Regulatory Network Research is a reference for researchers and professionals in computer science, systems biology, and bioinformatics, as well as upper undergraduate, graduate, and postgraduate students. Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Toyko, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012 he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.

This book provides a basic yet unified overview of theory and methodologies for evolutionary developmental systems. Based on the author’s extensive research into the synergies between various approaches to artificial intelligence including evolutionary computation, artificial neural networks, and systems biology, it also examines the inherent links between biological intelligence and artificial intelligence. The book begins with an introduction to computational algorithms used to understand and simulate biological evolution and development, including evolutionary algorithms, gene regulatory network models, multi-cellular models for neural and morphological development, and computational models of neural plasticity. Chap. 2 discusses important properties of biological gene regulatory systems, including network motifs, network connectivity, robustness and evolvability. Going a step further, Chap. 3 presents methods for synthesizing regulatory motifs from scratch and creating more complex regulatory dynamics by combining basic regulatory motifs using evolutionary algorithms. Multi-cellular growth models, which can be used to simulate either neural or morphological development, are presented in Chapters 4 and 5. Chap. 6 examines the synergies and coupling between neural and morphological evolution and development. In turn, Chap. 7 provides preliminary yet promising examples of how evolutionary developmental systems can help in self-organized pattern generation, referred to as morphogenetic self-organization, highlighting the great potentials of evolutionary developmental systems. Finally, Chap. 8 rounds out the book, stressing the importance and promise of the evolutionary developmental approach to artificial intelligence. Featuring a wealth of diagrams, graphs and charts to aid in comprehension, this book offers a valuable asset for graduate students, researchers and practitioners who are interested in pursuing a different approach to artificial intelligence.

Generally, spontaneous pattern formation phenomena are random and repetitive, whereas elaborate devices are the deterministic product of human design. Yet, biological organisms and collective insect constructions are exceptional examples of complex systems that are both self-organized and architectural. This book is the first initiative of its kind toward establishing a new field of research, Morphogenetic Engineering, to explore the modeling and implementation of “self-architecturing” systems. Particular emphasis is placed on the programmability and computational abilities of self-organization, properties that are often underappreciated in complex systems science—while, conversely, the benefits of self-organization are often underappreciated in engineering methodologies. Altogether, the aim of this work is to provide a framework for and examples of a larger class of “self-architecturing” systems, while addressing fundamental questions such as br” How do biological organisms carry out morphogenetic tasks so reliably? br” Can we extrapolate their self-formation capabilities to engineered systems?br” Can physical systems be endowed with information (or informational systems be embedded in physics) so as to create autonomous morphologies and functions?br” What are the core principles and best practices for the design and engineering of such morphogenetic systems?

Self-organizing approaches inspired from biological systems, such as social insects, genetic, molecular and cellular systems under morphogenesis, and human mental development, has enjoyed great success in advanced robotic systems that need to work in dynamic and changing environments. Compared with classical control methods for robotic systems, the major advantages of bio-inspired self-organizing robotic systems include robustness, self-repair and self-healing in the presence of system failures and/or malfunctions, high adaptability to environmental changes, and autonomous self-organization and self-reconfiguration without a centralized control. “Bio-inspired Self-organizing Robotic Systems” provides a valuable reference for scientists, practitioners and research students working on developing control algorithms for self-organizing engineered collective systems, such as swarm robotic systems, self-reconfigurable modular robots, smart material based robotic devices, unmanned aerial vehicles, and satellite constellations.

This book constitutes the refereed proceedings of the Third International Workshop on Self-Organizing Systems, IWSOS 2008, held in Vienna, Austria, December 10-12, 2008. The 20 revised full papers and 13 revised short papers presented were carefully selected from the 70 full and 24 short paper submissions from authors from 33 different countries. The papers are organized in topical sections on peer-to-peer systems, overlay networks as well as resource and service management.

This book covers the basic theory, practical details and advanced research of the implementation of evolutionary methods on physical substrates. Most of the examples are from electronic engineering applications, including transistor-level design and system-level implementation. The authors present an overview of the successes achieved, and the book will act as a point of reference for both academic and industrial researchers.