Biological Development model for the Design of Robust Digital System Heng Liu Doctor of Philosophy Intelligent Systems Research Group Electronics Department University of York September 2007 Abstract and Keywords Abstract This thesis presents a biologically-inspired developmental model for the design of digital circuits. Circuits have been evolved that exhibit the ability to self-repair and correct transient faults to recover correct functionality. The method devised gives no explicit coordinate information to the evolved cell circuits. The method presented has been implemented fully in electronic hardware. This allowed developmental circuits to be evolved considerably more quickly than in software simulation. The methods presented have been applied to produce a self-repairing two bit multiplier and an autonomous robot controller circuit. Results are presented that shows that after introduction of faults, both circuits can autonomously recover correct functionality. Keywords Fault-tolerance, Evolvable hardware, FPGA, Development principle, Multi- cellular organism, Evolutionary algorithm, Cartesian Genetic Programming, French Flag, Multiplier, Digital circuit, Autonomous Robot Controller i Acknowledgement Acknowledgement No matter how much to write, it is just impossible to express my deep and genuine appreciation to every person who supported and contributed to my research in terms of financial, technical and mental aspects. I will try my best to acknowledge those without whom it would have been less productive or even impossible. Without the unconditional financial support from my parents, the study of my Britain degree would have been absolutely unfeasible at all. Furthermore, they have always had intuitive ideas, constructive suggestions and supportive encouragement; especially during I am in the most arduous situation of my research. I am proud of being born in this family and being your son. This research was made possible under the excellent supervision of Prof. Andy Tyrrell and Dr. Julian Miller. I would like to thank them for their continuous support and guidance of the project as well as their suggestions and direction. In addition, I highly appreciate the efforts they exerted to find financial support for my further research. To my wife, Mrs. Fei Xu, who is ready to give me unconditional backup and encourage me whenever I encounter problems. You know, it is hard for both of us in the year I am abroad. However we together make it! We love each other no less than, if not more than, one year ago. I am proud of being your companions. Thank you for all your valuable support and the peace of mind feeling you grant me. My lab mates, Andy, Marcus, Dapeng Xu, Chao Wu, Rachael and Simon, also deserve my credit. Thanks for all your assistance and suggestions, as well as the laughs and times shared with me. To my dear friends with whom I have had plenty of un-forgettable wonderful time, it has been a real fortune having you such good friends to communicate with, express my feelings and discuss general topics. ii Contents Contents Abstract..................................................................................................................i Keywords ...............................................................................................................i Acknowledgement ................................................................................................ii Figure Index.........................................................................................................ix Table Index .........................................................................................................xii Chapter 1 Introduction........................................................................................1 1.1 Research Motivation and Objective.......................................................3 1.2 Hypothesis..............................................................................................4 1.3 Achievements.........................................................................................4 1.4 Structure of the Thesis ...........................................................................5 Chapter 2 Evolutionary Design of Electronic Systems.....................................7 2.1 Introduction............................................................................................7 2.2 Principles of Evolutionary Design .........................................................9 2.3 Evolutionary Algorithms......................................................................13 2.3.1 Common Features ............................................................................13 2.3.2 Overview of EAs...............................................................................16 2.3.3 Comparison of different EAs............................................................18 2.4 Evolvable Hardware.............................................................................19 2.4.1 Classification of Evolvable Hardware.............................................19 2.4.2 Extrinsic Evolvable Hardware.........................................................20 2.4.3 Intrinsic Evolvable Hardware..........................................................22 2.5 Limitation of EHW ..............................................................................24 iii Contents 2.6 Summary ..............................................................................................24 Chapter 3 Development Principles and Development Systems .....................26 3.1 Biological Development Principles......................................................26 3.1.1 Basic Concepts.................................................................................26 3.1.1.1 Chromosomes and Genes.........................................................27 3.1.1.2 Genotype and Phenotype..........................................................27 3.1.2 Biological Living Organism Cells....................................................28 3.1.3 Stages of Development .....................................................................30 3.1.4 Characteristics of Biological Development .....................................31 3.2 Mathematical Abstractions of Development........................................32 3.2.1 Gene Regulatory Network Abstractions...........................................32 3.2.2 L-Systems .........................................................................................33 3.3 Developmental Systems.......................................................................35 3.3.1 Gene Regulatory Networks ..............................................................35 3.3.2 L-Systems and other Rewriting Rule Based Systems........................37 3.3.3 Cell Programs ..................................................................................39 3.3.4 Other Systems...................................................................................40 3.4 Summary ..............................................................................................43 Chapter 4 Fault-tolerant Techniques...............................................................44 4.1 Fundamental Concepts and Definitions ...............................................44 4.1.1 Classification of System Faults ........................................................46 4.1.2 Phases of Fault Tolerance ...............................................................48 4.1.2.1 Error detection.........................................................................48 4.1.2.2 Damage confinement and assessment......................................49 4.1.2.3 Error recovery..........................................................................49 4.1.2.4 Fault treatment and continued system service.........................50 iv Contents 4.2 History of Fault Tolerance Systems.....................................................50 4.3 Conventional Fault-tolerant Design .....................................................52 4.3.1 Hardware Redundancy.....................................................................52 4.3.2 Information Redundancy..................................................................53 4.3.3 Software Redundancy.......................................................................54 4.3.4 Time Redundancy.............................................................................54 4.4 Conventional Transient Fault-tolerant Techniques..............................54 4.5 Bio-inspired Fault-tolerant Techniques ...............................................55 4.5.1 Phylogeny.........................................................................................56 4.5.2 Ontogeny ..........................................................................................56 4.5.3 Epigenesis ........................................................................................57 4.6 Summary ..............................................................................................57 Chapter 5 Development Cellular Model for Digital System ..........................59 5.1 Transforming of Biological Principles to Digital Systems ..................59 5.2 Design Consideration...........................................................................61 5.3 Digital Cell Structure and Inter-Cell Connections...............................63 5.4 Chemical Diffusion ..............................................................................67 5.5 Digital Organism Growth.....................................................................68