"Going back to our roots": second generation biocomputing

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin

Evolutionary morphogenesis for multi-cellular systems

With a gene required for each phenotypic trait, direct genetic encodings may show poor scalability to increasing phenotype length. Developmental systems may alleviate this problem by providing more efficient indirect genotype to phenotype mappings. A novel classification of multi-cellular developmental systems in evolvable hardware is introduced. It shows a category of developmental systems that up to now has rarely been explored. We argue that this category is where most of the benefits of developmental systems lie (e.g. speed, scalability, robustness, inter-cellular and environmental interactions that allow fault-tolerance or adaptivity). This article describes a very simple genetic encoding and developmental system designed for multi-cellular circuits that belongs to this category. We refer to it as the morphogenetic system. The morphogenetic system is inspired by gene expression and cellular differentiation. It focuses on low computational requirements which allows fast execution and a compact hardware implementation. The morphogenetic system shows better scalability compared to a direct genetic encoding in the evolution of structures of differentiated cells, and its dynamics provides fault-tolerance up to high fault rates. It outperforms a direct genetic encoding when evolving spiking neural networks for pattern recognition and robot navigation. The results obtained with the morphogenetic system indicate that this "minimalist” approach to developmental systems merits further stud

Diagnosis of an EPS module

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Electrotécnica e ComputadoresThis thesis addresses and contextualizes the problem of diagnostic of an Evolvable Production System (EPS). An EPS is a complex and lively entity composed of intelligent modules that interact through bio-inspired mechanisms, to ensure high system availability and seamless reconfiguration. The actual economic situation together with the increasing demand of high quality and low priced customized products imposed a shift in the production policies of enterprises. Shop floors have to become more agile and flexible to accommodate the new production paradigms. Rather than selling products enterprises are establishing a trend of offering services to explore business opportunities. The new production paradigms, potentiated by the advances in Information Technologies (IT), especially in web related standards and technologies as well as the progressive acceptance of the multi-agent systems (MAS) concept and related technologies, envision collections of modules whose individual and collective function adapts and evolves ensuring the fitness and adequacy of the shop floor in tackling profitable but volatile business opportunities. Despite the richness of the interactions and the effort set in modelling them, their potential to favour fault propagation and interference, in these complex environments, has been ignored from a diagnostic point of view. With the increase of distributed and autonomous components that interact in the execution of processes current diagnostic approaches will soon be insufficient. While current system dynamics are complex and to a certain extent unpredictable the adoption of the next generation of approaches and technologies comes at the cost of a yet increased complexity.Whereas most of the research in such distributed industrial systems is focused in the study and establishment of control structures, the problem of diagnosis has been left relatively unattended. There are however significant open challenges in the diagnosis of such modular systems including: understanding fault propagation and ensuring scalability and co-evolution. This work provides an implementation of a state-of-the-art agent-based interaction-oriented architecture compliant with the EPS paradigm that supports the introduction of a new developed diagnostic algorithm that has the ability to cope with the modern manufacturing paradigm challenges and to provide diagnostic analysis that explores the network dimension of multi-agent systems

Exploiting development to enhance the scalability of hardware evolution.

Evolutionary algorithms do not scale well to the large, complex circuit design problems typical of the real world. Although techniques based on traditional design decomposition have been proposed to enhance hardware evolution's scalability, they often rely on traditional domain knowledge that may not be appropriate for evolutionary search and might limit evolution's opportunity to innovate. It has been proposed that reliance on such knowledge can be avoided by introducing a model of biological development to the evolutionary algorithm, but this approach has not yet achieved its potential. Prior demonstrations of how development can enhance scalability used toy problems that are not indicative of evolving hardware. Prior attempts to apply development to hardware evolution have rarely been successful and have never explored its effect on scalability in detail. This thesis demonstrates that development can enhance scalability in hardware evolution, primarily through a statistical comparison of hardware evolution's performance with and without development using circuit design problems of various sizes. This is reinforced by proposing and demonstrating three key mechanisms that development uses to enhance scalability: the creation of modules, the reuse of modules, and the discovery of design abstractions. The thesis includes several minor contributions: hardware is evolved using a common reconfigurable architecture at a lower level of abstraction than reported elsewhere. It is shown that this can allow evolution to exploit the architecture more efficiently and perhaps search more effectively. Also the benefits of several features of developmental models are explored through the biases they impose on the evolutionary search. Features that are explored include the type of environmental context development uses and the constraints on symmetry and information transmission they impose, genetic operators that may improve the robustness of gene networks, and how development is mapped to hardware. Also performance is compared against contemporary developmental models

An Open Avionics and Software Architecture to Support Future NASA Exploration Missions

The presentation describes an avionics and software architecture that has been developed through NASAs Advanced Exploration Systems (AES) division. The architecture is open-source, highly reliable with fault tolerance, and utilizes standard capabilities and interfaces, which are scalable and customizable to support future exploration missions. Specific focus areas of discussion will include command and data handling, software, human interfaces, communication and wireless systems, and systems engineering and integration

Hardware morphogenetic developmental system

Indirect genotype to phenotype mappings in the form of developmental systems may allow better scalability to larger phenotypes in evolvable hardware. This report reviews developmental systems used in evolvable hardware and it proposes a new classifications based on hardware characteristics. It then describes a genetic encoding and developmental system called the morphogenetic system which has been designed for multi-cellular circuits. This morphogenetic system is inspired upon gene expression and cell differentiation but it focuses on efficient hardware implementation. An hardware implementation on the dynamically reconfigurable POEtic circuit is described. It uses serial arithmetics and time-multiplexing to minimize ressource use

Risk of employing an evolvable production system

Nowadays manufacturing companies are facing a more challenging environment due to the unpredictability of the markets in order to survive. Enterprises need to keep innovating and deliver products with new internal or external characteristics. There are strategies and solutions, to different organisational level from strategic to operational, when technology is growing faster in operational level, more specifically in manufacturing system. This means that companies have to deal with the changes of the emergent manufacturing systems while it can be expensive and not easy to be implement. An agile manufacturing system can help to cope with the markets changeability. Evolvable Production Systems (EPS) is an emergent paradigm which aims to bring new solutions to deal with changeability. The proposed paradigm is characterised by modularity and intends to introduce high flexibility and dynamism at shop floor level through the use of the evolution of new computational devices and technology. This new approach brings to enterprises the ability to plug and unplug new devices and allowing fast reformulation of the production line without reprogramming. There is no doubt about the advantages and benefits of this emerging technology but the feasibility and applicability is still under questioned. Most researches in this area are focused on technical side, explaining the advantages of those systems while there are no sufficient works discussing the implementation risks from different perspective, including business owner. The main objective of this work is to propose a methodology and model to identify, classify and measure potential risk associated with an implementation of this emergent paradigm. To quantify the proposed comprehensive risk model, an Intelligent Decision system is developed employing Fuzzy Inference System to deal with the knowledge of experts, as there are no historical data and sufficient research on this area. The result can be the vulnerability assessment of implementing EPS technology in manufacturing companies when the focus is more on SMEs. The present dissertation used the experts’ knowledge and experiences, who were involved in FP7 project IDEAS, which is one of the leading projects in this area