"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

Generalized disjunction decomposition for evolvable hardware

Evolvable hardware (EHW) refers to self-reconfiguration hardware design, where the configuration is under the control of an evolutionary algorithm (EA). One of the main difficulties in using EHW to solve real-world problems is scalability, which limits the size of the circuit that may be evolved. This paper outlines a new type of decomposition strategy for EHW, the “generalized disjunction decomposition” (GDD), which allows the evolution of large circuits. The proposed method has been extensively tested, not only with multipliers and parity bit problems traditionally used in the EHW community, but also with logic circuits taken from the Microelectronics Center of North Carolina (MCNC) benchmark library and randomly generated circuits. In order to achieve statistically relevant results, each analyzed logic circuit has been evolved 100 times, and the average of these results is presented and compared with other EHW techniques. This approach is necessary because of the probabilistic nature of EA; the same logic circuit may not be solved in the same way if tested several times. The proposed method has been examined in an extrinsic EHW system using the$(1 + lambda)$evolution strategy. The results obtained demonstrate that GDD significantly improves the evolution of logic circuits in terms of the number of generations, reduces computational time as it is able to reduce the required time for a single iteration of the EA, and enables the evolution of larger circuits never before evolved. In addition to the proposed method, a short overview of EHW systems together with the most recent applications in electrical circuit design is provided

ParaFPGA : parallel computing with flexible hardware

ParaFPGA 2009 is a Mini-Symposium on parallel computing with field programmable gate arrays (FPGAs), held in conjunction with the ParCo conference on parallel computing. FPGAs allow to map an algorithm directly onto the hardware, optimize the architecture for parallel execution, and dynamically reconfigure the system in between different phases of the computation. Compared to e.g. Cell processors, GPGPU's (general-purpose GPU's) and other high-performance devices, FPGAs are considered as flexible hardware in the sense that the building blocks of one or more single or multiple FPGAs can be interconnected freely to build a highly parallel system. In this Mini-Symposium the following topics are addressed: clustering FPGAs, evolvable hardware using FPGAs and fast dynamic reconfiguration

Self-repair ability of evolved self-assembling systems in cellular automata

Self-repairing systems are those that are able to reconfigure themselves following disruptions to bring them back into a defined normal state. In this paper we explore the self-repair ability of some cellular automata-like systems, which differ from classical cellular automata by the introduction of a local diffusion process inspired by chemical signalling processes in biological development. The update rules in these systems are evolved using genetic programming to self-assemble towards a target pattern. In particular, we demonstrate that once the update rules have been evolved for self-assembly, many of those update rules also provide a self-repair ability without any additional evolutionary process aimed specifically at self-repair

Open-ended evolution to discover analogue circuits for beyond conventional applications

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s10710-012-9163-8. Copyright @ Springer 2012.Analogue circuits synthesised by means of open-ended evolutionary algorithms often have unconventional designs. However, these circuits are typically highly compact, and the general nature of the evolutionary search methodology allows such designs to be used in many applications. Previous work on the evolutionary design of analogue circuits has focused on circuits that lie well within analogue application domain. In contrast, our paper considers the evolution of analogue circuits that are usually synthesised in digital logic. We have developed four computational circuits, two voltage distributor circuits and a time interval metre circuit. The approach, despite its simplicity, succeeds over the design tasks owing to the employment of substructure reuse and incremental evolution. Our findings expand the range of applications that are considered suitable for evolutionary electronics

On evolution of relatively large combinational logic circuits

Evolvable hardware (EHW) (Yao and Higuchi, 1999) is a technique introduced to automatically design circuits where the circuit configuration is carried out by evolutionary algorithms. One of the main difficulties in using EHW to solve real-world problems is the scalability. Until now, several strategies have been proposed to avoid this problem, but none of them completely tackle the issue. In this paper three different methods for evolving the most complex circuits have been tested for their scalability. These methods are bi-directional incremental evolution (SO-BIE); generalised disjunction decomposition (GD-BIE) and evolutionary strategies (ES) with dynamic mutation rate. In order to achieve the generalised conclusions the chosen approaches were tested using multipliers, traditionally used in EHW, but also logic circuits taken from MCNC (Yang, 1991) benchmark library and randomly generated circuits. The analysis of the approaches demonstrated that PLA-based ES is capable of evolving logic circuits of up to 12 inputs. The use of SO-BIE allows the generation of fully functional circuits of 14 inputs and GD-BIE is estimated to be able to evolve circuits of 21 inputs

Absolutely free extrinsic evolution of passive low-pass filter

Evolutionary electronics is a brunch of evolvable hardware, where the evolutionary algorithm is applied towards electronic circuits. The success of evolutionary search most of all depends on variable length representation methodology. The low-pass filter is a standard task in evolutionary electronics to start with. The results of evolution enable one to qualify whether the methodology is good for further experiments. In this paper the maximum freedom for evolutionary search has been proclaimed as a main target during development of new VLR methodology. The introduction of R-support elements enables to perform an unconstrained evolution of analogue circuits for the first time. The proposed algorithm has been tested on the example of analogue low-pass filter. The experimental results demonstrate that the evolved filter is comparable with filters evolved previously using genetic programming and genetic algorithms techniques. The obtained results are compared in details with low-pass filters previously designed

A novel genetic algorithm for evolvable hardware

Evolutionary algorithms are used for solving search and optimization problems. A new field in which they are also applied is evolvable hardware, which refers to a self-configurable electronic system. However, evolvable hardware is not widely recognized as a tool for solving real-world applications, because of the scalability problem, which limits the size of the system that may be evolved. In this paper a new genetic algorithm, particularly designed for evolving logic circuits, is presented and tested for its scalability. The proposed algorithm designs and optimizes logic circuits based on a Programmable Logic Array (PLA) structure. Furthermore it allows the evolution of large logic circuits, without the use of any decomposition techniques. The experimental results, based on the evolution of several logic circuits taken from three different benchmarks, prove that the proposed algorithm is very fast, as only a few generations are required to fully evolve the logic circuits. In addition it optimizes the evolved circuits better than the optimization offered by other evolutionary algorithms based on a PLA and FPGA structures

Self-Reconfigurable Analog Arrays: Off-The Shelf Adaptive Electronics for Space Applications

Development of analog electronic solutions for space avionics is expensive and lengthy. Lack of flexible analog devices, counterparts to digital Field Programmable Gate Arrays (FPGA), prevents analog designers from benefits of rapid prototyping. This forces them to expensive and lengthy custom design, fabrication, and qualification of application specific integrated circuits (ASIC). The limitations come from two directions: commercial Field Programmable Analog Arrays (FPAA) have limited variability in the components offered on-chip; and they are only qualified for best case scenarios for military grade (-55C to +125C). In order to avoid huge overheads, there is a growing trend towards avoiding thermal and radiation protection by developing extreme environment electronics, which maintain correct operation while exposed to temperature extremes (-180degC to +125degC). This paper describes a recent FPAA design, the Self-Reconfigurable Analog Array (SRAA) developed at JPL. It overcomes both limitations, offering a variety of analog cells inside the array together with the possibility of self-correction at extreme temperatures

Improving EHW performance introducing a new decomposition strategy

This paper describes a new type of decomposition strategy for Evolvable Hardware, which tackles the problem of scalability. Several logic circuits from the MCNC benchmark have been evolved and compared with other Evolvable Hardware techniques. The results demonstrate that the proposed method improves the evolution of logic circuits in terms of time and fitness function in comparison with BIE and standard EHW