487 research outputs found
"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
Degeneracy: a link between evolvability, robustness and complexity in biological systems
A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability) and evidence of an intimate relationship between robustness and complexity in biology.
This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability
Genetic Learning Algorithms Combined With Novel Binary Hill Climbing Used for Online Walking-Pattern Generation in Legged Robots
According to Darwin every species on this planet have developed froma small group of simple molecules into all the modern species living among us today. The reason why some species survive and others don’t is what Darwin called Natural Selection, which means that every individual have to fight for its existence. Those who are best fit will survive. This has brought life to the well known saying: "Survival of the Fittest". The best fit will have the best chance to reproduce, to pass its well fitted, surviving qualities on to their offspring. And the offspring of two well-equipped parents will have a high probability of adaptation, and so the circle
of life goes on...
A set of evolutionary search methods have been extracted from the Darwinian theories of evolution. These have been evolving in computer environments for several decades and have been passing through different areas of computer science, from theoretical tuning problems, algorithm developing, clustering, chip design, and several real world applications have been the foci the last years.
In this thesis Genetic Algorithms and Evolvable Hardware is used for evolving gaits in a walking biped robot controller. The focus is fast learning in a real-time environment. An incremental approach combining a genetic algorithm with hill climbing is proposed. This combination interacts in an efficient way to generate precise walking patterns in less than 15 generations. Our proposal is compared to various versions of Genetic Algorithms and stochastic search, and finally tested on a pneumatic biped walking robot
Intrinsically Evolvable Artificial Neural Networks
Dedicated hardware implementations of neural networks promise to provide faster, lower power operation when compared to software implementations executing on processors. Unfortunately, most custom hardware implementations do not support intrinsic training of these networks on-chip. The training is typically done using offline software simulations and the obtained network is synthesized and targeted to the hardware offline. The FPGA design presented here facilitates on-chip intrinsic training of artificial neural networks. Block-based neural networks (BbNN), the type of artificial neural networks implemented here, are grid-based networks neuron blocks. These networks are trained using genetic algorithms to simultaneously optimize the network structure and the internal synaptic parameters. The design supports online structure and parameter updates, and is an intrinsically evolvable BbNN platform supporting functional-level hardware evolution. Functional-level evolvable hardware (EHW) uses evolutionary algorithms to evolve interconnections and internal parameters of functional modules in reconfigurable computing systems such as FPGAs. Functional modules can be any hardware modules such as multipliers, adders, and trigonometric functions. In the implementation presented, the functional module is a neuron block. The designed platform is suitable for applications in dynamic environments, and can be adapted and retrained online. The online training capability has been demonstrated using a case study. A performance characterization model for RC implementations of BbNNs has also been presented
Born to learn: The inspiration, progress, and future of evolved plastic artificial neural networks
Biological plastic neural networks are systems of extraordinary computational
capabilities shaped by evolution, development, and lifetime learning. The
interplay of these elements leads to the emergence of adaptive behavior and
intelligence. Inspired by such intricate natural phenomena, Evolved Plastic
Artificial Neural Networks (EPANNs) use simulated evolution in-silico to breed
plastic neural networks with a large variety of dynamics, architectures, and
plasticity rules: these artificial systems are composed of inputs, outputs, and
plastic components that change in response to experiences in an environment.
These systems may autonomously discover novel adaptive algorithms, and lead to
hypotheses on the emergence of biological adaptation. EPANNs have seen
considerable progress over the last two decades. Current scientific and
technological advances in artificial neural networks are now setting the
conditions for radically new approaches and results. In particular, the
limitations of hand-designed networks could be overcome by more flexible and
innovative solutions. This paper brings together a variety of inspiring ideas
that define the field of EPANNs. The main methods and results are reviewed.
Finally, new opportunities and developments are presented
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Automatic design of analogue circuits
This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Evolvable Hardware (EHW) is a promising area in electronics today. Evolutionary Algorithms (EA), together with a circuit simulation tool or real hardware, automatically designs a circuit for a given problem. The circuits evolved may have unconventional designs and be less dependent on the personal knowledge of a designer. Nowadays, EA are represented by Genetic Algorithms (GA), Genetic Programming (GP) and Evolutionary Strategy (ES). While GA is definitely the most popular tool, GP has rapidly developed in recent years and is notable by its outstanding results. However, to date the use of ES for analogue circuit synthesis has been limited to a few applications.
This work is devoted to exploring the potential of ES to create novel analogue designs. The narrative of the thesis starts with a framework of an ES-based system generating simple circuits, such as low pass filters. Then it continues with a step-by-step progression to increasingly sophisticated designs that require additional strength from the system. Finally, it describes the modernization of the system using novel techniques that enable the synthesis of complex multi-pin circuits that are newly evolved.
It has been discovered that ES has strong power to synthesize analogue circuits. The circuits evolved in the first part of the thesis exceed similar results made previously using other techniques in a component economy, in the better functioning of the evolved circuits and in the computing power spent to reach the results. The target circuits for evolution in the second half are chosen by the author to challenge the capability of the developed system. By functioning, they do not belong to the conventional analogue domain but to applications that are usually adopted by digital circuits. To solve the design tasks, the system has been gradually developed to support the ability of evolving increasingly complex circuits.
As a final result, a state-of-the-art ES-based system has been developed that possesses a novel mutation paradigm, with an ability to create, store and reuse substructures, to adapt the mutation, selection parameters and population size, utilize automatic incremental evolution and use the power of parallel computing. It has been discovered that with the ability to synthesis the most up-to-date multi-pin complex analogue circuits that have ever been automatically synthesized before, the system is capable of synthesizing circuits that are problematic for conventional design with application domains that lay beyond the conventional application domain for analogue circuits
Hardware evolution of a digital circuit using a custom VLSI architecture
This research investigates three solutions to overcoming portability and scalability concerns in the Evolutionary Hardware (EHW) field. Firstly, the study explores if the V-FPGA—a new, portable Virtual-Reconfigurable-Circuit architecture—is a practical and viable evolution platform. Secondly, the research looks into two possible ways of making EHW systems more scalable: by optimising the system’s genetic algorithm; and by decomposing the solution circuit into smaller, evolvable sub-circuits or modules. GA optimisation is done is by: omitting a canonical GA’s crossover operator (i.e. by using an algorithm); applying evolution constraints; and optimising the fitness function. The circuit decomposition is done in order to demonstrate modular evolution. Three two-bit multiplier circuits and two sub-circuits of a simple, but real-world control circuit are evolved. The results show that the evolved multiplier circuits, when compared to a conventional multiplier, are either equal or more efficient. All the evolved circuits improve two of the four critical paths, and all are unique. Thus, it is experimentally shown that the V-FPGA is a viable hardware-platform on which hardware evolution can be implemented; and how hardware evolution is able to synthesise novel, optimised versions of conventional circuits. By comparing the and canonical GAs, the results verify that optimised GAs can find solutions quicker, and with fewer attempts. Part of the optimisation also includes a comprehensive critical-path analysis, where the findings show that the identification of dependent critical paths is vital in enhancing a GA’s efficiency. Finally, by demonstrating the modular evolution of a finite-state machine’s control circuit, it is found that although the control circuit as a whole makes use of more than double the available hardware resources on the V-FPGA and is therefore not evolvable, the evolution of each state’s sub-circuit is possible. Thus, modular evolution is shown to be a successful tool when dealing with scalability
geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research
8 pages, 5 figures, 3 additional files.-- Software.[Background] Bioinformatics and medical informatics are two research fields that serve the needs of different but related communities. Both domains share the common goal of providing new algorithms, methods and technological solutions to biomedical research, and contributing to the treatment and cure of diseases. Although different microarray techniques have been successfully used to investigate useful information for cancer diagnosis at the gene expression level, the true integration of existing methods into day-to-day clinical practice is still a long way off. Within this context, case-based reasoning emerges as a suitable paradigm specially intended for the development of biomedical informatics applications and decision support systems, given the support and collaboration involved in such a translational development. With the goals of removing barriers against multi-disciplinary collaboration and facilitating the dissemination and transfer of knowledge to real practice, case-based reasoning systems have the potential to be applied to translational research mainly because their computational reasoning paradigm is similar to the way clinicians gather, analyze and process information in their own practice of clinical medicine.[Results] In addressing the issue of bridging the existing gap between biomedical researchers and clinicians who work in the domain of cancer diagnosis, prognosis and treatment, we have developed and made accessible a common interactive framework. Our geneCBR system implements a freely available software tool that allows the use of combined techniques that can be applied to gene selection, clustering, knowledge extraction and prediction for aiding diagnosis in cancer research. For biomedical researches, geneCBR expert mode offers a core workbench for designing and testing new techniques and experiments. For pathologists or oncologists, geneCBR diagnostic mode implements an effective and reliable system that can diagnose cancer subtypes based on the analysis of microarray data using a CBR architecture. For programmers, geneCBR programming mode includes an advanced edition module for run-time modification of previous coded techniques.[Conclusion] geneCBR is a new translational tool that can effectively support the integrative work of programmers, biomedical researches and clinicians working together in a common framework. The code is freely available under the GPL license and can be obtained at http://www.genecbr.org (webcite).This work is supported in part by the projects Research on Translational Bioinformatics
(ref. 08VIB6) from University of Vigo and Development of computational
tools for the classification and clustering of gene expression data in order
to discover meaningful biological information in cancer diagnosis (ref.
VA100A08) from JCyL (Spain). The work of D. Glez-Peña is supported by
a "María Barbeito" contract from Xunta de Galicia.Peer reviewe
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