Genetically Engineered Adaptive Resonance Theory (art) Neural Network Architectures

Fuzzy ARTMAP (FAM) is currently considered to be one of the premier neural network architectures in solving classification problems. One of the limitations of Fuzzy ARTMAP that has been extensively reported in the literature is the category proliferation problem. That is Fuzzy ARTMAP has the tendency of increasing its network size, as it is confronted with more and more data, especially if the data is of noisy and/or overlapping nature. To remedy this problem a number of researchers have designed modifications to the training phase of Fuzzy ARTMAP that had the beneficial effect of reducing this phenomenon. In this thesis we propose a new approach to handle the category proliferation problem in Fuzzy ARTMAP by evolving trained FAM architectures. We refer to the resulting FAM architectures as GFAM. We demonstrate through extensive experimentation that an evolved FAM (GFAM) exhibits good (sometimes optimal) generalization, small size (sometimes optimal size), and requires reasonable computational effort to produce an optimal or sub-optimal network. Furthermore, comparisons of the GFAM with other approaches, proposed in the literature, which address the FAM category proliferation problem, illustrate that the GFAM has a number of advantages (i.e. produces smaller or equal size architectures, of better or as good generalization, with reduced computational complexity). Furthermore, in this dissertation we have extended the approach used with Fuzzy ARTMAP to other ART architectures, such as Ellipsoidal ARTMAP (EAM) and Gaussian ARTMAP (GAM) that also suffer from the ART category proliferation problem. Thus, we have designed and experimented with genetically engineered EAM and GAM architectures, named GEAM and GGAM. Comparisons of GEAM and GGAM with other ART architectures that were introduced in the ART literature, addressing the category proliferation problem, illustrate similar advantages observed by GFAM (i.e, GEAM and GGAM produce smaller size ART architectures, of better or improved generalization, with reduced computational complexity). Moverover, to optimally cover the input space of a problem, we proposed a genetically engineered ART architecture that combines the category structures of two different ART networks, FAM and EAM. We named this architecture UART (Universal ART). We analyzed the order of search in UART, that is the order according to which a FAM category or an EAM category is accessed in UART. This analysis allowed us to better understand UART\u27s functionality. Experiments were also conducted to compare UART with other ART architectures, in a similar fashion as GFAM and GEAM were compared. Similar conclusions were drawn from this comparison, as in the comparison of GFAM and GEAM with other ART architectures. Finally, we analyzed the computational complexity of the genetically engineered ART architectures and we compared it with the computational complexity of other ART architectures, introduced into the literature. This analytical comparison verified our claim that the genetically engineered ART architectures produce better generalization and smaller sizes ART structures, at reduced computational complexity, compared to other ART approaches. In review, a methodology was introduced of how to combine the answers (categories) of ART architectures, using genetic algorithms. This methodology was successfully applied to FAM, EAM and FAM and EAM ART architectures, with success, resulting in ART neural networks which outperformed other ART architectures, previously introduced into the literature, and quite often produced ART architectures that attained optimal classification results, at reduced computational complexity

Frontiers of Adaptive Design, Synthetic Biology and Growing Skins for Ephemeral Hybrid Structures

The history of membranes is one of adaptation, from the development in living organisms to man-made versions, with a great variety of uses in temporary design: clothing, building, packaging, etc. Being versatile and simple to integrate, membranes have a strong sustainability potential, through an essential use of material resources and multifunctional design, representing one of the purest cases where “design follows function.” The introduction of new engineered materials and techniques, combined with a growing interest for Nature-inspired technologies are progressively merging man-made artifacts and biological processes with a high potential for innovation. This chapter introduces, through a number of examples, the broad variety of hybrid membranes in the contest of experimental Design, Art and Architecture, categorized following two different stages of biology-inspired approach with the aim of identifying potential developments. Biomimicry, is founded on the adoption of practices from nature in architecture though imitation: solutions are observed on a morphological, structural or procedural level and copied to design everything from nanoscale materials to building technologies. Synthetic biology relies on hybrid procedures mixing natural and synthetic materials and processes

Bionanomaterials from plant viruses

Plant virus capsids have emerged as useful biotemplates for material synthesis. All plant virus capsids are assembled with high-precision, three-dimensional structures providing nanoscale architectures that are highly monodisperse, can be produced in large quantities and that cannot replicate in mammalian cells (so are safe). Such exceptional characteristics make plant viruses strong candidates for application as biotemplates for novel and new material synthesis

Transmitter and Receiver Architectures for Molecular Communications: A Survey on Physical Design with Modulation, Coding, and Detection Techniques

Inspired by nature, molecular communications (MC), i.e., the use of molecules to encode, transmit, and receive information, stands as the most promising communication paradigm to realize the nanonetworks. Even though there has been extensive theoretical research toward nanoscale MC, there are no examples of implemented nanoscale MC networks. The main reason for this lies in the peculiarities of nanoscale physics, challenges in nanoscale fabrication, and highly stochastic nature of the biochemical domain of envisioned nanonetwork applications. This mandates developing novel device architectures and communication methods compatible with MC constraints. To that end, various transmitter and receiver designs for MC have been proposed in the literature together with numerable modulation, coding, and detection techniques. However, these works fall into domains of a very wide spectrum of disciplines, including, but not limited to, information and communication theory, quantum physics, materials science, nanofabrication, physiology, and synthetic biology. Therefore, we believe it is imperative for the progress of the field that an organized exposition of cumulative knowledge on the subject matter can be compiled. Thus, to fill this gap, in this comprehensive survey, we review the existing literature on transmitter and receiver architectures toward realizing MC among nanomaterial-based nanomachines and/or biological entities and provide a complete overview of modulation, coding, and detection techniques employed for MC. Moreover, we identify the most significant shortcomings and challenges in all these research areas and propose potential solutions to overcome some of them.This work was supported in part by the European Research Council (ERC) Projects MINERVA under Grant ERC-2013-CoG #616922 and MINERGRACE under Grant ERC-2017-PoC #780645

Roadmap on semiconductor-cell biointerfaces.

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world

Recent Advances and Current Developments in Tissue Scaffolding

A bio-scaffold can be broadly termed as a structure used to substitute an organ either permanently or temporarily to restore functionality. The material that can be used varies with the application intended. Tissue engineering is one such application demanding certain requirements to be met before it is applied. One of the applications in tissue engineering is the tissue scaffold, which provides either a permanent or temporary support to the damaged tissues/organ until the functionalities are restored. A biomaterial can exhibit specific interactions with cells that will lead to stereotyped responses. The use of a particular material and morphology depends on various factors such as osteoinduction, osteoconduction, angiogenesis, growth rates of cells and degradation rate of the material in case of temporary scaffolds, etc. The current work reviews the state of art in tissue scaffolds and focuses on permanent scaffold materials and applications with a brief overview of temporary scaffold materials and their disadvantages

Biology of Applied Digital Ecosystems

A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex, dynamic problems. However, the biological processes that contribute to these properties have not been made explicit in Digital Ecosystems research. Here, we discuss how biological properties contribute to the self-organising features of biological ecosystems, including population dynamics, evolution, a complex dynamic environment, and spatial distributions for generating local interactions. The potential for exploiting these properties in artificial systems is then considered. We suggest that several key features of biological ecosystems have not been fully explored in existing digital ecosystems, and discuss how mimicking these features may assist in developing robust, scalable self-organising architectures. An example architecture, the Digital Ecosystem, is considered in detail. The Digital Ecosystem is then measured experimentally through simulations, with measures originating from theoretical ecology, to confirm its likeness to a biological ecosystem. Including the responsiveness to requests for applications from the user base, as a measure of the 'ecological succession' (development).Comment: 9 pages, 4 figure, conferenc