Download or read book Novel Methods for Learning and Adaptation in Chemical Reaction Networks written by and published by . This book was released on 2015 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be re-programmed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. Currently, biochemistry lacks a systems vision on how the user-level programming interface and abstraction with a subsequent translation to chemistry should look like. By developing adaptation in chemistry, we could replace multiple hard-wired systems with a single programmable template that can be (re)trained to match a desired input-output profile benefiting smart drug delivery, pattern recognition, and chemical computing. I aimed to address these challenges by proposing several approaches to learning and adaptation in Chemical Reaction Networks (CRNs), a type of simulated chemistry, where species are unstructured, i.e., they are identified by symbols rather than molecular structure, and their dynamics or concentration evolution are driven by reactions and reaction rates that follow mass-action and Michaelis-Menten kinetics. Several CRN and experimental DNA-based models of neural networks exist. However, these models successfully implement only the forward-pass, i.e., the input-weight integration part of a perceptron model. Learning is delegated to a non-chemical system that computes the weights before converting them to molecular concentrations. Autonomous learning, i.e., learning implemented fully inside chemistry has been absent from both theoretical and experimental research. The research in this thesis offers the first constructive evidence that learning in CRNs is, in fact, possible. I have introduced the original concept of a chemical binary perceptron that can learn all 14 linearly-separable logic functions and is robust to the perturbation of rate constants. That shows learning is universal and substrate-free. To simplify the model I later proposed and applied the "asymmetric" chemical arithmetic providing a compact solution for representing negative numbers in chemistry. To tackle more difficult tasks and to serve more complicated biochemical applications, I introduced several key modular building blocks, each addressing certain aspects of chemical information processing and learning. These parts organically combined into gradually more complex systems. First, instead of simple static Boolean functions, I tackled analog time-series learning and signal processing by modeling an analog chemical perceptron. To store past input concentrations as a sliding window I implemented a chemical delay line, which feeds the values to the underlying chemical perceptron. That allows the system to learn, e.g., the linear moving-average and to some degree predict a highly nonlinear NARMA benchmark series. Another important contribution to the area of chemical learning, which I have helped to shape, is the composability of perceptrons into larger multi-compartment networks. Each compartment hosts a single chemical perceptron and compartments communicate with each other through a channel-mediated exchange of molecular species. Besides the feedforward pass, I implemented the chemical error backpropagation analogous to that of feedforward neural networks. Also, after applying mass-action kinetics for the catalytic reactions, I succeeded to systematically analyze the ODEs of my models and derive the closed exact and approximative formulas for both the input-weight integration and the weight update with a learning rate annealing. I proved mathematically that the formulas of certain chemical perceptrons equal the formal linear and sigmoid neurons, essentially bridging neural networks and adaptive CRNs. For all my models the basic methodology was to first design species and reactions, and then set the rate constants either "empirically" by hand, automatically by a standard genetic algorithm (GA), or analytically if possible. I performed all simulations in my COEL framework, which is the first cloud-based chemistry modeling tool, accessible at http://coel-sim.org. I minimized the amount of required molecular species and reactions to make wet chemical implementation possible. I applied an automatized mapping technique, Soloveichik's CRN-to-DNA-strand-displacement transformation, to the chemical linear perceptron and the manual signalling delay line and obtained their full DNA-strand specified implementations. As an alternative DNA-based substrate, I mapped these two models also to deoxyribozyme-mediated cleavage reactions reducing the size of the displacement variant to a third. Both DNA-based incarnations could directly serve as blue-prints for wet biochemicals. Besides an actual synthesis of my models and conducting an experiment in a biochemical laboratory, the most promising future work is to employ so-called reservoir computing (RC), which is a novel machine learning method based on recurrent neural networks. The RC approach is relevant because for time-series prediction it is clearly superior to classical recurrent networks. It can also be implemented in various ways, such as electrical circuits, physical systems, such as a colony of Escherichia Coli, and water. RC's loose structural assumptions therefore suggest that it could be expressed in a chemical form as well. This could further enhance the expressivity and capabilities of chemically-embedded learning. My chemical learning systems may have applications in the area of medical diagnosis and smart medication, e.g., concentration signal processing and monitoring, and the detection of harmful species, such as chemicals produced by cancer cells in a host (cancer miRNAs) or the detection of a severe event, defined as a linear or nonlinear temporal concentration pattern. My approach could replace hard-coded solutions and would allow to specify, train, and reuse chemical systems without redesigning them. With time-series integration, biochemical computers could keep a record of changing biological systems and act as diagnostic aids and tools in preventative and highly personalized medicine.
Download or read book Foundations of Chemical Reaction Network Theory written by Martin Feinberg and published by Springer. This book was released on 2019-01-31 with total page 475 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an authoritative introduction to the rapidly growing field of chemical reaction network theory. In particular, the book presents deep and surprising theorems that relate the graphical and algebraic structure of a reaction network to qualitative properties of the intricate system of nonlinear differential equations that the network induces. Over the course of three main parts, Feinberg provides a gradual transition from a tutorial on the basics of reaction network theory, to a survey of some of its principal theorems, and, finally, to a discussion of the theory’s more technical aspects. Written with great clarity, this book will be of value to mathematicians and to mathematically-inclined biologists, chemists, physicists, and engineers who want to contribute to chemical reaction network theory or make use of its powerful results.
Download or read book The Modelling and Synthesis of Chemical Reaction Networks written by Max Alexander Norman Whitby and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Construction of Chemical Reaction Networks written by I. Nemes and published by . This book was released on 1976 with total page 14 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Out of Equilibrium Supra molecular Systems and Materials written by Nicolas Giuseppone and published by John Wiley & Sons. This book was released on 2021-03-30 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: A must-have resource that covers everything from out-of-equilibrium chemical systems and materials to dissipative self-assemblies Out-of-Equilibrium Supramolecular Systems and Materials presents a comprehensive overview of the synthetic approaches that use supramolecular bonds in various out-of-thermodynamic equilibrium situations. With contributions from noted experts on the topic, the text contains information on the design of dissipative self-assemblies that maintain their structures when fueled by an external source of energy. The contributors also examine molecules and nanoscale objects and materials that can produce mechanical work based on molecular machines. Additionally, the book explores non-equilibrium supramolecular polymers that can be trapped in kinetically stable states, as well as out-of-equilibrium chemical systems and oscillators that are important to understand the emergence of complex behaviors and, in particular, the origin of life. This important book: Offers comprehensive coverage of fields from design of dissipative self-assemblies to non-equilibrium supramolecular polymers Presents information on a highly emerging and interdisciplinary topic Includes contributions from internationally renowned scientists Written for chemists, physical chemists, biochemists, material scientists, Out-of-Equilibrium Supramolecular Systems and Materials is an indispensable resource written by top scientists in the field.
Download or read book Differential Evolution written by Anyong Qing and published by John Wiley & Sons. This book was released on 2009-07-23 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Differential evolution is a very simple but very powerful stochastic optimizer. Since its inception, it has proved very efficient and robust in function optimization and has been applied to solve problems in many scientific and engineering fields. In Differential Evolution , Dr. Qing begins with an overview of optimization, followed by a state-of-the-art review of differential evolution, including its fundamentals and up-to-date advances. He goes on to explore the relationship between differential evolution strategies, intrinsic control parameters, non-intrinsic control parameters, and problem features through a parametric study. Findings and recommendations on the selection of strategies and intrinsic control parameter values are presented. Lastly, after an introductory review of reported applications in electrical and electronic engineering fields, different research groups demonstrate how the methods can be applied to such areas as: multicast routing, multisite mapping in grid environments, antenna arrays, analog electric circuit sizing, electricity markets, stochastic tracking in video sequences, and color quantization. Contains a systematic and comprehensive overview of differential evolution Reviews the latest differential evolution research Describes a comprehensive parametric study conducted over a large test bed Shows how methods can be practically applied to mobile communications grid computing circuits image processing power engineering Sample applications demonstrated by research groups in the United Kingdom, Australia, Italy, Turkey, China, and Eastern Europe Provides access to companion website with code examples for download Differential Evolution is ideal for application engineers, who can use the methods described to solve specific engineering problems. It is also a valuable reference for post-graduates and researchers working in evolutionary computation, design optimization and artificial intelligence. Researchers in the optimization field or engineers and managers involved in operations research will also find the book a helpful introduction to the topic.
Download or read book Computational Modeling From Chemistry To Materials To Biology Proceedings Of The 25th Solvay Conference On Chemistry written by Kurt Wuthrich and published by World Scientific. This book was released on 2020-12-21 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chaired by K Wüthrich (Nobel Laureate in Chemistry, 2002) and co-chaired by B Weckhuysen, this by-invitation-only conference has gathered 39 participants — who are leaders in the field of computational modeling and its applications in Chemistry, Material Sciences and Biology. Highlights of the Conference Proceedings are short, prepared statements by all the participants and the records of lively discussions on the current and future perspectives in the field of computational modeling, from chemistry to materials to biology.
Download or read book Adaptation and Hybridization in Computational Intelligence written by Iztok Fister and published by Springer. This book was released on 2015-01-24 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt: This carefully edited book takes a walk through recent advances in adaptation and hybridization in the Computational Intelligence (CI) domain. It consists of ten chapters that are divided into three parts. The first part illustrates background information and provides some theoretical foundation tackling the CI domain, the second part deals with the adaptation in CI algorithms, while the third part focuses on the hybridization in CI. This book can serve as an ideal reference for researchers and students of computer science, electrical and civil engineering, economy, and natural sciences that are confronted with solving the optimization, modeling and simulation problems. It covers the recent advances in CI that encompass Nature-inspired algorithms, like Artificial Neural networks, Evolutionary Algorithms and Swarm Intelligence –based algorithms.
Download or read book 34th European Symposium on Computer Aided Process Engineering 15th International Symposium on Process Systems Engineering written by Flavio Manenti and published by Elsevier. This book was released on 2024-06-28 with total page 3634 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 34th European Symposium on Computer Aided Process Engineering / 15th International Symposium on Process Systems Engineering, contains the papers presented at the 34th European Symposium on Computer Aided Process Engineering / 15th International Symposium on Process Systems Engineering joint event. It is a valuable resource for chemical engineers, chemical process engineers, researchers in industry and academia, students, and consultants for chemical industries. Presents findings and discussions from the 34th European Symposium on Computer Aided Process Engineering / 15th International Symposium on Process Systems Engineering joint event
Download or read book Applying Particle Swarm Optimization written by Burcu Adıgüzel Mercangöz and published by Springer Nature. This book was released on 2021-05-13 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explains the theoretical structure of particle swarm optimization (PSO) and focuses on the application of PSO to portfolio optimization problems. The general goal of portfolio optimization is to find a solution that provides the highest expected return at each level of portfolio risk. According to H. Markowitz’s portfolio selection theory, as new assets are added to an investment portfolio, the total risk of the portfolio’s decreases depending on the correlations of asset returns, while the expected return on the portfolio represents the weighted average of the expected returns for each asset. The book explains PSO in detail and demonstrates how to implement Markowitz’s portfolio optimization approach using PSO. In addition, it expands on the Markowitz model and seeks to improve the solution-finding process with the aid of various algorithms. In short, the book provides researchers, teachers, engineers, managers and practitioners with many tools they need to apply the PSO technique to portfolio optimization.
Download or read book Computational Management written by Srikanta Patnaik and published by Springer Nature. This book was released on 2021-05-29 with total page 682 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers a timely review of cutting-edge applications of computational intelligence to business management and financial analysis. It covers a wide range of intelligent and optimization techniques, reporting in detail on their application to real-world problems relating to portfolio management and demand forecasting, decision making, knowledge acquisition, and supply chain scheduling and management.
Download or read book Evolutionary Computation written by Ashish M. Gujarathi and published by CRC Press. This book was released on 2016-12-01 with total page 652 pages. Available in PDF, EPUB and Kindle. Book excerpt: Edited by professionals with years of experience, this book provides an introduction to the theory of evolutionary algorithms and single- and multi-objective optimization, and then goes on to discuss to explore applications of evolutionary algorithms for many uses with real-world applications. Covering both the theory and applications of evolutionary computation, the book offers exhaustive coverage of several topics on nontraditional evolutionary techniques, details working principles of new and popular evolutionary algorithms, and discusses case studies on both scientific and real-world applications of optimization
Download or read book New Frontiers in the Study of Social Phenomena written by Federico Cecconi and published by Springer. This book was released on 2016-03-11 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book studies social phenomena in a new way, by making judicious use of computer technology. The book addresses the entire spectrum of classic studies in social science, from experiments to the computational models, with a multidisciplinary approach. The book is suitable for those who want to get a picture of what it means to do social research today, and also to get an indication of the major open issues. The book is connected to a database of code for simulations, experimental data and allows to activate a subscription to a teaching tool using NetLogo, a programming language widely used in the social studies. The authors are researchers with first-hand experience research projects, both basic and applied. The work will be useful for those who want to understand more of the social, economic and political phenomena via computer applications.
Download or read book Adaptive and Natural Computing Algorithms written by Marco Tomassini and published by Springer. This book was released on 2013-04-12 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book constitutes the refereed proceedings of the 11th International Conference on Adaptive and Natural Computing Algorithms, ICANNGA 2013, held in Lausanne, Switzerland, in April 2013. The 51 revised full papers presented were carefully reviewed and selected from a total of 91 submissions. The papers are organized in topical sections on neural networks, evolutionary computation, soft computing, bioinformatics and computational biology, advanced computing, and applications.
Download or read book Theoretical Immunology Part Two written by Alan S. Perelson and published by CRC Press. This book was released on 2018-02-19 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: Assuming that the complex phenomena underlying the operation of the immune system may be better understood through the collaborative efforts of theorists and experimentalists viewing the same phenomena in different ways, the Sante Fe Institute and the Theoretical Division of Los Alamos National Laboratory cosponsored a workshop entitled "Theoretical Immunology." The workshop focused on themes spanning the field of immunology, with emphasis on areas where the theorists have made the most progress. This book covers the discussions a that workshop on the topics of immune surveillance, mathematical models of HIV infection, complexities of antigen-antibody systems, immune suppression and tolerance, and idiotypie networks. In each of these areas there is reason to believe that advances can be made either through interactions among experimentalists and theorists or through the critical look experimentalists and theorists will bring to bear upon one another's work.
Download or read book Chemical Reaction Engineering written by Octave Levenspiel and published by John Wiley & Sons. This book was released on 1998-09-01 with total page 689 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical reaction engineering is concerned with the exploitation of chemical reactions on a commercial scale. It's goal is the successful design and operation of chemical reactors. This text emphasizes qualitative arguments, simple design methods, graphical procedures, and frequent comparison of capabilities of the major reactor types. Simple ideas are treated first, and are then extended to the more complex.
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2008 with total page 800 pages. Available in PDF, EPUB and Kindle. Book excerpt:
