The Kinetic Basis of Morphogenesis

It has been shown recently (Shalygo, 2014) that stationary and dynamic patterns can arise in the proposed one-component model of the analog (continuous state) kinetic automaton, or kinon for short, defined as a reflexive dynamical system with active transport. This paper presents extensions of the model, which increase further its complexity and tunability, and shows that the extended kinon model can produce spatio-temporal patterns pertaining not only to pattern formation but also to morphogenesis in real physical and biological systems. The possible applicability of the model to morphogenetic engineering and swarm robotics is also discussed.Comment: 8 pages. Submitted to the 13th European Conference on Artificial Life (ECAL-2015) on March 10, 2015. Accepted on April 28, 201

Deep Learning as a Parton Shower

We make the connection between certain deep learning architectures and the renormalisation group explicit in the context of QCD by using a deep learning network to construct a toy parton shower model. The model aims to describe proton-proton collisions at the Large Hadron Collider. A convolutional autoencoder learns a set of kernels that efficiently encode the behaviour of fully showered QCD collision events. The network is structured recursively so as to ensure self-similarity, and the number of trained network parameters is low. Randomness is introduced via a novel custom masking layer, which also preserves existing parton splittings by using layer-skipping connections. By applying a shower merging procedure, the network can be evaluated on unshowered events produced by a matrix element calculation. The trained network behaves as a parton shower that qualitatively reproduces jet-based observables.Comment: 26 pages, 13 figure

Local Causal States and Discrete Coherent Structures

Coherent structures form spontaneously in nonlinear spatiotemporal systems and are found at all spatial scales in natural phenomena from laboratory hydrodynamic flows and chemical reactions to ocean, atmosphere, and planetary climate dynamics. Phenomenologically, they appear as key components that organize the macroscopic behaviors in such systems. Despite a century of effort, they have eluded rigorous analysis and empirical prediction, with progress being made only recently. As a step in this, we present a formal theory of coherent structures in fully-discrete dynamical field theories. It builds on the notion of structure introduced by computational mechanics, generalizing it to a local spatiotemporal setting. The analysis' main tool employs the \localstates, which are used to uncover a system's hidden spatiotemporal symmetries and which identify coherent structures as spatially-localized deviations from those symmetries. The approach is behavior-driven in the sense that it does not rely on directly analyzing spatiotemporal equations of motion, rather it considers only the spatiotemporal fields a system generates. As such, it offers an unsupervised approach to discover and describe coherent structures. We illustrate the approach by analyzing coherent structures generated by elementary cellular automata, comparing the results with an earlier, dynamic-invariant-set approach that decomposes fields into domains, particles, and particle interactions.Comment: 27 pages, 10 figures; http://csc.ucdavis.edu/~cmg/compmech/pubs/dcs.ht

Generative Design in Minecraft (GDMC), Settlement Generation Competition

This paper introduces the settlement generation competition for Minecraft, the first part of the Generative Design in Minecraft challenge. The settlement generation competition is about creating Artificial Intelligence (AI) agents that can produce functional, aesthetically appealing and believable settlements adapted to a given Minecraft map - ideally at a level that can compete with human created designs. The aim of the competition is to advance procedural content generation for games, especially in overcoming the challenges of adaptive and holistic PCG. The paper introduces the technical details of the challenge, but mostly focuses on what challenges this competition provides and why they are scientifically relevant.Comment: 10 pages, 5 figures, Part of the Foundations of Digital Games 2018 proceedings, as part of the workshop on Procedural Content Generatio

A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

The Differential Scheme and Quantum Computation

It is well-known that standard models of computation are representable as simple dynamical systems that evolve in discrete time, and that systems that evolve in continuous time are often representable by dynamical systems governed by ordinary differential equations. In many applications, e.g., molecular networks and hybrid Fermi-Pasta-Ulam systems, one must work with dynamical systems comprising both discrete and continuous components. Reasoning about and verifying the properties of the evolving state of such systems is currently a piecemeal affair that depends on the nature of major components of a system: e.g., discrete vs. continuous components of state, discrete vs. continuous time, local vs. distributed clocks, classical vs. quantum states and state evolution. We present the Differential Scheme as a unifying framework for reasoning about and verifying the properties of the evolving state of a system, whether the system in question evolves in discrete time, as for standard models of computation, or continuous time, or a combination of both. We show how instances of the differential scheme can accommodate classical computation. We also generalize a relatively new model of quantum computation, the quantum cellular automaton, with an eye towards extending the differential scheme to accommodate quantum computation and hybrid classical/quantum computation. All the components of a specific instance of the differential scheme are Convergence Spaces. Convergence spaces generalize notions of continuity and convergence. The category of convergence spaces, Conv, subsumes both simple discrete structures (e.g., digraphs), and complex continuous structures (e.g., topological spaces, domains, and the standard fields of analysis: R and C). We present novel uses for convergence spaces, and extend their theory by defining differential calculi on Conv. It is to the use of convergence spaces that the differential scheme owes its generality and flexibility

Cellular Automata and Randomization: A Structural Overview

The chapter overviews the methods, algorithms, and architectures for random number generators based on cellular automata, as presented in the scientific literature. The variations in linear and two-dimensional cellular automata model and their features are discussed in relation to their applications as randomizers. Additional memory layers, functional nonuniformity in space or time, and global feedback are examples of such variations. Successful applications of cellular automata random number/signal generators (both software and hardware) reported in the scientific literature are also reviewed. The chapter includes an introductory presentation of the mathematical (ideal) model of cellular automata and its implementation as a computing model, emphasizing some important theoretical debates regarding the complexity and universality of cellular automata