Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov–Zhabotinsky reaction

Interaction computing (IC) aims to map the properties of integrable low-dimensional non-linear dynamical systems to the discrete domain of finite-state automata in an attempt to reproduce in software the self-organizing and dynamically stable properties of sub-cellular biochemical systems. As the work reported in this paper is still at the early stages of theory development it focuses on the analysis of a particularly simple chemical oscillator, the Belousov-Zhabotinsky (BZ) reaction. After retracing the rationale for IC developed over the past several years from the physical, biological, mathematical, and computer science points of view, the paper presents an elementary discussion of the Krohn-Rhodes decomposition of finite-state automata, including the holonomy decomposition of a simple automaton, and of its interpretation as an abstract positional number system. The method is then applied to the analysis of the algebraic properties of discrete finite-state automata derived from a simplified Petri net model of the BZ reaction. In the simplest possible and symmetrical case the corresponding automaton is, not surprisingly, found to contain exclusively cyclic groups. In a second, asymmetrical case, the decomposition is much more complex and includes five different simple non-abelian groups whose potential relevance arises from their ability to encode functionally complete algebras. The possible computational relevance of these findings is discussed and possible conclusions are drawn

Chasing diagrams in cryptography

Cryptography is a theory of secret functions. Category theory is a general theory of functions. Cryptography has reached a stage where its structures often take several pages to define, and its formulas sometimes run from page to page. Category theory has some complicated definitions as well, but one of its specialties is taming the flood of structure. Cryptography seems to be in need of high level methods, whereas category theory always needs concrete applications. So why is there no categorical cryptography? One reason may be that the foundations of modern cryptography are built from probabilistic polynomial-time Turing machines, and category theory does not have a good handle on such things. On the other hand, such foundational problems might be the very reason why cryptographic constructions often resemble low level machine programming. I present some preliminary explorations towards categorical cryptography. It turns out that some of the main security concepts are easily characterized through the categorical technique of *diagram chasing*, which was first used Lambek's seminal `Lecture Notes on Rings and Modules'.Comment: 17 pages, 4 figures; to appear in: 'Categories in Logic, Language and Physics. Festschrift on the occasion of Jim Lambek's 90th birthday', Claudia Casadio, Bob Coecke, Michael Moortgat, and Philip Scott (editors); this version: fixed typos found by kind reader

Calibrating Generative Models: The Probabilistic Chomsky-Schützenberger Hierarchy

A probabilistic Chomsky–Schützenberger hierarchy of grammars is introduced and studied, with the aim of understanding the expressive power of generative models. We offer characterizations of the distributions definable at each level of the hierarchy, including probabilistic regular, context-free, (linear) indexed, context-sensitive, and unrestricted grammars, each corresponding to familiar probabilistic machine classes. Special attention is given to distributions on (unary notations for) positive integers. Unlike in the classical case where the "semi-linear" languages all collapse into the regular languages, using analytic tools adapted from the classical setting we show there is no collapse in the probabilistic hierarchy: more distributions become definable at each level. We also address related issues such as closure under probabilistic conditioning

How the Dimension of Space Affects the Products of Pre-Biotic Evolution: The Spatial Population Dynamics of Structural Complexity and The Emergence of Membranes

We show that autocatalytic networks of epsilon-machines and their population dynamics differ substantially between spatial (geographically distributed) and nonspatial (panmixia) populations. Generally, regions of spacetime-invariant autocatalytic networks---or domains---emerge in geographically distributed populations. These are separated by functional membranes of complementary epsilon-machines that actively translate between the domains and are responsible for their growth and stability. We analyze both spatial and nonspatial populations, determining the algebraic properties of the autocatalytic networks that allow for space to affect the dynamics and so generate autocatalytic domains and membranes. In addition, we analyze populations of intermediate spatial architecture, delineating the thresholds at which spatial memory (information storage) begins to determine the character of the emergent auto-catalytic organization.Comment: 9 pages, 7 figures, 2 tables; http://cse.ucdavis.edu/~cmg/compmech/pubs/ss.ht

Equations of States in Statistical Learning for a Nonparametrizable and Regular Case

Many learning machines that have hierarchical structure or hidden variables are now being used in information science, artificial intelligence, and bioinformatics. However, several learning machines used in such fields are not regular but singular statistical models, hence their generalization performance is still left unknown. To overcome these problems, in the previous papers, we proved new equations in statistical learning, by which we can estimate the Bayes generalization loss from the Bayes training loss and the functional variance, on the condition that the true distribution is a singularity contained in a learning machine. In this paper, we prove that the same equations hold even if a true distribution is not contained in a parametric model. Also we prove that, the proposed equations in a regular case are asymptotically equivalent to the Takeuchi information criterion. Therefore, the proposed equations are always applicable without any condition on the unknown true distribution

Spectral Simplicity of Apparent Complexity, Part I: The Nondiagonalizable Metadynamics of Prediction

Virtually all questions that one can ask about the behavioral and structural complexity of a stochastic process reduce to a linear algebraic framing of a time evolution governed by an appropriate hidden-Markov process generator. Each type of question---correlation, predictability, predictive cost, observer synchronization, and the like---induces a distinct generator class. Answers are then functions of the class-appropriate transition dynamic. Unfortunately, these dynamics are generically nonnormal, nondiagonalizable, singular, and so on. Tractably analyzing these dynamics relies on adapting the recently introduced meromorphic functional calculus, which specifies the spectral decomposition of functions of nondiagonalizable linear operators, even when the function poles and zeros coincide with the operator's spectrum. Along the way, we establish special properties of the projection operators that demonstrate how they capture the organization of subprocesses within a complex system. Circumventing the spurious infinities of alternative calculi, this leads in the sequel, Part II, to the first closed-form expressions for complexity measures, couched either in terms of the Drazin inverse (negative-one power of a singular operator) or the eigenvalues and projection operators of the appropriate transition dynamic.Comment: 24 pages, 3 figures, 4 tables; current version always at http://csc.ucdavis.edu/~cmg/compmech/pubs/sdscpt1.ht