An Introduction to String Diagrams for Computer Scientists

This document is an elementary introduction to string diagrams. It takes a computer science perspective: rather than using category theory as a starting point, we build on intuitions from formal language theory, treating string diagrams as a syntax with its semantics. After the basic theory, pointers are provided to contemporary applications of string diagrams in various fields of science

Concepts and analogies in cybernetics: Mathematical investigations of the role of analogy in concept formation and problem solving; with emphasis for conflict resolution via object and morphism eliminations

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.We address two problematic areas of cybernetics; nam. Analogical Problem Solving (APS) and Analogical Learning (AL). Both these human faculties do unquestionably require Intelligence. In addition, we point out that shifting of representations is the main unified theme underlying these two intellectual tasks. We focus our attention on the formulation and clarification of the notion of analogy, which has been loosely treated and used in the literature; and also on its role in shifting of representations. We describe analogizing situations in a new representational scheme, borrowed from mathematics and modified and extended to cater for our targets. We call it k-structure, closely resembling semantic networks and directed graphs; the main components of it are the so-called objects and morphisms. We argue and substantiate the need for such a representation scheme, by analysing what its constituents stand for and by cataloguing its virtues, the main one being its visual appeal and its mathematical clarity, and by listing its disadvantages when it is compared to other representation systems. Emphasis is also given to its descriptive power and usefulness by implementing it in a number of APS and AL situations. Besides representation issues, attention is paid to intelligence mechanisms which are involved in APS and AL. A cornerstone in APS and a fundamental theme in AL is the 'skeletization of k-structures'. APS is conceived as 'harmonization of skeletons'. The methodology we develop involves techniques which are computer implemented and extensively studied in theoretic terms via a proposed theory for extended k-structures. To name but a few: 1. 'the separation of the context of a concept from the concept itself', based on the ideas of k-opens and k-spaces; 2, 'object and morphism elimination' of a controversial nature; and 3. 'conflict or deadlock or dilemma resolution' which naturally arises in a k-structure interaction. The overall system, is then applied to capture the essence of EVANS' (1963) analogy-type problems and WINSTOM (1970) learning-type situations. In our attempt not to be too informal, we use basic notions and terminology from abstract Algebra, Topology and Category theory. We rather tend to be "non-logical" (analogical) in EVANS' and WINSTON's sense; "non-numeric", in MESAROVIC (1970) terms (we rather deal with abstract conceptual entities); "non-linguistic" (we do not touch natural language); and "non-resolution" oriented, in the sense of BLEDSOE (1977). However, we give hints sometimes about logical deductive axiomatic systems, employing First Order Predicate Calculus (FOPC); and about semiotics, by which we denote syntactic-semantic-pragmatic features of our system and issues of the problem domains it is acting upon. We believe in what we call: shift from the traditional 'Heuristic search paradigm' era to the 'Analogy-paradigm' era underlying Artificial Intelligence and Cybernetics. We justify this merely by listing a number of A. I. works, which employ, in some way or another, the concept of analogy, over the last fifteen years or so, where a noticeable peak is obvious during the last years and especially in 1977. Finally, we hope that if the proposed conceptual framework and techniques developed do not straightforwardly constitute some kind of platform for Artificial Intelligence, at least it would give some insights into and illuminate our understanding of the two most fundamental faculties the human brain is occupied with; namely problem solving and learning

Proof Support for Common Logic

We present an extension of the Heterogeneous Tool Set HETS that enables proof support for Common Logic. This is achieved via logic translations that relate Common Logic and some of its sublogics to already supported logics and automated theorem proving systems. We thus provide the first full theorem proving support for Common Logic, including the possibility of verifying meta-theoretical relationships between Common Logic theories

Matrix Graph Grammars

This book objective is to develop an algebraization of graph grammars. Equivalently, we study graph dynamics. From the point of view of a computer scientist, graph grammars are a natural generalization of Chomsky grammars for which a purely algebraic approach does not exist up to now. A Chomsky (or string) grammar is, roughly speaking, a precise description of a formal language (which in essence is a set of strings). On a more discrete mathematical style, it can be said that graph grammars -- Matrix Graph Grammars in particular -- study dynamics of graphs. Ideally, this algebraization would enforce our understanding of grammars in general, providing new analysis techniques and generalizations of concepts, problems and results known so far.Comment: 321 pages, 75 figures. This book has is publisehd by VDM verlag, ISBN 978-363921255

Non-commutative fermion mass matrix and gravity

The first part is an introductory description of a small cross-section of the literature on algebraic methods in non-perturbative quantum gravity with a specific focus on viewing algebra as a laboratory in which to deepen understanding of the nature of geometry. This helps to set the context for the second part, in which we describe a new algebraic characterisation of the Dirac operator in non-commutative geometry and then use it in a calculation on the form of the fermion mass matrix. Assimilating and building on the various ideas described in the first part, the final part consists of an outline of a speculative perspective on (non-commutative) quantum spectral gravity. This is the second of a pair of papers so far on this project.Comment: To appear in Int. J. Mod. Phys. A Previous title: An outlook on quantum gravity from an algebraic perspective. 39 pages, 1 xy-pic figure, LaTex Reasons for new version: added references, change of title and some comments more up-to-dat

Analysis of Generative Chemistries

For the modelling of chemistry we use undirected, labelled graphs as explicit models of molecules and graph transformation rules for modelling generalised chemical reactions. This is used to define artificial chemistries on the level of individual bonds and atoms, where formal graph grammars implicitly represent large spaces of chemical compounds. We use a graph rewriting formalism, rooted in category theory, called the Double Pushout approach, which directly expresses the transition state of chemical reactions. Using concurrency theory for transformation rules, we define algorithms for the composition of rewrite rules in a chemically intuitive manner that enable automatic abstraction of the level of detail in chemical pathways. Based on this rule composition we define an algorithmic framework for generation of vast reaction networks for specific spaces of a given chemistry, while still maintaining the level of detail of the model down to the atomic level. The framework also allows for computation with graphs and graph grammars, which is utilised to model non-trivial chemical systems. The graph generation relies on graph isomorphism testing, and we review the general individualisation-refinement paradigm used in the state-of-the-art algorithms for graph canonicalisation, isomorphism testing, and automorphism discovery. We present a model for chemical pathways based on a generalisation of network flows from ordinary directed graphs to directed hypergraphs. The model allows for reasoning about the flow of individual molecules in general pathways, and the introduction of chemically motivated routing constraints. It further provides the foundation for defining specialised pathway motifs, which is illustrated by defining necessary topological constraints for both catalytic and autocatalytic pathways. We also prove that central types of pathway questions are NP-complete, even for restricted classes of reaction networks. The complete pathway model, including constraints for catalytic and autocatalytic pathways, is implemented using integer linear programming. This implementation is used in a tree search method to enumerate both optimal and near-optimal pathway solutions. The formal methods are applied to multiple chemical systems: the enzyme catalysed beta-lactamase reaction, variations of the glycolysis pathway, and the formose process. In each of these systems we use rule composition to abstract pathways and calculate traces for isotope labelled carbon atoms. The pathway model is used to automatically enumerate alternative non-oxidative glycolysis pathways, and enumerate thousands of candidates for autocatalytic pathways in the formose process

Graph-based software specification and verification

The (in)correct functioning of many software systems heavily influences how\ud we qualify our daily lives. Software companies as well as academic computer\ud science research groups spend much effort on applying and developing techniques for improving the correctness of software systems. In this dissertation\ud we focus on using and developing graph-based techniques to specify and verify\ud the behaviour of software systems in general, and object-oriented systems more\ud specifically. We elaborate on two ways to improve the correctness (and thereby\ud the quality) of such systems.\ud Firstly, we investigate the potential of using the graph transformation tech-\ud nique to formally specify the dynamic semantics of (object-oriented) program-\ud ming languages. Those semantics are typically specified in natural language.\ud Such specifications are often hard to understand or even ambiguous. We show\ud how the graph transformation framework provides formal and intuitive means\ud for their specification.\ud Secondly, we develop techniques to verify systems of which the behaviour is\ud specified as graph production systems. For the verification of such systems, we\ud introduce an algorithm that combines a well-known on-the-\ud y model checking\ud algorithm with ideas from bounded model checking. One of the main prob-\ud lems of model checking is the state-explosion problem. This problem is often\ud tackled using partial order reduction techniques. Unfortunately, many such\ud techniques are based on assumptions that do not hold for graph production sys-\ud tems. Therefore, we develop a new dynamic partial order reduction algorithm\ud based on selecting so-called probe sets and prove its correctness.\ud Most of the techniques developed in this dissertation have been implemented\ud in the graph transformation tool GROOVE

Sustainability of systems interoperability in dynamic business networks

Dissertação para obtenção do Grau de Doutor em Engenharia Electrotécnica e de ComputadoresCollaborative networked environments emerged with the spread of the internet, contributing to overcome past communication barriers, and identifying interoperability as an essential property to support businesses development. When achieved seamlessly, efficiency is increased in the entire product life cycle support. However, due to the different sources of knowledge, models and semantics, enterprise organisations are experiencing difficulties exchanging critical information, even when they operate in the same business environments. To solve this issue, most of them try to attain interoperability by establishing peer-to-peer mappings with different business partners, or use neutral data and product standards as the core for information sharing, in optimized networks. In current industrial practice, the model mappings that regulate enterprise communications are only defined once, and most of them are hardcoded in the information systems. This solution has been effective and sufficient for static environments, where enterprise and product models are valid for decades. However, more and more enterprise systems are becoming dynamic, adapting and looking forward to meet further requirements; a trend that is causing new interoperability disturbances and efficiency reduction on existing partnerships. Enterprise Interoperability (EI) is a well established area of applied research, studying these problems, and proposing novel approaches and solutions. This PhD work contributes to that research considering enterprises as complex and adaptive systems, swayed to factors that are making interoperability difficult to sustain over time. The analysis of complexity as a neighbouring scientific domain, in which features of interoperability can be identified and evaluated as a benchmark for developing a new foundation of EI, is here proposed. This approach envisages at drawing concepts from complexity science to analyse dynamic enterprise networks and proposes a framework for sustaining systems interoperability, enabling different organisations to evolve at their own pace, answering the upcoming requirements but minimizing the negative impact these changes can have on their business environment