Differential Hoare Logics and Refinement Calculi for Hybrid Systems with Isabelle/HOL

We present simple new Hoare logics and refinement calculi for hybrid systems in the style of differential dynamic logic. (Refinement) Kleene algebra with tests is used for reasoning about the program structure and generating verification conditions at this level. Lenses capture hybrid program stores in a generic algebraic way. The approach has been formalised with the Isabelle/HOL proof assistant. A number of examples explains the workflow with the resulting verification components

Towards a quantitative alloy

Dissertação de mestrado integrado em Engenharia InformáticaWhen one comes across a new problem that needs to be solved, by abstracting from its associated details in a simple and concise way through the use of formal methods, one is able to better understand the matter at hand. Alloy (Jackson, 2012), a declarative specification language based on relational logic, is an example of an effective modelling tool, allowing high-level specification of potentially very complex systems. However, along with the irrelevant information, measurable data of the system is often lost in the abstraction as well, making it not as adequate for certain situations. The Alloy Analyzer represents the relations under analysis by Boolean matrices. By extending this type of structure to: • numeric matrices, over N0 , one is able to work with multirelations, i.e. relations whose arcs are weighted; each tuple is thus associated with a natural number, which allows reasoning in a similar fashion as in optimization problems and integer programming techniques; • left-Stochastic matrices, one is able to model faulty behaviour and other forms of quantitative information about software systems in a probabilistic way; in particular, this introduces the notion of a probabilistic contract in software design. Such an increase in Alloy’s capabilities strengthens its position in the area of formal methods for software design, in particular towards becoming a quantitative formal method. This dissertation explores the motivation and importance behind quantitative analysis by studying and establishing theoretical foundations through categorial approaches to accomplish such reasoning in Alloy. This starts by reviewing the required tools to support such groundwork and proceeds to the design and implementation of such a quantitative Alloy extension. This project aims to promote the evolution of quantitative formal methods by successfully achieving quantitative abstractions in Alloy, extending its support to these concepts and implementing them in the Alloy Analyzer.Quando se depara com um novo problema que precisa de ser resolvido, ao abstrair dos seus detalhes associados de forma simples e concisa recorrendo a métodos formais, é possível compreender melhor o assunto em questão. Alloy (Jackson, 2012), uma linguagem de especificação declarativa baseada em lógica relacional, é um exemplo de uma ferramenta de modelação eficaz, possibilitando especificações de alto-nível de sistemas potencialmente bastante complexos. Contudo, em conjunto com a informação irrelevante, os dados mensuráveis são muitas vezes também perdidos na abstração, tornando-a não tão adequada para certas situações. O Alloy Analyzer representa as relações sujeitas a análise através de matrizes Booleanas. Ao estender este tipo de estrutura para: • matrizes numéricas, em N0 , é possível lidar com multirelações, i.e., relações cujos arcos são pesados; cada tuplo é consequentemente associado a um número natural, o que proporciona uma linha de raciocínio semelhante à de técnicas de problemas de otimização e de programação inteira; • matrizes estocásticas, permitindo a modelação de comportamento defeituoso e de outros tipos de informação quantitativa de sistemas de software probabilisticamente; em particular, é introduzida a noção de contrato probabilístico em design de software. Tal aumento às capacidades do Alloy, fortalece a sua posição na área de métodos formais para design de software, em particular, a caminho de se tornar um método formal quantitativo. Esta dissertação explora a motivação e a importância subjacente à análise quantitativa, a partir do estudo e consolidação dos fundamentos teóricos através de abordagens categóricas de forma a conseguir suportar esse tipo de raciocínio em Alloy. Inicialmente, as ferramentas imprescindíveis para assegurar tal base são analisadas, passando de seguida ao planeamento e posterior implementação de tal extensão quantitativa do Alloy. Este projecto pretende promover a evolução dos métodos formais quantitativos através da concretização de abstracção quantitativa em Alloy, estendendo a sua base para suportar estes conceitos e assim implementá los no Alloy Analyzer

Convolution algebras: Relational convolution, generalised modalities and incidence algebras

Convolution is a ubiquitous operation in mathematics and computing. The Kripke semantics for substructural and interval logics motivates its study for quantale-valued functions relative to ternary relations. The resulting notion of relational convolution leads to generalised binary and unary modal operators for qualitative and quantitative models, and to more conventional variants, when ternary relations arise from identities over partial semigroups. Convolution-based semantics for fragments of categorial, linear and incidence (segment or interval) logics are provided as qualitative applications. Quantitative examples include algebras of durations and mean values in the duration calculus

Exploration of Chemical Space: Formal, chemical and historical aspects

Starting from the observation that substances and reactions are the central entities of chemistry, I have structured chemical knowledge into a formal space called a directed hypergraph, which arises when substances are connected by their reactions. I call this hypernet chemical space. In this thesis, I explore different levels of description of this space: its evolution over time, its curvature, and categorical models of its compositionality. The vast majority of the chemical literature focuses on investigations of particular aspects of some substances or reactions, which have been systematically recorded in comprehensive databases such as Reaxys for the last 200 years. While complexity science has made important advances in physics, biology, economics, and many other fields, it has somewhat neglected chemistry. In this work, I propose to take a global view of chemistry and to combine complexity science tools, modern data analysis techniques, and geometric and compositional theories to explore chemical space. This provides a novel view of chemistry, its history, and its current status. We argue that a large directed hypergraph, that is, a model of directed relations between sets, underlies chemical space and that a systematic study of this structure is a major challenge for chemistry. Using the Reaxys database as a proxy for chemical space, we search for large-scale changes in a directed hypergraph model of chemical knowledge and present a data-driven approach to navigate through its history and evolution. These investigations focus on the mechanistic features by which this space has been expanding: the role of synthesis and extraction in the production of new substances, patterns in the selection of starting materials, and the frequency with which reactions reach new regions of chemical space. Large-scale patterns that emerged in the last two centuries of chemical history are detected, in particular, in the growth of chemical knowledge, the use of reagents, and the synthesis of products, which reveal both conservatism and sharp transitions in the exploration of the space. Furthermore, since chemical similarity of substances arises from affinity patterns in chemical reactions, we quantify the impact of changes in the diversity of the space on the formulation of the system of chemical elements. In addition, we develop formal tools to probe the local geometry of the resulting directed hypergraph and introduce the Forman-Ricci curvature for directed and undirected hypergraphs. This notion of curvature is characterized by applying it to social and chemical networks with higher order interactions, and then used for the investigation of the structure and dynamics of chemical space. The network model of chemistry is strongly motivated by the observation that the compositional nature of chemical reactions must be captured in order to build a model of chemical reasoning. A step forward towards categorical chemistry, that is, a formalization of all the flavors of compositionality in chemistry, is taken by the construction of a categorical model of directed hypergraphs. We lifted the structure from a lineale (a poset version of a symmetric monoidal closed category) to a category of Petri nets, whose wiring is a bipartite directed graph equivalent to a directed hypergraph. The resulting construction, based on the Dialectica categories introduced by Valeria De Paiva, is a symmetric monoidal closed category with finite products and coproducts, which provides a formal way of composing smaller networks into larger in such a way that the algebraic properties of the components are preserved in the resulting network. Several sets of labels, often used in empirical data modeling, can be given the structure of a lineale, including: stoichiometric coefficients in chemical reaction networks, reaction rates, inhibitor arcs, Boolean interactions, unknown or incomplete data, and probabilities. Therefore, a wide range of empirical data types for chemical substances and reactions can be included in our model

Proceedings of the 1st International Conference on Algebras, Graphs and Ordered Sets (ALGOS 2020)

International audienceOriginating in arithmetics and logic, the theory of ordered sets is now a field of combinatorics that is intimately linked to graph theory, universal algebra and multiple-valued logic, and that has a wide range of classical applications such as formal calculus, classification, decision aid and social choice.This international conference “Algebras, graphs and ordered set” (ALGOS) brings together specialists in the theory of graphs, relational structures and ordered sets, topics that are omnipresent in artificial intelligence and in knowledge discovery, and with concrete applications in biomedical sciences, security, social networks and e-learning systems. One of the goals of this event is to provide a common ground for mathematicians and computer scientists to meet, to present their latest results, and to discuss original applications in related scientific fields. On this basis, we hope for fruitful exchanges that can motivate multidisciplinary projects.The first edition of ALgebras, Graphs and Ordered Sets (ALGOS 2020) has a particular motivation, namely, an opportunity to honour Maurice Pouzet on his 75th birthday! For this reason, we have particularly welcomed submissions in areas related to Maurice’s many scientific interests:• Lattices and ordered sets• Combinatorics and graph theory• Set theory and theory of relations• Universal algebra and multiple valued logic• Applications: formal calculus, knowledge discovery, biomedical sciences, decision aid and social choice, security, social networks, web semantics..

A Category Theoretical Approach to the Concurrent Semantics of Rewriting: Adhesive Categories and Related Concepts

This thesis studies formal semantics for a family of rewriting formalisms that have arisen as category theoretical abstractions of the so-called algebraic approaches to graph rewriting. The latter in turn generalize and combine features of term rewriting and Petri nets. Two salient features of (the abstract versions of) graph rewriting are a suitable class of categories which captures the structure of the objects of rewriting, and a notion of independence or concurrency of rewriting steps – as in the theory of Petri nets. Category theoretical abstractions of graph rewriting such as double pushout rewriting encapsulate the complex details of the structures that are to be rewritten by considering them as objects of a suitable abstract category, for example an adhesive one. The main difficulty of the development of appropriate categorical frameworks is the identification of the essential properties of the category of graphs which allow to develop the theory of graph rewriting in an abstract framework. The motivations for such an endeavor are twofold: to arrive at a succint description of the fundamental principles of rewriting systems in general, and to apply well-established verification and analysis techniques of the theory of Petri nets (and also term rewriting systems) to a wide range of distributed and concurrent systems in which states have a "graph-like" structure. The contributions of this thesis thus can be considered as two sides of the same coin: on the one side, concepts and results for Petri nets (and graph grammars) are generalized to an abstract category theoretical setting; on the other side, suitable classes of "graph-like" categories which capture the essential properties of the category of graphs are identified. Two central results are the following: first, (concatenable) processes are faithful partial order representations of equivalence classes of system runs which only differ w.r.t. the rescheduling of causally independent events; second, the unfolding of a system is established as the canonical partial order representation of all possible events (following the work of Winskel). Weakly ω-adhesive categories are introduced as the theoretical foundation for the corresponding formal theorems about processes and unfoldings. The main result states that an unfolding procedure for systems which are given as single pushout grammars in weakly ω-adhesive categories exists and can be characetrised as a right adjoint functor from a category of grammars to the subcategory of occurrence grammars. This result specializes to and improves upon existing results concerning the coreflective semantics of the unfolding of graph grammars and Petri nets (under an individual token interpretation). Moreover, the unfolding procedure is in principle usable as the starting point for static analysis techniques such as McMillan’s finite complete prefix method. Finally, the adequacy of weakly ω-adhesive categories as a categorical framework is argued for by providing a comparison with the notion of topos, which is a standard abstraction of the categories of sets (and graphs)