Commutative Languages and their Composition by Consensual Methods

Commutative languages with the semilinear property (SLIP) can be naturally recognized by real-time NLOG-SPACE multi-counter machines. We show that unions and concatenations of such languages can be similarly recognized, relying on -- and further developing, our recent results on the family of consensually regular (CREG) languages. A CREG language is defined by a regular language on the alphabet that includes the terminal alphabet and its marked copy. New conditions, for ensuring that the union or concatenation of CREG languages is closed, are presented and applied to the commutative SLIP languages. The paper contributes to the knowledge of the CREG family, and introduces novel techniques for language composition, based on arithmetic congruences that act as language signatures. Open problems are listed.Comment: In Proceedings AFL 2014, arXiv:1405.527

UML model refactoring as refinement: a coalgebraic perspective

Although increasingly popular, Model Driven Architecture (MDA) still lacks suitable formal foundations on top of which rigorous methodologies for the description, analysis and transformation of models could be built. This paper aims to contribute in this direction: building on previous work by the authors on coalgebraic refinement for software components and architectures, it discusses refactoring of models within a coalgebraic semantic framework. Architectures are defined through aggregation based on a coalgebraic semantics for (subsets of) UML. On the other hand, such aggregations, no matter how large and complex they are, can always be dealt with as coalgebras themselves. This paves the way to a discipline of models’ transformations which, being invariant under either behavioural equivalence or refinement, are able to formally capture a large number of refactoring patterns. The main ideas underlying this research are presented through a detailed example in the context of refactoring of UML class diagrams.The work reported in this paper is partially supported by a grant from the GLANCE funding program of NWO, through project CooPer (600.643.000.05N12)

OWA-based fuzzy m-ary adjacency relations in Social Network Analysis.

In this paper we propose an approach to Social Network Analysis (SNA) based on fuzzy m-ary adjacency relations. In particular, we show that the dimension of the analysis can naturally be increased and interesting results can be derived. Therefore, fuzzy m-ary adjacency relations can be computed starting from fuzzy binary relations and introducing OWA-based aggregations. The behavioral assumptions derived from the measure and the exam of individual propensity to connect with other suggest that OWA operators can be considered particularly suitable in characterizing such relationships.reciprocal relation; fuzzy preference relation; priority vector; normalization

The cultural epigenetics of psychopathology: The missing heritability of complex diseases found?

We extend a cognitive paradigm for gene expression based on the asymptotic limit theorems of information theory to the epigenetic epidemiology of mental disorders. In particular, we recognize the fundamental role culture plays in human biology, another heritage mechanism parallel to, and interacting with, the more familiar genetic and epigenetic systems. We do this via a model through which culture acts as another tunable epigenetic catalyst that both directs developmental trajectories, and becomes convoluted with individual ontology, via a mutually-interacting crosstalk mediated by a social interaction that is itself culturally driven. We call for the incorporation of embedding culture as an essential component of the epigenetic regulation of human mental development and its dysfunctions, bringing what is perhaps the central reality of human biology into the center of biological psychiatry. Current US work on gene-environment interactions in psychiatry must be extended to a model of gene-environment-culture interaction to avoid becoming victim of an extreme American individualism that threatens to create paradigms particular to that culture and that are, indeed, peculiar in the context of the world's cultures. The cultural and epigenetic systems of heritage may well provide the 'missing' heritability of complex diseases now under so much intense discussion

Transposing partial components: an exercise on coalgebraic refinement

A partial component is a process which fails or dies at some stage, thus exhibiting a finite, more ephemeral behaviour than expected (eg, operating system crash). Partiality --- which is the rule rather than exception in formal modelling --- can be treated mathematically via totalization techniques. In the case of partial functions, totalization involves error values and exceptions. In the context of a coalgebraic approach to component semantics, this paper argues that the behavioural counterpart to such functional techniques should extend behaviour with try-again cycles preventing from component collapse, thus extending totalization or transposition from the algebraic to the coalgebraic context. We show that a refinement relationship holds between original and totalized components which is reasoned about in a coalgebraic approach to component refinement expressed in the pointfree binary relation calculus. As part of the pragmatic aims of this research, we also address the factorization of every such totalized coalgebra into two coalgebraic components --- the original one and an added front-end --- which cooperate in a client-serverstyle.Fundação para a Ciência e a Tecnologia (FCT) - PURe Project under contract POSI/ICHS/44304/2002

A proposal for ontology formalization based on category theory

This work proposes a formalization of domain ontologies based in category theory as a framework for the study and representation of conceptual models. Category theory is a branch of mathematics that studies the structure in systems of composable relations. Domain ontologies are conceptual models that enable the reuse of domain knowledge and the execution of inferential processes over said knowledge. In order to achieve such goals, concepts must be modeled intensionally. The established set-theoretic foundations of current conceptual models are incompatible with the intended intensionality of ontological models. Category theory, on the other hand, does not default to extensionality in the same way set theory does, and offers, therefore, a better-suited mathematical foundation. Additionally, category theory’s focus on relations matches the primary attention of construction and representation of ontologies, which is turned towards the relations between the domain concepts. The present work builds upon these motivations and formalizes ontologies as categories of concepts and conceptual relations. We subsequently analyze the categorical constructions present in ontologies, and the consequences of this formalization for categories of ontologies.O presente trabalho propõe uma formalização de ontologias de domínio baseada em teoria das categorias como um arcabouço para o estudo e representação de modelos conceituais. A teoria das categorias é uma área da matemática que estuda a estrutura presente em sistemas de relações componíveis. Ontologias de domínio são modelos conceituais que permitem o reuso de conhecimento de domínio e a execução de processos de inferência sobre tal conhecimento. Para atingir tais objetivos, os conceitos devem ser modelados de forma intensional. As fundamentações dos modelos conceituais baseadas em teoria dos conjuntos atualmente aceitas são incompatíveis com a pretendida intensionalidade de modelos ontológicos. A teoria das categorias, por outro lado, não está comprometida com extensionalidade da mesma forma que a teoria dos conjuntos e, portanto, mostra-se uma fundamentação matemática mais adequada. Ainda, o fato de que a teoria das categorias tem seu foco principalmente em relações melhor se relaciona à atenção primária presente na construção e representação de ontologias, que é orientada às relações entre os conceitos do domínio. Este trabalho parte destas motivações e formaliza ontologias como categorias de conceitos e relações conceituais. Subsequentemente são analisadas as construções categoriais presentes em ontologias e as consequências desta formalização para categorias de ontologias

Improving programmability and performance for scientific applications

With modern advancements in hardware and software technology scaling towards new limits, our compute machines are reaching new potentials to tackle more challenging problems. While the size and complexity of both the problems and solutions increases, the programming methodologies must remain at a level that can be understood by programmers and scientists alike. In our work, this problem is encountered when developing an optimized framework to best exploit the semantic properties of a finite-element solver. In efforts to address this problem, we explore programming and runtime models which decouple algorithmic complexity, parallelism concerns, and hardware mapping. We build upon these frameworks to exploit domain-specific semantics using high-level transformations and modifications to obtain performance through algorithmic and runtime optimizations. We first discusses optimizations performed on a computational mechanics solver using a novel coupling technique for multi-time scale methods for discrete finite element domains. We exploit domain semantics using a high-level dynamic runtime scheme to reorder and balance workloads to greatly improve runtime performance. The framework presented automatically chooses a near-optimal coupling solution and runs a work-stealing parallel executor to run effectively on multi-core systems. In my latter work, I focus on the parallel programming model, Concurrent Collections (CnC), to seamlessly bridge the gap between performance and programmability. Because challenging problems in various domains, not limited to computation mechanics, requires both domain expertise and programming prowess, there is a need for ways to separate those concerns. This thesis describes methods and techniques to obtain scalable performance using CnC programming while limiting the burden of programming. These high level techniques are presented for two high-performance applications corresponding to hydrodynamics and multi-grid solvers