Free De Morgan Bisemigroups and Bisemilattices

We give a geometric representation of free De Morgan bisemigroups, free commutative De Morgan bisemigroups and free De Morgan bisemilattices, using labeled graphs

2-Nested Simulation is not Finitely Equationally Axiomatizable

2-nested simulation was introduced by Groote and Vaandrager [10] as the coarsest equivalence included in completed trace equivalence for which the tyft/tyxt format is a congruence format. In the lineartime-branching time spectrum of van Glabbeek [8], 2-nested simulationis one of the few equivalences for which no finite equational axiomatization is presented. In this paper we prove that such an axiomatizationdoes not exist for 2-nested simulation.Keywords: Concurrency, process algebra, basic CCS, 2-nested simulation, equational logic, complete axiomatizations

A Presheaf Semantics of Value-Passing Processes

This paper investigates presheaf models for process calculi withvalue passing. Denotational semantics in presheaf models are shownto correspond to operational semantics in that bisimulation obtainedfrom open maps is proved to coincide with bisimulation as definedtraditionally from the operational semantics. Both "early" and "late"semantics are considered, though the more interesting "late" semanticsis emphasised. A presheaf model and denotational semantics is proposedfor a language allowing process passing, though there remainsthe problem of relating the notion of bisimulation obtained from openmaps to a more traditional definition from the operational semantics.A tentative beginning is made of a "domain theory" supportingpresheaf models

Comparative Methods for Gene Structure Prediction in Homologous Sequences

The increasing number of sequenced genomes motivates the use of evolutionary patterns to detect genes. We present a series of comparative methods for gene finding in homologous prokaryotic or eukaryotic sequences. Based on a model of legal genes and a similarity measure between genes, we find the pair of legal genes of maximum similarity. We develop methods based on genes models and alignment based similarity measures of increasing complexity, which take into account many details of real gene structures, e.g. the similarity of the proteins encoded by the exons. When using a similarity measure based on an exiting alignment, the methods run in linear time. When integrating the alignment and prediction process which allows for more fine grained similarity measures, the methods run in quadratic time. We evaluate the methods in a series of experiments on synthetic and real sequence data, which show that all methods are competitive but that taking the similarity of the encoded proteins into account really boost the performance

A Presheaf Semantics of Value-Passing Processes

This paper investigates presheaf models for process calculi withvalue passing. Denotational semantics in presheaf models are shownto correspond to operational semantics in that bisimulation obtainedfrom open maps is proved to coincide with bisimulation as definedtraditionally from the operational semantics. Both "early" and "late"semantics are considered, though the more interesting "late" semanticsis emphasised. A presheaf model and denotational semantics is proposedfor a language allowing process passing, though there remainsthe problem of relating the notion of bisimulation obtained from openmaps to a more traditional definition from the operational semantics.A tentative beginning is made of a "domain theory" supportingpresheaf models

Theory and Practice of Action Semantics

Action Semantics is a framework for the formal descriptionof programming languages. Its main advantage over other frameworksis pragmatic: action-semantic descriptions (ASDs) scale up smoothly torealistic programming languages. This is due to the inherent extensibilityand modifiability of ASDs, ensuring that extensions and changes tothe described language require only proportionate changes in its description.(In denotational or operational semantics, adding an unforeseenconstruct to a language may require a reformulation of the entire description.)After sketching the background for the development of action semantics,we summarize the main ideas of the framework, and provide a simpleillustrative example of an ASD. We identify which features of ASDsare crucial for good pragmatics. Then we explain the foundations ofaction semantics, and survey recent advances in its theory and practicalapplications. Finally, we assess the prospects for further developmentand use of action semantics.The action semantics framework was initially developed at the Universityof Aarhus by the present author, in collaboration with David Watt(University of Glasgow). Groups and individuals scattered around fivecontinents have since contributed to its theory and practice

Nested Semantics over Finite Trees are Equationally Hard

This paper studies nested simulation and nested trace semantics over the language BCCSP, a basic formalism to express finite process behaviour. It is shown that none of these semantics affords finite (in)equational axiomatizations over BCCSP. In particular, for each of the nested semantics studied in this paper, the collection of sound, closed (in)equations over a singleton action set is not finitely based

Introduction to the Literature on Semantics

An introduction to the literature on semantics. Included are pointers to the literature on axiomatic semantics, denotational semantics, operational semantics, and type theory

A Categorical View on Algebraic Lattices in Formal Concept Analysis

Formal concept analysis has grown from a new branch of the mathematical field of lattice theory to a widely recognized tool in Computer Science and elsewhere. In order to fully benefit from this theory, we believe that it can be enriched with notions such as approximation by computation or representability. The latter are commonly studied in denotational semantics and domain theory and captured most prominently by the notion of algebraicity, e.g. of lattices. In this paper, we explore the notion of algebraicity in formal concept analysis from a category-theoretical perspective. To this end, we build on the the notion of approximable concept with a suitable category and show that the latter is equivalent to the category of algebraic lattices. At the same time, the paper provides a relatively comprehensive account of the representation theory of algebraic lattices in the framework of Stone duality, relating well-known structures such as Scott information systems with further formalisms from logic, topology, domains and lattice theory.Comment: 36 page

Abstract Constraint Data Types

Martin Wirsing is one of the earliest contributors to the area of Algebraic Specification (e.g., [2]), which he explored in a variety of domains over many years. Throughout his career, he has also inspired countless researchers in related areas. This paper is inspired by one of the domains that he explored thirty years or so after his first contributions when leading the FET Integrated Project SENSORIA [14]: the use of constraint systems to deal with non-functional requirements and preferences [13,8]. Following in his footsteps, we provide an extension of the traditional notion of algebraic data type specification to encompass soft-constraints as formalised in [1]. Finally, we relate this extension with institutions [6] and recent work on graded consequence in institutions [3].Peer ReviewedPostprint (author’s final draft