On the Completeness of Spider Diagrams Augmented with Constants

Diagrammatic reasoning can be described formally by a number of diagrammatic logics; spider diagrams are one of these, and are used for expressing logical statements about set membership and containment. Here, existing work on spider diagrams is extended to include constant spiders that represent specific individuals. We give a formal syntax and semantics for the extended diagram language before introducing a collection of reasoning rules encapsulating logical equivalence and logical consequence. We prove that the resulting logic is sound, complete and decidable

Visual Specification Patterns

Visual modelling notations such as constraint diagrams can be used for the behavioural specifications of software components. This includes specifying invariants on classes or types and preconditions and postconditions of operations. However, one current problem in specifying components comes from the fact that editing constraints manually is time consuming and error prone and so we may adopt a pattern-based approach to alleviate this problem. One way to simplify the definition of constraints is to identify and capture those recurring constraints in the form of visual specification patterns. Such patterns would facilitate the automatic generation of diagrammatic constraints. This paper identifies some specification patterns that frequently occur when specifying software components and provides a diagrammatic representation of these patterns. This will form the basis of a library of specification patterns that could be used in the context of tools. We also show how such patterns can be combined in order to specify more complex constraints

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology

<p>Abstract</p> <p>Background</p> <p>Bio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologies is a prior condition for diverse and efficient reasoning, and hence querying and hypothesis validation. Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training.</p> <p>Results</p> <p>Analogous to design patterns in software engineering, Ontology Design Patterns are solutions to typical modelling problems that bio-ontologists can use when building bio-ontologies. They offer a means of creating rich and rigorous bio-ontologies with reduced effort. The concept of Ontology Design Patterns is described and documentation and application methodologies for Ontology Design Patterns are presented. Some real-world use cases of Ontology Design Patterns are provided and tested in the Cell Cycle Ontology. Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented (<url>http://odps.sourceforge.net/</url>).</p> <p>Conclusions</p> <p>Ontology Design Patterns provide a method for rich and rigorous modelling in bio-ontologies. They also offer advantages at different development levels (such as design, implementation and communication) enabling, if used, a more modular, well-founded and richer representation of the biological knowledge. This representation will produce a more efficient knowledge management in the long term.</p

The Meaning of UML Models

The Unified Modelling Language (UML) is intended to express complex ideas in an intuitive and easily understood way. It is important because it is widely used in software engineering and other disciplines. Although an official definition document exists, there is much debate over the precise meaning of UML models. ¶ In response, the academic community have put forward many different proposals for formalising UML, but it is not at all obvious how to decide between them. Indeed, given that UML practitioners are inclined to reject formalisms as non-intuitive, it is not even obvious that the definition should be “formal” at all. Rather than searching for yet another formalisation of UML, our main aim is to determine what would constitute a good definition of UML. ¶ The first chapter sets the UML definition problem in a broad context, relating it to work in logic and the philosophy of science. ..

Analysis of Hardware Descriptions

The design process for integrated circuits requires a lot of analysis of circuit descriptions. An important class of analyses determines how easy it will be to determine if a physical component suffers from any manufacturing errors. As circuit complexities grow rapidly, the problem of testing circuits also becomes increasingly difficult. This thesis explores the potential for analysing a recent high level hardware description language called Ruby. In particular, we are interested in performing testability analyses of Ruby circuit descriptions. Ruby is ammenable to algebraic manipulation, so we have sought transformations that improve testability while preserving behaviour. The analysis of Ruby descriptions is performed by adapting a technique called abstract interpretation. This has been used successfully to analyse functional programs. This technique is most applicable where the analysis to be captured operates over structures isomorphic to the structure of the circuit. Many digital systems analysis tools require the circuit description to be given in some special form. This can lead to inconsistency between representations, and involves additional work converting between representations. We propose using the original description medium, in this case Ruby, for performing analyses. A related technique, called non-standard interpretation, is shown to be very useful for capturing many circuit analyses. An implementation of a system that performs non-standard interpretation forms the central part of the work. This allows Ruby descriptions to be analysed using alternative interpretations such test pattern generation and circuit layout interpretations. This system follows a similar approach to Boute's system semantics work and O'Donnell's work on Hydra. However, we have allowed a larger class of interpretations to be captured and offer a richer description language. The implementation presented here is constructed to allow a large degree of code sharing between different analyses. Several analyses have been implemented including simulation, test pattern generation and circuit layout. Non-standard interpretation provides a good framework for implementing these analyses. A general model for making non-standard interpretations is presented. Combining forms that combine two interpretations to produce a new interpretation are also introduced. This allows complex circuit analyses to be decomposed in a modular manner into smaller circuit analyses which can be built independently

Experimenting with computing

AbstractWe distinguish two kinds of experimental activity: post-theory and exploratory. Post-theory experiment enjoys computer support that is well-aligned to the classical theory of computation. Exploratory experiment, in contrast, arguably demands a broader conception of computing. Empirical Modelling (EM) is proposed as a more appropriate conceptual framework in which to provide computational support for exploratory experiment. In the process, it promises to provide integrated computational support for both exploratory and post-theory experiment. We first sketch the motivation for EM and illustrate its potential for supporting experimentation, then briefly highlight the semantic challenge it poses and the philosophical implications

Integrating knowledge about complex adaptive systems: insights from modelling the Eastern Baltic cod

Currently, the Eastern Baltic cod (EBC) is in continuing decline. Supporting management efforts to assist in its recovery will require a functional understanding of the dynamics of the EBC and the Baltic ecosystem. However, aquatic environments are challenging to research as they are elusive, encompass many scientific disciplines and are complex adaptive systems. This thesis explores how modelling and simulation methods can be applied and adapted to meet the specific needs of fisheries biologies’ current challenges regarding the EBC and potentially those of other stocks in similar situations.Aktuell verschlechtert sich der Zustand des Ostdorsches anhaltend und unterstützende Bewirtschaftungsmaßnahmen zu identifizieren erfordert ein funktionales Verständnis des Bestands und des Ökosystems Ostsee. Die Erforschung aquatischer Systeme ist jedoch schwierig: sie sind flüchtig, umfassen eine Vielzahl an Disziplinen und sind komplexe adaptiver Systeme. Diese Arbeit untersucht, wie Modellierungs- und Simulationsmethoden angewendet und angepasst werden können, um den Anforderungen der Fischereibiologie beim Ostdorsch und potentiell bei anderer Bestände in ähnlichen Situationen zu begegnen

Dwelling on ontology - semantic reasoning over topographic maps

The thesis builds upon the hypothesis that the spatial arrangement of topographic features, such as buildings, roads and other land cover parcels, indicates how land is used. The aim is to make this kind of high-level semantic information explicit within topographic data. There is an increasing need to share and use data for a wider range of purposes, and to make data more definitive, intelligent and accessible. Unfortunately, we still encounter a gap between low-level data representations and high-level concepts that typify human qualitative spatial reasoning. The thesis adopts an ontological approach to bridge this gap and to derive functional information by using standard reasoning mechanisms offered by logic-based knowledge representation formalisms. It formulates a framework for the processes involved in interpreting land use information from topographic maps. Land use is a high-level abstract concept, but it is also an observable fact intimately tied to geography. By decomposing this relationship, the thesis correlates a one-to-one mapping between high-level conceptualisations established from human knowledge and real world entities represented in the data. Based on a middle-out approach, it develops a conceptual model that incrementally links different levels of detail, and thereby derives coarser, more meaningful descriptions from more detailed ones. The thesis verifies its proposed ideas by implementing an ontology describing the land use ‘residential area’ in the ontology editor Protégé. By asserting knowledge about high-level concepts such as types of dwellings, urban blocks and residential districts as well as individuals that link directly to topographic features stored in the database, the reasoner successfully infers instances of the defined classes. Despite current technological limitations, ontologies are a promising way forward in the manner we handle and integrate geographic data, especially with respect to how humans conceptualise geographic space

LL(O)D and NLP perspectives on semantic change for humanities research

CC BY 4.0This paper presents an overview of the LL(O)D and NLP methods, tools and data for detecting and representing semantic change, with its main application in humanities research. The paper’s aim is to provide the starting point for the construction of a workflow and set of multilingual diachronic ontologies within the humanities use case of the COST Action Nexus Linguarum, European network for Web-centred linguistic data science, CA18209. The survey focuses on the essential aspects needed to understand the current trends and to build applications in this area of study