A Formal Framework for Linguistic Annotation

`Linguistic annotation' covers any descriptive or analytic notations applied to raw language data. The basic data may be in the form of time functions -- audio, video and/or physiological recordings -- or it may be textual. The added notations may include transcriptions of all sorts (from phonetic features to discourse structures), part-of-speech and sense tagging, syntactic analysis, `named entity' identification, co-reference annotation, and so on. While there are several ongoing efforts to provide formats and tools for such annotations and to publish annotated linguistic databases, the lack of widely accepted standards is becoming a critical problem. Proposed standards, to the extent they exist, have focussed on file formats. This paper focuses instead on the logical structure of linguistic annotations. We survey a wide variety of existing annotation formats and demonstrate a common conceptual core, the annotation graph. This provides a formal framework for constructing, maintaining and searching linguistic annotations, while remaining consistent with many alternative data structures and file formats.Comment: 49 page

Modelling Cell Cycle using Different Levels of Representation

Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform computerised simulations of biological systems, which are called in silico experiments, to attain important insights and predictions about the system behaviour with a considerably lower cost. Computer visualisation is an important part of this approach, since it provides a realistic representation of the system behaviour. We define a formal methodology to model biological systems using different levels of representation: a purely formal representation, which we call molecular level, models the biochemical dynamics of the system; visualisation-oriented representations, which we call visual levels, provide views of the biological system at a higher level of organisation and are equipped with the necessary spatial information to generate the appropriate visualisation. We choose Spatial CLS, a formal language belonging to the class of Calculi of Looping Sequences, as the formalism for modelling all representation levels. We illustrate our approach using the budding yeast cell cycle as a case study

Formalizing graphical notations

The thesis describes research into graphical notations for software engineering, with a principal interest in ways of formalizing them. The research seeks to provide a theoretical basis that will help in designing both notations and the software tools that process them. The work starts from a survey of literature on notation, followed by a review of techniques for formal description and for computational handling of notations. The survey concentrates on collecting views of the benefits and the problems attending notation use in software development; the review covers picture description languages, grammars and tools such as generic editors and visual programming environments. The main problem of notation is found to be a lack of any coherent, rigorous description methods. The current approaches to this problem are analysed as lacking in consensus on syntax specification and also lacking a clear focus on a defined concept of notated expression. To address these deficiencies, the thesis embarks upon an exploration of serniotic, linguistic and logical theory; this culminates in a proposed formalization of serniosis in notations, using categorial model theory as a mathematical foundation. An argument about the structure of sign systems leads to an analysis of notation into a layered system of tractable theories, spanning the gap between expressive pictorial medium and subject domain. This notion of 'tectonic' theory aims to treat both diagrams and formulae together. The research gives details of how syntactic structure can be sketched in a mathematical sense, with examples applying to software development diagrams, offering a new solution to the problem of notation specification. Based on these methods, the thesis discusses directions for resolving the harder problems of supporting notation design, processing and computer-aided generic editing. A number of future research areas are thereby opened up. For practical trial of the ideas, the work proceeds to the development and partial implementation of a system to aid the design of notations and editors. Finally the thesis is evaluated as a contribution to theory in an area which has not attracted a standard approach

A logic for application level QoS

Service Oriented Computing (SOC) has been proposed as a paradigm to describe computations of applications on wide area distributed systems. Awareness of Quality of Service (QoS) is emerging as a new exigency in both design and implementation of SOC applications. We do not refer to QoS aspects related to low-level performance and focus on those high-level non-functional features perceived by end-users as application dependent requirements, e.g., the price of a given service, or the payment mode, or else the availability of a resource (e.g., a file in a given format). In this paper we present a logic which includes mechanisms to consider the three main dimensions of systems, namely their structure, behaviour and QoS aspects. The evaluation of a formula is a value of a constraint-semiring and not just a boolean value expressing whether or not the formula holds. This permits to express not only topological and temporal properties but also QoS properties of systems. The logic is interpreted on SHReQ, a formal framework for specifying systems that handles abstract high-level QoS aspects combining Synchronised Hyperedge Replacement with constraint-semirings

Maintaining Structured Experiences for Robots via Human Demonstrations: An Architecture To Convey Long-Term Robot\u2019s Beliefs

This PhD thesis presents an architecture for structuring experiences, learned through demonstrations, in a robot memory. To test our architecture, we consider a specific application where a robot learns how objects are spatially arranged in a tabletop scenario. We use this application as a mean to present a few software development guidelines for building architecture for similar scenarios, where a robot is able to interact with a user through a qualitative shared knowledge stored in its memory. In particular, the thesis proposes a novel technique for deploying ontologies in a robotic architecture based on semantic interfaces. To better support those interfaces, it also presents general-purpose tools especially designed for an iterative development process, which is suitable for Human-Robot Interaction scenarios. We considered ourselves at the beginning of the first iteration of the design process, and our objective was to build a flexible architecture through which evaluate different heuristic during further development iterations. Our architecture is based on a novel algorithm performing a oneshot structured learning based on logic formalism. We used a fuzzy ontology for dealing with uncertain environments, and we integrated the algorithm in the architecture based on a specific semantic interface. The algorithm is used for building experience graphs encoded in the robot\u2019s memory that can be used for recognising and associating situations after a knowledge bootstrapping phase. During this phase, a user is supposed to teach and supervise the beliefs of the robot through multimodal, not physical, interactions. We used the algorithm to implement a cognitive like memory involving the encoding, storing, retrieving, consolidating, and forgetting behaviours, and we showed that our flexible design pattern could be used for building architectures where contextualised memories are managed with different purposes, i.e. they contains representation of the same experience encoded with different semantics. The proposed architecture has the main purposes of generating and maintaining knowledge in memory, but it can be directly interfaced with perceiving and acting components if they provide, or require, symbolical knowledge. With the purposes of showing the type of data considered as inputs and outputs in our tests, this thesis also presents components to evaluate point clouds, engage dialogues, perform late data fusion and simulate the search of a target position. Nevertheless, our design pattern is not meant to be coupled only with those components, which indeed have a large room of improvement

Prospects for Declarative Mathematical Modeling of Complex Biological Systems

Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation program, in a general-purpose programming language. Examples of such computations on models include model analysis, relatively general-purpose model-reduction maps, and the initial phases of model implementation, all of which should preserve or approximate the mathematical semantics of a complex biological model. The potential advantages are particularly relevant in the case of developmental modeling, wherein complex spatial structures exhibit dynamics at molecular, cellular, and organogenic levels to relate genotype to multicellular phenotype. Multiscale modeling can benefit from both the expressive power of declarative modeling languages and the application of model reduction methods to link models across scale. Based on previous work, here we define declarative modeling of complex biological systems by defining the operator algebra semantics of an increasingly powerful series of declarative modeling languages including reaction-like dynamics of parameterized and extended objects; we define semantics-preserving implementation and semantics-approximating model reduction transformations; and we outline a "meta-hierarchy" for organizing declarative models and the mathematical methods that can fruitfully manipulate them