On AGM for Non-Classical Logics

The AGM theory of belief revision provides a formal framework to represent the dynamics of epistemic states. In this framework, the beliefs of the agent are usually represented as logical formulas while the change operations are constrained by rationality postulates. In the original proposal, the logic underlying the reasoning was supposed to be supraclassical, among other properties. In this paper, we present some of the existing work in adapting the AGM theory for non-classical logics and discuss their interconnections and what is still missing for each approach.

Reasoning about Requirements Evolution Using Clustered Belief Revision

During the development of system requirements, software system specifications are often inconsistent. Inconsistencies may arise for different reasons, for example, when multiple conflicting viewpoints are embodied in the specification, or when the specification itself is at a transient stage of evolution. These inconsistencies cannot always be resolved immediately. As a result, we argue that a formal framework for the analysis of evolving specifications should be able to tolerate inconsistency by allowing reasoning in the presence of inconsistency without trivialisation, and circumvent inconsistency by enabling impact analyses of potential changes to be carried out. This paper shows how clustered belief revision can help in this process. Clustered belief revision allows for the grouping of requirements with similar functionality into clusters and the assignment of priorities between them. By analysing the result of a cluster, an engineer can either choose to rectify problems in the specification or to postpone the changes until more information becomes available.

Regularized nonnegative shared subspace learning

Joint modeling of related data sources has the potential to improve various data mining tasks such as transfer learning, multitask clustering, information retrieval etc. However, diversity among various data sources might outweigh the advantages of the joint modeling, and thus may result in performance degradations. To this end, we propose a regularized shared subspace learning framework, which can exploit the mutual strengths of related data sources while being immune to the effects of the variabilities of each source. This is achieved by further imposing a mutual orthogonality constraint on the constituent subspaces which segregates the common patterns from the source specific patterns, and thus, avoids performance degradations. Our approach is rooted in nonnegative matrix factorization and extends it further to enable joint analysis of related data sources. Experiments performed using three real world data sets for both retrieval and clustering applications demonstrate the benefits of regularization and validate the effectiveness of the model. Our proposed solution provides a formal framework appropriate for jointly analyzing related data sources and therefore, it is applicable to a wider context in data mining.

Computational studies to understand the role of social learning in team familiarity and its effects on team performance

This paper concerns social learning modes and their effects on team performance. Social learning, such as by observing others' actions and their outcomes, allows members of a team to learn what other members know. Knowing what other members know can reduce task communication and co-ordination overhead, which helps the team to perform faster since members can devote their attention to their tasks. This paper describes agent-based simulation studies using a computational model that implements different social learning modes as parameters that can be controlled in the simulations. The results show that social learning from both direct and indirect observations positively contributes to learning about what others know, but the value of social learning is sensitive to prior familiarity such that minimum thresholds of team familiarity are needed to realise the benefits of social learning. This threshold increases with task complexity. These findings clarify the level of influence that sociality has on social learning and sets up a formal framework by which to conduct studies on how social context influences learning and group performance.

Optimal communication amongst team members

We present a formal framework based on the theory of game with incomplete information [5] for modelling the coordination and communication problem among team of collaborative agents, and define what it means by optimal communication in this setting. Although computing an optimal communication strategy for the team is hard in general, we illustrate with an example of collaborative negotiation and meeting scheduling that computation can be substantially reduced when domain dependent assumptions are introduced.

Should payments for biodiversity conservation be based on action or results?

There is growing interest in the potential of payments for ecosystem services (PES) to encourage land managers to protect and enhance the environment. However, questions remain about how PES agreements should be designed. There is a division between schemes that structure payments by action or by results, with most biodiversity PES schemes, including European agri-environment schemes, paying by action; for example incentivising land managers to carry out actions believed to increase biodiversity. Payment by results is a common incentive structure in the private sector (e.g. labourers doing piece work or no-win no-fee lawyers) but rarer in PES. Using a theoretical modelling approach, we investigate the conditions under which each way of structuring payments may be more cost-effective in a biodiversity PES. Payment by action is favoured where there is a clear action that can be specified at an appropriate level and to which biodiversity is sensitive. We found that payment by results is favoured in degraded landscapes as incentives are created for managers to use their private knowledge and join the scheme only if they can produce the biodiversity services targeted by the scheme. Payment by results is also favoured where biodiversity is less sensitive to conservation action and when it is difficult for a central agency to determine an appropriate level of conservation action. This is because payment by results allows individual managers to optimise their level of action. The relative cost of monitoring action (compliance with an agreement to manage in a certain way) versus results (the presence of biodiversity) has a substantial effect on which payment structure is more efficient only when the central agency can accurately set an appropriate level of action. We illustrate these principles with examples based on agri-environment schemes. Synthesis and applications. Payment by results deserves more attention from those designing biodiversity PES (be they agri-environment schemes in agricultural landscapes or direct payment schemes in more intact ecosystems). This paper provides a formal framework to help policy makers identify the conditions under which payment by results or payment by action is most likely to yield cost-effective biodiversity conservation. © 2011 The Authors. Journal of Applied Ecology © 2011 British Ecological Society.

A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

Abstract Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

Censors for Boolean Description Logic

Protecting different kinds of information has become an important area of research. One aspect is to provide effective means to avoid that secrets can be deduced from the answers of legitimate queries. In the context of atomic propositional databases several methods have been developed to achieve this goal. However, in those databases it is not possible to formalize structural information. Also they are quite restrictive with respect to the specification of secrets. In this paper we extend those methods to match the much greater expressive power of Boolean description logics. In addition to the formal framework, we provide a discussion of various kinds of censors and establish different levels of security they can provide.

Advanced Topics in Resource Analysis: Certification, Incrementality, Concurrency and Array-Sensitivity

El Análisis de Consumo de Recursos o Análisis de Coste trata de aproximar el coste de ejecutar un programa como una función dependiente de sus datos de entrada. A pesar de que existen trabajos previos a esta tesis doctoral que desarrollan potentes marcos para el análisis de coste de programas orientados a objetos, algunos aspectos avanzados, como la eficiencia, la precisión y la fiabilidad de los resultados, todavía deben ser estudiados en profundidad. Esta tesis aborda estos aspectos desde cuatro perspectivas diferentes: (1) Las estructuras de datos compartidas en la memoria del programa son una pesadilla para el análisis estático de programas. Trabajos recientes proponen una serie de condiciones de localidad para poder mantener de forma consistente información sobre los atributos de los objetos almacenados en memoria compartida, reemplazando éstos por variables locales no almacenadas en la memoria compartida. En esta tesis presentamos dos extensiones a estos trabajos: la primera es considerar, no sólo los accesos a los atributos, sino también los accesos a los elementos almacenados en arrays; la segunda se centra en los casos en los que las condiciones de localidad no se cumplen de forma incondicional, para lo cual, proponemos una técnica para encontrar las precondiciones necesarias para garantizar la consistencia de la información acerca de los datos almacenados en memoria. (2) El objetivo del análisis incremental es, dado un programa, los resultados de su análisis y una serie de cambios sobre el programa, obtener los nuevos resultados del análisis de la forma más eficiente posible, evitando reanalizar aquellos fragmentos de código que no se hayan visto afectados por los cambios. Los analizadores actuales todavía leen y analizan el programa completo de forma no incremental. Esta tesis presenta un análisis de coste incremental, que, dado un cambio en el programa, reconstruye la información sobre el coste del programa de todos los métodos afectados por el cambio de forma incremental. Para esto, proponemos (i) un algoritmo multi-dominio y de punto fijo que puede ser utilizado en todos los análisis globales necesarios para inferir el coste, y (ii) una novedosa forma de almacenar las expresiones de coste que nos permite reconstruir de forma incremental únicamente las funciones de coste de aquellos componentes afectados por el cambio. (3) Las garantías de coste obtenidas de forma automática por herramientas de análisis estático no son consideradas totalmente fiables salvo que la implementación de la herramienta o los resultados obtenidos sean verificados formalmente. Llevar a cabo el análisis de estas herramientas es una tarea titánica, ya que se trata de herramientas de gran tamaño y complejidad. En esta tesis nos centramos en el desarrollo de un marco formal para la verificación de las garantías de coste obtenidas por los analizadores en lugar de analizar las herramientas. Hemos implementado esta idea mediante la herramienta COSTA, un analizador de coste para programas Java y KeY, una herramienta de verificación de programas Java. De esta forma, COSTA genera las garantías de coste, mientras que KeY prueba la validez formal de los resultados obtenidos, generando de esta forma garantías de coste verificadas. (4) Hoy en día la concurrencia y los programas distribuidos son clave en el desarrollo de software. Los objetos concurrentes son un modelo de concurrencia asentado para el desarrollo de sistemas concurrentes. En este modelo, los objetos son las unidades de concurrencia y se comunican entre ellos mediante llamadas asíncronas a sus métodos. La distribución de las tareas sugiere que el análisis de coste debe inferir el coste de los diferentes componentes distribuidos por separado. En esta tesis proponemos un análisis de coste sensible a objetos que, utilizando los resultados obtenidos mediante un análisis de apunta-a, mantiene el coste de los diferentes componentes de forma independiente. Abstract Resource Analysis (a.k.a. Cost Analysis) tries to approximate the cost of executing programs as functions on their input data sizes and without actually having to execute the programs. While a powerful resource analysis framework on object-oriented programs existed before this thesis, advanced aspects to improve the efficiency, the accuracy and the reliability of the results of the analysis still need to be further investigated. This thesis tackles this need from the following four different perspectives. (1) Shared mutable data structures are the bane of formal reasoning and static analysis. Analyses which keep track of heap-allocated data are referred to as heap-sensitive. Recent work proposes locality conditions for soundly tracking field accesses by means of ghost non-heap allocated variables. In this thesis we present two extensions to this approach: the first extension is to consider arrays accesses (in addition to object fields), while the second extension focuses on handling cases for which the locality conditions cannot be proven unconditionally by finding aliasing preconditions under which tracking such heap locations is feasible. (2) The aim of incremental analysis is, given a program, its analysis results and a series of changes to the program, to obtain the new analysis results as efficiently as possible and, ideally, without having to (re-)analyze fragments of code that are not affected by the changes. During software development, programs are permanently modified but most analyzers still read and analyze the entire program at once in a non-incremental way. This thesis presents an incremental resource usage analysis which, after a change in the program is made, is able to reconstruct the upper-bounds of all affected methods in an incremental way. To this purpose, we propose (i) a multi-domain incremental fixed-point algorithm which can be used by all global analyses required to infer the cost, and (ii) a novel form of cost summaries that allows us to incrementally reconstruct only those components of cost functions affected by the change. (3) Resource guarantees that are automatically inferred by static analysis tools are generally not considered completely trustworthy, unless the tool implementation or the results are formally verified. Performing full-blown verification of such tools is a daunting task, since they are large and complex. In this thesis we focus on the development of a formal framework for the verification of the resource guarantees obtained by the analyzers, instead of verifying the tools. We have implemented this idea using COSTA, a state-of-the-art cost analyzer for Java programs and KeY, a state-of-the-art verification tool for Java source code. COSTA is able to derive upper-bounds of Java programs while KeY proves the validity of these bounds and provides a certificate. The main contribution of our work is to show that the proposed tools cooperation can be used for automatically producing verified resource guarantees. (4) Distribution and concurrency are today mainstream. Concurrent objects form a well established model for distributed concurrent systems. In this model, objects are the concurrency units that communicate via asynchronous method calls. Distribution suggests that analysis must infer the cost of the diverse distributed components separately. In this thesis we propose a novel object-sensitive cost analysis which, by using the results gathered by a points-to analysis, can keep the cost of the diverse distributed components separate.

Método para la Construcción Automática de Ontologías Basado en Patrones Lingüísticos

La tesis que se presenta tiene como propósito la construcción automática de ontologías a partir de textos, enmarcándose en el área denominada Ontology Learning. Esta disciplina tiene como objetivo automatizar la elaboración de modelos de dominio a partir de fuentes información estructurada o no estructurada, y tuvo su origen con el comienzo del milenio, a raíz del crecimiento exponencial del volumen de información accesible en Internet. Debido a que la mayoría de información se presenta en la web en forma de texto, el aprendizaje automático de ontologías se ha centrado en el análisis de este tipo de fuente, nutriéndose a lo largo de los años de técnicas muy diversas provenientes de áreas como la Recuperación de Información, Extracción de Información, Sumarización y, en general, de áreas relacionadas con el procesamiento del lenguaje natural. La principal contribución de esta tesis consiste en que, a diferencia de la mayoría de las técnicas actuales, el método que se propone no analiza la estructura sintáctica superficial del lenguaje, sino que estudia su nivel semántico profundo. Su objetivo, por tanto, es tratar de deducir el modelo del dominio a partir de la forma con la que se articulan los significados de las oraciones en lenguaje natural. Debido a que el nivel semántico profundo es independiente de la lengua, el método permitirá operar en escenarios multilingües, en los que es necesario combinar información proveniente de textos en diferentes idiomas. Para acceder a este nivel del lenguaje, el método utiliza el modelo de las interlinguas. Estos formalismos, provenientes del área de la traducción automática, permiten representar el significado de las oraciones de forma independiente de la lengua. Se utilizará en concreto UNL (Universal Networking Language), considerado como la única interlingua de propósito general que está normalizada. La aproximación utilizada en esta tesis supone la continuación de trabajos previos realizados tanto por su autor como por el equipo de investigación del que forma parte, en los que se estudió cómo utilizar el modelo de las interlinguas en las áreas de extracción y recuperación de información multilingüe. Básicamente, el procedimiento definido en el método trata de identificar, en la representación UNL de los textos, ciertas regularidades que permiten deducir las piezas de la ontología del dominio. Debido a que UNL es un formalismo basado en redes semánticas, estas regularidades se presentan en forma de grafos, generalizándose en estructuras denominadas patrones lingüísticos. Por otra parte, UNL aún conserva ciertos mecanismos de cohesión del discurso procedentes de los lenguajes naturales, como el fenómeno de la anáfora. Con el fin de aumentar la efectividad en la comprensión de las expresiones, el método provee, como otra contribución relevante, la definición de un algoritmo para la resolución de la anáfora pronominal circunscrita al modelo de la interlingua, limitada al caso de pronombres personales de tercera persona cuando su antecedente es un nombre propio. El método propuesto se sustenta en la definición de un marco formal, que ha debido elaborarse adaptando ciertas definiciones provenientes de la teoría de grafos e incorporando otras nuevas, con el objetivo de ubicar las nociones de expresión UNL, patrón lingüístico y las operaciones de encaje de patrones, que son la base de los procesos del método. Tanto el marco formal como todos los procesos que define el método se han implementado con el fin de realizar la experimentación, aplicándose sobre un artículo de la colección EOLSS “Encyclopedia of Life Support Systems” de la UNESCO. ABSTRACT The purpose of this thesis is the automatic construction of ontologies from texts. This thesis is set within the area of Ontology Learning. This discipline aims to automatize domain models from structured or unstructured information sources, and had its origin with the beginning of the millennium, as a result of the exponential growth in the volume of information accessible on the Internet. Since most information is presented on the web in the form of text, the automatic ontology learning is focused on the analysis of this type of source, nourished over the years by very different techniques from areas such as Information Retrieval, Information Extraction, Summarization and, in general, by areas related to natural language processing. The main contribution of this thesis consists of, in contrast with the majority of current techniques, the fact that the method proposed does not analyze the syntactic surface structure of the language, but explores his deep semantic level. Its objective, therefore, is trying to infer the domain model from the way the meanings of the sentences are articulated in natural language. Since the deep semantic level does not depend on the language, the method will allow to operate in multilingual scenarios, where it is necessary to combine information from texts in different languages. To access to this level of the language, the method uses the interlingua model. These formalisms, coming from the area of machine translation, allow to represent the meaning of the sentences independently of the language. In this particular case, UNL (Universal Networking Language) will be used, which considered to be the only interlingua of general purpose that is standardized. The approach used in this thesis corresponds to the continuation of previous works carried out both by the author of this thesis and by the research group of which he is part, in which it is studied how to use the interlingua model in the areas of multilingual information extraction and retrieval. Basically, the procedure defined in the method tries to identify certain regularities at the UNL representation of texts that allow the deduction of the parts of the ontology of the domain. Since UNL is a formalism based on semantic networks, these regularities are presented in the form of graphs, generalizing in structures called linguistic patterns. On the other hand, UNL still preserves certain mechanisms of discourse cohesion from natural languages, such as the phenomenon of the anaphora. In order to increase the effectiveness in the understanding of expressions, the method provides, as another significant contribution, the definition of an algorithm for the resolution of pronominal anaphora limited to the model of the interlingua, in the case of third person personal pronouns when its antecedent is a proper noun. The proposed method is based on the definition of a formal framework, adapting some definitions from Graph Theory and incorporating new ones, in order to locate the notions of UNL expression and linguistic pattern, as well as the operations of pattern matching, which are the basis of the method processes. Both the formal framework and all the processes that define the method have been implemented in order to carry out the experimentation, applying on an article of the "Encyclopedia of Life Support Systems" of the UNESCO-EOLSS collection.

System for robot control inspired by the functionality and organisation of the human nervous system

This paper presents a model of a control system for robot systems inspired by the functionality and organisation of human neuroregulatory system. Our model was specified using software agents within a formal framework and implemented through Web Services. This approach allows the implementation of the control logic of a robot system with relative ease, in an incremental way, using the addition of new control centres to the system as its behaviour is observed or needs to be detailed with greater precision, without the need to modify existing functionality. The tests performed verify that the proposed model has the general characteristics of biological systems together with the desirable features of software, such as robustness, flexibility, reuse and decoupling.

Contrasting mutual sexual selection on homologous signal traits in Drosophila serrata

The nature of male mating preferences, and how they differ from female mating preferences in species with conventional sex roles, has received little attention in sexual selection studies. We estimated the form and strength of sexual selection as a consequence of male and female mating preferences in a laboratory-based population of Drosophila serrata. The differences between sexual selection on male and female signal traits (cuticular hydrocarbons [CHCs]) were evaluated within a formal framework of linear and nonlinear selection gradients. Females tended to exert linear sexual selection on male CHCs, whereas males preferred intermediate female CHC phenotypes leading to convex (stabilizing) selection gradients. Possible mechanisms determining the nonlinear nature of sexual selection on female CHCs are proposed.

Good-turing estimation for the frequentist n-tuple classifier

We present results concerning the application of the Good-Turing (GT) estimation method to the frequentist n-tuple system. We show that the Good-Turing method can, to a certain extent rectify the Zero Frequency Problem by providing, within a formal framework, improved estimates of small tallies. We also show that it leads to better tuple system performance than Maximum Likelihood estimation (MLE). However, preliminary experimental results suggest that replacing zero tallies with an arbitrary constant close to zero before MLE yields better performance than that of GT system.

XML storage and retrieval using the semantic binary object -oriented database system (SEM-ODB)

Over the past five years, XML has been embraced by both the research and industrial community due to its promising prospects as a new data representation and exchange format on the Internet. The widespread popularity of XML creates an increasing need to store XML data in persistent storage systems and to enable sophisticated XML queries over the data. The currently available approaches to addressing the XML storage and retrieval issue have the limitations of either being not mature enough (e.g. native approaches) or causing inflexibility, a lot of fragmentation and excessive join operations (e.g. non-native approaches such as the relational database approach). ^ In this dissertation, I studied the issue of storing and retrieving XML data using the Semantic Binary Object-Oriented Database System (Sem-ODB) to leverage the advanced Sem-ODB technology with the emerging XML data model. First, a meta-schema based approach was implemented to address the data model mismatch issue that is inherent in the non-native approaches. The meta-schema based approach captures the meta-data of both Document Type Definitions (DTDs) and Sem-ODB Semantic Schemas, thus enables a dynamic and flexible mapping scheme. Second, a formal framework was presented to ensure precise and concise mappings. In this framework, both schemas and the conversions between them are formally defined and described. Third, after major features of an XML query language, XQuery, were analyzed, a high-level XQuery to Semantic SQL (Sem-SQL) query translation scheme was described. This translation scheme takes advantage of the navigation-oriented query paradigm of the Sem-SQL, thus avoids the excessive join problem of relational approaches. Finally, the modeling capability of the Semantic Binary Object-Oriented Data Model (Sem-ODM) was explored from the perspective of conceptually modeling an XML Schema using a Semantic Schema. ^ It was revealed that the advanced features of the Sem-ODB, such as multi-valued attributes, surrogates, the navigation-oriented query paradigm, among others, are indeed beneficial in coping with the XML storage and retrieval issue using a non-XML approach. Furthermore, extensions to the Sem-ODB to make it work more effectively with XML data were also proposed. ^

Quality of Judgment Assessment

The intersection of Artificial Intelligence and The Law stands for a multifaceted matter, and its effects set the advances on culture, organization, as well as the social matters, when the emergent information technologies are taken into consideration. From this point of view, the weight of formal and informal Conflict Resolution settings should be highlighted, and the use of defective data, information or knowledge must be emphasized. Indeed, it is hard to do it with traditional problem solving methodologies. Therefore, in this work the focus is on the development of decision support systems, in terms of its knowledge representation and reasoning procedures, under a formal framework based on Logic Programming, complemented with an approach to computing centered on Artificial Neural Networks. It is intended to evaluate the Quality-of-Judgments and the respective Degree-of-Confidence that one has on such happenings.