Extending the 2P-Kt ecosystem: CLP and Labelled LP

The ability to create hybrid systems that blend different paradigms has now become a requirement for complex AI systems usually made of more than a component. In this way, it is possible to exploit the advantages of each paradigm and exploit the potential of different approaches such as symbolic and non-symbolic approaches. In particular, symbolic approaches are often exploited for their efficiency, effectiveness and ability to manage large amounts of data, while symbolic approaches are exploited to ensure aspects related to explainability, fairness, and trustworthiness in general. The thesis lies in this context, in particular in the design and development of symbolic technologies that can be easily integrated and interoperable with other AI technologies. 2P-Kt is a symbolic ecosystem developed for this purpose, it provides a logic-programming (LP) engine which can be easily extended and customized to deal with specific needs. The aim of this thesis is to extend 2P-Kt to support constraint logic programming (CLP) as one of the main paradigms for solving highly combinatorial problems given a declarative problem description and a general constraint-propagation engine. A real case study concerning school timetabling is described to show a practical usage of the CLP(FD) library implemented. Since CLP represents only a particular scenario for extending LP to domain-specific scenarios, in this thesis we present also a more general framework: Labelled Prolog, extending LP with labelled terms and in particular labelled variables. The designed framework shows how it is possible to frame all variations and extensions of LP under a single language reducing the huge amount of existing languages and libraries and focusing more on how to manage different domain needs using labels which can be associated with every kind of term. Mapping of CLP into Labeled Prolog is also discussed as well as the benefits of the provided approach.

Survival and quality of life of patients with oral and oropharyngeal cancer at 1-year follow-up of tumor resection

OBJECTIVE: This study aimed to assess the survival and life quality evolution of patients subjected to surgical excision of oral and oropharyngeal squamous cell carcinoma. MATERIAL AND METHODS: Forty-seven patients treated at a Brazilian healthcare unit specialized in head and neck surgery between 2006 and 2007 were enrolled in the study. The gathering of data comprised reviewing hospital files and applying the University of Washington Quality of Life (UW-QOL) questionnaire previously and 1 year after the surgery. Comparative analysis used Poisson regression to assess factors associated with survival and a paired t-test to compare preoperative and 1-year postoperative QOL ratings. RESULTS: 1 year after surgery, 7 patients were not found (dropout of the cohort); 15 had died and 25 fulfilled the UW-QOL again. The risk of death was associated with having regional metastasis previously to surgery (relative risk=2.18; 95% confidence interval=1.09-5.17) and tumor size T3 or T4 (RR=2.30; 95%CI=1.05-5.04). Survivors presented significantly (p<0.05) poorer overall and domain-specific ratings of quality of life. Chewing presented the largest reduction: from 74.0 before surgery to 34.0 one year later. Anxiety was the only domain whose average rating increased (from 36.0 to 70.7). CONCLUSIONS: The prospective assessment of survival and quality of life may contribute to anticipate interventions aimed at reducing the incidence of functional limitations in patients with oral and oropharyngeal cancer.

Rehabilitation of executive dysfunction: A controlled trial of an attention and problem solving treatment group

In this study, the effectiveness of a group-based attention and problem solving (APS) treatment approach to executive impairments in patients with frontal lobe lesions was investigated. Thirty participants with lesions in the frontal lobes, 16 with left frontal (LF) and 14 with right frontal (RF) lesions, were allocated into three groups, each with 10 participants. The APS treatment was initially compared to two other control conditions, an information/education (IE) approach and treatment-as-usual or traditional rehabilitation (TR), with each of the control groups subsequently receiving the APS intervention in a crossover design. This design allowed for an evaluation of the treatment through assessment before and after treatment and on follow up, six months later. There was an improvement on some executive and functional measures after the implementation of the APS programme in the three groups. Size, and to a lesser extent laterality, of lesion affected baseline performance on measures of executive function, but there was no apparent relationship between size, laterality or site of lesion and level of benefit from the treatment intervention. The results were discussed in terms of models of executive functioning and the effectiveness of domain specific interventions in the rehabilitation of executive dysfunction.

MDA-based re-engineering with Object-Z

This paper describes a practical application of MDA and reverse engineering based on a domain-specific modelling language. A well defined metamodel of a domain-specific language is useful for verification and validation of associated tools. We apply this approach to SIFA, a security analysis tool. SIFA has evolved as requirements have changed, and it has no metamodel. Hence, testing SIFA’s correctness is difficult. We introduce a formal metamodelling approach to develop a well-defined metamodel of the domain. Initially, we develop a domain model in EMF by reverse engineering the SIFA implementation. Then we transform EMF to Object-Z using model transformation. Finally, we complete the Object-Z model by specifying system behavior. The outcome is a well-defined metamodel that precisely describes the domain and the security properties that it analyses. It also provides a reliable basis for testing the current SIFA implementation and forward engineering its successor.

Protein targeting to the plasma membrane of adult skeletal muscle fiber: An organized mosaic of functional domains

The plasma membrane of differentiated skeletal muscle fibers comprises the sarcolemma, the transverse (T) tubule network, and the neuromuscular and muscle-tendon junctions. We analyzed the organization of these domains in relation to defined surface markers, beta -dystroglycan, dystrophin, and caveolin-3, These markers were shown to exhibit highly organized arrays along the length of the fiber. Caveolin-3 and beta -dystroglycan/dystrophin showed distinct, but to some extent overlapping, labeling patterns and both markers left transverse tubule openings clear. This labeling pattern revealed microdomains over the entire plasma membrane with the exception of the neuromuscular and muscle-tendon junctions which formed distinct demarcated macrodomains. Our results suggest that the entire plasma membrane of mature muscle comprises a mosaic of T tubule domains together with sareolemmal caveolae and beta -dystroglycan domains. The domains identified with these markers were examined with respect to targeting of viral proteins and other expressed domain-specific markers, We found that each marker protein was targeted to distinct microdomains, The macrodomains were intensely labeled with all our markers. Replacing the cytoplasmic tail of the vesicular stomatitis virus glycoprotein with that of CD4 resulted in retargeting from one domain to another. The domain-specific protein distribution at the muscle cell surface may be generated by targeting pathways requiring specific sorting information but this trafficking is different from the conventional apical-basolateral division. (C) 2001 Academic Press.

Quality in Hospital Administrative Databases

The clinical content of administrative databases includes, among others, patient demographic characteristics, and codes for diagnoses and procedures. The data in these databases is standardized, clearly defined, readily available, less expensive than collected by other means, and normally covers hospitalizations in entire geographic areas. Although with some limitations, this data is often used to evaluate the quality of healthcare. Under these circumstances, the quality of the data, for instance, errors, or it completeness, is of central importance and should never be ignored. Both the minimization of data quality problems and a deep knowledge about this data (e.g., how to select a patient group) are important for users in order to trust and to correctly interpret results. In this paper we present, discuss and give some recommendations for some problems found in these administrative databases. We also present a simple tool that can be used to screen the quality of data through the use of domain specific data quality indicators. These indicators can significantly contribute to better data, to give steps towards a continuous increase of data quality and, certainly, to better informed decision-making.

Automatização de testes à framework myMIS

Atualmente, verifica-se um aumento na necessidade de software feito à medida do cliente, que se consiga adaptar de forma rápida as constantes mudanças da sua área de negócio. Cada cliente tem os seus problemas concretos que precisa de resolver, não lhe sendo muitas vezes possível dispensar uma elevada quantidade de recursos para atingir os fins pretendidos. De forma a dar resposta a estes problemas surgiram várias arquiteturas e metodologias de desenvolvimento de software, que permitem o desenvolvimento ágil de aplicações altamente configuráveis, que podem ser personalizadas por qualquer utilizador das mesmas. Este dinamismo, trazido para as aplicações sobre a forma de modelos que são personalizados pelos utilizadores e interpretados por uma plataforma genérica, cria maiores desafios no momento de realizar testes, visto existir um número de variáveis consideravelmente maior que numa aplicação com uma arquitetura tradicional. É necessário, em todos os momentos, garantir a integridade de todos os modelos, bem como da plataforma responsável pela sua interpretação, sem ser necessário o desenvolvimento constante de aplicações para suportar os testes sobre os diferentes modelos. Esta tese debruça-se sobre uma aplicação, a plataforma myMIS, que permite a interpretação de modelos orientados à gestão, escritos numa linguagem específica de domínio, sendo realizada a avaliação do estado atual e definida uma proposta de práticas de testes a aplicar no desenvolvimento da mesma. A proposta resultante desta tese permitiu verificar que, apesar das dificuldades inerentes à arquitetura da aplicação, o desenvolvimento de testes de uma forma genérica é possível, podendo as mesmas lógicas ser utilizadas para o teste de diversos modelos distintos.

A framework for supporting knowledge representation – an ontological based approach

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

Linked Data based Health Information Representation, Visualization and Retrieval System on the Semantic Web

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Família de DSLs para integrated modular avionics

Na atualidade existe a necessidade de produzir novos aviões de forma rápida, eficiente e económica com o objetivo de abrir novas rotas de voo, expansão das já existentes e substituição de aviões em fim de vida útil. Neste contexto, e sem nunca deixar de cumprir os apertados requisitos do domínio que incluem a exigência de elevada qualidade, a indústria adotou a arquitetura IMA que permite executar várias aplicações aviónicas num único sistema de computação partilhado. Com esta arquitetura, o desenvolvimento do software para as aeronaves ganhou uma elevada relevância, sendo necessário gerar código automaticamente, reutilizar código já testado proveniente de outras aplicações anteriormente desenvolvidas e garantir o mais cedo possível que o software desenvolvido se encontra de acordo com os standards. Apesar da complexidade do domínio, desenvolveu-se uma ferramenta que permite produzir a estrutura do código de novas aplicações para a aviónica. Aferramenta lida com a variabilidade das diversas linhas de produto e reduz o tempo de desenvolvimento. Uma DSL poderia ser uma solução apropriada, pois permite cobrir diversos requisitos exigidos, no entanto, esta solução não é exequível porque seria necessário produzir uma linguagem para cada configuração de software aviónico diferente se pretendêssemos tirar partido da especificidade. Com esta dissertação, solucionou-se esta dificuldade com recurso à noção de família de DSLs. Trata-se de um conjunto de linguagens para um domínio específico, que apresentam um conjunto comum de conceitos chave, mas que adaptam alguns desses conceitos para cumprir a variabilidade dos requisitos. Utilizou-se a abordagem MDD para desenvolver um gerador automático de DSLs que é capaz de produzir a linguagem desejada de acordo com a configuração de software pretendida para a partição pertencente a um módulo aviónico. As linguagens geradas apresentam um nível de usabilidade adequada para o domínio, bem como têm a capacidade de validar as construções efetuadas usando a DSL e produzir os artefactos pretendidos.

Towards an engine for coordination-based architectural reconfigurations

Software reconfigurability became increasingly relevant to the architectural process due to the crescent dependency of modern societies on reliable and adaptable systems. Such systems are supposed to adapt themselves to surrounding environmental changes with minimal service disruption, if any. This paper introduces an engine that statically applies reconfigurations to (formal) models of software architectures. Reconfigurations are specified using a domain specific language— ReCooPLa—which targets the manipulation of software coordinationstructures,typicallyusedinservice-orientedarchitectures(soa).Theengine is responsible for the compilation of ReCooPLa instances and their application to the relevant coordination structures. The resulting configurations are amenable to formal analysis of qualitative and quantitative (probabilistic) properties.

Metodologies de Desenvolupament Dirigides per Models

En aquest treball, s'introduiran dos de les metodologies de desenvolupament dirigides per models més significatives: Model Driven Architecture (MDA) i Domain Specific Modeling (DSM). Així mateix, es presentarà un estudi comparatiu d'algunes de les diferents eines existents actualment al mercat que els hi donen suport.

Body context and posture affect mental imagery of hands.

Different visual stimuli have been shown to recruit different mental imagery strategies. However the role of specific visual stimuli properties related to body context and posture in mental imagery is still under debate. Aiming to dissociate the behavioural correlates of mental processing of visual stimuli characterized by different body context, in the present study we investigated whether the mental rotation of stimuli showing either hands as attached to a body (hands-on-body) or not (hands-only), would be based on different mechanisms. We further examined the effects of postural changes on the mental rotation of both stimuli. Thirty healthy volunteers verbally judged the laterality of rotated hands-only and hands-on-body stimuli presented from the dorsum- or the palm-view, while positioning their hands on their knees (front postural condition) or behind their back (back postural condition). Mental rotation of hands-only, but not of hands-on-body, was modulated by the stimulus view and orientation. Additionally, only the hands-only stimuli were mentally rotated at different speeds according to the postural conditions. This indicates that different stimulus-related mechanisms are recruited in mental rotation by changing the bodily context in which a particular body part is presented. The present data suggest that, with respect to hands-only, mental rotation of hands-on-body is less dependent on biomechanical constraints and proprioceptive input. We interpret our results as evidence for preferential processing of visual- rather than kinesthetic-based mechanisms during mental transformation of hands-on-body and hands-only, respectively.

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

Summarization of specialized discourse: the case of medical articles in Spanish

In this article, we present the current state of our work on a linguistically-motivated model for automatic summarization of medical articles in Spanish. The model takes into account the results of an empirical study which reveals that, on the one hand, domain-specific summarization criteria can often be derived from the summaries of domain specialists, and, on the other hand, adequate summarization strategies must be multidimensional, i.e., cover various types of linguistic clues. We take into account the textual, lexical, discursive, syntactic and communicative dimensions. This is novel in the field of summarization. The experiments carried out so far indicate that our model is suitable to provide high quality summarizations.