Derivation methods for hybrid knowledge bases with rules and ontologies

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia InformáticaFirst of all, I would like to thank my advisor, José Júlio Alferes, for his incredible support. Right from the start, during the first semester of this work, when we were 2700 km apart and meeting regularly via Skype, until the end of this dissertation, he was always committed and available for discussions, even when he had lots of other urgent things to do. A really special thanks to Terrance Swift, whom acted as an advisor, helping me a lot in the second implementation, and correcting all XSB’s and CDF’s bugs. This implementation wouldn’t surely have reached such a fruitful end without his support. I would also like to thank all my colleagues and friends at FCT for the great work environment and for not letting me take myself too serious. A special thanks to my colleagues from Dresden for encouraging me to work even when there were so many other interesting things to do as an Erasmus student. I’m indebted to Luís Leal, Bárbara Soares, Jorge Soares and Cecília Calado, who kindly accepted to read a preliminary version of this report and gave me their valuable comments. For giving me working conditions and a partial financial support, I acknowledge the Departamento de Informática of the Faculdade de Ciências e Tecnologias of Universidade Nova de Lisboa. Last, but definitely not least, I would like to thank my parents and all my family for their continuous encouragement and motivation. A special thanks to Bruno for his love, support and patience

Integrating rules and ontologies in the first-order stable model semantics (preliminary report

Abstract. We present an approach to integrating rules and ontologies on the basis of the first-order stable model semantics defined by Ferraris, Lee and Lifschitz. We show that a few existing integration proposals can be uniformly related to the first-order stable model semantics.

Automatically selecting patients for clinical trials with justifications

Clinical trials are human research studies that are used to evaluate the effectiveness of a surgical, medical, or behavioral intervention. They have been widely used by researchers to determine whether a new treatment, such as a new medication, is safe and effective in humans. A clinical trial is frequently performed to determine whether a new treatment is more successful than the current treatment or has less harmful side effects. However, clinical trials have a high failure rate. One method applied is to find patients based on patient records. Unfortunately, this is a difficult process. This is because this process is typically performed manually, making it time-consuming and error-prone. Consequently, clinical trial deadlines are often missed, and studies do not move forward. Time can be a determining factor for success. Therefore, it would be advantageous to have automatic support in this process. Since it is also important to be able to validate whether the patients were selected correctly for the trial, avoiding eventual health problems, it would be important to have a mechanism to present justifications for the selected patients. In this dissertation, we present one possible solution to solve the problem of patient selection for clinical trials. We developed the necessary algorithms and created a simple and intuitive web application that features the selection of patients for clinical trials automatically. This was achieved by combining knowledge expressed in different formalisms. We integrated medical knowledge using ontologies, with criteria that were expressed using nonmonotonic rules. To address the validation procedure automatically, we developed a mechanism that generates the justifications for each selection together with the results of the patients who were selected. In the end, it is expected that a user can easily enter a set of trial criteria, and the application will generate the results of the selected patients and their respective justifications, based on the criteria inserted, medical information and a database of patient information.Os ensaios clínicos são estudos de pesquisa em humanos, utilizados para avaliar a eficácia de uma intervenção cirúrgica, médica ou comportamental. Estes estudos, têm sido amplamente utilizados pelos investigadores para determinar se um novo tratamento, como é o caso de um novo medicamento, é seguro e eficaz em humanos. Um ensaio clínico é realizado frequentemente, para determinar se um novo tratamento tem mais sucesso do que o tratamento atual ou se tem menos efeitos colaterais prejudiciais. No entanto, os ensaios clínicos têm uma taxa de insucesso alta. Um método aplicado é encontrar pacientes com base em registos. Infelizmente, este é um processo difícil. Isto deve-se ao facto deste processo ser normalmente realizado à mão, o que o torna demorado e propenso a erros. Consequentemente, o prazo dos ensaios clínicos é muitas vezes ultrapassado e os estudos acabam por não avançar. O tempo pode ser por vezes um fator determinante para o sucesso. Seria então vantajoso ter algum apoio automático neste processo. Visto que também seria importante validar se os pacientes foram selecionados corretamente para o ensaio, evitando até eventuais problemas de saúde, seria importante ter um mecanismo que apresente justificações para os pacientes selecionados. Nesta dissertação, apresentamos uma possível solução para resolver o problema da seleção de pacientes para ensaios clínicos, através da criação de uma aplicação web, intuitiva e fácil de utilizar, que apresenta a seleção de pacientes para ensaios clínicos de forma automática. Isto foi alcançado através da combinação de conhecimento expresso em diferentes formalismos. Integrámos o conhecimento médico usando ontologias, com os critérios que serão expressos usando regras não monotónicas. Para tratar do processo de validação, desenvolvemos um mecanismo que gera justificações para cada seleção juntamente com os resultados dos pacientes selecionados. No final, é esperado que o utilizador consiga inserir facilmente um conjunto de critérios de seleção, e a aplicação irá gerar os resultados dos pacientes selecionados e as respetivas justificações, com base nos critérios inseridos, informações médicas e uma base de dados com informações dos pacientes

Reasoning with Forest Logic Programs and f-hybrid Knowledge Bases

Open Answer Set Programming (OASP) is an undecidable framework for integrating ontologies and rules. Although several decidable fragments of OASP have been identified, few reasoning procedures exist. In this article, we provide a sound, complete, and terminating algorithm for satisfiability checking w.r.t. Forest Logic Programs (FoLPs), a fragment of OASP where rules have a tree shape and allow for inequality atoms and constants. The algorithm establishes a decidability result for FoLPs. Although believed to be decidable, so far only the decidability for two small subsets of FoLPs, local FoLPs and acyclic FoLPs, has been shown. We further introduce f-hybrid knowledge bases, a hybrid framework where \SHOQ{} knowledge bases and forest logic programs co-exist, and we show that reasoning with such knowledge bases can be reduced to reasoning with forest logic programs only. We note that f-hybrid knowledge bases do not require the usual (weakly) DL-safety of the rule component, providing thus a genuine alternative approach to current integration approaches of ontologies and rules

The EZSMT Solver: Constraint Answer Set Solving meets SMT

Constraint answer set programming is a promising research direction that integrates answer set programming with constraint processing. It is often informally related to the field of Satisfiability Modulo Theories. Yet, the exact formal link is obscured as the terminology and concepts used in these two research areas differ. In this thesis, by connecting these two areas, we begin the cross-fertilization of not only of the theoretical foundations of both areas but also of the existing solving technologies. We present the system EZSMT, one of the first solvers of this nature, which is able to take a large class of constraint answer set programs and rewrite them into Satisfiability Modulo Theories programs so that Satisfiability Modulo Theories technology can be used to process these programs

Multi-Context Reasoning in Continuous Data-Flow Environments

The field of artificial intelligence, research on knowledge representation and reasoning has originated a large variety of formats, languages, and formalisms. Over the decades many different tools emerged to use these underlying concepts. Each one has been designed with some specific application in mind and are even used nowadays, where the internet is seen as a service to be sufficient for the age of Industry 4.0 and the Internet of Things. In that vision of a connected world, with these many different formalisms and systems, a formal way to uniformly exchange information, such as knowledge and belief is imperative. That alone is not enough, because even more systems get integrated into the online world and nowadays we are confronted with a huge amount of continuously flowing data. Therefore a solution is needed to both, allowing the integration of information and dynamic reaction to the data which is provided in such continuous data-flow environments. This work aims to present a unique and novel pair of formalisms to tackle these two important needs by proposing an abstract and general solution. We introduce and discuss reactive Multi-Context Systems (rMCS), which allow one to utilise different knowledge representation formalisms, so-called contexts which are represented as an abstract logic framework, and exchange their beliefs through bridge rules with other contexts. These multiple contexts need to mutually agree on a common set of beliefs, an equilibrium of belief sets. While different Multi-Context Systems already exist, they are only solving this agreement problem once and are neither considering external data streams, nor are they reasoning continuously over time. rMCS will do this by adding means of reacting to input streams and allowing the bridge rules to reason with this new information. In addition we propose two different kind of bridge rules, declarative ones to find a mutual agreement and operational ones for adapting the current knowledge for future computations. The second framework is more abstract and allows computations to happen in an asynchronous way. These asynchronous Multi-Context Systems are aimed at modelling and describing communication between contexts, with different levels of self-management and centralised management of communication and computation. In this thesis rMCS will be analysed with respect to usability, consistency management, and computational complexity, while we will show how asynchronous Multi-Context Systems can be used to capture the asynchronous ideas and how to model an rMCS with it. Finally we will show how rMCSs are positioned in the current world of stream reasoning and that it can capture currently used technologies and therefore allows one to seamlessly connect different systems of these kinds with each other. Further on this also shows that rMCSs are expressive enough to simulate the mechanics used by these systems to compute the corresponding results on its own as an alternative to already existing ones. For asynchronous Multi-Context Systems, we will discuss how to use them and that they are a very versatile tool to describe communication and asynchronous computation