A Goal-Directed Implementation of Query Answering for Hybrid MKNF Knowledge Bases

Ontologies and rules are usually loosely coupled in knowledge representation formalisms. In fact, ontologies use open-world reasoning while the leading semantics for rules use non-monotonic, closed-world reasoning. One exception is the tightly-coupled framework of Minimal Knowledge and Negation as Failure (MKNF), which allows statements about individuals to be jointly derived via entailment from an ontology and inferences from rules. Nonetheless, the practical usefulness of MKNF has not always been clear, although recent work has formalized a general resolution-based method for querying MKNF when rules are taken to have the well-founded semantics, and the ontology is modeled by a general oracle. That work leaves open what algorithms should be used to relate the entailments of the ontology and the inferences of rules. In this paper we provide such algorithms, and describe the implementation of a query-driven system, CDF-Rules, for hybrid knowledge bases combining both (non-monotonic) rules under the well-founded semantics and a (monotonic) ontology, represented by a CDF Type-1 (ALQ) theory. To appear in Theory and Practice of Logic Programming (TPLP

Combining open and closed world reasoning for the semantic web

Dissertação para obtenção do Grau de Doutor em InformáticaOne important problem in the ongoing standardization of knowledge representation languages for the Semantic Web is combining open world ontology languages, such as the OWL-based ones, and closed world rule-based languages. The main difficulty of such a combination is that both formalisms are quite orthogonal w.r.t. expressiveness and how decidability is achieved. Combining non-monotonic rules and ontologies is thus a challenging task that requires careful balancing between expressiveness of the knowledge representation language and the computational complexity of reasoning. In this thesis, we will argue in favor of a combination of ontologies and nonmonotonic rules that tightly integrates the two formalisms involved, that has a computational complexity that is as low as possible, and that allows us to query for information instead of calculating the whole model. As our starting point we choose the mature approach of hybrid MKNF knowledge bases, which is based on an adaptation of the Stable Model Semantics to knowledge bases consisting of ontology axioms and rules. We extend the two-valued framework of MKNF logics to a three-valued logics, and we propose a well-founded semantics for non-disjunctive hybrid MKNF knowledge bases. This new semantics promises to provide better efficiency of reasoning,and it is faithful w.r.t. the original two-valued MKNF semantics and compatible with both the OWL-based semantics and the traditional Well- Founded Semantics for logic programs. We provide an algorithm based on operators to compute the unique model, and we extend SLG resolution with tabling to a general framework that allows us to query a combination of non-monotonic rules and any given ontology language. Finally, we investigate concrete instances of that procedure w.r.t. three tractable ontology languages, namely the three description logics underlying the OWL 2 pro les.Fundação para a Ciência e Tecnologia - grant contract SFRH/BD/28745/200

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

Ontology-based knowledge representation and semantic search information retrieval: case study of the underutilized crops domain

The aim of using semantic technologies in domain knowledge modeling is to introduce the semantic meaning of concepts in knowledge bases, such that they are both human-readable as well as machine-understandable. Due to their powerful knowledge representation formalism and associated inference mechanisms, ontology-based approaches have been increasingly adopted to formally represent domain knowledge. The primary objective of this thesis work has been to use semantic technologies in advancing knowledge-sharing of Underutilized crops as a domain and investigate the integration of underlying ontologies developed in OWL (Web Ontology Language) with augmented SWRL (Semantic Web Rule Language) rules for added expressiveness. The work further investigated generating ontologies from existing data sources and proposed the reverse-engineering approach of generating domain specific conceptualization through competency questions posed from possible ontology users and domain experts. For utilization, a semantic search engine (the Onto-CropBase) has been developed to serve as a Web-based access point for the Underutilized crops ontology model. Relevant linked-data in Resource Description Framework Schema (RDFS) were added for comprehensiveness in generating federated queries. While the OWL/SWRL combination offers a highly expressive ontology language for modeling knowledge domains, the combination is found to be lacking supplementary descriptive constructs to model complex real-life scenarios, a necessary requirement for a successful Semantic Web application. To this end, the common logic programming formalisms for extending Description Logic (DL)-based ontologies were explored and the state of the art in SWRL expressiveness extensions determined with a view to extending the SWRL formalism. Subsequently, a novel fuzzy temporal extension to the Semantic Web Rule Language (FT-SWRL), which combines SWRL with fuzzy logic theories based on the valid-time temporal model, has been proposed to allow modeling imprecise temporal expressions in domain ontologies

OPTIMIZATION OF NONSTANDARD REASONING SERVICES

The increasing adoption of semantic technologies and the corresponding increasing complexity of application requirements are motivating extensions to the standard reasoning paradigms and services supported by such technologies. This thesis focuses on two of such extensions: nonmonotonic reasoning and inference-proof access control. Expressing knowledge via general rules that admit exceptions is an approach that has been commonly adopted for centuries in areas such as law and science, and more recently in object-oriented programming and computer security. The experiences in developing complex biomedical knowledge bases reported in the literature show that a direct support to defeasible properties and exceptions would be of great help. On the other hand, there is ample evidence of the need for knowledge confidentiality measures. Ontology languages and Linked Open Data are increasingly being used to encode the private knowledge of companies and public organizations. Semantic Web techniques facilitate merging different sources of knowledge and extract implicit information, thereby putting at risk security and the privacy of individuals. But the same reasoning capabilities can be exploited to protect the confidentiality of knowledge. Both nonmonotonic inference and secure knowledge base access rely on nonstandard reasoning procedures. The design and realization of these algorithms in a scalable way (appropriate to the ever-increasing size of ontologies and knowledge bases) is carried out by means of a diversified range of optimization techniques such as appropriate module extraction and incremental reasoning. Extensive experimental evaluation shows the efficiency of the developed optimization techniques: (i) for the first time performance compatible with real-time reasoning is obtained for large nonmonotonic ontologies, while (ii) the secure ontology access control proves to be already compatible with practical use in the e-health application scenario.

Ontology-based knowledge representation and semantic search information retrieval: case study of the underutilized crops domain

The aim of using semantic technologies in domain knowledge modeling is to introduce the semantic meaning of concepts in knowledge bases, such that they are both human-readable as well as machine-understandable. Due to their powerful knowledge representation formalism and associated inference mechanisms, ontology-based approaches have been increasingly adopted to formally represent domain knowledge. The primary objective of this thesis work has been to use semantic technologies in advancing knowledge-sharing of Underutilized crops as a domain and investigate the integration of underlying ontologies developed in OWL (Web Ontology Language) with augmented SWRL (Semantic Web Rule Language) rules for added expressiveness. The work further investigated generating ontologies from existing data sources and proposed the reverse-engineering approach of generating domain specific conceptualization through competency questions posed from possible ontology users and domain experts. For utilization, a semantic search engine (the Onto-CropBase) has been developed to serve as a Web-based access point for the Underutilized crops ontology model. Relevant linked-data in Resource Description Framework Schema (RDFS) were added for comprehensiveness in generating federated queries. While the OWL/SWRL combination offers a highly expressive ontology language for modeling knowledge domains, the combination is found to be lacking supplementary descriptive constructs to model complex real-life scenarios, a necessary requirement for a successful Semantic Web application. To this end, the common logic programming formalisms for extending Description Logic (DL)-based ontologies were explored and the state of the art in SWRL expressiveness extensions determined with a view to extending the SWRL formalism. Subsequently, a novel fuzzy temporal extension to the Semantic Web Rule Language (FT-SWRL), which combines SWRL with fuzzy logic theories based on the valid-time temporal model, has been proposed to allow modeling imprecise temporal expressions in domain ontologies

Practical reasoning for defeasable description logics.

Doctor of Philosophy in Mathematics, Statistics and Computer Science. University of KwaZulu-Natal, Durban 2016.Description Logics (DLs) are a family of logic-based languages for formalising ontologies. They have useful computational properties allowing the development of automated reasoning engines to infer implicit knowledge from ontologies. However, classical DLs do not tolerate exceptions to speci ed knowledge. This led to the prominent research area of nonmonotonic or defeasible reasoning for DLs, where most techniques were adapted from seminal works for propositional and rst-order logic. Despite the topic's attention in the literature, there remains no consensus on what \sensible" defeasible reasoning means for DLs. Furthermore, there are solid foundations for several approaches and yet no serious implementations and practical tools. In this thesis we address the aforementioned issues in a broad sense. We identify the preferential approach, by Kraus, Lehmann and Magidor (KLM) in propositional logic, as a suitable abstract framework for de ning and studying the precepts of sensible defeasible reasoning. We give a generalisation of KLM's precepts, and their arguments motivating them, to the DL case. We also provide several preferential algorithms for defeasible entailment in DLs; evaluate these algorithms, and the main alternatives in the literature, against the agreed upon precepts; extensively test the performance of these algorithms; and ultimately consolidate our implementation in a software tool called Defeasible-Inference Platform (DIP). We found some useful entailment regimes within the preferential context that satisfy all the KLM properties, and some that have scalable performance in real world ontologies even without extensive optimisation

A semantic web rule language for geospatial domains

Retrieval of geographically-referenced information on the Internet is now a common activity. The web is increasingly being seen as a medium for the storage and exchange of geographic data sets in the form of maps. The geospatial-semantic web (GeoWeb) is being developed to address the need for access to current and accurate geo-information. The potential applications of the GeoWeb are numerous, ranging from specialised application domains for storing and analysing geo-information to more common applications by casual users for querying and visualising geo-data, e.g. finding locations of services, descriptions of routes, etc. Ontologies are at the heart of W3C's semantic web initiative to provide the necessary machine understanding to the sheer volumes of information contained on the internet. For the GeoWeb to succeed the development of ontologies for the geographic domain are crucial. Semantic web technologies to represent ontologies have been developed and standardised. OWL, the Web Ontology Language, is the most expressive of these enabling a rich form of reasoning, thanks to its formal description logic underpinnings. Building geo-ontologies involves a continuous process of update to the originally modelled data to reflect change over time as well as to allow for ontology expansion by integrating new data sets, possibly from different sources. One of the main challenges in this process is finding means of ensuring the integrity of the geo-ontology and maintaining its consistency upon further evolution. Representing and reasoning with geographic ontologies in OWL is limited. Firstly, OWL is not an integrity checking language due to it's non-unique name and open world assumptions. Secondly, it can not represent spatial datatypes, can not compute information using spatial operators and does not have any form of spatial index. Finally, OWL does not support complex property composition needed to represent qualitative spatial reasoning over spatial concepts. To address OWL's representational inefficiencies, new ontology languages have been proposed based on the intersection or union of OWL (in particular the DL family corresponding to OWL) with logic programs (rule languages). In this work, a new Semantic Web Spatial Rule Language (SWSRL) is proposed, based on the syntactic core of the Description Logic Programs paradigm (DLP), and the semantics of a Logic Program. The language is built to support the expression of geospatial ontological axioms and geospatial integrity and deduction rules. A hybrid framework to integrate both qualitative symbolic information in SWSRL with quantitative, geometric information using spatial datatypes in a spatial database is proposed. Two notable features of SWSRL are 1) the language is based on a prioritised de fault logic that allows the expression of default integrity rules and their exceptions and 2) the implementation of the language uses an interleaved mode of inference for on the fly computation (either qualitative or quantitative) deduction of spatial relations. SWSRL supports an OGC complaint spatial syntax, and a standardised definition of rule meta data. Both features aid the construction, description, identification and categorisation of designed and implemented rules within large rule sets. The language and the developed engine are evaluated using synthetic as well as real data sets in the context of developing geographic ontologies for geographic information retrieval on the Semantic Web. Empirical experiments are also presented to test the scalability and applicability of the developed framework