Polynomial-Time Reasoning Support for Design and Maintenance of Large-Scale Biomedical Ontologies

Description Logics (DLs) belong to a successful family of knowledge representation formalisms with two key assets: formally well-defined semantics which allows to represent knowledge in an unambiguous way and automated reasoning which allows to infer implicit knowledge from the one given explicitly. This thesis investigates various reasoning techniques for tractable DLs in the EL family which have been implemented in the CEL system. It suggests that the use of the lightweight DLs, in which reasoning is tractable, is beneficial for ontology design and maintenance both in terms of expressivity and scalability. The claim is supported by a case study on the renown medical ontology SNOMED CT and extensive empirical evaluation on several large-scale biomedical ontologies

SAT Encoding of Unification in ELHR+ w.r.t. Cycle-Restricted Ontologies

Unification in Description Logics has been proposed as an inference service that can, for example, be used to detect redundancies in ontologies. For the Description Logic EL, which is used to define several large biomedical ontologies, unification is NP-complete. An NP unification algorithm for EL based on a translation into propositional satisfiability (SAT) has recently been presented. In this report, we extend this SAT encoding in two directions: on the one hand, we add general concept inclusion axioms, and on the other hand, we add role hierarchies (H) and transitive roles (R+). For the translation to be complete, however, the ontology needs to satisfy a certain cycle restriction. The SAT translation depends on a new rewriting-based characterization of subsumption w.r.t. ELHR+-ontologies

Unification in the Description Logic EL Without Top Constructor

Unification in Description Logics has been proposed as a novel inference service that can, for example, be used to detect redundancies in ontologies. The inexpressive Description Logic EL is of particular interest in this context since, on the one hand, several large biomedical ontologies are defined using EL. On the other hand, unification in EL has recently been shown to be NP-complete, and thus of considerably lower complexity than unification in other DLs of similarly restricted expressive power. However, EL allows the use of the top concept (>), which represents the whole interpretation domain, whereas the large medical ontology SNOMEDCT makes no use of this feature. Surprisingly, removing the top concept from EL makes the unification problem considerably harder. More precisely, we will show that unification in EL without the top concept is PSpace-complete.This is an updated version of the original report that includes Appendix A on locality of unifiers

Design and foundations of ontologies with meta-modelling.

Ontologies are broadly used and proved modelling artifacts to conceptualize a domain. In particular the W3C standard ontology language OWL, based on description logics, allows the ontology engineer to formally represent a domain as a set of assertions about concepts, individuals and roles. Nowadays, complex applications leads to combine autonomously built ontologies into ontology networks by relating them through di erent kind of relations. Some relations, such as the mapping of two concepts from di erent ontologies, can be expressed by the standard ontology language OWL, i.e. by the description logics behind it. However, there are other kind of relations that are not soundly represented by OWL, such as the meta-modelling relation. The meta-modelling relation has to do with the modelling of the same real object with di erent abstraction levels, e.g. as a concept in one ontology and as an individual in another ontology. Even though there are a set of approaches that extend description logics to deal with meta-modelling, they do not solve relevant requirements of some real scenarios. The present thesis work introduces an extension to the description logic SHIQ which provides a exible syntax and a strong semantics, and moreover ensures the well-foundedness of the interpretation domain. This approach is di erent from existing meta-modelling approaches either in the syntax or in the semantics (or both), and moreover ensures the well-foundedness of the domain which is an original contribution from the theoretical point of view. The meta-modelling extension of SHIQ introduced in the present work is justi ed by a detailed description of a set of real case studies, with an analysis of the bene ts of the new approach to solve some relevant requirements. Finally, the present work addresses the methodological issue by introducing a design pattern to help the ontology engineer in the use of the proposed meta-modelling approach

Quantitative Methods for Similarity in Description Logics

Description Logics (DLs) are a family of logic-based knowledge representation languages used to describe the knowledge of an application domain and reason about it in formally well-defined way. They allow users to describe the important notions and classes of the knowledge domain as concepts, which formalize the necessary and sufficient conditions for individual objects to belong to that concept. A variety of different DLs exist, differing in the set of properties one can use to express concepts, the so-called concept constructors, as well as the set of axioms available to describe the relations between concepts or individuals. However, all classical DLs have in common that they can only express exact knowledge, and correspondingly only allow exact inferences. Either we can infer that some individual belongs to a concept, or we can't, there is no in-between. In practice though, knowledge is rarely exact. Many definitions have their exceptions or are vaguely formulated in the first place, and people might not only be interested in exact answers, but also in alternatives that are "close enough". This thesis is aimed at tackling how to express that something "close enough", and how to integrate this notion into the formalism of Description Logics. To this end, we will use the notion of similarity and dissimilarity measures as a way to quantify how close exactly two concepts are. We will look at how useful measures can be defined in the context of DLs, and how they can be incorporated into the formal framework in order to generalize it. In particular, we will look closer at two applications of thus measures to DLs: Relaxed instance queries will incorporate a similarity measure in order to not just give the exact answer to some query, but all answers that are reasonably similar. Prototypical definitions on the other hand use a measure of dissimilarity or distance between concepts in order to allow the definitions of and reasoning with concepts that capture not just those individuals that satisfy exactly the stated properties, but also those that are "close enough"

Thirty years of artificial intelligence in medicine (AIME) conferences: A review of research themes

Over the past 30 years, the international conference on Artificial Intelligence in MEdicine (AIME) has been organized at different venues across Europe every 2 years, establishing a forum for scientific exchange and creating an active research community. The Artificial Intelligence in Medicine journal has published theme issues with extended versions of selected AIME papers since 1998

Mechanised Uniform Interpolation for Modal Logics K, GL, and iSL

The uniform interpolation property in a given logic can be understood as the definability of propositional quantifiers. We mechanise the computation of these quantifiers and prove correctness in the Coq proof assistant for three modal logics, namely: (1) the modal logic K, for which a pen-and-paper proof exists; (2) Gödel-Löb logic GL, for which our formalisation clarifies an important point in an existing, but incomplete, sequent-style proof; and (3) intuitionistic strong Löb logic iSL, for which this is the first proof-theoretic construction of uniform interpolants. Our work also yields verified programs that allow one to compute the propositional quantifiers on any formula in this logic

Mechanised Uniform Interpolation for Modal Logics K, GL, and iSL

The uniform interpolation property in a given logic can be understood as the definability of propositional quantifiers. We mechanise the computation of these quantifiers and prove correctness in the Coq proof assistant for three modal logics, namely: (1) the modal logic K, for which a pen-and-paper proof exists; (2) Gödel-Löb logic GL, for which our formalisation clarifies an important point in an existing, but incomplete, sequent-style proof; and (3) intuitionistic strong Löb logic iSL, for which this is the first proof-theoretic construction of uniform interpolants. Our work also yields verified programs that allow one to compute the propositional quantifiers on any formula in this logic

Temporalised Description Logics for Monitoring Partially Observable Events

Inevitably, it becomes more and more important to verify that the systems surrounding us have certain properties. This is indeed unavoidable for safety-critical systems such as power plants and intensive-care units. We refer to the term system in a broad sense: it may be man-made (e.g. a computer system) or natural (e.g. a patient in an intensive-care unit). Whereas in Model Checking it is assumed that one has complete knowledge about the functioning of the system, we consider an open-world scenario and assume that we can only observe the behaviour of the actual running system by sensors. Such an abstract sensor could sense e.g. the blood pressure of a patient or the air traffic observed by radar. Then the observed data are preprocessed appropriately and stored in a fact base. Based on the data available in the fact base, situation-awareness tools are supposed to help the user to detect certain situations that require intervention by an expert. Such situations could be that the heart-rate of a patient is rather high while the blood pressure is low, or that a collision of two aeroplanes is about to happen. Moreover, the information in the fact base can be used by monitors to verify that the system has certain properties. It is not realistic, however, to assume that the sensors always yield a complete description of the current state of the observed system. Thus, it makes sense to assume that information that is not present in the fact base is unknown rather than false. Moreover, very often one has some knowledge about the functioning of the system. This background knowledge can be used to draw conclusions about the possible future behaviour of the system. Employing description logics (DLs) is one way to deal with these requirements. In this thesis, we tackle the sketched problem in three different contexts: (i) runtime verification using a temporalised DL, (ii) temporalised query entailment, and (iii) verification in DL-based action formalisms