Datalog± Ontology Consolidation

Knowledge bases in the form of ontologies are receiving increasing attention as they allow to clearly represent both the available knowledge, which includes the knowledge in itself and the constraints imposed to it by the domain or the users. In particular, Datalog ± ontologies are attractive because of their property of decidability and the possibility of dealing with the massive amounts of data in real world environments; however, as it is the case with many other ontological languages, their application in collaborative environments often lead to inconsistency related issues. In this paper we introduce the notion of incoherence regarding Datalog± ontologies, in terms of satisfiability of sets of constraints, and show how under specific conditions incoherence leads to inconsistent Datalog ± ontologies. The main contribution of this work is a novel approach to restore both consistency and coherence in Datalog± ontologies. The proposed approach is based on kernel contraction and restoration is performed by the application of incision functions that select formulas to delete. Nevertheless, instead of working over minimal incoherent/inconsistent sets encountered in the ontologies, our operators produce incisions over non-minimal structures called clusters. We present a construction for consolidation operators, along with the properties expected to be satisfied by them. Finally, we establish the relation between the construction and the properties by means of a representation theorem. Although this proposal is presented for Datalog± ontologies consolidation, these operators can be applied to other types of ontological languages, such as Description Logics, making them apt to be used in collaborative environments like the Semantic Web.Fil: Deagustini, Cristhian Ariel David. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Martinez, Maria Vanina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Falappa, Marcelo Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Simari, Guillermo Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; Argentin

Dealing with Inconsistencies and Updates in Description Logic Knowledge Bases

The main purpose of an "Ontology-based Information System" (OIS) is to provide an explicit description of the domain of interest, called ontology, and let all the functions of the system be based on such representation, thus freeing the users from the knowledge about the physical repositories where the real data reside. The functionalities that an OIS should provide to the user include both query answering, whose goal is to extract information from the system, and update, whose goal is to modify the information content of the system in order to reflect changes in the domain of interest. The "ontology" is a formal, high quality intentional representation of the domain, designed in such a way to avoid inconsistencies in the modeling of concepts and relationships. On the contrary, the extensional level of the system, constituted by a set of autonomous, heterogeneous data sources, is built independently from the conceptualization represented by the ontology, and therefore may contain information that is incoherent with the ontology itself. This dissertation presents a detailed study on the problem of dealing with inconsistencies in OISs, both in query answering, and in performing updates. We concentrate on the case where the knowledge base in the OISs is expressed in Description Logics, especially the logics of the DL-lite family. As for query answering, we propose both semantical frameworks that are inconsistency-tolerant, and techniques for answering unions of conjunctive queries posed to OISs under such inconsistency-tolerant semantics. As for updates, we present an approach to compute the result of updating a possibly inconsistent OIS with both insertion and deletion of extensional knowledge

RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

The interaction of representation and reasoning

Automated reasoning is an enabling technology for many applications of informatics. These applications include verifying that a computer program meets its specification; enabling a robot to form a plan to achieve a task and answering questions by combining information from diverse sources, e.g. on the Internet, etc. How is automated reasoning possible? Firstly, knowledge of a domain must be stored in a computer, usually in the form of logical formulae. This knowledge might, for instance, have been entered manually, retrieved from the Internet or perceived in the environment via sensors, such as cameras. Secondly, rules of inference are applied to old knowledge to derive new knowledge. Automated reasoning techniques have been adapted from logic, a branch of mathematics that was originally designed to formalize the reasoning of humans, especially mathematicians. My special interest is in the way that representation and reasoning interact. Successful reasoning is dependent on appropriate representation of both knowledge and successful methods of reasoning. Failures of reasoning can suggest changes of representation. This process of representational change can also be automated. We will illustrate the automation of representational change by drawing on recent work in my research group

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

Principles of Periodontology

Periodontal diseases are among the most common diseases affecting humans. Dental biofilm is a contributor to the etiology of most periodontal diseases. It is also widely accepted that immunological and inflammatory responses to biofilm components are manifested by signs and symptoms of periodontal disease. The outcome of such interaction is modulated by risk factors (modifiers), either inherent (genetic) or acquired (environmental), significantly affecting the initiation and progression of different periodontal disease phenotypes. While definitive genetic determinants responsible for either susceptibility or resistance to periodontal disease have yet to be identified, many factors affecting the pathogenesis have been described, including smoking, diabetes, obesity, medications, and nutrition. Currently, periodontal diseases are classified based upon clinical disease traits using radiographs and clinical examination. Advances in genomics, molecular biology, and personalized medicine may result in new guidelines for unambiguous disease definition and diagnosis in the future. Recent studies have implied relationships between periodontal diseases and systemic conditions. Answering critical questions regarding host‐parasite interactions in periodontal diseases may provide new insight in the pathogenesis of other biomedical disorders. Therapeutic efforts have focused on the microbial nature of the infection, as active treatment centers on biofilm disruption by non‐surgical mechanical debridement with antimicrobial and sometimes anti‐inflammatory adjuncts. The surgical treatment aims at gaining access to periodontal lesions and correcting unfavorable gingival/osseous contours to achieve a periodontal architecture that will provide for more effective oral hygiene and periodontal maintenance. In addition, advances in tissue engineering have provided innovative means to regenerate/repair periodontal defects, based upon principles of guided tissue regeneration and utilization of growth factors/biologic mediators. To maintain periodontal stability, these treatments need to be supplemented with long‐term maintenance (supportive periodontal therapy) programs

Coronectomy of deeply impacted lower third molar : incidence of outcomes and complications after one year follow-up

Objectives: The purpose of present study was to assess the surgical management of impacted third molar with proximity to the inferior alveolar nerve and complications associated with coronectomy in a series of patients undergoing third molar surgery. Material and Methods: The position of the mandibular canal in relation to the mandibular third molar region and mandibular foramen in the front part of the mandible (i.e., third molar in close proximity to the inferior alveolar nerve [IAN] or not) was identified on panoramic radiographs of patients scheduled for third molar extraction. Results: Close proximity to the IAN was observed in 64 patients (35 females, 29 males) with an impacted mandibular third molar. Coronectomy was performed in these patients. The most common complication was tooth migration away from the mandibular canal (n = 14), followed by root exposure (n = 5). Re-operation to remove the root was performed in cases with periapical infection and root exposure. Conclusions: The results indicate that coronectomy can be considered a reasonable and safe treatment alternative for patients who demonstrate elevated risk for injury to the inferior alveolar nerve with removal of the third molars. Coronectomy did not increase the incidence of damage to the inferior alveolar nerve and would be safer than complete extraction in situations in which the root of the mandibular third molar overlaps or is in close proximity to the mandibular canal

Pseudo-contractions as Gentle Repairs

Updating a knowledge base to remove an unwanted consequence is a challenging task. Some of the original sentences must be either deleted or weakened in such a way that the sentence to be removed is no longer entailed by the resulting set. On the other hand, it is desirable that the existing knowledge be preserved as much as possible, minimising the loss of information. Several approaches to this problem can be found in the literature. In particular, when the knowledge is represented by an ontology, two different families of frameworks have been developed in the literature in the past decades with numerous ideas in common but with little interaction between the communities: applications of AGM-like Belief Change and justification-based Ontology Repair. In this paper, we investigate the relationship between pseudo-contraction operations and gentle repairs. Both aim to avoid the complete deletion of sentences when replacing them with weaker versions is enough to prevent the entailment of the unwanted formula. We show the correspondence between concepts on both sides and investigate under which conditions they are equivalent. Furthermore, we propose a unified notation for the two approaches, which might contribute to the integration of the two areas