Knowledge graphs (KGs) have become the preferred technology for representing, sharing and adding knowledge to modern AI applications. While KGs have become a mainstream technology, the RDF/SPARQL-centric toolset for operating with them at scale is heterogeneous, difficult to integrate and only covers a subset of the operations that are commonly needed in data science applications. In this paper, we present KGTK, a data science-centric toolkit to represent, create, transform, enhance and analyze KGs. KGTK represents graphs in tables and leverages popular libraries developed for data science applications, enabling a wide audience of developers to easily construct knowledge graph pipelines for their applications. We illustrate KGTK with real-world scenarios in which we have used KGTK to integrate and manipulate large KGs, such as Wikidata, DBpedia and ConceptNet, in our own work.

In this paper, based on a fuzzy entropy feature selection framework, different methods have been implemented and compared to improve the key components of the framework. Those methods include the combinations of three ideal vector calculations, three maximal similarity classifiers and three fuzzy entropy functions. Different feature removal orders based on the fuzzy entropy values were also compared. The proposed method was evaluated on three publicly available biomedical datasets. From the experiments, we concluded the optimized combination of the ideal vector, similarity classifier and fuzzy entropy function for feature selection. The optimized framework was also compared with other six classical filter-based feature selection methods. The proposed method was ranked as one of the top performers together with the Correlation and ReliefF methods. More importantly, the proposed method achieved the most stable performance for all three datasets when the features being gradually removed. This indicates a better feature ranking performance than the other compared methods.

We focus on handling conflicting and uncertain information in lightweight ontologies, where uncertainty is represented in a possibilistic logic setting. We use DL-Lite, a tractable fragment of Description Logic, to specify terminological knowledge (i.e., TBox). We assume the TBox to be stable and coherent, while its combination with a set of assertional facts (i.e., ABox) may be inconsistent. We address the problem of dealing with conflicts when the reliability relation between sources is only partially ordered. We propose to represent the uncertain ABox as a symbolic weighted base, where a strict partial preorder is applied on the weights. In this context, we provide a strategy for computing a single repair for the ABox, called the partial possibilistic repair. The idea is to consider all compatible bases of a partially preordered ABox (which intuitively encode total extensions of the partial preorder), compute their associated possibilistic repairs, before intersecting those repairs. We define the notion of π-accepted assertions and provide an equivalent characterization, therefore ensuring tractable computations of our method.

Bounded-memory computability continues to be in the focus of those areas of AI and databases that deal with feasible computations over streams be it feasible arithmetical calculations on low-level streams or feasible query answering for declaratively specified queries on relational data streams or even feasible query answering for high-level queries on streams w.r.t. a set of constraints in an ontology such as in the paradigm of Ontology-Based Data Access (OBDA). In classical OBDA, a high-level query is answered by transforming it into a query on data source level. The transformation requires a rewriting step, where knowledge from an ontology is incorporated into the query, followed by an unfolding step with respect to a set of mappings. Given an OBDA setting it is very difficult to decide, whether and how a query can be answered efficiently. In particular it is difficult to decide whether a query can be answered in bounded memory, i.e., in constant space w.r.t. an infinitely growing prefix of a data stream. This work presents criteria for bounded-memory computability of select-project-join (SPJ) queries over streams with application time. Deciding whether an SPJ query can be answered in constant space is easier than for high-level queries, as neither an ontology nor a set of mappings are part of the input. Using the transformation process of classical OBDA, these criteria then can help deciding the efficiency of answering high-level queries on streams.

Machine learning algorithms are now synonymous with finding patterns in data but not all patterns are suitable for statistics based data-driven techniques, for example when these patterns don't have explicitly labelled targets to learn from. In some cases, these patterns can be expressed precisely as a rule. Reasoning is the process of matching rule-based patterns or verifying that they don't exist in a graph. Because these patterns are found with deductive logic they can be found more efficiently and interpreted more easily than Machine Learning patterns which are induced from the data. This article will introduce some common patterns and how you can express them in the rule language, Datalog, using RDFox, a knowledge graph and semantic reasoning engine developed by Oxford Semantic Technologies.

Increased availability of electronic health records (EHR) has enabled researchers to study various medical questions. Cohort selection for the hypothesis under investigation is one of the main consideration for EHR analysis. For uncommon diseases, cohorts extracted from EHRs contain very limited number of records - hampering the robustness of any analysis. Data augmentation methods have been successfully applied in other domains to address this issue mainly using simulated records. In this paper, we present ODVICE, a data augmentation framework that leverages the medical concept ontology to systematically augment records using a novel ontologically guided Monte-Carlo graph spanning algorithm. The tool allows end users to specify a small set of interactive controls to control the augmentation process. We analyze the importance of ODVICE by conducting studies on MIMIC-III dataset for two learning tasks. Our results demonstrate the predictive performance of ODVICE augmented cohorts, showing ~30% improvement in area under the curve (AUC) over the non-augmented dataset and other data augmentation strategies.

In this paper, an overview of the state of the art on knowledge graph generation is provided, with focus on the two prevalent mapping languages: the W3C recommended R2RML and its generalisation RML. We look into details on their differences and explain how knowledge graphs, in the form of RDF graphs, can be generated with each one of the two mapping languages. Then we assess if the vocabulary terms were properly applied to the data and no violations occurred on their use, either using R2RML or RML to generate the desired knowledge graph.

This Chapter describes a new technique, called "knowledge patterns", for helping construct axiom-rich, formal ontologies, based on identifying and explicitly representing recurring patterns of knowledge (theory schemata) in the ontology, and then stating how those patterns map onto domain-specific concepts in the ontology. From a modeling perspective, knowledge patterns provide an important insight into the structure of a formal ontology: rather than viewing a formal ontology simply as a list of terms and axioms, knowledge patterns views it as a collection of abstract, modular theories (the "knowledge patterns") plus a collection of modeling decisions stating how different aspects of the world can be modeled using those theories. Knowledge patterns make both those abstract theories and their mappings to the domain of interest explicit, thus making modeling decisions clear, and avoiding some of the ontological confusion that can otherwise arise. In addition, from a computational perspective, knowledge patterns provide a simple and computationally efficient mechanism for facilitating knowledge reuse. We describe the technique and an application built using them, and then critique its strengths and weaknesses. We conclude that this technique enables us to better explicate both the structure and modeling decisions made when constructing a formal axiom-rich ontology.

Ontologies are the prime way of organizing data in the Semantic Web. Often, it is necessary to combine several, independently developed ontologies to obtain a knowledge graph fully representing a domain of interest. The complementarity of existing ontologies can be leveraged by merging them. Existing approaches for ontology merging mostly implement a binary merge. However, with the growing number and size of relevant ontologies across domains, scalability becomes a central challenge. A multi-ontology merging technique offers a potential solution to this problem. We present CoMerger, a scalable multiple ontologies merging method. For efficient processing, rather than successively merging complete ontologies pairwise, we group related concepts across ontologies into partitions and merge first within and then across those partitions. The experimental results on well-known datasets confirm the feasibility of our approach and demonstrate its superiority over binary strategies. A prototypical implementation is freely accessible through a live web portal.