Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a new concept is pre-discovered and cannot support out-of-KB mention discovery; (ii) only using the concept label as the input along with the KB and thus lacking the contexts of a concept label; and (iii) mostly focusing on concept placement w.r.t a taxonomy of atomic concepts, instead of complex concepts, i.e., with logical operators. To address these issues, we propose a new benchmark, adapting MedMentions dataset (PubMed abstracts) with SNOMED CT versions in 2014 and 2017 under the Diseases sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic product. We provide usage on the evaluation with the dataset for out-of-KB mention discovery and concept placement, adapting recent Large Language Model based methods.

Discovering entity mentions that are out of a Knowledge Base (KB) from texts plays a critical role in KB maintenance, but has not yet been fully explored. The current methods are mostly limited to the simple threshold-based approach and feature-based classification, and the datasets for evaluation are relatively rare. We propose BLINKout, a new BERT-based Entity Linking (EL) method which can identify mentions that do not have corresponding KB entities by matching them to a special NIL entity. To better utilize BERT, we propose new techniques including NIL entity representation and classification, with synonym enhancement. We also apply KB Pruning and Versioning strategies to automatically construct out-of-KB datasets from common in-KB EL datasets. Results on five datasets of clinical notes, biomedical publications, and Wikipedia articles in various domains show the advantages of BLINKout over existing methods to identify out-of-KB mentions for the medical ontologies, UMLS, SNOMED CT, and the general KB, WikiData.

Digital Twins (DT) facilitate monitoring and reasoning processes in cyber-physical systems. They have progressively gained popularity over the past years because of intense research activity and industrial advancements. Cognitive Twins is a novel concept, recently coined to refer to the involvement of Semantic Web technology in DTs. Recent studies address the relevance of ontologies and knowledge graphs in the context of DTs, in terms of knowledge representation, interoperability and automatic reasoning. However, there is no comprehensive analysis of how semantic technologies, and specifically ontologies, are utilized within DTs. This Systematic Literature Review (SLR) is based on the analysis of 82 research articles, that either propose or benefit from ontologies with respect to DT. The paper uses different analysis perspectives, including a structural analysis based on a reference DT architecture, and an application-specific analysis to specifically address the different domains, such as Manufacturing and Infrastructure. The review also identifies open issues and possible research directions on the usage of ontologies and knowledge graphs in DTs.

The study of Description Logics have been historically mostly focused on features that can be translated to decidable fragments of first-order logic. In this paper, we leave this restriction behind and look for useful and decidable extensions outside first-order logic. We introduce universally quantified concepts, which take the form of variables that can be replaced with arbitrary concepts, and define two semantics of this extension. A schema semantics allows replacements of concept variables only by concepts from a particular language, giving us axiom schemata similar to modal logics. A second-order semantics allows replacement of concept variables with arbitrary subsets of the domain, which is similar to quantified predicates in second-order logic. To study the proposed semantics, we focus on the extension of the description logic $\mathcal{EL}$. We show that for a useful fragment of the extension, the conclusions entailed by the different semantics coincide, allowing us to use classical $\mathcal{EL}$ reasoning algorithms even for the second-order semantics. For a slightly smaller, but still useful, fragment, we were also able to show polynomial decidability of the extension. This fragment, in particular, can express a generalized form of role chain axioms, positive self restrictions, and some forms of (local) role-value-maps from KL-ONE, without requiring any additional constructors.

A seller wants to sell an item to n buyers. Buyer valuations are drawn i.i.d. from a distribution unknown to the seller; the seller only knows that the support is included in [a, b]. To be robust, the seller chooses a DSIC mechanism that optimizes the worst-case performance relative to the first-best benchmark. Our analysis unifies the regret and the ratio objectives. For these objectives, we derive an optimal mechanism and the corresponding performance in quasi-closed form, as a function of the support information and the number of buyers n. Our analysis reveals three regimes of support information and a new class of robust mechanisms. i.) With "low" support information, the optimal mechanism is a second-price auction (SPA) with random reserve, a focal class in earlier literature. ii.) With "high" support information, SPAs are strictly suboptimal, and an optimal mechanism belongs to a class of mechanisms we introduce, which we call pooling auctions (POOL); whenever the highest value is above a threshold, the mechanism still allocates to the highest bidder, but otherwise the mechanism allocates to a uniformly random buyer, i.e., pools low types. iii.) With "moderate" support information, a randomization between SPA and POOL is optimal. We also characterize optimal mechanisms within nested central subclasses of mechanisms: standard mechanisms that only allocate to the highest bidder, SPA with random reserve, and SPA with no reserve. We show strict separations in terms of performance across classes, implying that deviating from standard mechanisms is necessary for robustness.

The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies. Facilitating the integration of a dataset with other types of data increases the likelihood of reuse, and the potential of answering novel research questions. Ontologies are a useful tool for semantically tagging datasets as adding relevant metadata increases the understanding of how data was produced and increases its interoperability. Ontologies provide concepts for a particular domain as well as the relationships between concepts. By tagging data with ontology terms, data becomes both human and machine interpretable, allowing for increased reuse and interoperability. However, the task of identifying ontologies relevant to a particular research domain or technology is challenging, especially within the diverse realm of fundamental plant research. In this review, we outline the ontologies most relevant to the fundamental plant sciences and how they can be used to annotate data related to plant-specific experiments within metadata frameworks, such as Investigation-Study-Assay (ISA). We also outline repositories and platforms most useful for identifying applicable ontologies or finding ontology terms.

Model-Based Anomaly Detection has been a successful approach to identify deviations from the expected behavior of Cyber-Physical Production Systems. Since manual creation of these models is a time-consuming process, it is advantageous to learn them from data and represent them in a generic formalism like timed automata. However, these models - and by extension, the detected anomalies - can be challenging to interpret due to a lack of additional information about the system. This paper aims to improve model-based anomaly detection in CPPS by combining the learned timed automaton with a formal knowledge graph about the system. Both the model and the detected anomalies are described in the knowledge graph in order to allow operators an easier interpretation of the model and the detected anomalies. The authors additionally propose an ontology of the necessary concepts. The approach was validated on a five-tank mixing CPPS and was able to formally define both automata model as well as timing anomalies in automata execution.

A scientific paper can be divided into two major constructs which are Metadata and Full-body text. Metadata provides a brief overview of the paper while the Full-body text contains key-insights that can be valuable to fellow researchers. To retrieve metadata and key-insights from scientific papers, knowledge acquisition is a central activity. It consists of gathering, analyzing and organizing knowledge embedded in scientific papers in such a way that it can be used and reused whenever needed. Given the wealth of scientific literature, manual knowledge acquisition is a cumbersome task. Thus, computer-assisted and (semi-)automatic strategies are generally adopted. Our purpose in this research was two fold: curate Open Research Knowledge Graph (ORKG) with papers related to ontology learning and define an approach using ORKG as a computer-assisted tool to organize key-insights extracted from research papers. This approach was used to document the "epidemiological surveillance systems design and implementation" research problem and to prepare the related work of this paper. It is currently used to document "food information engineering", "Tabular data to Knowledge Graph Matching" and "Question Answering" research problems and "Neuro-symbolic AI" domain.

Wikidata is one of the largest public general-purpose Knowledge Bases (KBs). Yet, due to its collaborative nature, its schema and taxonomy have become convoluted. For the YAGO 4 KB, we combined Wikidata with the ontology from Schema.org, which reduced and cleaned up the taxonomy and constraints and made it possible to run automated reasoners on the data. However, it also cut away large parts of the Wikidata taxonomy. In this paper, we present our effort to merge the entire Wikidata taxonomy into the YAGO KB as much as possible. We pay particular attention to logical constraints and a careful distinction of classes and instances. Our work creates YAGO 4.5, which adds a rich layer of informative classes to YAGO, while at the same time keeping the KB logically consistent.

In this paper, a new perspective is suggested for unsupervised Ontology Matching (OM) or Ontology Alignment (OA) by treating it as a translation task. Ontologies are represented as graphs, and the translation is performed from a node in the source ontology graph to a path in the target ontology graph. The proposed framework, Truveta Mapper (TM), leverages a multi-task sequence-to-sequence transformer model to perform alignment across multiple ontologies in a zero-shot, unified and end-to-end manner. Multi-tasking enables the model to implicitly learn the relationship between different ontologies via transfer-learning without requiring any explicit cross-ontology manually labeled data. This also enables the formulated framework to outperform existing solutions for both runtime latency and alignment quality. The model is pre-trained and fine-tuned only on publicly available text corpus and inner-ontologies data. The proposed solution outperforms state-of-the-art approaches, Edit-Similarity, LogMap, AML, BERTMap, and the recently presented new OM frameworks in Ontology Alignment Evaluation Initiative (OAEI22), offers log-linear complexity, and overall makes the OM task efficient and more straightforward without much post-processing involving mapping extension or mapping repair. We are open sourcing our solution.