Ontological knowledge, which comprises classes and properties and their relationships, is integral to world knowledge. It is significant to explore whether Pretrained Language Models (PLMs) know and understand such knowledge. However, existing PLM-probing studies focus mainly on factual knowledge, lacking a systematic probing of ontological knowledge. In this paper, we focus on probing whether PLMs store ontological knowledge and have a semantic understanding of the knowledge rather than rote memorization of the surface form. To probe whether PLMs know ontological knowledge, we investigate how well PLMs memorize: (1) types of entities; (2) hierarchical relationships among classes and properties, e.g., Person is a subclass of Animal and Member of Sports Team is a subproperty of Member of ; (3) domain and range constraints of properties, e.g., the subject of Member of Sports Team should be a Person and the object should be a Sports Team. To further probe whether PLMs truly understand ontological knowledge beyond memorization, we comprehensively study whether they can reliably perform logical reasoning with given knowledge according to ontological entailment rules. Our probing results show that PLMs can memorize certain ontological knowledge and utilize implicit knowledge in reasoning. However, both the memorizing and reasoning performances are less than perfect, indicating incomplete knowledge and understanding.

Knowledge graphs (KGs) have emerged as a prominent data representation and management paradigm. Being usually underpinned by a schema (e.g. an ontology), KGs capture not only factual information but also contextual knowledge. In some tasks, a few KGs established themselves as standard benchmarks. However, recent works outline that relying on a limited collection of datasets is not sufficient to assess the generalization capability of an approach. In some data-sensitive fields such as education or medicine, access to public datasets is even more limited. To remedy the aforementioned issues, we release PyGraft, a Python-based tool that generates highly customized, domain-agnostic schemas and knowledge graphs. The synthesized schemas encompass various RDFS and OWL constructs, while the synthesized KGs emulate the characteristics and scale of real-world KGs. Logical consistency of the generated resources is ultimately ensured by running a description logic (DL) reasoner. By providing a way of generating both a schema and KG in a single pipeline, PyGraft's aim is to empower the generation of a more diverse array of KGs for benchmarking novel approaches in areas such as graph-based machine learning (ML), or more generally KG processing. In graph-based ML in particular, this should foster a more holistic evaluation of model performance and generalization capability, thereby going beyond the limited collection of available benchmarks. PyGraft is available at: https://github.com/nicolas-hbt/pygraft.

Relation Extraction (RE) is the task of extracting semantic relationships between entities in a sentence and aligning them to relations defined in a vocabulary, which is generally in the form of a Knowledge Graph (KG) or an ontology. Various approaches have been proposed so far to address this task. However, applying these techniques to biomedical text often yields unsatisfactory results because it is hard to infer relations directly from sentences due to the nature of the biomedical relations. To address these issues, we present a novel technique called ReOnto, that makes use of neuro symbolic knowledge for the RE task. ReOnto employs a graph neural network to acquire the sentence representation and leverages publicly accessible ontologies as prior knowledge to identify the sentential relation between two entities. The approach involves extracting the relation path between the two entities from the ontology. We evaluate the effect of using symbolic knowledge from ontologies with graph neural networks. Experimental results on two public biomedical datasets, BioRel and ADE, show that our method outperforms all the baselines (approximately by 3\%).

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.