Machine learning with Semantic Web ontologies follows several strategies, one of which involves projecting ontologies into graph structures and applying graph embeddings or graph-based machine learning methods to the resulting graphs. Several methods have been developed that project ontology axioms into graphs. However, these methods are limited in the type of axioms they can project (totality), whether they are invertible (injectivity), and how they exploit semantic information. These limitations restrict the kind of tasks to which they can be applied. Category-theoretical semantics of logic languages formalizes interpretations using categories instead of sets, and categories have a graph-like structure. We developed CatE, which uses the category-theoretical formulation of the semantics of the Description Logic $\mathcal{ALC}$ to generate a graph representation for ontology axioms. The CatE projection is total and injective, and therefore overcomes limitations of other graph-based ontology embedding methods which are generally not invertible. We apply CatE to a number of different tasks, including deductive and inductive reasoning, and we demonstrate that CatE improves over state of the art ontology embedding methods. Furthermore, we show that CatE can also outperform model-theoretic ontology embedding methods in machine learning tasks in the biomedical domain.

Several approaches have been developed that generate embeddings for Description Logic ontologies and use these embeddings in machine learning. One approach of generating ontologies embeddings is by first embedding the ontologies into a graph structure, i.e., introducing a set of nodes and edges for named entities and logical axioms, and then applying a graph embedding to embed the graph in $\mathbb{R}^n$. Methods that embed ontologies in graphs (graph projections) have different formal properties related to the type of axioms they can utilize, whether the projections are invertible or not, and whether they can be applied to asserted axioms or their deductive closure. We analyze, qualitatively and quantitatively, several graph projection methods that have been used to embed ontologies, and we demonstrate the effect of the properties of graph projections on the performance of predicting axioms from ontology embeddings. We find that there are substantial differences between different projection methods, and both the projection of axioms into nodes and edges as well ontological choices in representing knowledge will impact the success of using ontology embeddings to predict axioms.

This paper shines a light on the potential of definition-based semantic models for detecting idiomatic and semi-idiomatic multiword expressions (MWEs) in clinical terminology. Our study focuses on biomedical entities defined in the UMLS ontology and aims to help prioritize the translation efforts of these entities. In particular, we develop an effective tool for scoring the idiomaticity of biomedical MWEs based on the degree of similarity between the semantic representations of those MWEs and a weighted average of the representation of their constituents. We achieve this using a biomedical language model trained to produce similar representations for entity names and their definitions, called BioLORD. The importance of this definition-based approach is highlighted by comparing the BioLORD model to two other state-of-the-art biomedical language models based on Transformer: SapBERT and CODER. Our results show that the BioLORD model has a strong ability to identify idiomatic MWEs, not replicated in other models. Our corpus-free idiomaticity estimation helps ontology translators to focus on more challenging MWEs.

Standpoint EL is a multi-modal extension of the popular description logic EL that allows for the integrated representation of domain knowledge relative to diverse standpoints or perspectives. Advantageously, its satisfiability problem has recently been shown to be in PTime, making it a promising framework for large-scale knowledge integration. In this paper, we show that we can further push the expressivity of this formalism, arriving at an extended logic, called Standpoint EL+, which allows for axiom negation, role chain axioms, self-loops, and other features, while maintaining tractability. This is achieved by designing a satisfiability-checking deduction calculus, which at the same time addresses the need for practical algorithms. We demonstrate the feasibility of our calculus by presenting a prototypical Datalog implementation of its deduction rules.

When building a new application we are increasingly confronted with the need of reusing and integrating pre-existing knowledge. Nevertheless, it is a fact that this prior knowledge is virtually impossible to reuse as-is. This is true also in domains, e.g., eHealth, where a lot of effort has been put into developing high-quality standards and reference ontologies, e.g. FHIR1. In this paper, we propose an integrated methodology, called iTelos, which enables data and knowledge reuse towards the construction of Interoperable Electronic Health Records (iEHR). The key intuition is that the data level and the schema level of an application should be developed independently, thus allowing for maximum flexibility in the reuse of the prior knowledge, but under the overall guidance of the needs to be satisfied, formalized as competence queries. This intuition is implemented by codifying all the requirements, including those concerning reuse, as part of a purpose defined a priori, which is then used to drive a middle-out development process where the application schema and data are continuously aligned. The proposed methodology is validated through its application to a large-scale case study.

Investigating whether pre-trained language models (LMs) can function as knowledge bases (KBs) has raised wide research interests recently. However, existing works focus on simple, triple-based, relational KBs, but omit more sophisticated, logic-based, conceptualised KBs such as OWL ontologies. To investigate an LM's knowledge of ontologies, we propose OntoLAMA, a set of inference-based probing tasks and datasets from ontology subsumption axioms involving both atomic and complex concepts. We conduct extensive experiments on ontologies of different domains and scales, and our results demonstrate that LMs encode relatively less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference (NLI) but can improve on SI significantly when a small number of samples are given. We will open-source our code and datasets.

Existing task-oriented conversational search systems heavily rely on domain ontologies with pre-defined slots and candidate value sets. In practical applications, these prerequisites are hard to meet, due to the emerging new user requirements and ever-changing scenarios. To mitigate these issues for better interaction performance, there are efforts working towards detecting out-of-vocabulary values or discovering new slots under unsupervised or semi-supervised learning paradigm. However, overemphasizing on the conversation data patterns alone induces these methods to yield noisy and arbitrary slot results. To facilitate the pragmatic utility, real-world systems tend to provide a stringent amount of human labelling quota, which offers an authoritative way to obtain accurate and meaningful slot assignments. Nonetheless, it also brings forward the high requirement of utilizing such quota efficiently. Hence, we formulate a general new slot discovery task in an information extraction fashion and incorporate it into an active learning framework to realize human-in-the-loop learning. Specifically, we leverage existing language tools to extract value candidates where the corresponding labels are further leveraged as weak supervision signals. Based on these, we propose a bi-criteria selection scheme which incorporates two major strategies, namely, uncertainty-based sampling and diversity-based sampling to efficiently identify terms of interest. We conduct extensive experiments on several public datasets and compare with a bunch of competitive baselines to demonstrate the effectiveness of our method. We have made the code and data used in this paper publicly available.

Ontologies play a critical role in Semantic Web technologies by providing a structured and standardized way to represent knowledge and enabling machines to understand the meaning of data. Several taxonomies and ontologies have been generated, but individuals target one domain, and only some of those have been found expensive in time and manual effort. Also, they need more coverage of unconventional topics representing a more holistic and comprehensive view of the knowledge landscape and interdisciplinary collaborations. Thus, there needs to be an ontology covering Science and Technology and facilitate multidisciplinary research by connecting topics from different fields and domains that may be related or have commonalities. To address these issues, we present an automatic Science and Technology Ontology (S&TO) that covers unconventional topics in different science and technology domains. The proposed S&TO can promote the discovery of new research areas and collaborations across disciplines. The ontology is constructed by applying BERTopic to a dataset of 393,991 scientific articles collected from Semantic Scholar from October 2021 to August 2022, covering four fields of science. Currently, S&TO includes 5,153 topics and 13,155 semantic relations. S&TO model can be updated by running BERTopic on more recent datasets.

In reverse engineering of database queries, we aim to construct a query from a given set of answers and non-answers; it can then be used to explore the data further or as an explanation of the answers and non-answers. We investigate this query-by-example problem for queries formulated in positive fragments of linear temporal logic LTL over timestamped data, focusing on the design of suitable query languages and the combined and data complexity of deciding whether there exists a query in the given language that separates the given answers from non-answers. We consider both plain LTL queries and those mediated by LTL-ontologies.

Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts. We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-based framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations. The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes). We discuss the usefulness of the weak supervision approach and propose directions for future studies.