We present a method for extracting general modules for ontologies formulated in the description logic ALC. A module for an ontology is an ideally substantially smaller ontology that preserves all entailments for a user-specified set of terms. As such, it has applications such as ontology reuse and ontology analysis. Different from classical modules, general modules may use axioms not explicitly present in the input ontology, which allows for additional conciseness. So far, general modules have only been investigated for lightweight description logics. We present the first work that considers the more expressive description logic ALC. In particular, our contribution is a new method based on uniform interpolation supported by some new theoretical results. Our evaluation indicates that our general modules are often smaller than classical modules and uniform interpolants computed by the state-of-the-art, and compared with uniform interpolants, can be computed in a significantly shorter time. Moreover, our method can be used for, and in fact improves, the computation of uniform interpolants and classical modules.

Datalog reasoning based on the semina\"ive evaluation strategy evaluates rules using traditional join plans, which often leads to redundancy and inefficiency in practice, especially when the rules are complex. Hypertree decompositions help identify efficient query plans and reduce similar redundancy in query answering. However, it is unclear how this can be applied to materialisation and incremental reasoning with recursive Datalog programs. Moreover, hypertree decompositions require additional data structures and thus introduce nonnegligible overhead in both runtime and memory consumption. In this paper, we provide algorithms that exploit hypertree decompositions for the materialisation and incremental evaluation of Datalog programs. Furthermore, we combine this approach with standard Datalog reasoning algorithms in a modular fashion so that the overhead caused by the decompositions is reduced. Our empirical evaluation shows that, when the program contains complex rules, the combined approach is usually significantly faster than the baseline approach, sometimes by orders of magnitude.

We propose bounded fitting as a scheme for learning description logic concepts in the presence of ontologies. A main advantage is that the resulting learning algorithms come with theoretical guarantees regarding their generalization to unseen examples in the sense of PAC learning. We prove that, in contrast, several other natural learning algorithms fail to provide such guarantees. As a further contribution, we present the system SPELL which efficiently implements bounded fitting for the description logic $\mathcal{ELH}^r$ based on a SAT solver, and compare its performance to a state-of-the-art learner.

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.