Ontology Embedding: A Survey of Methods, Applications and Resources

Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies can directly support are quite limited in learning, approximation and prediction. One straightforward solution is to integrate statistical analysis and machine learning. To this end, automatically learning vector representation for knowledge of an ontology i.e., ontology embedding has been widely investigated in recent years. Numerous papers have been published on ontology embedding, but a lack of systematic reviews hinders researchers from gaining a comprehensive understanding of this field. To bridge this gap, we write this survey paper, which first introduces different kinds of semantics of ontologies, and formally defines ontology embedding from the perspectives of both mathematics and machine learning, as well as its property of faithfulness. Based on this, it systematically categorises and analyses a relatively complete set of over 80 papers, according to the ontologies and semantics that they aim at, and their technical solutions including geometric modeling, sequence modeling and graph propagation. This survey also introduces the applications of ontology embedding in ontology engineering, machine learning augmentation and life sciences, presents a new library mOWL, and discusses the challenges and future directions.

Enhancing Geometric Ontology Embeddings for $\mathcal{EL}^{++}$ with Negative Sampling and Deductive Closure Filtering

Ontology embeddings map classes, relations, and individuals in ontologies into $\mathbb{R}^n$, and within $\mathbb{R}^n$ similarity between entities can be computed or new axioms inferred. For ontologies in the Description Logic $\mathcal{EL}^{++}$, several embedding methods have been developed that explicitly generate models of an ontology. However, these methods suffer from some limitations; they do not distinguish between statements that are unprovable and provably false, and therefore they may use entailed statements as negatives. Furthermore, they do not utilize the deductive closure of an ontology to identify statements that are inferred but not asserted. We evaluated a set of embedding methods for $\mathcal{EL}^{++}$ ontologies based on high-dimensional ball representation of concept descriptions, incorporating several modifications that aim to make use of the ontology deductive closure. In particular, we designed novel negative losses that account both for the deductive closure and different types of negatives. We demonstrate that our embedding methods improve over the baseline ontology embedding in the task of knowledge base or ontology completion.

CatE: Embedding $\mathcal{ALC}$ ontologies using category-theoretical semantics

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.

From axioms over graphs to vectors, and back again: evaluating the properties of graph-based ontology embeddings

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.