Olga Mashkova

Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf

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.

Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf

Ontology embeddings map classes, roles, 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 optimization-based 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, 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 and formulated evaluation methods for knowledge base completion. We demonstrate that our embedding methods improve over the baseline ontology embedding in the task of knowledge base or ontology completion.

Jiaoyan Chen, Olga Mashkova, Fernando Zhapa-Camacho et al.

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. 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 as well as its property of faithfulness. Based on this, it systematically categorizes and analyses a relatively complete set of over 80 papers, according to the ontologies 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.

Aram Avetisyan, Shahane Tigranyan, Ariana Asatryan et al.

Numerous studies are aimed at diagnosing heart diseases based on 12-lead electrocardiographic (ECG) records using deep learning methods. These studies usually use specific datasets that differ in size and parameters, such as patient metadata, number of doctors annotating ECGs, types of devices for ECG recording, data preprocessing techniques, etc. It is well-known that high-quality deep neural networks trained on one ECG dataset do not necessarily perform well on another dataset or clinical settings. In this paper, we propose a methodology to improve the quality of heart disease prediction regardless of the dataset by training neural networks on a variety of datasets with further fine-tuning for the specific dataset. To show its applicability, we train different neural networks on a large private dataset TIS containing various ECG records from multiple hospitals and on a relatively small public dataset PTB-XL. We demonstrate that training the networks on a large dataset and fine-tuning it on a small dataset from another source outperforms the networks trained only on one small dataset. We also show how the ability of a deep neural networks to generalize allows to improve classification quality of more diseases.