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.

We present an ontology design pattern for modeling Names as part of Roles, to capture scenarios where an Agent performs different Roles using different Names associated with the different Roles. Examples of an Agent performing a Role using different Names are rather ubiquitous, e.g., authors who write under different pseudonyms, or different legal names for citizens of more than one country. The proposed pattern is a modified merger of a standard Agent Role and a standard Name pattern stub.

Cross-lingual and cross-domain knowledge alignment without sufficient external resources is a fundamental and crucial task for fusing irregular data. As the element-wise fusion process aiming to discover equivalent objects from different knowledge graphs (KGs), entity alignment (EA) has been attracting great interest from industry and academic research recent years. Most of existing EA methods usually explore the correlation between entities and relations through neighbor nodes, structural information and external resources. However, the complex intrinsic interactions among triple elements and role information are rarely modeled in these methods, which may lead to the inadequate illustration for triple. In addition, external resources are usually unavailable in some scenarios especially cross-lingual and cross-domain applications, which reflects the little scalability of these methods. To tackle the above insufficiency, a novel universal EA framework (OTIEA) based on ontology pair and role enhancement mechanism via triple-aware attention is proposed in this paper without introducing external resources. Specifically, an ontology-enhanced triple encoder is designed via mining intrinsic correlations and ontology pair information instead of independent elements. In addition, the EA-oriented representations can be obtained in triple-aware entity decoder by fusing role diversity. Finally, a bidirectional iterative alignment strategy is deployed to expand seed entity pairs. The experimental results on three real-world datasets show that our framework achieves a competitive performance compared with baselines.

In recent years, the field of neural machine translation (NMT) for SPARQL query generation has witnessed a significant growth. Recently, the incorporation of the copy mechanism with traditional encoder-decoder architectures and the use of pre-trained encoder-decoders have set new performance benchmarks. This paper presents a large variety of experiments that replicate and expand upon recent NMT-based SPARQL generation studies, comparing pre-trained and non-pre-trained models, question annotation formats, and the use of a copy mechanism for non-pre-trained and pre-trained models. Our results show that either adding the copy mechanism or using a question annotation improves performances for nonpre-trained models and for pre-trained models, setting new baselines for three popular datasets.

Effectively representing medical concepts and patients is important for healthcare analytical applications. Representing medical concepts for healthcare analytical tasks requires incorporating medical domain knowledge and prior information from patient description data. Current methods, such as feature engineering and mapping medical concepts to standardized terminologies, have limitations in capturing the dynamic patterns from patient description data. Other embedding-based methods have difficulties in incorporating important medical domain knowledge and often require a large amount of training data, which may not be feasible for most healthcare systems. Our proposed framework, MD-Manifold, introduces a novel approach to medical concept and patient representation. It includes a new data augmentation approach, concept distance metric, and patient-patient network to incorporate crucial medical domain knowledge and prior data information. It then adapts manifold learning methods to generate medical concept-level representations that accurately reflect medical knowledge and patient-level representations that clearly identify heterogeneous patient cohorts. MD-Manifold also outperforms other state-of-the-art techniques in various downstream healthcare analytical tasks. Our work has significant implications in information systems research in representation learning, knowledge-driven machine learning, and using design science as middle-ground frameworks for downstream explorative and predictive analyses. Practically, MD-Manifold has the potential to create effective and generalizable representations of medical concepts and patients by incorporating medical domain knowledge and prior data information. It enables deeper insights into medical data and facilitates the development of new analytical applications for better healthcare outcomes.

We present a tool for modelling and reasoning with knowledge from various diverse (and possibly conflicting) viewpoints. The theoretical underpinnings are provided by enhancing base logics by standpoints according to a recently introduced formalism that we also recall. The tool works by translating the standpoint-enhanced version of the description logic SROIQ to its plain (i.e. classical) version. Existing reasoners can then be directly used to provide automated support for reasoning about diverse standpoints.