Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new Bio-ML track at OAEI 2022.

Applying deep learning techniques, particularly language models (LMs), in ontology engineering has raised widespread attention. However, deep learning frameworks like PyTorch and Tensorflow are predominantly developed for Python programming, while widely-used ontology APIs, such as the OWL API and Jena, are primarily Java-based. To facilitate seamless integration of these frameworks and APIs, we present Deeponto, a Python package designed for ontology engineering. The package encompasses a core ontology processing module founded on the widely-recognised and reliable OWL API, encapsulating its fundamental features in a more "Pythonic" manner and extending its capabilities to include other essential components including reasoning, verbalisation, normalisation, projection, and more. Building on this module, Deeponto offers a suite of tools, resources, and algorithms that support various ontology engineering tasks, such as ontology alignment and completion, by harnessing deep learning methodologies, primarily pre-trained LMs. In this paper, we also demonstrate the practical utility of Deeponto through two use-cases: the Digital Health Coaching in Samsung Research UK and the Bio-ML track of the Ontology Alignment Evaluation Initiative (OAEI).

Recent embedding-based methods have achieved great successes on exploiting entity alignment from knowledge graph (KG) embeddings of multiple modals. In this paper, we study embedding-based entity alignment (EEA) from a perspective of generative models. We show that EEA is a special problem where the main objective is analogous to that in a typical generative model, based on which we theoretically prove the effectiveness of the recently developed generative adversarial network (GAN)-based EEA methods. We then reveal that their incomplete objective limits the capacity on both entity alignment and entity synthesis (i.e., generating new entities). We mitigate this problem by introducing a generative EEA (abbr., GEEA) framework with the proposed mutual variational autoencoder (M-VAE) as the generative model. M-VAE can convert an entity from one KG to another and generate new entities from random noise vectors. We demonstrate the power of GEEA with theoretical analysis and empirical experiments on both entity alignment and entity synthesis tasks.

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.

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.

Business Knowledge Graphs (KGs) are important to many enterprises today, providing factual knowledge and structured data that steer many products and make them more intelligent. Despite their promising benefits, building business KG necessitates solving prohibitive issues of deficient structure and multiple modalities. In this paper, we advance the understanding of the practical challenges related to building KG in non-trivial real-world systems. We introduce the process of building an open business knowledge graph (OpenBG) derived from a well-known enterprise, Alibaba Group. Specifically, we define a core ontology to cover various abstract products and consumption demands, with fine-grained taxonomy and multimodal facts in deployed applications. OpenBG is an open business KG of unprecedented scale: 2.6 billion triples with more than 88 million entities covering over 1 million core classes/concepts and 2,681 types of relations. We release all the open resources (OpenBG benchmarks) derived from it for the community and report experimental results of KG-centric tasks. We also run up an online competition based on OpenBG benchmarks, and has attracted thousands of teams. We further pre-train OpenBG and apply it to many KG- enhanced downstream tasks in business scenarios, demonstrating the effectiveness of billion-scale multimodal knowledge for e-commerce. All the resources with codes have been released at \url{https://github.com/OpenBGBenchmark/OpenBG}.

Automating ontology construction and curation is an important but challenging task in knowledge engineering and artificial intelligence. Prediction by machine learning techniques such as contextual semantic embedding is a promising direction, but the relevant research is still preliminary especially for expressive ontologies in Web Ontology Language (OWL). In this paper, we present a new subsumption prediction method named BERTSubs for classes of OWL ontology. It exploits the pre-trained language model BERT to compute contextual embeddings of a class, where customized templates are proposed to incorporate the class context (e.g., neighbouring classes) and the logical existential restriction. BERTSubs is able to predict multiple kinds of subsumers including named classes from the same ontology or another ontology, and existential restrictions from the same ontology. Extensive evaluation on five real-world ontologies for three different subsumption tasks has shown the effectiveness of the templates and that BERTSubs can dramatically outperform the baselines that use (literal-aware) knowledge graph embeddings, non-contextual word embeddings and the state-of-the-art OWL ontology embeddings.

Large-scale pre-trained language models (PLMs) such as BERT have recently achieved great success and become a milestone in natural language processing (NLP). It is now the consensus of the NLP community to adopt PLMs as the backbone for downstream tasks. In recent works on knowledge graph question answering (KGQA), BERT or its variants have become necessary in their KGQA models. However, there is still a lack of comprehensive research and comparison of the performance of different PLMs in KGQA. To this end, we summarize two basic KGQA frameworks based on PLMs without additional neural network modules to compare the performance of nine PLMs in terms of accuracy and efficiency. In addition, we present three benchmarks for larger-scale KGs based on the popular SimpleQuestions benchmark to investigate the scalability of PLMs. We carefully analyze the results of all PLMs-based KGQA basic frameworks on these benchmarks and two other popular datasets, WebQuestionSP and FreebaseQA, and find that knowledge distillation techniques and knowledge enhancement methods in PLMs are promising for KGQA. Furthermore, we test ChatGPT, which has drawn a great deal of attention in the NLP community, demonstrating its impressive capabilities and limitations in zero-shot KGQA. We have released the code and benchmarks to promote the use of PLMs on KGQA.

Entity alignment (EA) for knowledge graphs (KGs) plays a critical role in knowledge engineering. Existing EA methods mostly focus on utilizing the graph structures and entity attributes (including literals), but ignore images that are common in modern multi-modal KGs. In this study we first constructed Multi-OpenEA -- eight large-scale, image-equipped EA benchmarks, and then evaluated some existing embedding-based methods for utilizing images. In view of the complementary nature of visual modal information and logical deduction, we further developed a new multi-modal EA method named LODEME using logical deduction and multi-modal KG embedding, with state-of-the-art performance achieved on Multi-OpenEA and other existing multi-modal EA benchmarks.

Visual Relation Detection (VRD) aims to detect relationships between objects for image understanding. Most existing VRD methods rely on thousands of training samples of each relationship to achieve satisfactory performance. Some recent papers tackle this problem by few-shot learning with elaborately designed pipelines and pre-trained word vectors. However, the performance of existing few-shot VRD models is severely hampered by the poor generalization capability, as they struggle to handle the vast semantic diversity of visual relationships. Nonetheless, humans have the ability to learn new relationships with just few examples based on their knowledge. Inspired by this, we devise a knowledge-augmented, few-shot VRD framework leveraging both textual knowledge and visual relation knowledge to improve the generalization ability of few-shot VRD. The textual knowledge and visual relation knowledge are acquired from a pre-trained language model and an automatically constructed visual relation knowledge graph, respectively. We extensively validate the effectiveness of our framework. Experiments conducted on three benchmarks from the commonly used Visual Genome dataset show that our performance surpasses existing state-of-the-art models with a large improvement.