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).

Knowledge Graph (KG) completion is the problem of extending an incomplete KG with missing facts. A key feature of Machine Learning approaches for KG completion is their ability to learn inference patterns, so that the predicted facts are the results of applying these patterns to the KG. Standard completion benchmarks, however, are not well-suited for evaluating models' abilities to learn patterns, because the training and test sets of these benchmarks are a random split of a given KG and hence do not capture the causality of inference patterns. We propose a novel approach for designing KG completion benchmarks based on the following principles: there is a set of logical rules so that the missing facts are the results of the rules' application; the training set includes both premises matching rule antecedents and the corresponding conclusions; the test set consists of the results of applying the rules to the training set; the negative examples are designed to discourage the models from learning rules not entailed by the rule set. We use our methodology to generate several benchmarks and evaluate a wide range of existing KG completion systems. Our results provide novel insights on the ability of existing models to induce inference patterns from incomplete KGs.

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.

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.

In recent years, there has been increasing interest in explanation methods for neural model predictions that offer precise formal guarantees. These include abductive (respectively, contrastive) methods, which aim to compute minimal subsets of input features that are sufficient for a given prediction to hold (respectively, to change a given prediction). The corresponding decision problems are, however, known to be intractable. In this paper, we investigate whether tractability can be regained by focusing on neural models implementing a monotonic function. Although the relevant decision problems remain intractable, we can show that they become solvable in polynomial time by means of greedy algorithms if we additionally assume that the activation functions are continuous everywhere and differentiable almost everywhere. Our experiments suggest favourable performance of our algorithms.

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.

Machine learning methods especially deep neural networks have achieved great success but many of them often rely on a number of labeled samples for training. In real-world applications, we often need to address sample shortage due to e.g., dynamic contexts with emerging prediction targets and costly sample annotation. Therefore, low-resource learning, which aims to learn robust prediction models with no enough resources (especially training samples), is now being widely investigated. Among all the low-resource learning studies, many prefer to utilize some auxiliary information in the form of Knowledge Graph (KG), which is becoming more and more popular for knowledge representation, to reduce the reliance on labeled samples. In this survey, we very comprehensively reviewed over $90$ papers about KG-aware research for two major low-resource learning settings -- zero-shot learning (ZSL) where new classes for prediction have never appeared in training, and few-shot learning (FSL) where new classes for prediction have only a small number of labeled samples that are available. We first introduced the KGs used in ZSL and FSL studies as well as the existing and potential KG construction solutions, and then systematically categorized and summarized KG-aware ZSL and FSL methods, dividing them into different paradigms such as the mapping-based, the data augmentation, the propagation-based and the optimization-based. We next presented different applications, including not only KG augmented tasks in Computer Vision and Natural Language Processing (e.g., image classification, text classification and knowledge extraction), but also tasks for KG curation (e.g., inductive KG completion), and some typical evaluation resources for each task. We eventually discussed some challenges and future directions on aspects such as new learning and reasoning paradigms, and the construction of high quality KGs.

Ontology alignment (a.k.a ontology matching (OM)) plays a critical role in knowledge integration. Owing to the success of machine learning in many domains, it has been applied in OM. However, the existing methods, which often adopt ad-hoc feature engineering or non-contextual word embeddings, have not yet outperformed rule-based systems especially in an unsupervised setting. In this paper, we propose a novel OM system named BERTMap which can support both unsupervised and semi-supervised settings. It first predicts mappings using a classifier based on fine-tuning the contextual embedding model BERT on text semantics corpora extracted from ontologies, and then refines the mappings through extension and repair by utilizing the ontology structure and logic. Our evaluation with three alignment tasks on biomedical ontologies demonstrates that BERTMap can often perform better than the leading OM systems LogMap and AML.

Smart factories are equipped with machines that can sense their manufacturing environments, interact with each other, and control production processes. Smooth operation of such factories requires that the machines and engineering personnel that conduct their monitoring and diagnostics share a detailed common industrial knowledge about the factory, e.g., in the form of knowledge graphs. Creation and maintenance of such knowledge is expensive and requires automation. In this work we show how machine learning that is specifically tailored towards industrial applications can help in knowledge graph completion. In particular, we show how knowledge completion can benefit from event logs that are common in smart factories. We evaluate this on the knowledge graph from a real world-inspired smart factory with encouraging results.

Conjunctive query (CQ) answering over knowledge bases is an important reasoning task. However, with expressive ontology languages such as OWL, query answering is computationally very expensive. The PAGOdA system addresses this issue by using a tractable reasoner to compute lower and upper-bound approximations, falling back to a fully-fledged OWL reasoner only when these bounds don't coincide. The effectiveness of this approach critically depends on the quality of the approximations, and in this paper we explore a technique for computing closer approximations via RSA, an ontology language that subsumes all the OWL 2 profiles while still maintaining tractability. We present a novel approximation of OWL 2 ontologies into RSA, and an algorithm to compute a closer (than PAGOdA) lower bound approximation using the RSA combined approach. We have implemented these algorithms in a prototypical CQ answering system, and we present a preliminary evaluation of our system that shows significant performance improvements w.r.t. PAGOdA.