Ernesto Jiménez-Ruiz

Yuan He, Jiaoyan Chen, Ernesto Jiménez-Ruiz et al. · oxford

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.

Yuan He, Jiaoyan Chen, Hang Dong et al. · oxford

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 BioML track at OAEI 2022.

Jiaoyan Chen, Hang Dong, Janna Hastings et al.

The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.

Zhuoxun Zheng, Baifan Zhou, Dongzhuoran Zhou et al.

Industrial analytics that includes among others equipment diagnosis and anomaly detection heavily relies on integration of heterogeneous production data. Knowledge Graphs (KGs) as the data format and ontologies as the unified data schemata are a prominent solution that offers high quality data integration and a convenient and standardised way to exchange data and to layer analytical applications over it. However, poor design of ontologies of high degree of mismatch between them and industrial data naturally lead to KGs of low quality that impede the adoption and scalability of industrial analytics. Indeed, such KGs substantially increase the training time of writing queries for users, consume high volume of storage for redundant information, and are hard to maintain and update. To address this problem we propose an ontology reshaping approach to transform ontologies into KG schemata that better reflect the underlying data and thus help to construct better KGs. In this poster we present a preliminary discussion of our on-going research, evaluate our approach with a rich set of SPARQL queries on real-world industry data at Bosch and discuss our findings.

Erik Bryhn Myklebust, Ernesto Jimenez-Ruiz, Jiaoyan Chen et al.

Extrapolation of adverse biological (toxic) effects of chemicals is an important contribution to expand available hazard data in (eco)toxicology without the use of animals in laboratory experiments. In this work, we extrapolate effects based on a knowledge graph (KG) consisting of the most relevant effect data as domain-specific background knowledge. An effect prediction model, with and without background knowledge, was used to predict mean adverse biological effect concentration of chemicals as a prototypical type of stressors. The background knowledge improves the model prediction performance by up to 40\% in terms of $R^2$ (\ie coefficient of determination). We use the KG and KG embeddings to provide quantitative and qualitative insights into the predictions. These insights are expected to improve the confidence in effect prediction. Larger scale implementation of such extrapolation models should be expected to support hazard and risk assessment, by simplifying and reducing testing needs.

Sevinj Teymurova, Ernesto Jiménez-Ruiz, Tillman Weyde et al.

Ontology alignment is integral to achieving semantic interoperability as the number of available ontologies covering intersecting domains is increasing. This paper proposes OWL2Vec4OA, an extension of the ontology embedding system OWL2Vec*. While OWL2Vec* has emerged as a powerful technique for ontology embedding, it currently lacks a mechanism to tailor the embedding to the ontology alignment task. OWL2Vec4OA incorporates edge confidence values from seed mappings to guide the random walk strategy. We present the theoretical foundations, implementation details, and experimental evaluation of our proposed extension, demonstrating its potential effectiveness for ontology alignment tasks.

Pedro Giesteira Cotovio, Ernesto Jimenez-Ruiz, Catia Pesquita

Knowledge Graphs (KG) are the backbone of many data-intensive applications since they can represent data coupled with its meaning and context. Aligning KGs across different domains and providers is necessary to afford a fuller and integrated representation. A severe limitation of current KG alignment (KGA) algorithms is that they fail to articulate logical thinking and reasoning with lexical, structural, and semantic data learning. Deep learning models are increasingly popular for KGA inspired by their good performance in other tasks, but they suffer from limitations in explainability, reasoning, and data efficiency. Hybrid neurosymbolic learning models hold the promise of integrating logical and data perspectives to produce high-quality alignments that are explainable and support validation through human-centric approaches. This paper examines the current state of the art in KGA and explores the potential for neurosymbolic integration, highlighting promising research directions for combining these fields.

Cliff O'Reilly, Ernesto Jimenez-Ruiz, Tillman Weyde

Connecting LLMs with formal knowledge representation and reasoning is a promising approach to address their shortcomings. Embeddings and sparse autoencoders are widely used to represent textual content, but the semantics are entangled with syntactic and language-specific information. We propose a method that isolates concept semantics in Large Langue Models by averaging concept activations derived via Sparse Autoencoders. We create English text representations from OWL ontology classes, translate the English into French and Chinese and then pass these texts as prompts to the Gemma 2B LLM. Using the open source Gemma Scope suite of Sparse Autoencoders, we obtain concept activations for each class and language version. We average the different language activations to derive a conceptual average. We then correlate the conceptual averages with a ground truth mapping between ontology classes. Our results give a strong indication that the conceptual average aligns to the true relationship between classes when compared with a single language by itself. The result hints at a new technique which enables mechanistic interpretation of internal network states with higher accuracy.

David Herron, Ernesto Jiménez-Ruiz, Giacomo Tarroni et al.

NeSy4VRD is a multifaceted resource designed to support the development of neurosymbolic AI (NeSy) research. NeSy4VRD re-establishes public access to the images of the VRD dataset and couples them with an extensively revised, quality-improved version of the VRD visual relationship annotations. Crucially, NeSy4VRD provides a well-aligned, companion OWL ontology that describes the dataset domain.It comes with open source infrastructure that provides comprehensive support for extensibility of the annotations (which, in turn, facilitates extensibility of the ontology), and open source code for loading the annotations to/from a knowledge graph. We are contributing NeSy4VRD to the computer vision, NeSy and Semantic Web communities to help foster more NeSy research using OWL-based knowledge graphs.

Marco Cremaschi, Blerina Spahiu, Matteo Palmonari et al.

Tabular data plays a pivotal role in various fields, making it a popular format for data manipulation and exchange, particularly on the web. The interpretation, extraction, and processing of tabular information are invaluable for knowledge-intensive applications. Notably, significant efforts have been invested in annotating tabular data with ontologies and entities from background knowledge graphs, a process known as Semantic Table Interpretation (STI). STI automation aids in building knowledge graphs, enriching data, and enhancing web-based question answering. This survey aims to provide a comprehensive overview of the STI landscape. It starts by categorizing approaches using a taxonomy of 31 attributes, allowing for comparisons and evaluations. It also examines available tools, assessing them based on 12 criteria. Furthermore, the survey offers an in-depth analysis of the Gold Standards used for evaluating STI approaches. Finally, it provides practical guidance to help end-users choose the most suitable approach for their specific tasks while also discussing unresolved issues and suggesting potential future research directions.

Sviatoslav Lushnei, Dmytro Shumskyi, Severyn Shykula et al.

Ontology alignment plays a crucial role in integrating diverse data sources across domains. There is a large plethora of systems that tackle the ontology alignment problem, yet challenges persist in producing highly quality correspondences among a set of input ontologies. Human-in-the-loop during the alignment process is essential in applications requiring very accurate mappings. User involvement is, however, expensive when dealing with large ontologies. In this paper, we explore the feasibility of using Large Language Models (LLM) as an alternative to the domain expert. The use of the LLM focuses only on the validation of the subset of correspondences where an ontology alignment system is very uncertain. We have conducted an extensive evaluation over several matching tasks of the Ontology Alignment Evaluation Initiative (OAEI), analysing the performance of several state-of-the-art LLMs using different ontology-driven prompt templates. The LLM results are also compared against simulated Oracles with variable error rates.

Piero A. Bonatti, John Domingue, Anna Lisa Gentile et al.

Computer-Using Agents (CUA) enable users to automate increasingly-complex tasks using graphical interfaces such as browsers. As many potential tasks require personal data, we propose Computer-Using Personal Agents (CUPAs) that have access to an external repository of the user's personal data. Compared with CUAs, CUPAs offer users better control of their personal data, the potential to automate more tasks involving personal data, better interoperability with external sources of data, and better capabilities to coordinate with other CUPAs in order to solve collaborative tasks involving the personal data of multiple users.

Alex Clay, Ernesto Jiménez-Ruiz

LLMs are frequently used tools for conversational generation. Without additional information LLMs can generate lower quality responses due to lacking relevant content and hallucinations, as well as the perception of poor emotional capability, and an inability to maintain a consistent character. Knowledge graphs are commonly used forms of external knowledge and may provide solutions to these challenges. This paper introduces three proposals, utilizing knowledge graphs to enhance LLM generation. Firstly, dynamic knowledge graph embeddings and recommendation could allow for the integration of new information and the selection of relevant knowledge for response generation. Secondly, storing entities with emotional values as additional features may provide knowledge that is better emotionally aligned with the user input. Thirdly, integrating character information through narrative bubbles would maintain character consistency, as well as introducing a structure that would readily incorporate new information.

Jiaoyan Chen, Yuan He, Yuxia Geng et al.

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.

Erik B. Myklebust, Ernesto Jiménez-Ruiz, Jiaoyan Chen et al.

We have created a knowledge graph based on major data sources used in ecotoxicological risk assessment. We have applied this knowledge graph to an important task in risk assessment, namely chemical effect prediction. We have evaluated nine knowledge graph embedding models from a selection of geometric, decomposition, and convolutional models on this prediction task. We show that using knowledge graph embeddings can increase the accuracy of effect prediction with neural networks. Furthermore, we have implemented a fine-tuning architecture that adapts the knowledge graph embeddings to the effect prediction task and leads to better performance. Finally, we evaluate certain characteristics of the knowledge graph embedding models to shed light on the individual model performance.

Jiaoyan Chen, Pan Hu, Ernesto Jimenez-Ruiz et al.

Semantic embedding of knowledge graphs has been widely studied and used for prediction and statistical analysis tasks across various domains such as Natural Language Processing and the Semantic Web. However, less attention has been paid to developing robust methods for embedding OWL (Web Ontology Language) ontologies which can express a much wider range of semantics than knowledge graphs and have been widely adopted in domains such as bioinformatics. In this paper, we propose a random walk and word embedding based ontology embedding method named OWL2Vec*, which encodes the semantics of an OWL ontology by taking into account its graph structure, lexical information and logical constructors. Our empirical evaluation with three real world datasets suggests that OWL2Vec* benefits from these three different aspects of an ontology in class membership prediction and class subsumption prediction tasks. Furthermore, OWL2Vec* often significantly outperforms the state-of-the-art methods in our experiments.

Ernesto Jiménez-Ruiz, Asan Agibetov, Jiaoyan Chen et al.

Large ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In this paper we present an approach that combines a neural embedding model and logic-based modules to accurately divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive evaluation using the datasets of the Ontology Alignment Evaluation Initiative. The results are encouraging and suggest that the proposed method is adequate in practice and can be integrated within the workflow of systems unable to cope with very large ontologies.

Erik Bryhn Myklebust, Ernesto Jimenez-Ruiz, Jiaoyan Chen et al.

Ecological risk assessment requires large amounts of chemical effect data from laboratory experiments. Due to experimental effort and animal welfare concerns it is desired to extrapolate data from existing sources. To cover the required chemical effect data several data sources need to be integrated to enable their interoperability. In this paper we introduce the Toxicological Effect and Risk Assessment (TERA) knowledge graph, which aims at providing such integrated view, and the data preparation and steps followed to construct this knowledge graph. We also present the applications of TERA for chemical effect prediction and the potential applications within the Semantic Web community.

Erik Bryhn Myklebust, Ernesto Jimenez-Ruiz, Jiaoyan Chen et al.

Exploring the effects a chemical compound has on a species takes a considerable experimental effort. Appropriate methods for estimating and suggesting new effects can dramatically reduce the work needed to be done by a laboratory. In this paper we explore the suitability of using a knowledge graph embedding approach for ecotoxicological effect prediction. A knowledge graph has been constructed from publicly available data sets, including a species taxonomy and chemical classification and similarity. The publicly available effect data is integrated to the knowledge graph using ontology alignment techniques. Our experimental results show that the knowledge graph based approach improves the selected baselines.

Jiaoyan Chen, Ernesto Jimenez-Ruiz, Ian Horrocks

Ontology-based knowledge bases (KBs) like DBpedia are very valuable resources, but their usefulness and usability is limited by various quality issues. One such issue is the use of string literals instead of semantically typed entities. In this paper we study the automated canonicalization of such literals, i.e., replacing the literal with an existing entity from the KB or with a new entity that is typed using classes from the KB. We propose a framework that combines both reasoning and machine learning in order to predict the relevant entities and types, and we evaluate this framework against state-of-the-art baselines for both semantic typing and entity matching.

Jiaoyan Chen, Ernesto Jimenez-Ruiz, Ian Horrocks et al.

The usefulness of tabular data such as web tables critically depends on understanding their semantics. This study focuses on column type prediction for tables without any meta data. Unlike traditional lexical matching-based methods, we propose a deep prediction model that can fully exploit a table's contextual semantics, including table locality features learned by a Hybrid Neural Network (HNN), and inter-column semantics features learned by a knowledge base (KB) lookup and query answering algorithm.It exhibits good performance not only on individual table sets, but also when transferring from one table set to another.

Yuxia Geng, Jiaoyan Chen, Ernesto Jimenez-Ruiz et al.

Transfer learning which aims at utilizing knowledge learned from one problem (source domain) to solve another different but related problem (target domain) has attracted wide research attentions. However, the current transfer learning methods are mostly uninterpretable, especially to people without ML expertise. In this extended abstract, we brief introduce two knowledge graph (KG) based frameworks towards human understandable transfer learning explanation. The first one explains the transferability of features learned by Convolutional Neural Network (CNN) from one domain to another through pre-training and fine-tuning, while the second justifies the model of a target domain predicted by models from multiple source domains in zero-shot learning (ZSL). Both methods utilize KG and its reasoning capability to provide rich and human understandable explanations to the transfer procedure.

Jiaoyan Chen, Ernesto Jimenez-Ruiz, Ian Horrocks et al.

Automatically annotating column types with knowledge base (KB) concepts is a critical task to gain a basic understanding of web tables. Current methods rely on either table metadata like column name or entity correspondences of cells in the KB, and may fail to deal with growing web tables with incomplete meta information. In this paper we propose a neural network based column type annotation framework named ColNet which is able to integrate KB reasoning and lookup with machine learning and can automatically train Convolutional Neural Networks for prediction. The prediction model not only considers the contextual semantics within a cell using word representation, but also embeds the semantics of a column by learning locality features from multiple cells. The method is evaluated with DBPedia and two different web table datasets, T2Dv2 from the general Web and Limaye from Wikipedia pages, and achieves higher performance than the state-of-the-art approaches.

Ernesto Jimenez-Ruiz, Asan Agibetov, Matthias Samwald et al.

Large ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In the paper we present an approach that combines a lexical index, a neural embedding model and locality modules to effectively divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive evaluation using the datasets of the Ontology Alignment Evaluation Initiative. The results are encouraging and suggest that the proposed methods are adequate in practice and can be integrated within the workflow of state-of-the-art systems.

Christian Meilicke, Ondrej Sváb-Zamazal, Cássia Trojahn et al.

In the field of ontology matching, the most systematic evaluation of matching systems is established by the Ontology Alignment Evaluation Initiative (OAEI), which is an annual campaign for evaluating ontology matching systems organized by different groups of researchers. In this paper, we report on the results of an intermediary OAEI campaign called OAEI 2011.5. The evaluations of this campaign are divided in five tracks. Three of these tracks are new or have been improved compared to previous OAEI campaigns. Overall, we evaluated 18 matching systems. We discuss lessons learned, in terms of scalability, multilingual issues and the ability do deal with real world cases from different domains.