arXiv subjects

Ian Horrocks

Publications and source records attributed to Ian Horrocks.

At least 19 recordsLinked to original sources

arXiv2025

Sound Logical Explanations for Mean Aggregation Graph Neural Networks

Graph neural networks (GNNs) are frequently used for knowledge graph completion. Their black-box nature has motivated work that uses sound logical rules to explain predictions and characterise their expressivity. However, despite the prevalence of GNNs that use mean as an aggregation function, explainability and expressivity results are lacking for them. We consider GNNs with mean aggregation and non-negative weights (MAGNNs), proving the precise class of monotonic rules that can be sound for them, as well as providing a restricted fragment of first-order logic to explain any MAGNN prediction. Our experiments show that restricting mean-aggregation GNNs to have non-negative weights yields comparable or improved performance on standard inductive benchmarks, that sound rules are obtained in practice, that insightful explanations can be generated in practice, and that the sound rules can expose issues in the trained models.

cs.LG↗

arXiv2025

From Neural Networks to Logical Theories: The Correspondence between Fibring Modal Logics and Fibring Neural Networks

Fibring of modal logics is a well-established formalism for combining countable families of modal logics into a single fibred language with common semantics, characterized by fibred models. Inspired by this formalism, fibring of neural networks was introduced as a neurosymbolic framework for combining learning and reasoning in neural networks. Fibring of neural networks uses the (pre-)activations of a trained network to evaluate a fibring function computing the weights of another network whose outputs are injected back into the original network. However, the exact correspondence between fibring of neural networks and fibring of modal logics was never formally established. In this paper, we close this gap by formalizing the idea of fibred models \emph{compatible} with fibred neural networks. Using this correspondence, we then derive non-uniform logical expressiveness results for Graph Neural Networks (GNNs), Graph Attention Networks (GATs) and Transformer encoders. Longer-term, the goal of this paper is to open the way for the use of fibring as a formalism for interpreting the logical theories learnt by neural networks with the tools of computational logic.

cs.AI↗

arXiv2025

Language Models as Ontology Encoders

OWL (Web Ontology Language) ontologies which are able to formally represent complex knowledge and support semantic reasoning have been widely adopted across various domains such as healthcare and bioinformatics. Recently, ontology embeddings have gained wide attention due to its potential to infer plausible new knowledge and approximate complex reasoning. However, existing methods face notable limitations: geometric model-based embeddings typically overlook valuable textual information, resulting in suboptimal performance, while the approaches that incorporate text, which are often based on language models, fail to preserve the logical structure. In this work, we propose a new ontology embedding method OnT, which tunes a Pretrained Language Model (PLM) via geometric modeling in a hyperbolic space for effectively incorporating textual labels and simultaneously preserving class hierarchies and other logical relationships of Description Logic EL. Extensive experiments on four real-world ontologies show that OnT consistently outperforms the baselines including the state-of-the-art across both tasks of prediction and inference of axioms. OnT also demonstrates strong potential in real-world applications, indicated by its robust transfer learning abilities and effectiveness in real cases of constructing a new ontology from SNOMED CT. Data and code are available at https://github.com/HuiYang1997/OnT.

cs.AI↗

arXiv2025

Supposedly Equivalent Facts That Aren't? Entity Frequency in Pre-training Induces Asymmetry in LLMs

Understanding and mitigating hallucinations in Large Language Models (LLMs) is crucial for ensuring reliable content generation. While previous research has primarily focused on "when" LLMs hallucinate, our work explains "why" and directly links model behaviour to the pre-training data that forms their prior knowledge. Specifically, we demonstrate that an asymmetry exists in the recognition of logically equivalent facts, which can be attributed to frequency discrepancies of entities appearing as subjects versus objects. Given that most pre-training datasets are inaccessible, we leverage the fully open-source OLMo series by indexing its Dolma dataset to estimate entity frequencies. Using relational facts (represented as triples) from Wikidata5M, we construct probing datasets to isolate this effect. Our experiments reveal that facts with a high-frequency subject and a low-frequency object are better recognised than their inverse, despite their logical equivalence. The pattern reverses in low-to-high frequency settings, and no statistically significant asymmetry emerges when both entities are high-frequency. These findings highlight the influential role of pre-training data in shaping model predictions and provide insights for inferring the characteristics of pre-training data in closed or partially closed LLMs.

cs.CL↗

arXiv2024

Relational Graph Convolutional Networks Do Not Learn Sound Rules

Graph neural networks (GNNs) are frequently used to predict missing facts in knowledge graphs (KGs). Motivated by the lack of explainability for the outputs of these models, recent work has aimed to explain their predictions using Datalog, a widely used logic-based formalism. However, such work has been restricted to certain subclasses of GNNs. In this paper, we consider one of the most popular GNN architectures for KGs, R-GCN, and we provide two methods to extract rules that explain its predictions and are sound, in the sense that each fact derived by the rules is also predicted by the GNN, for any input dataset. Furthermore, we provide a method that can verify that certain classes of Datalog rules are not sound for the R-GCN. In our experiments, we train R-GCNs on KG completion benchmarks, and we are able to verify that no Datalog rule is sound for these models, even though the models often obtain high to near-perfect accuracy. This raises some concerns about the ability of R-GCN models to generalise and about the explainability of their predictions. We further provide two variations to the training paradigm of R-GCN that encourage it to learn sound rules and find a trade-off between model accuracy and the number of learned sound rules.

cs.LG↗

arXiv2024

Ontology Embedding: A Survey of Methods, Applications and Resources

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.

cs.AI↗

arXiv2024

A Language Model based Framework for New Concept Placement in Ontologies

We investigate the task of inserting new concepts extracted from texts into an ontology using language models. We explore an approach with three steps: edge search which is to find a set of candidate locations to insert (i.e., subsumptions between concepts), edge formation and enrichment which leverages the ontological structure to produce and enhance the edge candidates, and edge selection which eventually locates the edge to be placed into. In all steps, we propose to leverage neural methods, where we apply embedding-based methods and contrastive learning with Pre-trained Language Models (PLMs) such as BERT for edge search, and adapt a BERT fine-tuning-based multi-label Edge-Cross-encoder, and Large Language Models (LLMs) such as GPT series, FLAN-T5, and Llama 2, for edge selection. We evaluate the methods on recent datasets created using the SNOMED CT ontology and the MedMentions entity linking benchmark. The best settings in our framework use fine-tuned PLM for search and a multi-label Cross-encoder for selection. Zero-shot prompting of LLMs is still not adequate for the task, and we propose explainable instruction tuning of LLMs for improved performance. Our study shows the advantages of PLMs and highlights the encouraging performance of LLMs that motivates future studies.

cs.CL↗

arXiv2024

Language Models as Hierarchy Encoders

Interpreting hierarchical structures latent in language is a key limitation of current language models (LMs). While previous research has implicitly leveraged these hierarchies to enhance LMs, approaches for their explicit encoding are yet to be explored. To address this, we introduce a novel approach to re-train transformer encoder-based LMs as Hierarchy Transformer encoders (HiTs), harnessing the expansive nature of hyperbolic space. Our method situates the output embedding space of pre-trained LMs within a Poincar\'e ball with a curvature that adapts to the embedding dimension, followed by training on hyperbolic clustering and centripetal losses. These losses are designed to effectively cluster related entities (input as texts) and organise them hierarchically. We evaluate HiTs against pre-trained LMs, standard fine-tuned LMs, and several hyperbolic embedding baselines, focusing on their capabilities in simulating transitive inference, predicting subsumptions, and transferring knowledge across hierarchies. The results demonstrate that HiTs consistently outperform all baselines in these tasks, underscoring the effectiveness and transferability of our re-trained hierarchy encoders.

cs.CL↗

arXiv2023

Optimised Storage for Datalog Reasoning

Materialisation facilitates Datalog reasoning by precomputing all consequences of the facts and the rules so that queries can be directly answered over the materialised facts. However, storing all materialised facts may be infeasible in practice, especially when the rules are complex and the given set of facts is large. We observe that for certain combinations of rules, there exist data structures that compactly represent the reasoning result and can be efficiently queried when necessary. In this paper, we present a general framework that allows for the integration of such optimised storage schemes with standard materialisation algorithms. Moreover, we devise optimised storage schemes targeting at transitive rules and union rules, two types of (combination of) rules that commonly occur in practice. Our experimental evaluation shows that our approach significantly improves memory consumption, sometimes by orders of magnitude, while remaining competitive in terms of query answering time.

cs.DB↗

arXiv2023

Exploring Large Language Models for Ontology Alignment

This work investigates the applicability of recent generative Large Language Models (LLMs), such as the GPT series and Flan-T5, to ontology alignment for identifying concept equivalence mappings across ontologies. To test the zero-shot performance of Flan-T5-XXL and GPT-3.5-turbo, we leverage challenging subsets from two equivalence matching datasets of the OAEI Bio-ML track, taking into account concept labels and structural contexts. Preliminary findings suggest that LLMs have the potential to outperform existing ontology alignment systems like BERTMap, given careful framework and prompt design.

cs.AI↗

arXiv2023

DeepOnto: A Python Package for Ontology Engineering with Deep Learning

Integrating deep learning techniques, particularly language models (LMs), with knowledge representation techniques like ontologies has raised widespread attention, urging the need of a platform that supports both paradigms. Although packages such as OWL API and Jena offer robust support for basic ontology processing features, they lack the capability to transform various types of information within ontologies into formats suitable for downstream deep learning-based applications. Moreover, widely-used ontology APIs are primarily Java-based while deep learning frameworks like PyTorch and Tensorflow are mainly for Python programming. To address the needs, we present DeepOnto, a Python package designed for ontology engineering with deep learning. 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 incorporate other essential components including reasoning, verbalisation, normalisation, taxonomy, 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 methods, 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).

cs.AI↗

arXiv2023

Ontology Enrichment from Texts: A Biomedical Dataset for Concept Discovery and Placement

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a new concept is pre-discovered and cannot support out-of-KB mention discovery; (ii) only using the concept label as the input along with the KB and thus lacking the contexts of a concept label; and (iii) mostly focusing on concept placement w.r.t a taxonomy of atomic concepts, instead of complex concepts, i.e., with logical operators. To address these issues, we propose a new benchmark, adapting MedMentions dataset (PubMed abstracts) with SNOMED CT versions in 2014 and 2017 under the Diseases sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic product. We provide usage on the evaluation with the dataset for out-of-KB mention discovery and concept placement, adapting recent Large Language Model based methods.

cs.CL↗

arXiv2023

Revisiting Inferential Benchmarks for Knowledge Graph Completion

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.

cs.AI↗

arXiv2023

Enhancing Datalog Reasoning with Hypertree Decompositions

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.

cs.DB↗

arXiv2023

Language Model Analysis for Ontology Subsumption Inference

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.

cs.CL↗

arXiv2023

Reveal the Unknown: Out-of-Knowledge-Base Mention Discovery with Entity Linking

Discovering entity mentions that are out of a Knowledge Base (KB) from texts plays a critical role in KB maintenance, but has not yet been fully explored. The current methods are mostly limited to the simple threshold-based approach and feature-based classification, and the datasets for evaluation are relatively rare. We propose BLINKout, a new BERT-based Entity Linking (EL) method which can identify mentions that do not have corresponding KB entities by matching them to a special NIL entity. To better utilize BERT, we propose new techniques including NIL entity representation and classification, with synonym enhancement. We also apply KB Pruning and Versioning strategies to automatically construct out-of-KB datasets from common in-KB EL datasets. Results on five datasets of clinical notes, biomedical publications, and Wikipedia articles in various domains show the advantages of BLINKout over existing methods to identify out-of-KB mentions for the medical ontologies, UMLS, SNOMED CT, and the general KB, WikiData.

cs.CL↗

arXiv2023

Dual Box Embeddings for the Description Logic EL++

OWL ontologies, whose formal semantics are rooted in Description Logic (DL), have been widely used for knowledge representation. Similar to Knowledge Graphs (KGs), ontologies are often incomplete, and maintaining and constructing them has proved challenging. While classical deductive reasoning algorithms use the precise formal semantics of an ontology to predict missing facts, recent years have witnessed growing interest in inductive reasoning techniques that can derive probable facts from an ontology. Similar to KGs, a promising approach is to learn ontology embeddings in a latent vector space, while additionally ensuring they adhere to the semantics of the underlying DL. While a variety of approaches have been proposed, current ontology embedding methods suffer from several shortcomings, especially that they all fail to faithfully model one-to-many, many-to-one, and many-to-many relations and role inclusion axioms. To address this problem and improve ontology completion performance, we propose a novel ontology embedding method named Box$^2$EL for the DL EL++, which represents both concepts and roles as boxes (i.e., axis-aligned hyperrectangles), and models inter-concept relationships using a bumping mechanism. We theoretically prove the soundness of Box$^2$EL and conduct an extensive experimental evaluation, achieving state-of-the-art results across a variety of datasets on the tasks of subsumption prediction, role assertion prediction, and approximating deductive reasoning.

cs.AI↗

arXiv2022

Zero-shot and Few-shot Learning with Knowledge Graphs: A Comprehensive Survey

Machine learning especially deep neural networks have achieved great success but many of them often rely on a number of labeled samples for supervision. As sufficient labeled training data are not always ready due to e.g., continuously emerging prediction targets and costly sample annotation in real world applications, machine learning with sample shortage is now being widely investigated. Among all these studies, many prefer to utilize auxiliary information including those in the form of Knowledge Graph (KG) to reduce the reliance on labeled samples. In this survey, we have comprehensively reviewed over 90 papers about KG-aware research for two major sample shortage settings -- zero-shot learning (ZSL) where some classes to be predicted have no labeled samples, and few-shot learning (FSL) where some classes to be predicted have only a small number of labeled samples that are available. We first introduce KGs used in ZSL and FSL as well as their construction methods, and then systematically categorize and summarize 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 present different applications, including not only KG augmented prediction tasks such as image classification, question answering, text classification and knowledge extraction, but also KG completion tasks, and some typical evaluation resources for each task. We eventually discuss some challenges and open problems from different perspectives.

cs.LG↗