Ontologies
Applying Ontologies and Knowledge Augmented Large Language Models to Industrial Automation: A Decision-Making Guidance for Achieving Human-Robot Collaboration in Industry 5.0
Oyekan, John, Turner, Christopher, Bax, Michael, Graf, Erich
The rapid advancement of Large Language Models (LLMs) has resulted in interest in their potential applications within manufacturing systems, particularly in the context of Industry 5.0. However, determining when to implement LLMs versus other Natural Language Processing (NLP) techniques, ontologies or knowledge graphs, remains an open question. This paper offers decision-making guidance for selecting the most suitable technique in various industrial contexts, emphasizing human-robot collaboration and resilience in manufacturing. We examine the origins and unique strengths of LLMs, ontologies, and knowledge graphs, assessing their effectiveness across different industrial scenarios based on the number of domains or disciplines required to bring a product from design to manufacture. Through this comparative framework, we explore specific use cases where LLMs could enhance robotics for human-robot collaboration, while underscoring the continued relevance of ontologies and knowledge graphs in low-dependency or resource-constrained sectors. Additionally, we address the practical challenges of deploying these technologies, such as computational cost and interpretability, providing a roadmap for manufacturers to navigate the evolving landscape of Language based AI tools in Industry 5.0. Our findings offer a foundation for informed decision-making, helping industry professionals optimize the use of Language Based models for sustainable, resilient, and human-centric manufacturing. We also propose a Large Knowledge Language Model architecture that offers the potential for transparency and configuration based on complexity of task and computing resources available.
Semantic-Aware Interpretable Multimodal Music Auto-Tagging
Patakis, Andreas, Lyberatos, Vassilis, Kantarelis, Spyridon, Dervakos, Edmund, Stamou, Giorgos
Music auto-tagging is essential for organizing and discovering music in extensive digital libraries. While foundation models achieve exceptional performance in this domain, their outputs often lack interpretability, limiting trust and usability for researchers and end-users alike. In this work, we present an interpretable framework for music auto-tagging that leverages groups of musically meaningful multimodal features, derived from signal processing, deep learning, ontology engineering, and natural language processing. To enhance interpretability, we cluster features semantically and employ an expectation maximization algorithm, assigning distinct weights to each group based on its contribution to the tagging process. Our method achieves competitive tagging performance while offering a deeper understanding of the decision-making process, paving the way for more transparent and user-centric music tagging systems.
Exploring a Large Language Model for Transforming Taxonomic Data into OWL: Lessons Learned and Implications for Ontology Development
Soares, Filipi Miranda, Saraiva, Antonio Mauro, Pires, Luรญs Ferreira, Santos, Luiz Olavo Bonino da Silva, Moreira, Dilvan de Abreu, Corrรชa, Fernando Elias, Braghetto, Kelly Rosa, Drucker, Debora Pignatari, Delbem, Alexandre Clรกudio Botazzo
Managing scientific names in ontologies that represent species taxonomies is challenging due to the ever-evolving nature of these taxonomies. Manually maintaining these names becomes increasingly difficult when dealing with thousands of scientific names. To address this issue, this paper investigates the use of ChatGPT-4 to automate the development of the :Organism module in the Agricultural Product Types Ontology (APTO) for species classification. Our methodology involved leveraging ChatGPT-4 to extract data from the GBIF Backbone API and generate OWL files for further integration in APTO. Two alternative approaches were explored: (1) issuing a series of prompts for ChatGPT-4 to execute tasks via the BrowserOP plugin and (2) directing ChatGPT-4 to design a Python algorithm to perform analogous tasks. Both approaches rely on a prompting method where we provide instructions, context, input data, and an output indicator. The first approach showed scalability limitations, while the second approach used the Python algorithm to overcome these challenges, but it struggled with typographical errors in data handling. This study highlights the potential of Large language models like ChatGPT-4 to streamline the management of species names in ontologies. Despite certain limitations, these tools offer promising advancements in automating taxonomy-related tasks and improving the efficiency of ontology development.
A Domain Ontology for Modeling the Book of Purification in Islam
This paper aims to address a gap in major Islamic topics by developing an ontology for the Book of Purification in Islam. Many authoritative Islamic texts begin with the Book of Purification, as it is essential for performing prayer (the second pillar of Islam after Shahadah, the profession of faith) and other religious duties such as Umrah and Hajj. The ontology development strategy followed six key steps: (1) domain identification, (2) knowledge acquisition, (3) conceptualization, (4) classification, (5) integration and implementation, and (6) ontology generation. This paper includes examples of the constructed tables and classifications. The focus is on the design and analysis phases, as technical implementation is beyond the scope of this study. However, an initial implementation is provided to illustrate the steps of the proposed strategy. The developed ontology ensures reusability by formally defining and encoding the key concepts, attributes, and relationships related to the Book of Purification. This structured representation is intended to support knowledge sharing and reuse.
Ontology- and LLM-based Data Harmonization for Federated Learning in Healthcare
Kokash, Natallia, Wang, Lei, Gillespie, Thomas H., Belloum, Adam, Grosso, Paola, Quinney, Sara, Li, Lang, de Bono, Bernard
The rise of electronic health records (EHRs) has unlocked new opportunities for medical research, but privacy regulations and data heterogeneity remain key barriers to large-scale machine learning. Federated learning (FL) enables collaborative modeling without sharing raw data, yet faces challenges in harmonizing diverse clinical datasets. This paper presents a two-step data alignment strategy integrating ontologies and large language models (LLMs) to support secure, privacy-preserving FL in healthcare, demonstrating its effectiveness in a real-world project involving semantic mapping of EHR data.
Conversational Lexicography: Querying Lexicographic Data on Knowledge Graphs with SPARQL through Natural Language
Sennrich, Kilian, Ahmadi, Sina
Knowledge graphs offer an excellent solution for representing the lexical-semantic structures of lexicographic data. However, working with the SPARQL query language represents a considerable hurdle for many non-expert users who could benefit from the advantages of this technology. This paper addresses the challenge of creating natural language interfaces for lexicographic data retrieval on knowledge graphs such as Wikidata. We develop a multidimensional taxonomy capturing the complexity of Wikidata's lexicographic data ontology module through four dimensions and create a template-based dataset with over 1.2 million mappings from natural language utterances to SPARQL queries. Our experiments with GPT-2 (124M), Phi-1.5 (1.3B), and GPT-3.5-Turbo reveal significant differences in model capabilities. While all models perform well on familiar patterns, only GPT-3.5-Turbo demonstrates meaningful generalization capabilities, suggesting that model size and diverse pre-training are crucial for adaptability in this domain. However, significant challenges remain in achieving robust generalization, handling diverse linguistic data, and developing scalable solutions that can accommodate the full complexity of lexicographic knowledge representation.
Cell ontology guided transcriptome foundation model
Transcriptome foundation models (TFMs) hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks. To this end, we present single cell, Cell-ontology guided TFM (scCello). We introduce cell-type coherence loss and ontology alignment loss, which are minimized along with the masked gene expression prediction loss during the pre-training.
Managing FAIR Knowledge Graphs as Polyglot Data End Points: A Benchmark based on the rdf2pg Framework and Plant Biology Data
Brandizi, Marco, Bobed, Carlos, Garulli, Luca, de Klerk, Arnรฉ, Hassani-Pak, Keywan
Linked data and labelled property graphs (LPG) are two data management approaches with complementary strengths and weaknesses, making their integration beneficial for sharing datasets and supporting software ecosystems. In thi s paper, we introduce rdf2pg, an extensible framework for mapping RDF data to semantically equivalent LPG formats and databases. Utilising this framework, we perform a comparative analysis of three popular graph databases - Virtuoso, Neo4j, and ArcadeDB - and the well - known graph query languages SPARQL, Cypher, and Gremlin. Our qualitative and quantitative assessments underline the strengths and limitations of these graph database technologies. Additionally, we highlight the potent ial of rdf2pg as a versatile tool for enabling polyglot access to knowledge graphs, aligning with established standards of linked data and the semantic web.
MEDMKG: Benchmarking Medical Knowledge Exploitation with Multimodal Knowledge Graph
Wang, Xiaochen, Zhong, Yuan, Zhang, Lingwei, Dai, Lisong, Wang, Ting, Ma, Fenglong
Medical deep learning models depend heavily on domain-specific knowledge to perform well on knowledge-intensive clinical tasks. Prior work has primarily leveraged unimodal knowledge graphs, such as the Unified Medical Language System (UMLS), to enhance model performance. However, integrating multimodal medical knowledge graphs remains largely underexplored, mainly due to the lack of resources linking imaging data with clinical concepts. To address this gap, we propose MEDMKG, a Medical Multimodal Knowledge Graph that unifies visual and textual medical information through a multi-stage construction pipeline. MEDMKG fuses the rich multimodal data from MIMIC-CXR with the structured clinical knowledge from UMLS, utilizing both rule-based tools and large language models for accurate concept extraction and relationship modeling. To ensure graph quality and compactness, we introduce Neighbor-aware Filtering (NaF), a novel filtering algorithm tailored for multimodal knowledge graphs. We evaluate MEDMKG across three tasks under two experimental settings, benchmarking twenty-four baseline methods and four state-of-the-art vision-language backbones on six datasets. Results show that MEDMKG not only improves performance in downstream medical tasks but also offers a strong foundation for developing adaptive and robust strategies for multimodal knowledge integration in medical artificial intelligence.
Theoretical Foundations for Semantic Cognition in Artificial Intelligence
This monograph presents a modular cognitive architecture for artificial intelligence grounded in the formal modeling of belief as structured semantic state. Belief states are defined as dynamic ensembles of linguistic expressions embedded within a navigable manifold, where operators enable assimilation, abstraction, nullification, memory, and introspection. Drawing from philosophy, cognitive science, and neuroscience, we develop a layered framework that enables self-regulating epistemic agents capable of reflective, goal-directed thought. At the core of this framework is the epistemic vacuum: a class of semantically inert cognitive states that serves as the conceptual origin of belief space. From this foundation, the Null Tower arises as a generative structure recursively built through internal representational capacities. The theoretical constructs are designed to be implementable in both symbolic and neural systems, including large language models, hybrid agents, and adaptive memory architectures. This work offers a foundational substrate for constructing agents that reason, remember, and regulate their beliefs in structured, interpretable ways.