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.

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.

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.

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.

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.

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.

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.

Since Edmund Husserl coined the term "Formal Ontologies" in the early 20th century, a field that identifies itself with this particular branch of sciences has gained increasing attention. Many authors, and even Husserl himself have developed what they claim to be formal ontologies. I argue that under close inspection, none of these so claimed formal ontologies are truly formal in the Husserlian sense. More concretely, I demonstrate that they violate the two most important notions of formal ontology as developed in Husserl's Logical Investigations, namely a priori validity independent of perception and formalism as the total absence of content. I hence propose repositioning the work previously understood as formal ontology as the foundational ontology it really is. This is to recognize the potential of a truly formal ontology in the Husserlian sense. Specifically, I argue that formal ontology following his conditions, allows us to formulate ontological structures, which could capture what is more objectively without presupposing a particular framework arising from perception. I further argue that the ability to design the formal structure deliberately allows us to create highly scalable and interoperable information artifacts. As concrete evidence, I showcase that a class of formal ontology, which uses the axioms of vector spaces, is able to express most of the conceptualizations found in foundational ontologies. Most importantly, I argue that many information systems, specifically artificial intelligence, are likely already using some type of vector ontologies to represent reality in their internal worldviews and elaborate on the evidence that humans do as well. I hence propose a thorough investigation of the ability of vector ontologies to act as a human-machine interoperable ontological framework that allows us to understand highly sophisticated machines and machines to understand us.

Public procurement plays a critical role in government operations, ensuring the efficient allocation of resources and fostering economic growth. However, traditional procurement data is often stored in rigid, tabular formats, limiting its analytical potential and hindering transparency. This research presents a methodological framework for transforming structured procurement data into a semantic knowledge graph, leveraging ontological modeling and automated data transformation techniques. By integrating RDF and SPARQL-based querying, the system enhances the accessibility and interpretability of procurement records, enabling complex semantic queries and advanced analytics. Furthermore, by incorporating machine learning-driven predictive modeling, the system extends beyond conventional data analysis, offering insights into procurement trends and risk assessment. This work contributes to the broader field of public procurement intelligence by improving data transparency, supporting evidence-based decision-making, and enabling in-depth analysis of procurement activities in North Macedonia.

Taiwanese China Studies (CS) has developed into a rich, interdisciplinary research field shaped by the unique geopolitical position and long standing academic engagement with Mainland China. This study responds to the growing need to systematically revisit and reorganize decades of Taiwan based CS scholarship by proposing an AI assisted approach that transforms unstructured academic texts into structured, interactive knowledge representations. We apply generative AI (GAI) techniques and large language models (LLMs) to extract and standardize entity relation triples from 1,367 peer reviewed CS articles published between 1996 and 2019. These triples are then visualized through a lightweight D3.js based system, forming the foundation of a domain specific knowledge graph and vector database for the field. This infrastructure allows users to explore conceptual nodes and semantic relationships across the corpus, revealing previously uncharted intellectual trajectories, thematic clusters, and research gaps. By decomposing textual content into graph structured knowledge units, our system enables a paradigm shift from linear text consumption to network based knowledge navigation. In doing so, it enhances scholarly access to CS literature while offering a scalable, data driven alternative to traditional ontology construction. This work not only demonstrates how generative AI can augment area studies and digital humanities but also highlights its potential to support a reimagined scholarly infrastructure for regional knowledge systems.