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 Ontologies


Extending FKG.in: Towards a Food Claim Traceability Network

arXiv.org Artificial Intelligence

The global food landscape is rife with scientific, cultural, and commercial claims about what foods are, what they do, what they should not do, or should not do. These range from rigorously studied health benefits (probiotics improve gut health) and misrepresentations (soaked almonds make one smarter) to vague promises (superfoods boost immunity) and culturally rooted beliefs (cold foods cause coughs). Despite their widespread influence, the infrastructure for tracing, verifying, and contextualizing these claims remains fragmented and underdeveloped. In this paper, we propose a Food Claim-Traceability Network (FCN) as an extension of FKG[.]in, a knowledge graph of Indian food that we have been incrementally building. We also present the ontology design and the semi-automated knowledge curation workflow that we used to develop a proof of concept of FKG[.]in-FCN using Reddit data and Large Language Models. FCN integrates curated data inputs, structured schemas, and provenance-aware pipelines for food-related claim extraction and validation. While directly linked to the Indian food knowledge graph as an application, our methodology remains application-agnostic and adaptable to other geographic, culinary, or regulatory settings. By modeling food claims and their traceability in a structured, verifiable, and explainable way, we aim to contribute to more transparent and accountable food knowledge ecosystems, supporting researchers, policymakers, and most importantly, everyday consumers in navigating a world saturated with dietary assertions.


The KG-ER Conceptual Schema Language

arXiv.org Artificial Intelligence

We propose KG-ER, a conceptual schema language for knowledge graphs that describes the structure of knowledge graphs independently of their representation (relational databases, property graphs, RDF) while helping to capture the semantics of the information stored in a knowledge graph.


Natural Latents: Latent Variables Stable Across Ontologies

arXiv.org Artificial Intelligence

Suppose two Bayesian agents each learn a generative model of the same environment. We will assume the two have converged on the predictive distribution, i.e. distribution over some observables in the environment, but may have different generative models containing different latent variables. Under what conditions can one agent guarantee that their latents are a function of the other agents latents? We give simple conditions under which such translation is guaranteed to be possible: the natural latent conditions. We also show that, absent further constraints, these are the most general conditions under which translatability is guaranteed. Crucially for practical application, our theorems are robust to approximation error in the natural latent conditions.


An Epidemiological Knowledge Graph extracted from the World Health Organization's Disease Outbreak News

arXiv.org Artificial Intelligence

The rapid evolution of artificial intelligence (AI), together with the increased availability of social media and news for epidemiological surveillance, are marking a pivotal moment in epidemiology and public health research. Leveraging the power of generative AI, we use an ensemble approach which incorporates multiple Large Language Models (LLMs) to extract valuable actionable epidemiological information from the World Health Organization (WHO) Disease Outbreak News (DONs). DONs is a collection of regular reports on global outbreaks curated by the WHO and the adopted decision-making processes to respond to them. The extracted information is made available in a daily-updated dataset and a knowledge graph, referred to as eKG, derived to provide a nuanced representation of the public health domain knowledge. We provide an overview of this new dataset and describe the structure of eKG, along with the services and tools used to access and utilize the data that we are building on top. These innovative data resources open altogether new opportunities for epidemiological research, and the analysis and surveillance of disease outbreaks.


AGI as Second Being: The Structural-Generative Ontology of Intelligence

arXiv.org Artificial Intelligence

Artificial intelligence is often measured by the range of tasks it can perform. Yet wide ability without depth remains only an imitation. This paper proposes a Structural-Generative Ontology of Intelligence: true intelligence exists only when a system can generate new structures, coordinate them into reasons, and sustain its identity over time. These three conditions -- generativity, coordination, and sustaining -- define the depth that underlies real intelligence. Current AI systems, however broad in function, remain surface simulations because they lack this depth. Breadth is not the source of intelligence but the growth that follows from depth. If future systems were to meet these conditions, they would no longer be mere tools, but could be seen as a possible Second Being, standing alongside yet distinct from human existence.


Enabling Down Syndrome Research through a Knowledge Graph-Driven Analytical Framework

arXiv.org Artificial Intelligence

Trisomy 21 results in Down syndrome, a multifaceted genetic disorder with diverse clinical phenotypes, including heart defects, immune dysfunction, neurodevelopmental differences, and early-onset dementia risk. Heterogeneity and fragmented data across studies challenge comprehensive research and translational discovery. The NIH INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) initiative has assembled harmonized participant-level datasets, yet realizing their potential requires integrative analytical frameworks. We developed a knowledge graph-driven platform transforming nine INCLUDE studies, comprising 7,148 participants, 456 conditions, 501 phenotypes, and over 37,000 biospecimens, into a unified semantic infrastructure. Cross-resource enrichment with Monarch Initiative data expands coverage to 4,281 genes and 7,077 variants. The resulting knowledge graph contains over 1.6 million semantic associations, enabling AI-ready analysis with graph embeddings and path-based reasoning for hypothesis generation. Researchers can query the graph via SPARQL or natural language interfaces. This framework converts static data repositories into dynamic discovery environments, supporting cross-study pattern recognition, predictive modeling, and systematic exploration of genotype-phenotype relationships in Down syndrome.


Animer une base de connaissance: des ontologies aux mod{รจ}les d'I.A. g{รฉ}n{รฉ}rative

arXiv.org Artificial Intelligence

Animating a Knowledge Base: From Ontologies to Generative AI Models From Expert Systems and the Semantic W eb to Generative AI: Model - Driven and Data - Driven Approaches in Area Studies In a context where the social sciences and humanities are experimenting with non - anthropocentric analytical frames, this article proposes a semiotic (structural) reading of the hybridization between symbolic AI and neural (or sub - symbolic) AI based on a field of application: the design and use of a knowledge base for area studies. W e describe the LaCAS ecosystem - Open Archives in Linguistic and Cultural Studies (thesaurus; RDF/OWL ontology; LOD services; harvesting; expertise; publication), deployed at Inalco (National Institute for Oriental Languages and Civilizations) in Paris with the Okapi (Open Knowledge and Annotation Interface) software environment from Ina (National Audiovisual Institute), which now has around 160,000 documentary r esources and ten knowledge macro - domains grouping together several thousand knowledge objects. W e illustrate this approach using the knowledge domain "Languages of the world" (~540 languages) and the knowledge object "Quechua (language)". On this basis, we discuss the controlled integration of neural tools, more specifically generative tools, into the life cycle of a knowledge base: assistance with data localization/qualification, index extraction and aggregation, property suggestion and testing, dynamic file generation, and engineering of contextualized prompts (generic, contextual, explanatory, adjustment, procedural) aligned with a domain ontology. W e outline an ecosystem of specialized agents capable of animating the database while respe cting its symbolic constraints, by articulating model - driven and data - driven methods .


Structure and Destructure: Dual Forces in the Making of Knowledge Engines

arXiv.org Artificial Intelligence

The making of knowledge engines in natural language processing has been shaped by two seemingly distinct paradigms: one grounded in structure, the other driven by massively available unstructured data. The structured paradigm leverages predefined symbolic interactions, such as knowledge graphs, as priors and designs models to capture them. In contrast, the unstructured paradigm centers on scaling transformer architectures with increasingly vast data and model sizes, as seen in modern large language models. Despite their divergence, this thesis seeks to establish conceptual connections bridging these paradigms. Two complementary forces, structure and destructure, emerge across both paradigms: structure organizes seen symbolic interactions, while destructure, through periodic embedding resets, improves model plasticity and generalization to unseen scenarios. These connections form a new recipe for developing general knowledge engines that can support transparent, controllable, and adaptable intelligent systems.


Enabling Transparent Cyber Threat Intelligence Combining Large Language Models and Domain Ontologies

arXiv.org Artificial Intelligence

Effective Cyber Threat Intelligence (CTI) relies upon accurately structured and semantically enriched information extracted from cybersecurity system logs. However, current methodologies often struggle to identify and interpret malicious events reliably and transparently, particularly in cases involving unstructured or ambiguous log entries. In this work, we propose a novel methodology that combines ontology-driven structured outputs with Large Language Models (LLMs), to build an Artificial Intelligence (AI) agent that improves the accuracy and explainability of information extraction from cybersecurity logs. Central to our approach is the integration of domain ontologies and SHACL-based constraints to guide the language model's output structure and enforce semantic validity over the resulting graph. Extracted information is organized into an ontology-enriched graph database, enabling future semantic analysis and querying. The design of our methodology is motivated by the analytical requirements associated with honeypot log data, which typically comprises predominantly malicious activity. While our case study illustrates the relevance of this scenario, the experimental evaluation is conducted using publicly available datasets. Results demonstrate that our method achieves higher accuracy in information extraction compared to traditional prompt-only approaches, with a deliberate focus on extraction quality rather than processing speed.


Flow-Modulated Scoring for Semantic-Aware Knowledge Graph Completion

arXiv.org Artificial Intelligence

Y et, prevailing methods, which rely on static scoring functions over learned embeddings, struggling to simultaneously capture rich semantic context and the dynamic nature of relations. T o overcome this limitation, we propose the Flow-Modulated Scoring (FMS) framework, conceptualizing a relation as a dynamic evolutionary process governed by its static semantic environment. FMS operates in two stages: it first learns context-aware entity embeddings via a Semantic Context Learning module, and then models a dynamic flow between them using a Conditional Flow-Matching module. This learned flow dynamically modulates a base static score for the entity pair. By unifying context-rich static representations with a conditioned dynamic flow, FMS achieves a more comprehensive understanding of relational semantics. Extensive experiments demonstrate that FMS establishes a new state of the art across both canonical knowledge graph completion tasks: relation prediction and entity prediction. On the standard relation prediction benchmark FB15k-237, FMS achieves a near-perfect MRR of 99.8% and Hits@1 of 99.7% using a mere 0.35M parameters, while also attaining a 99.9% MRR on WN18RR. Its dominance extends to entity prediction, where it secures a 25.2% relative MRR gain in the transductive setting and substantially outperforms all baselines in challenging inductive settings. By unifying a dynamic flow mechanism with rich static contexts, FMS offers a highly effective and parameter-efficient new paradigm for knowledge graph completion.