Graph Neural Networks Applications Across Domains: All Insights You Need

Graph neural networks have moved from a niche representation-learning technique to the default model class wherever data carry relational structure. The interesting question is no longer whether message passing helps on a given dataset, but where graph structure earns its computational cost and where it does not. This survey organises the field around a single design space, derives the spectral and spatial formulations from shared first principles, and connects expressive power to the Weisfeiler-Leman hierarchy with explicit statements of what current architectures can and cannot separate. Against that methodological backbone we examine twelve application domains, among them recommendation and social networks, knowledge graphs and language-model integration, drug discovery and molecular property learning, healthcare and neuroscience, computer vision, traffic and urban computing, power and renewable-energy systems, wireless and sixth-generation networks, fraud and cybersecurity, industrial prognostics, materials science, and climate modelling. For each domain we specify the graph-construction choices and their costs, identify which architecture families dominate and why, and separate reported gains from artefacts of weak baselines or favourable splits. A cross-domain comparison exposes recurring patterns: heterophily and scale undercut the same models almost everywhere, temporal graphs remain harder than their static counterparts, and the architectures that top public leaderboards are seldom the ones that reach deployment. We treat over-smoothing, over-squashing, robustness, distribution shift, fairness, and explainability not as a closing checklist but as the constraints that decide adoption.

Zero-shot Tweet-Level Stance Detection Enhanced by External Knowledge and Reflective Chain-of-Thought Reasoning

Zero-shot tweet-level stance detection confronts two primary challenges: (1) mitigating the context sparsity inherent in short texts, and (2) establishing the relevance between implicit targets and textual content. While existing methods primarily focus on incorporating external knowledge, they neglect the intrinsic semantic cues embedded within key intra-textual entities. Furthermore, current models exhibit limited capability in determining the relevance of unseen targets to the given text, thereby struggling to differentiate between "neutral" and "irrelevant" stance labels. To address these issues, we first construct a four-class, multi-topic Japanese tweet dataset. To our knowledge, this is the first Japanese tweet-level dataset for stance detection. We then propose KIRP, a zero-shot stance detection framework. It integrates external knowledge with entity reorganization for data augmentation and employs prompt chaining for reasoning. Specifically, the framework incorporates knowledge graphs to supplement and reorganize key textual entities, while reflective Chain-of-Thought (CoT) reasoning extracts and validates implicit targets. To better distinguish "neutral" from "irrelevant" labels, we adopt stance-aware contrastive learning to capture discriminative features and design a three-layer iterative prototype network for fine-grained classification. Experimental results on SemEval-2016, WT-WT, and KIRP-D show that KIRP achieves state-of-the-art performance. KIRP obtains F1 scores of 84.05% (three-class) on SemEval-2016, and 84.99% and 79.18% (four-class) on WT-WT and KIRP-D, respectively.

Mapping Political-Elite Networks in Europe with a Multilingual Joint Entity-Relation Extraction Pipeline

Whether political elites organise into rent-seeking coalitions that capture public resources or civic networks that sustain governance is a central question in comparative politics. Yet observing these complex, informal, and adversarial ties at scale has historically required intensive manual coding, while automated text-as-data methods have largely been limited to simple co-occurrence. Recent large language model (LLM) approaches offer a path forward but often rely on proprietary APIs, lack cross-lingual capability, and struggle with scalable entity resolution. We present a modular, fully open-weight pipeline for multilingual joint entity-relation extraction that builds signed, temporal knowledge graphs from massive unstructured news corpora. It combines span-based named-entity recognition (NER) with a three-stage linking cascade mapping mentions to language-independent Wikidata identifiers; a high-throughput, ontology-constrained mixture-of-experts model then uses guided decoding to extract directed, signed relationships grounded in a domain ontology. A full-coverage spot-check against a 3491-relation gold standard shows high textual correctness (68.2% strict to 93.7% lenient). Two large-scale case studies validate the pipeline against the public record. In Austria, it reconstructs a political party's complete lifecycle, dating internal fractures and tracking personnel into successor factions and court convictions. In a Polish corpus, it uncovers the overlapping economic and governance networks of state-enterprise patronage, alongside the structurally balanced, signed conflict network of the polarized Civic Platform (Platforma Obywatelska, PO)--Law and Justice (Prawo i Sprawiedliwość, PiS) duopoly. By bridging raw multilingual text and structured relational data, our framework provides a robust, replicable foundation for cross-national empirical computational social science.

Fuzzy Quantification over OWL Ontologies and Knowledge Graphs

This paper presents a versatile framework for evaluating fuzzy quantification queries over both standard and fuzzy ontologies as well as knowledge graphs. The primary objective is the retrieval of individuals that satisfy queries articulated via Type I or Type II fuzzy quantified expressions. A key advantage of the proposed approach is its inherent adaptability: it remains entirely agnostic to the quantifier type, the underlying evaluation method, and the specific data source of the ontology (i.e., OWL ontologies or RDFS knowledge graphs). Furthermore, we present Q2S2, a publicly accessible implementation of this system developed to support future research.

MKG-RAG-Bench: Benchmarking Retrieval in Multimodal Knowledge Graph-Augmented Generation

Retrieval-augmented generation (RAG) over knowledge graphs has emerged as a promising approach for grounding large language models, yet existing benchmarks largely overlook the challenges of retrieval in multimodal knowledge graph RAG (MKG-RAG). In practice, retrieval is a critical bottleneck: multimodal knowledge is heterogeneous, difficult to align across modalities, and often poorly served by retrievers designed for unstructured corpora. To address this gap, we introduce MKG-RAG-Bench, a cross-domain benchmark explicitly designed to evaluate retrieval in MKG-RAG. MKG-RAG-Bench is constructed from two multimodal knowledge graphs spanning general and medical domains, and includes carefully aligned question-answering datasets that support controlled evaluation of both retrieval and downstream generation. The benchmark is built using an LLM-based curation pipeline that filters low-utility knowledge, generates structurally grounded queries with exact supervision, and systematically covers diverse modality configurations. Through extensive experiments across representative retriever families and modality settings, we show that effective multimodal retrieval remains challenging yet crucial for end-to-end MKG-RAG performance, and that retrieval quality strongly determines generation outcomes. By isolating retrieval as a first-class evaluation target, MKG-RAG-Bench provides a principled foundation for diagnosing current limitations and advancing multimodal knowledge graph RAG systems.

Knowledge-augmented Agentic AI for Mental Health Medication Information Seeking

Patients increasingly seek medication information online, yet safety knowledge for psychiatric drugs is split between regulatory adverse-event records, which are authoritative but abstract, and patient narratives, which are experience-near but unvalidated. Integrating them without conflating evidence and anecdote is especially consequential in psychiatry, where poorly contextualised information can amplify fear, nocebo responses, and non-adherence. Here we develop a provenance-aware, knowledge-graph-based multi-agent framework unifying 466,525 Reddit posts, 60,782 WebMD reviews, and twenty years of U.S. FDA Adverse Event Reporting System records for nine antidepressants. A large-language-model entity-recognition pipeline benchmarked against physician annotations reached highest F1 scores of 0.969 for medications and 0.973 for conditions. The two community platforms were far more concordant with each other (overlap up to a Jaccard similarity of 0.905) than with regulatory reports, indicating that patient-generated data form a partly independent safety signal. For sertraline, many adverse events appeared in community sources hundreds of days before the corresponding FDA date. A Neo4j knowledge graph grounded in ATC-N, ICD-10, and MedDRA vocabularies preserves provenance, keeping every claim traceable and regulatory facts distinct from patient experience. These results establish source-aware integration as a route to more auditable psychiatric medication information, with usefulness and patient benefit to be tested prospectively.

An Approach for a Supporting Multi-LLM System for Automated Certification Based on the German IT-Grundschutz

This paper presents a novel approach to perform semi-automated BSI IT-Grundschutz certification using a MultiLarge Language Model system (MLS) with Hybrid RetrievalAugmented Generation (HybridRAG). Facing the challenges of the Network and Information Security Directive 2 (NIS2) directive, a shortage of specialists, and high implementation costs, our MLS architecture aims to increase efficiency, reduce costs, and support certifiers in maintaining the quality of security concepts while meeting the increased demand for certifications of newly affected companies. The system combines Large Language Models (LLMs) and Knowledge Graphs (KGs) to support different phases of the certification process, including protection needs assessment, modeling, IT-Grundschutz check, measure consolidation, and subsequent realization. Our architecture addresses the growing demand for security concepts and offers an approach to handle the digital security challenges introduced by NIS2.

Is GraphRAG Needed? From Basic RAG to Graph-/Agentic Solutions with Context Optimization

As advanced RAG variants like GraphRAG and Agentic RAG emerge, one leading question is when and how to use them. Here, we introduce a framework for different RAG scenarios evaluation and comparison on semi-structured knowledge bases, including regular RAG, GraphRAG, Modular RAG and Agentic RAG. We provide implementation for 9 standardized RAG scenarios, and conduct experiments for a comprehensive comparison. These scenarios are designed for real use cases regarding data and domain restrictions, spanning from simple document-based retrieval to advanced features such as hybrid text-graph retrieval, integration with computed or pre-defined domain knowledge graphs, agentic multi-step planning, and agent-graph integration. Besides, we present a novel context engineering method for GraphRAG and Agentic RAG, addressing the context/memory overflow issues, efficiently managing text and graph retrievals with new representations and agentic loop design, leading to 19%-53% reduction on token usage. Moreover, further analysis identifies a retrieval-generation gap where expanded retrieval does not proportionally improve generation quality, suggesting retrieval-oriented metrics overstate advanced retrieval benefits. This work provides data-driven insights on when and how to use them for building production-ready intelligent RAG systems.

KG-TRACE: A Neuro-Symbolic Framework for Mechanistic Grounding in Antimicrobial Resistance Prediction

While WGS-based AMR prediction has reached high accuracy, existing models lack a mechanism to ground neural attributions in established biological pathways. We present KG-TRACE, a novel neuro-symbolic framework that integrates the WHO mutation knowledge graph (KG) as a structured biological constraint on a neural genomic model. Unlike existing methods that learn statistical patterns in isolation, KG-TRACE fuses genomic features and RotatE-based KG embeddings through a learned epistemic trust gate, dynamically weighting neural evidence against symbolic biological knowledge. Evaluated on the CRyPTIC M. tuberculosis cohort, KG-TRACE achieves an AUROC of 0.9760 for isoniazid, achieving competitive accuracy while its primary value lies in symbolic grounding, not predictive uplift. More importantly, we introduce the Biological Grounding Ratio (BGR), a dataset-level metric that quantifies alignment between neural attributions and established biology. Our framework achieves a 92.5% symbolic coverage of isoniazid-resistant predictions and effectively identifies MDR co-occurrence artifacts by issuing laboratory follow-up flags for 'UNCERTAIN' cases. We demonstrate that neuro-symbolic grounding provides a verifiable audit trail for clinicians, bridging the gap between predictive accuracy and clinical trust.

Agentic evolution of physically constrained foundation models

Artificial intelligence increasingly drives automated scientific discovery, yet contemporary generalist agents lack physical grounding, frequently hallucinating hardware-incompatible designs. Here, we present a physically grounded, multi-agent discovery engine that autonomously architects hardware-compliant computing systems. Anchored by an Evolutionary Knowledge Graph structuring past scientific innovations, the framework extracts an "algorithmic Chain-of-Thought" to transform blind stochastic search into directed structural evolution. Applied to the extreme testbed of foundation model deployment, the engine evolved two hardware-aware compression methodologies surpassing human-engineered heuristics: Q-Enhance mitigates long-context accuracy loss in dense models, and MoE-Salient-AQ outperforms state-of-the-art manual sparse Mixture-of-Experts designs by 3.7% at sub-3-bit regimes. Utilizing a bandwidth-efficient Sensitivity Profile, we successfully deployed a massive 235-billion-parameter model onto a constrained dual-A100 server, reducing memory requirements by 75% with a marginal 0.64% accuracy degradation. By transforming unconstrained combinatorial search into knowledge-driven autonomy, this establishes a scalable hardware-software co-design paradigm for machine-driven discovery within strict physical boundaries.