Traditional similarity-based schema matching methods fail to resolve semantic ambiguities and conflicts in complex, domain-specific mappings due to a lack of commonsense and domain-specific knowledge. In parallel, large language models (LLMs) without sufficient background knowledge tend to hallucinate, further complicating schema matching. To overcome these limitations, we introduce KG-RAG4SM, a Knowledge Graph-based Retrieval-Augmented Generation for Schema Matching. This method integrates novel retrieval mechanisms, including LLM-based, vector-based, graph traversal-based, and hybrid techniques with advanced reranking schemes to extract the most relevant subgraphs from large external KGs. Our approach achieves superior results without requiring re-training, as evidenced by improvements of 39.79% in precision and 30.56% in F1 score over LLM-based state-of-the-art (SOTA) methods (e.g., Jellyfish-8B) on the MIMIC dataset, and enhancements of 69.20% in precision and 21.99% in F1 score over pre-trained language model (PLM)-based SOTA methods (e.g., SMAT) on the Synthea dataset. Additionally, KG-RAG4SM scales effectively across KGs from commonsense KGs to domain-specific ones, while its instruction-tuning knowledge exclusion component ensures truthful performance in end-to-end schema matching tasks despite the suboptimal relevance of KG context. Our empirical analysis and case studies from real-world scenarios show that the hallucination problem in LLMs for schema matching is well mitigated by our solution.
Knowledge graph representation learning approaches provide a mapping between symbolic knowledge in the form of triples in a knowledge graph (KG) and their feature vectors. Knowledge graph embedding (KGE) models often represent relations in a KG as geometric transformations. Most state-of-the-art (SOTA) KGE models are derived from elementary geometric transformations (EGTs), such as translation, scaling, rotation, and reflection, or their combinations. These geometric transformations enable the models to effectively preserve specific structural and relational patterns of the KG. However, the current use of EGTs by KGEs remains insufficient without considering relation-specific transformations. Although recent models attempted to address this problem by ensembling SOTA baseline models in different ways, only a single or composite version of geometric transformations are used by such baselines to represent all the relations. In this paper, we propose a framework that evaluates how well each relation fits with different geometric transformations. Based on this ranking, the model can: (1) assign the best-matching transformation to each relation, or (2) use majority voting to choose one transformation type to apply across all relations. That is, the model learns a single relation-specific EGT in low dimensional vector space through an attention mechanism. Furthermore, we use the correlation between relations and EGTs, which are learned in a low dimension, for relation embeddings in a high dimensional vector space. The effectiveness of our models is demonstrated through comprehensive evaluations on three benchmark KGs as well as a real-world financial KG, witnessing a performance comparable to leading models
Knowledge graphs offer a structured representation of real-world entities and their relationships, enabling a wide range of applications from information retrieval to automated reasoning. In this paper, we conduct a systematic comparison between traditional rule-based approaches and modern deep learning methods for link prediction. We focus on KBGAT, a graph neural network model that leverages multi-head attention to jointly encode both entity and relation features within local neighborhood structures. To advance this line of research, we introduce \textbf{GCAT} (Graph Collaborative Attention Network), a refined model that enhances context aggregation and interaction between heterogeneous nodes. Experimental results on four widely-used benchmark datasets demonstrate that GCAT not only consistently outperforms rule-based methods but also achieves competitive or superior performance compared to existing neural embedding models. Our findings highlight the advantages of attention-based architectures in capturing complex relational patterns for knowledge graph completion tasks.
Link prediction infers missing or future relations between graph nodes, based on connection patterns. Scientific literature networks and knowledge graphs are typically large, sparse, and noisy, and often contain missing links between entities. We present an AI-driven hierarchical link prediction framework that integrates matrix factorization to infer hidden associations and steer discovery in complex material domains. Our method combines Hierarchical Nonnegative Matrix Factorization (HNMFk) and Boolean matrix factorization (BNMFk) with automatic model selection, as well as Logistic matrix factorization (LMF), we use to construct a three-level topic tree from a 46,862-document corpus focused on 73 transition-metal dichalcogenides (TMDs). These materials are studied in a variety of physics fields with many current and potential applications. An ensemble BNMFk + LMF approach fuses discrete interpretability with probabilistic scoring. The resulting HNMFk clusters map each material onto coherent topics like superconductivity, energy storage, and tribology. Also, missing or weakly connected links are highlight between topics and materials, suggesting novel hypotheses for cross-disciplinary exploration. We validate our method by removing publications about superconductivity in well-known superconductors, and show the model predicts associations with the superconducting TMD clusters. This shows the method finds hidden connections in a graph of material to latent topic associations built from scientific literature, especially useful when examining a diverse corpus of scientific documents covering the same class of phenomena or materials but originating from distinct communities and perspectives. The inferred links generating new hypotheses, produced by our method, are exposed through an interactive Streamlit dashboard, designed for human-in-the-loop scientific discovery.
Semantic context surrounding a triplet $(h, r, t)$ is crucial for Knowledge Graph Completion (KGC), providing vital cues for prediction. However, traditional node-based message passing mechanisms, when applied to knowledge graphs, often introduce noise and suffer from information dilution or over-smoothing by indiscriminately aggregating information from all neighboring edges. To address this challenge, we propose a semantic-aware relational message passing. A core innovation of this framework is the introduction of a \textbf{semantic-aware Top-K neighbor selection strategy}. Specifically, this strategy first evaluates the semantic relevance between a central node and its incident edges within a shared latent space, selecting only the Top-K most pertinent ones. Subsequently, information from these selected edges is effectively fused with the central node's own representation using a \textbf{multi-head attention aggregator} to generate a semantically focused node message. In this manner, our model not only leverages the structure and features of edges within the knowledge graph but also more accurately captures and propagates the contextual information most relevant to the specific link prediction task, thereby effectively mitigating interference from irrelevant information. Extensive experiments demonstrate that our method achieves superior performance compared to existing approaches on several established benchmarks.
Teaching large language models (LLMs) to use tools is crucial for improving their problem-solving abilities and expanding their applications. However, effectively using tools is challenging because it requires a deep understanding of tool functionalities and user intentions. Previous methods relied mainly on LLMs to generate instruction data, but the quality of these data was often insufficient. In this paper, we propose a new method that uses knowledge graphs to generate high-quality instruction data for LLMs. Knowledge graphs are manually curated datasets rich in semantic information. We begin by extracting various query pathways from a given knowledge graph, which are transformed into a broad spectrum of user queries. We then translate the relationships between entities into actionable tools and parse the pathways of each query into detailed solution steps, thereby creating high-quality instruction data. Our experiments show that fine-tuning on just a small sample of this synthetic data can significantly improve the tool utilization and overall capabilities of LLMs.
The rapid evolution of artificial intelligence has led to expectations of transformative scientific discovery, yet current systems remain fundamentally limited by their operational architectures, brittle reasoning mechanisms, and their separation from experimental reality. Building on earlier work, we contend that progress in AI-driven science now depends on closing three fundamental gaps -- the abstraction gap, the reasoning gap, and the reality gap -- rather than on model size/data/test time compute. Scientific reasoning demands internal representations that support simulation of actions and response, causal structures that distinguish correlation from mechanism, and continuous calibration. We define active inference AI systems for scientific discovery as those that (i) maintain long-lived research memories grounded in causal self-supervised foundation models, (ii) symbolic or neuro-symbolic planners equipped with Bayesian guardrails, (iii) grow persistent knowledge graphs where thinking generates novel conceptual nodes, reasoning establishes causal edges, and real-world interaction prunes false connections while strengthening verified pathways, and (iv) refine their internal representations through closed-loop interaction with both high-fidelity simulators and automated laboratories - an operational loop where mental simulation guides action and empirical surprise reshapes understanding. In essence, we outline an architecture where discovery arises from the interplay between internal models that enable counterfactual reasoning and external validation that grounds hypotheses in reality. It is also argued that the inherent ambiguity in feedback from simulations and experiments, and underlying uncertainties makes human judgment indispensable, not as a temporary scaffold but as a permanent architectural component.
Knowledge graphs (KGs) are useful for analyzing social structures, community dynamics, institutional memberships, and other complex relationships across domains from sociology to public health. While recent advances in large language models (LLMs) have improved the scalability and accessibility of automated KG extraction from large text corpora, the impacts of extraction errors on downstream analyses are poorly understood, especially for applied scientists who depend on accurate KGs for real-world insights. To address this gap, we conducted the first evaluation of KG extraction performance at two levels: (1) micro-level edge accuracy, which is consistent with standard NLP evaluations, and manual identification of common error sources; (2) macro-level graph metrics that assess structural properties such as community detection and connectivity, which are relevant to real-world applications. Focusing on affiliation graphs of person membership in organizations extracted from social register books, our study identifies a range of extraction performance where biases across most downstream graph analysis metrics are near zero. However, as extraction performance declines, we find that many metrics exhibit increasingly pronounced biases, with each metric tending toward a consistent direction of either over- or under-estimation. Through simulations, we further show that error models commonly used in the literature do not capture these bias patterns, indicating the need for more realistic error models for KG extraction. Our findings provide actionable insights for practitioners and underscores the importance of advancing extraction methods and error modeling to ensure reliable and meaningful downstream analyses.
This paper develops a comprehensive framework for artificial intelligence systems that operate under strict epistemic constraints, moving beyond stochastic language prediction to support structured reasoning, propositional commitment, and contradiction detection. It formalises belief representation, metacognitive processes, and normative verification, integrating symbolic inference, knowledge graphs, and blockchain-based justification to ensure truth-preserving, auditably rational epistemic agents.
As data and knowledge expand rapidly, adopting systematic methodologies for ontology generation has become crucial. With the daily increases in data volumes and frequent content changes, the demand for databases to store and retrieve information for the creation of knowledge graphs has become increasingly urgent. The previously established Knowledge Acquisition and Representation Methodology (KNARM) outlines a systematic approach to address these challenges and create knowledge graphs. However, following this methodology highlights the existing challenge of seamlessly integrating Neo4j databases with the Web Ontology Language (OWL). Previous attempts to integrate data from Neo4j into an ontology have been discussed, but these approaches often require an understanding of description logics (DL) syntax, which may not be familiar to many users. Thus, a more accessible method is necessary to bridge this gap. This paper presents a user-friendly approach that utilizes Python and its rdflib library to support ontology development. We showcase our novel approach through a Neo4j database we created by integrating data from the Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database. Using this dataset, we developed a Python script that automatically generates the required classes and their axioms, facilitating a smoother integration process. This approach offers a practical solution to the challenges of ontology generation in the context of rapidly growing adverse drug event datasets, supporting improved drug safety monitoring and public health decision-making.
Despite extensive research on Machine Learning-based Network Intrusion Detection Systems (ML-NIDS), their capability to detect diverse attack variants remains uncertain. Prior studies have largely relied on homogeneous datasets, which artificially inflate performance scores and offer a false sense of security. Designing systems that can effectively detect a wide range of attack variants remains a significant challenge. The progress of ML-NIDS continues to depend heavily on human expertise, which can embed subjective judgments of system designers into the model, potentially hindering its ability to generalize across diverse attack types. To address this gap, we propose KnowML, a framework for knowledge-guided machine learning that integrates attack knowledge into ML-NIDS. KnowML systematically explores the threat landscape by leveraging Large Language Models (LLMs) to perform automated analysis of attack implementations. It constructs a unified Knowledge Graph (KG) of attack strategies, on which it applies symbolic reasoning to generate KG-Augmented Input, embedding domain knowledge directly into the design process of ML-NIDS. We evaluate KnowML on 28 realistic attack variants, of which 10 are newly collected for this study. Our findings reveal that baseline ML-NIDS models fail to detect several variants entirely, achieving F1 scores as low as 0 %. In contrast, our knowledge-guided approach achieves up to 99 % F1 score while maintaining a False Positive Rate below 0.1 %.
Performance evaluation for Content-Based Image Retrieval (CBIR) remains a crucial but unsolved problem today especially in the medical domain. Various evaluation metrics have been discussed in the literature to solve this problem. Most of the existing metrics (e.g., precision, recall) are adapted from classification tasks which require manual labels as ground truth. However, such labels are often expensive and unavailable in specific thematic domains. Furthermore, medical images are usually associated with (radiological) case reports or annotated with descriptive captions in literature figures, such text contains information that can help to assess CBIR.Several researchers have argued that the medical concepts hidden in the text can serve as the basis for CBIR evaluation purpose. However, these works often consider these medical concepts as independent and isolated labels while in fact the subtle relationships between various concepts are neglected. In this work, we introduce the use of knowledge graphs to measure the distance between various medical concepts and propose a novel relevance measure for the evaluation of CBIR by defining an approximate matching-based relevance score between two sets of medical concepts which allows us to indirectly measure the similarity between medical images.We quantitatively demonstrate the effectiveness and feasibility of our relevance measure using a public dataset.
Large Language Models (LLMs) have achieved impressive capabilities in language understanding and generation, yet they continue to underperform on knowledge-intensive reasoning tasks due to limited access to structured context and multi-hop information. Retrieval-Augmented Generation (RAG) partially mitigates this by grounding generation in retrieved context, but conventional RAG and GraphRAG methods often fail to capture relational structure across nodes in knowledge graphs. We introduce Inference-Scaled GraphRAG, a novel framework that enhances LLM-based graph reasoning by applying inference-time compute scaling. Our method combines sequential scaling with deep chain-of-thought graph traversal, and parallel scaling with majority voting over sampled trajectories within an interleaved reasoning-execution loop. Experiments on the GRBench benchmark demonstrate that our approach significantly improves multi-hop question answering performance, achieving substantial gains over both traditional GraphRAG and prior graph traversal baselines. These findings suggest that inference-time scaling is a practical and architecture-agnostic solution for structured knowledge reasoning with LLMs
Multimodal electronic health record (EHR) data is useful for disease risk prediction based on medical domain knowledge. However, general medical knowledge must be adapted to specific healthcare settings and patient populations to achieve practical clinical use. Additionally, risk prediction systems must handle uncertainty from incomplete data and non-deterministic health outcomes while remaining explainable. These challenges can be alleviated by the integration of knowledge graphs (KGs) and Bayesian networks (BNs). We present a novel approach for constructing BNs from ontology-based KGs and multimodal EHR data for explainable disease risk prediction. Through an application use case of atrial fibrillation and real-world EHR data, we demonstrate that the approach balances generalised medical knowledge with patient-specific context, effectively handles uncertainty, is highly explainable, and achieves good predictive performance.
Time-continuous dynamic models are essential for various Cyber-Physical System (CPS) applications. To ensure effective usability in different lifecycle phases, such behavioral information in the form of differential equations must be contextualized and integrated with further CPS information. While knowledge graphs provide a formal description and structuring mechanism for this task, there is a lack of reusable ontological artifacts and methods to reduce manual instantiation effort. Hence, this contribution introduces two artifacts: Firstly, a modular semantic model based on standards is introduced to represent differential equations directly within knowledge graphs and to enrich them semantically. Secondly, a method for efficient knowledge graph generation is presented. A validation of these artifacts was conducted in the domain of aviation maintenance. Results show that differential equations of a complex Electro-Hydraulic Servoactuator can be formally represented in a knowledge graph and be contextualized with other lifecycle data, proving the artifacts' practical applicability.
Temporal knowledge graph reasoning aims to predict future events with knowledge of existing facts and plays a key role in various downstream tasks. Previous methods focused on either graph structure learning or semantic reasoning, failing to integrate dual reasoning perspectives to handle different prediction scenarios. Moreover, they lack the capability to capture the inherent differences between historical and non-historical events, which limits their generalization across different temporal contexts. To this end, we propose a Multi-Expert Structural-Semantic Hybrid (MESH) framework that employs three kinds of expert modules to integrate both structural and semantic information, guiding the reasoning process for different events. Extensive experiments on three datasets demonstrate the effectiveness of our approach.
This paper presents a formalised architecture for synthetic agents designed to retain immutable memory, verifiable reasoning, and constrained epistemic growth. Traditional AI systems rely on mutable, opaque statistical models prone to epistemic drift and historical revisionism. In contrast, we introduce the concept of the Merkle Automaton, a cryptographically anchored, deterministic computational framework that integrates formal automata theory with blockchain-based commitments. Each agent transition, memory fragment, and reasoning step is committed within a Merkle structure rooted on-chain, rendering it non-repudiable and auditably permanent. To ensure selective access and confidentiality, we derive symmetric encryption keys from ECDH exchanges contextualised by hierarchical privilege lattices. This enforces cryptographic access control over append-only DAG-structured knowledge graphs. Reasoning is constrained by formal logic systems and verified through deterministic traversal of policy-encoded structures. Updates are non-destructive and historied, preserving epistemic lineage without catastrophic forgetting. Zero-knowledge proofs facilitate verifiable, privacy-preserving inclusion attestations. Collectively, this architecture reframes memory not as a cache but as a ledger - one whose contents are enforced by protocol, bound by cryptography, and constrained by formal logic. The result is not an intelligent agent that mimics thought, but an epistemic entity whose outputs are provably derived, temporally anchored, and impervious to post hoc revision. This design lays foundational groundwork for legal, economic, and high-assurance computational systems that require provable memory, unforgeable provenance, and structural truth.
Large Language Models (LLMs) have shown strong inductive reasoning ability across various domains, but their reliability is hindered by the outdated knowledge and hallucinations. Retrieval-Augmented Generation mitigates these issues by grounding LLMs with external knowledge; however, most existing RAG pipelines rely on unstructured text, limiting interpretability and structured reasoning. Knowledge graphs, which represent facts as relational triples, offer a more structured and compact alternative. Recent studies have explored integrating knowledge graphs with LLMs for knowledge graph question answering (KGQA), with a significant proportion adopting the retrieve-then-reasoning paradigm. In this framework, graph-based retrievers have demonstrated strong empirical performance, yet they still face challenges in generalization ability. In this work, we propose RAPL, a novel framework for efficient and effective graph retrieval in KGQA. RAPL addresses these limitations through three aspects: (1) a two-stage labeling strategy that combines heuristic signals with parametric models to provide causally grounded supervision; (2) a model-agnostic graph transformation approach to capture both intra- and inter-triple interactions, thereby enhancing representational capacity; and (3) a path-based reasoning strategy that facilitates learning from the injected rational knowledge, and supports downstream reasoner through structured inputs. Empirically, RAPL outperforms state-of-the-art methods by $2.66\%-20.34\%$, and significantly reduces the performance gap between smaller and more powerful LLM-based reasoners, as well as the gap under cross-dataset settings, highlighting its superior retrieval capability and generalizability. Codes are available at: https://github.com/tianyao-aka/RAPL.
This paper presents a hierarchical knowledge graph framework for the structured understanding of visual narratives, focusing on multimodal media such as comics. The proposed method decomposes narrative content into multiple levels, from macro-level story arcs to fine-grained event segments. It represents them through integrated knowledge graphs that capture semantic, spatial, and temporal relationships. At the panel level, we construct multimodal graphs that link visual elements such as characters, objects, and actions with corresponding textual components, including dialogue and captions. These graphs are integrated across narrative levels to support reasoning over story structure, character continuity, and event progression. We apply our approach to a manually annotated subset of the Manga109 dataset and demonstrate its ability to support symbolic reasoning across diverse narrative tasks, including action retrieval, dialogue tracing, character appearance mapping, and panel timeline reconstruction. Evaluation results show high precision and recall across tasks, validating the coherence and interpretability of the framework. This work contributes a scalable foundation for narrative-based content analysis, interactive storytelling, and multimodal reasoning in visual media.
While Large Language Models (LLMs) excel at many natural language processing tasks, they often suffer from factual inaccuracies in knowledge-intensive scenarios. Integrating external knowledge resources, particularly knowledge graphs (KGs), provides a transparent and updatable foundation for more reliable reasoning. Knowledge Base Question Answering (KBQA), which queries and reasons over KGs, is central to this effort, especially for complex, multi-hop queries. However, multi-hop reasoning poses two key challenges: (1)~maintaining coherent reasoning paths, and (2)~avoiding prematurely discarding critical multi-hop connections. To address these issues, we introduce iQUEST, a question-guided KBQA framework that iteratively decomposes complex queries into simpler sub-questions, ensuring a structured and focused reasoning trajectory. Additionally, we integrate a Graph Neural Network (GNN) to look ahead and incorporate 2-hop neighbor information at each reasoning step. This dual approach strengthens the reasoning process, enabling the model to explore viable paths more effectively. Detailed experiments demonstrate the consistent improvement delivered by iQUEST across four benchmark datasets and four LLMs.