Oracle, will I ever learn? A study of prediction convergence and complementarity across link prediction models

Knowledge graphs have become an important source of structured knowledge for Web applications, including search, question answering, and recommender systems. In these applications, link prediction can serve either as a prediction task itself or as a means to enrich incomplete knowledge graphs for downstream tasks. Interestingly, different link prediction models, or even different training runs of the same model, can produce substantially different predictions for the same query. This suggests a variability in the capture of the underlying knowledge by models, thus raising a fundamental question: to what extent do different models capture complementary knowledge, and how much of this knowledge could be recovered by combining them? We propose to measure model complementarity through the performance of an oracle that, for each query, selects the best prediction among a considered set of models, hence providing an upper bound on the performance achievable through model combination. Across several architectures and benchmarks, we find a substantial gap between individual models and their oracle, revealing that different models capture complementary knowledge. Yet, this complementarity rapidly saturates as more models are added, leaving a persistent subset of queries unsolved even by a large number of models. These findings reveal both the potential of model complementarity and a fundamental limit to what current link prediction models can collectively recover; thereby highlighting the need for further research to build robust Web applications.

Hidden relationships in a document-derived property graph: top-k chunk embeddings and inverse-distance weighting over a dynamically evolving ontology

Large language models extracting knowledge graphs from text capture only explicitly stated facts, often leaving semantically related entities disconnected across documents. We present an additive, engine-neutral second pass that discovers these latent ties without altering extracted facts. Each document is chunked and embedded once; top-k nearest- neighbor queries across existing chunks yield candidate node pairs via entity membership maps. Candidate pairs are scored using Shepard inverse-distance weighting with a rescaled chord distance metric, avoiding the threshold-collapsing flaw of affine cosine scoring behind a k-NN gate. Un-gated per-pair accumulators form a commutative monoid, ensuring the pipeline is strictly order-independent and scales incrementally without recomputing prior documents. Implemented across FalkorDB, Kinetica, ArangoDB, and Neo4j, our method shows that 768- and 240-dimensional embeddings retain 92% and 72% edge fidelity against a 3072-D baseline while achieving a 25x faster top-k formulation.

OntoAligner-Ensemble: Voting-Based Fusion across Heterogeneous Ontology Alignment Techniques

Ontology alignment (OA) has evolved through several methodological paradigms, ranging from lexical and structural aligners to knowledge graph embedding (KGE) models and, more recently, Large Language Model (LLM)-based approaches. Although modern OA frameworks provide unified ecosystems for deploying these heterogeneous aligners, mechanisms for systematically reconciling their complementary and sometimes conflicting predictions remain relatively underexplored. We present OntoAligner-Ensemble, a modular and aligner-agnostic framework that combines candidate correspondences through a configurable two-stage process comprising voting-based fusion strategies followed by post-fusion selection policies. The framework supports any aligner implemented within OntoAligner that produces candidate correspondences, enabling diverse alignment paradigms to be integrated through a unified decision process. To demonstrate its effectiveness, we instantiate the framework using representative lightweight string-aligner, KGE-based, and Retrieval-Augmented Generation aligners powered by both open-weight and API-based LLMs. We evaluate individual aligners and ensemble configurations across eight benchmark tasks from five OAEI tracks spanning biomedical to beyond-equivalence. The results show that ensemble fusion consistently improves the balance between precision and recall and frequently outperforms standalone aligners across diverse domains. Furthermore, our analysis reveals that ensemble composition directly affects the precision-recall trade-off: heterogeneous cross-paradigm ensembles generally improve precision, whereas homogeneous LLM ensembles more often achieve higher overall F1-scores. These findings demonstrate that systematic ensemble learning offers a robust and reproducible strategy for OA while providing practical guidance for selecting ensemble compositions under different alignment scenarios.

SNAP-KG: Streaming Node Assignment via Projection for Knowledge Graph Entity Integration

Knowledge graph (KG) construction pipelines must continuously integrate newly arriving entities into a growing graph. Unlike inserting triples between existing nodes, a newly arriving entity has no graph connectivity: it emerges from the acquisition phase as a raw feature vector and must be assigned to a semantic community before entity resolution and link prediction can operate over a tractable candidate set. Existing multi-view graph clustering methods exploit multiple relation types as structural views, but are transductive: they assume a fixed graph and cannot assign unseen entities without retraining. We propose SNAP-KG (Streaming Node Assignment via Projection for Knowledge Graph Entity Integration), a framework supporting graph-structural multi-view relational clustering and inductive inference for streaming entities. SNAP-KG trains a projector to map a new entity directly to the learned embedding space using only raw features, enabling immediate cluster assignment without graph access or model retraining. Experiments on five benchmark multi-view graph datasets and a production-scale KG of 2.4 million nodes demonstrate multiple orders-of-magnitude inference speedups over retraining-based approaches and competitive clustering quality. As a candidate scoping mechanism for downstream tasks, SNAP-KG achieves 62-75% candidate search reduction on the five benchmark datasets and 97% on OGB-WikiKG2 for entity resolution and link prediction.

Neural Message Passing on Structural Interaction Graphs for Fully-Inductive Graph Neural Networks

A central obstacle in building graph foundation models is the input heterogeneity in terms of feature space dimensionality, semantics, and structure. Such heterogeneity limits the capability of graph neural networks to generalize to new graphs with unseen feature spaces. We address the transferability challenge with SIGIL, a framework that maps any attributed graph to a unified representation space of fixed dimension. Given a graph, SIGIL lifts it to a structural interaction graph, where nodes are the input feature dimensions and weighted, typed edges encode feature alignment across multiple orders of the graph's connectivity. A relational message-passing network embeds each feature dimension into a shared space, transforming the original node features, of arbitrary dimensionality, into representations transferable to any downstream graph. By construction, SIGIL is equivariant to permutations of nodes, feature dimensions, and labels. Additionally, when the input features are one-hot indicators of discrete relations, SIGIL recovers and strictly generalizes existing foundation models for knowledge graph reasoning. A single SIGIL model, pretrained on one graph, delivers strong fully-inductive link prediction. Also, SIGIL can be used to implement existing knowledge graph foundation models. As such, SIGIL unifies several existing regimes in graph foundation model design under a single framework

Improving Interoperability among Defence and National Security Ontologies: Analysis and Evaluation Tasks

The use of ontologies and knowledge graphs is becoming increasingly widespread in the defence and national security domain. Numerous ontologies have been developed through initiatives led by academia, industry, and government. Achieving interoperability across diverse defence and national security ontologies remains a major challenge due to the domain's breadth and specialisation. In this work, we analyse and document over 60 publicly available ontologies and introduce a new track for the Ontology Alignment Evaluation Initiative (OAEI). This track comprises eight matching tasks, consensus alignments and manually-curated (silver-standard) mappings. The consensus alignments are derived by aggregating the outputs of several state-of-the-art ontology alignment systems. The silver-standard is obtained from the manual validation of the consensus alignment together with a subset of the unique mappings (i.e., mappings suggested by only one system).

ProPRL: Property-Aware Prerequisite Relation Learning in Educational Knowledge Graphs

Prerequisite relation learning is central to adaptive instruction, yet existing methods often formulate it as conventional link prediction, limiting their ability to adaptively integrate complementary educational evidence for individual candidate pairs and to discourage contradictory reverse predictions. We propose ProPRL, a Property-aware Prerequisite Relation Learning framework. ProPRL first learns complementary concept representations from a concept-resource hypergraph and a directed learning-behavior graph, where direction-preserving personalized propagation aggregates multi-hop behavioral evidence. It then employs a Pair-conditioned Gate to adaptively weight and fuse the two views for each candidate ordered concept pair. Finally, an \textit{Irreversibility Constraint} introduces an anti-symmetry regularizer that penalizes simultaneously high confidence in both directions of the same concept pair. Experiments on multiple real-world educational datasets show that ProPRL achieves state-of-the-art performance on prerequisite relation learning.

The Graph Language: How Knowledge Graphs Speak to Large Language Models

Large Language Models (LLMs) excel at reasoning but benefit from grounding provided by Knowledge Graphs (KGs). However, integrating these paradigms is challenging. We introduce GRALAN, which enables KGs to speak directly in the LLM's semantic space through relational tokens that preserve graph structure. GRALAN-s trainable language mediator generates structured tokens for any frozen LLM, creating a foundation for knowledge-intensive applications. We demonstrate its effectiveness in question-answering by re-framing the task as entity classification over question-focused subgraphs. Experiments show that GRALAN significantly outperforms existing methods, particularly on complex multi-hop reasoning tasks, establishing a new paradigm for KG-LLM integration that maintains structural fidelity while leveraging LLMs' reasoning capabilities.

Fully Inductive Cardinality Estimation

Query optimization of Basic Graph Patterns (BGP) SPARQL queries over Knowledge Graphs (KG) requires accurate cardinality estimation. Recently published learned estimators outperform statistics- and sampling-based approaches, but share a limitation preventing their adoption in real-world triplestores: they are transductive and require retraining when the underlying graph changes or when applied to new graphs. We present FICE (Fully Inductive Cardinality Estimation), the first learned cardinality estimator for BGP queries over KGs that generalizes to entirely unseen graphs (including unseen relations), without any retraining. FICE is a graph neural network (GNN) with two coupled components. First, an encoder GNN over a factor-graph view of the KG produces entity and relation embeddings. We prove that BGP cardinality is a local function of the 2-hop neighborhood around bound terms in this view, motivating the local message-passing encoder. A decoder GNN then composes these embeddings along the join topology of the query to predict log-cardinality. The encoder and decoder are trained jointly, making the embeddings specialized for cardinality estimation. FICE is trained using neighborhood sampling to scale to KGs with millions of triples, and decouples embedding generation from cardinality decoding to enable estimation latency below a millisecond. Compared to learned and non-learned baselines over 10 KGs, FICE reduces the overall median q-error from 13.54 (for the best competitor) to 5.34 and dominates all approaches in tail behavior.

OntoExtend: A Framework for Requirement-driven and Scalable Ontology Extension with LLMs

Ontology extension refers to the process of enriching an existing ontology in response to emerging requirements, making it more complete. This task is a resource-intensive and error-prone process. Large Language Models (LLMs) have shown promising performance on generating ontologies from scratch, but current approaches rarely tie ontology extension explicitly to requirements or reusable core models, and offer limited, systematic evaluation of LLM outputs. This paper introduces OntoExtend, a requirements-driven framework for ontology extension with LLMs. It uses retrieval-augmented generation (RAG) over relevant input ontologies and requirements in the form of competency questions to propose grounded extensions. We evaluate OntoExtend on 39 CQs from two use cases: a public EU-project ontology, Onto-DESIDE, and an industrial ontology from Bosch. The generated fragments show few structural issues, satisfy all functional evaluation tests, and are rated by ontology engineers as requiring minor to moderate revision before integration. These results suggest that OntoExtend is useful as a drafting assistant for requirement-driven ontology extension in real world scenarios, while remaining sensitive to CQ specificity and modelling profile.

GRATE: Temporal Extensions for Inductive KG Foundation Models via Gated Rotary Attention

Knowledge graph foundation models such as Ultra and Trix achieve strong inductive transfer by learning relation-graph representations that generalise to unseen entities and relations. Extending this transferability to temporal knowledge graphs (TKGs) remains challenging: existing temporal models tie their parameters to dataset-specific entities, relations, or timestamps and are not designed to transfer to TKGs with disjoint vocabularies. We propose GRATE (Gated Rotary Attention for Temporal Encoding), an entity-side message function that adds no learnable parameters and encodes time through relative time differences by rotating each edge message according to its time gap to the query and applying a query-conditioned gate to select temporally relevant signals. GRATE integrates into NBFNet-style KG foundation models while preserving structural transferability. Existing TKG benchmarks evaluate within shared train/test vocabularies and cannot directly test cross-dataset temporal transfer; we therefore construct GDELTIndT and WIKIIndT, inductive transfer benchmark suites with disjoint entities, relations, and timestamps spanning both interpolation and extrapolation. Across these benchmarks and held-out forecasting datasets, a single jointly pretrained GRATE checkpoint improves over the static base model in most settings.

InductWave: Inductive Multi-Hop Logical Query Answering on Knowledge Graphs

Logical Multi-Hop Query Answering over Knowledge Graphs (KGs) can be formulated as querying, with an implicit completeness assumption. Current works mainly focus on Existential First Order Logic (EFO) queries. These EFO queries contain conjunction, disjunction, and negation operators. Most existing works employ transductive reasoning, meaning they are not capable of reasoning over entities unseen during training. In the real world, there is a resource scarcity, and we cannot train a model with all the nodes of a large KG. Hence, we propose InductWave, a wavelet-based inductive embedding method for logical query answering on large KGs. Here, the training graph consists of fewer nodes than the test graph. Our model performs on par with the baseline models while having half the number of message-passing layers. It outperforms all of them in most cases, with 75% of the layers. These fewer resource requirements enable us to evaluate InductWave on massive graphs, such as Wiki-KG. We test our model using extensive experiments across varying train-test graph proportions of the FB15k-(237) dataset, comparing it with the state-of-the-art models. The code and datasets for the model are available at https://github.com/kracr/inductwave/.

OntoLearner: A Modular Python Library for Ontology Learning with Large Language Models

Ontology learning (OL) aims to automatically construct structured knowledge models from text, yet progress remains fragmented across methods, domains, and evaluation practices. Despite decades of research, OL lacks a shared infrastructure for systematic evaluation and ontology access. This absence has hindered progress and fragmented research, leaving the central challenges of OL largely unaddressed. We introduce OntoLearner, a modular, cross-domain, and first-of-its-kind framework that unifies ontology access, large language model (LLM)-driven learning pipelines, and standardized benchmarking. OntoLearner releases 180 machine-readable ontologies spanning 22 domains and provides pipeline-ready datasets with train/dev/test splits for three core OL tasks: term typing, taxonomy discovery, and non-taxonomic relation extraction. Using this infrastructure, we conduct a large-scale empirical study of OL, evaluating 22 retrieval models and 12 LLMs across domains and tasks. The results converge on a finding that reframes the central challenge of OL: failure modes scale with ontological complexity rather than model size or architectural sophistication. The primary bottleneck is not model capability, but a structural mismatch between how models encode knowledge and how ontologies organize it. These findings establish that effective OL is reachable through the cross-domain, multi-task benchmarking enabled by OntoLearner. OntoLearner is open-source (MIT license) at https://github.com/sciknoworg/OntoLearner/.

Half a Link can Be Enough to Predict a Whole Link: Understanding Generalization in Knowledge Graph Foundation Models

Knowledge graph (KG) foundation models (KGFMs) are zero-shot generalizers: trained once, they can predict links on unseen graphs without retraining. However, understanding when and how they can robustly generalize across KGs is still an open question. In this paper, we shed some light on their generalization mechanisms highlighting how their performance on unseen KGs is not uniform when it comes to partially seen links, which we call half-links. In fact, we show that to predict a test triple $(h,r,t)$ it might suffice in practice to have observed the half-link $(h,r)$ or $(r,t)$ in the inference graph. This yields a taxonomy of four scenarios when combinations of these half-links are observed or not. In a rigorous stratified analysis over these scenarios, we reveal that SoTA KGFMs use seen half links for predictions, while unseen half-links pose different challenges. As such, our finer-grained taxonomy can be a diagnostic protocol for robust KGFM generalization and highlights where novel KGFMs can improve.

LLMs+Graphs: Toward Graph-Native, Synergistic AI Systems

Large Language Models (LLMs) have advanced rapidly, but their limitations in structured and multi-hop reasoning underscore the need for graph-native, synergistic artificial intelligence (AI) systems. Graph-structured data underpins critical applications across social, biological, financial, transportation, web, and knowledge domains, making it essential to understand how LLMs can leverage graph computation for grounded, context-rich inference. Three complementary synergies are emerging: LLMs augmented with graph computation for retrieval and reasoning; bidirectional integration between LLMs and knowledge graphs (KGs), where LLMs support KG construction and curation while KGs enforce semantic constraints and factual consistency; and AI agents strengthened by graph algorithms for planning, decision making, and multi-step reasoning. In parallel, LLMs introduce new capabilities for graph data management and graph machine learning (ML) through natural language interfaces and hybrid LLM-graph neural network (GNN) pipelines. This tutorial synthesizes the algorithms, systems, and design principles driving these converging directions, offering data science and data mining researchers a unified perspective on integrating LLMs, graph data management, graph mining, graph ML, and agentic computation into next-generation graph-native AI systems.

Extending Ontologies: From Dense Embeddings to Hybrid Quantum-Fuzzy Systems

LLMs have revolutionized knowledge representation and retrieval, but lack the explicit modeling that knowledge ontologies possess. This paper surveys the ways that ontologies and knowledge graphs have been integrated with dense embedding algorithms. All hitherto attempts involve a trade-off between probabilistic and crisp inference. This paper proposes a novel frontier for devising knowledge representation systems that can simultaneously accommodate probabilistic and crisp inference in the same representation. To this effect, the paper proposes neuro-quantum-fuzzy systems as knowledge representation systems that accommodate both classical and contextual inference implemented through quantum-neural networks (QNN).

Harnessing Structural Context for Entity Alignment Foundation Models

Entity alignment (EA) aims to identify equivalent entities across heterogeneous knowledge graphs (KGs) and is a key component of knowledge fusion and cross-KG reasoning. The recent EA foundation model demonstrates that alignment knowledge, once pretrained, can be directly applied to diverse previously unseen KG pairs. However, it still underuses structural context in two places: cross-KG interaction is weak during encoding, and final candidate ranking still relies too heavily on coarse similarity. We address these limitations with ContextEA, an enhanced encoder-decoder framework for transferable EA. On the encoder side, we introduce a cross-KG interaction encoder that unifies the two KGs with anchor bridges and performs earlier relation-aware cross-graph propagation. On the decoder side, we introduce a structural calibration decoder that calibrates alignment scores with entity-level, neighborhood-level, relation-level, and anchor-aware structural evidence. This design strengthens both structural context construction and structural context exploitation while remaining lightweight. Experiments on 29 EA datasets in OpenEA, SRPRS, and DBP show consistent gains over strong transferable baselines. Notably, the pretrained ContextEA already surpasses the finetuned baselines on all three benchmark groups, demonstrating substantially stronger transfer to unseen KGs. These results suggest that explicitly harnessing structural context is an effective direction for improving EA foundation models.

The Violation Situation Pattern: Persistent Representation of Compliance Violations in Knowledge Graphs

Existing compliance pipelines identify violations as transient query results, leaving no persistent representation of the violation itself or its lifecycle, evidence, and audit history. We address this limitation with the Violation Situation Pattern (VSP), a reusable ontology pattern that extends the Situation pattern of Gangemi and Mika by modeling each detected violation as a persistent first-class graph entity. Each violation is associated with a rule identifier, temporal validity interval, lifecycle state, and evidence links to the affected entities, while immutable lifecycle events provide a complete and queryable audit trail. We instantiate VSP on the schema of a deployed legal knowledge graph integrating corporate governance and contract data, populated with public contract corpora containing violations with established ground truth, and operationalize four deontic compliance rules. Rather than evaluating detection algorithms, we evaluate the pattern's robustness under rule evolution. Results show that repeated rule execution creates no duplicate violations, modifications to rule definitions preserve complete audit histories, and expanding rule scope maintains violation identity and lifecycle continuity. A case study using 73 regulatory enforcement decisions further demonstrates that compliance rules can evolve to capture additional confirmed violations without compromising the integrity of stored identities, evidence, or audit histories. These findings show that VSP enables compliance knowledge graphs to evolve without sacrificing traceability, explainability, or historical consistency. The complete implementation, queries, SHACL shapes, and evaluation dataset are publicly available to support the reproducibility of the reported results.

Evaluation of Pipelines for Data Integration into Knowledge Graphs

Integrating new data into knowledge graphs (KG) typically involves different tasks that are executed within workflows or pipelines There are many possible pipelines for a specific integration problem but there is not yet a general approach to evaluate the overall quality and performance of such pipelines to be able to determine the best choices. We therefore propose a new benchmark KGI-Bench to evaluate integration pipelines that ingest different kinds of input data into an existing KG. We evaluate pipelines by analyzing their output, i.e., the updated KG, with the three complementary quality metrics coverage, correctness and consistency. We also provide benchmark datasets (seed KG, overlapping input data of three formats, reference KG as a ground truth) for the movie domain. To demonstrate the applicability and usefulness of the proposed benchmark, we comparatively evaluate 12 pipelines and analyze their behavior across different input data formats and design choices.

Knowledge Graph Re-engineering Along the Ontological Continuum (extended version)

Knowledge graphs have become the primary vehicle for data integration and are critical to the success of modern AI, but the diversity of KG modelling practices, from lightweight vocabularies to richly axiomatised ontologies, makes integration and reuse expensive and brittle. This challenge is particularly acute in neuro-symbolic AI, where bridging neural and symbolic components depends on the ability to reengineer KGs to fit new requirements; GenAI now offers unprecedented automation capability, but without a principled understanding of the KG space, such automation remains conceptually ungrounded. We introduce the ontological continuum as that missing conceptualisation, a theoretical construct a theoretical construct whose characterisation framework is defined by two orthogonal distinctions: semantics vs pragmatics, and properties vs affordances; together these define a vocabulary to describe, compare, navigate, and transform KGs across the full range of modelling practices. The methodological stance is empirical: rather than prescribing how KGs should be modelled, the continuum aims to define a theory of the existent, derived from observation of real-world KG engineering practices and whose structure can be made formally explicit, for example, through Formal Concept Analysis (FCA). We ground the vision through a case study on provenance knowledge, showing how a single concern manifests differently across the continuum. We articulate five open research challenges and invite the community to develop the ontological continuum as a shared research agenda.

Position: How can Graphs Help Large Language Models?

With the rapid advancement of large language models (LLMs), classic graph learning tasks have greatly benefited from LLMs, including improved encoding of textual features, more efficient construction of graphs from text, and enhanced reasoning over knowledge graphs. In this paper, we ask a complementary question: How can graphs help LLMs? We address this question from three perspectives: 1) graphs provide an up-to-date knowledge source that helps reduce LLM hallucinations, 2) graph-based prompting techniques-such as Chain-of-Thought (CoT), Tree-of-Thought (ToT), and Graph-of-Thought (GoT)-enhance LLM reasoning capabilities, and 3) integrating graphs into LLMs improves their understanding of structured data, expanding their applicability to domains such as e-commerce, code, and relational databases (RDBs). We further outlook some future directions including designing sparse LLM architectures based on graphs and brain-inspired memory systems.