KG Embedding

KG: Knowledge Graph

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4 papers in the last four weeks, up 33% on the four weeks before. 0.0% of all new papers.

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Latest papers 37

Oct 7, 2026cs.LG

KGATE : a Knowledge Graph Embedding Training Environment

Knowledge graph embedding (KGE) models encode the entities and relations of a knowledge graph into a low-dimensional latent space, enabling tasks such as classification or link prediction. Most KGE models follow an autoencoder architecture, in which an encoder projects the knowledge graph into the latent space and a decoder reconstruct it. Combining both encoder and decoder components is increasingly needed, yet existing libraries rarely support complete autoencoders, are often unmaintained, rely on undocumented default hyperparameters, and produce results that cannot be compared across libraries. Here we present KGATE (Knowledge Graph Autoencoder Training Environment), a modular Python library built on PyTorch Geometric and TorchKGE. KGATE lets users assemble initializers, encoders, decoders, losses, negative samplers, and evaluation metrics as building blocks, or plug in their own block. KGATE includes a preprocessing procedure that controls data leakage, a builtin training pipeline, and reproducibility by design. Benchmarks against six existing KGE libraries show that KGATE training time is comparable with the fastest libraries while offering a broader set of features.

Benjamin Loire, Galadriel Brière, Célia Brahimi +2

Aix Marseille Univ., INSERM, Marseille Medical Genetics, Systems Biomedicine Team, Marseille, France · Neurology Therapeutic Area, R&D Servier Paris-Saclay Institut, Gif-sur-Yvette, France · LIRMM, Univ. Montpellier, CNRS, Montpellier, France +1

KG Embedding Autoencoders

Sep 29, 2026cs.AI

ImbalancE: Inference-Time Latent Search Against Degree Imbalance in Link Prediction

Knowledge Graph Embedding models have been extensively used to learn representations of entities and relations in Knowledge Graphs for predicting missing links. However, the quality of the learned representations varies a lot across different areas of the graph. If previous research has loosely linked the problem to relation types or degree bias, we show that it is more widespread and it correlates with the degree imbalance of the entities in test triples. In particular, the prediction of a target entity that has a degree much smaller than the degree of the anchor entity is extremely problematic. This is critical in recommender systems and other use cases, where these triples represent important corner cases. To address this issue, we propose an inference-time latent search optimization method capable of significantly improving model predictions on the most imbalanced triples. Built on top of a pre-trained model, it explores the embedding space at evaluation time, blending known and out-of-band information to mitigate the degree imbalance bias. We show the value of our approach on imbalanced triples from common benchmark datasets, where we outperform conventional methods, opening the door to the successful adoption of Knowledge Graph Embedding models on these critical corner cases.

Alberto Bernardi, Luca Costabello, Christophe Gueret

Accenture Labs, Dublin, Ireland

Inference-Time Optimization KG Embedding KG Completion

Sep 28, 2026cs.LG

Scalable GNN-based Knowledge Graph Representation Learning with Efficient Message Passing

Graph neural networks (GNNs) excel at representation learning on Knowledge Graphs (KGs), achieving stateof-the-art performance on tasks like link prediction or entity classification. However, their high computational complexity, inherent to their user-defined message passing (MP) algorithm, still prohibits their widespread adoption, especially for large KGs. Current efforts to mitigate the scalability bottlenecks of GNNs on KGs, such as subgraph sampling, are often task- and model-specific, and do not reliably guarantee lossless (if applicable) runtime/space reductions. To address this, we extend Relational Sparse Matrix Multiplication (RSPMM), originally designed to losslessly lower the space complexity of composition-based MP with pointwise composition functions, to support more expressive functions (e.g., 2x2 block-diagonal matrix multiplication, Givens rotation, circular correlation). Our method delivers significant task-independent reductions in runtime and space for current GNNs on KGs and facilitates efficient re-implementations of GNNs that maintain near state-of-the-art performance on challenging KG tasks, for a fraction of computational costs.

Huu Tan Mai, Cuong Xuan Chu, Heiko Paulheim +1

Bosch Center for Artificial Intelligence, Robert-Bosch-Campus 1, 71272 Renningen, Germany · University of Mannheim, Schloss, 68131 Mannheim, Germany

Graph Neural Networks Graph Representation Learning KG Embedding

Sep 16, 2026cs.AI

Hyperbolic Graph Representation Learning for Differential Diagnosis on Biomedical Knowledge Graphs

Biomedical knowledge graphs combine ontology-derived hierarchies with transversal associations among heterogeneous entities such as phenotypes, diseases, genes, proteins, and patients. This hybrid structure raises the question of whether hyperbolic embeddings, which naturally capture tree-like organization, remain useful beyond purely hierarchical graphs. We present a preliminary study of hyperbolic graph representation learning for Mendelian-disease differential diagnosis on a patient-integrated biomedical graph. Experiments on isolated ontology subgraphs show that hyperbolic models achieve strong performance in substantially lower dimensions than Euclidean baselines. We then evaluate the models on a link-prediction task that ranks candidate diseases for each patient. Results suggest that hyperbolic embeddings can exploit biomedical hierarchical structure while supporting diagnostic reasoning over heterogeneous patient-level graphs.

Pietro Miotto, Lucia Mellini, Tommaso Marzi +5

Department of Computer Science, Università degli Studi di Milano, Milan, Italy · Università della Svizzera italiana (USI), Lugano, Switzerland · Politecnico di Milano, Milan, Italy +2

KG Embedding Knowledge Graphs Differential Diagnosis Hyperbolic Representation Learning Biomedical KGs

Sep 14, 2026cs.AI

When Successful Knowledge Graph Edits Displace Correct Answers: Rank-Level Locality beyond Parameter Support

Editing a knowledge graph embedding (KGE) model to promote a desired answer can displace correct answers from the returned list. Locality tests based only on facts that reuse the edited parameter can miss this ranking effect. We introduce a common rank-displacement audit at three scopes: facts supported by the edited parameter, other correct answers to the target query, and correct answers across queries with the same relation. We also derive dimensional and geometric conditions for an update to improve the target while exactly preserving selected scores. On FB15k-237 with DistMult and ComplEx, direct promotion always moves the target into the top ten, but does so without damage in only 23.0--23.2% of edits. Strict preservation causes no measured damage, yet succeeds in only 1.3--1.4%. Support-regularized entity editing gives the highest joint success, 36.3--37.7%, while rank-truncated preservation reaches 32.8--34.7% and reduces the mean number of displaced answers from about 14 to 1.2. Experiments across dimensions, scorers, ranking conventions, and a learned editor show that locality depends on both the protected scope and the editing mechanism. KGE editing should therefore report correction success together with the incidence and severity of rank displacement.

Yi-Cheng Lai, Jerry Wang, Hsin-Ling Hsu +3

Institute of Information Science, Academia Sinica Taipei, Taiwan · University of Illinois Urbana-Champaign Urbana, IL, USA · National Chengchi University Taipei, Taiwan

Knowledge Editing KG Embedding

Sep 3, 2026cs.CL

Pattern Over-Generalization of Knowledge Graph Embedding

Knowledge graph embedding (KGE) demonstrates its effectiveness for predicting missing links in knowledge graphs (KGs) by projecting entities and relations into a low-dimensional vector space. It is crucial for KGE models to effectively capture inference patterns (patterns) inherent in KGs, such as symmetry/antisymmetry, inversion and composition. Although recent KGE models exhibit strong capabilities in modeling such diverse patterns, they suffer from inherent limitations stemming from pattern over-generalization, where embeddings learned from only a single pattern instance inevitably generalize that pattern to all related instances, i.e., generalize the pattern universally. To address this issue, we propose PogRE (Pattern Over-Generalization Robust Embedding), a simple but effective method that utilizes dense linear transformations and compound operations for relation representation. Our theoretical analysis demonstrates that a dense linear transformation allows a pattern to become progressively universal as more triples are observed in the pattern. Furthermore, after observing d+1 linearly independent entities (d+1 denotes the dimension of entity), the linear transformation guarantees universal generalization of the pattern across all related instances. Experimental results on three standard benchmark datasets show that PogRE outperforms existing state-of-the-art KGE models in link prediction. Moreover, our empirical results indicate that PogRE effectively addresses the negative impact of over-generalization.

Junsik Kim, Kangil Kim

Gwangju Institute of Science and Technology

Link Prediction KG Embedding KG Completion

Aug 31, 2026cs.AI

PyKEEN-NSX: A Modular Framework for Static, Dynamic and Schema-Aware Negative Sampling in PyKEEN

Embedding methods have become popular due to their scalability on link prediction and/or triple classification tasks on Knowledge Graphs (KGs). Embedding models are trained relying on both positive and negative samples of triples. However, since KGs generally contain only positive assertions, negative samples are artificially generated through negative sampling strategies, ranging from simple random corruption to more sophisticated approaches that exploit structural, semantic, or embedding information. The design and implementation of advanced negative samplers remains challenging, as most popular Knowledge Graph Embedding (KGE) libraries provide support only for basic strategies and lack a unified framework for developing more advanced and customized solutions. To address this gap, we introduce PyKEEN-NSX, an extension of PyKEEN, the popular KGE framework, that provides a modular engineered abstraction for negative sampling. The proposed architecture separates the generation of candidate negative pools, conditioned on an explicit context, from the selection strategy, enabling the development and integration of static, schema-aware and dynamic approaches within a consistent framework. Based on this abstraction, we implement six negative samplers, while remaining fully compatible with existing PyKEEN workflows and pipelines. As a proof of concept, we study negative availability across four datasets, showing that constrained pools frequently fall below the requested number of negatives, so that the encoded criterion is to a large extent replaced by the random fallback that supplements them.

Ivan Diliso, Nicola Fanizzi, Claudia d'Amato

1Dipartimento di Informatica, University of Bari Aldo Moro, Bari, Italy

KG Embedding KG Completion

Aug 11, 2026cs.AI

FITTER: Vocabulary-Agnostic Cross-Domain Inference on Temporal Knowledge Graphs

Temporal knowledge graphs are central to many uses of the Semantic Web, but existing completion methods assume the entities, relation names, and timestamps to be reasoned about are already known at training time, restricting each model to a single graph and vocabulary. We propose FITTER, the first fully-inductive structural model for temporal knowledge graph link prediction that supports cross-domain transfer: the inference graph may contain entirely unseen entities, relation names, and timestamps drawn from a different domain. FITTER represents each predicate by its interaction patterns with others and time through encodings of relative rather than absolute ordering; message-passing fuses local and global temporal context to produce vocabulary-agnostic embeddings. We prove the temporal encoding is time-shift invariant and evaluate FITTER on cross-domain, cross-graph transfer over six temporal knowledge graph benchmarks of diverse domains, granularities, and time spans. FITTER consistently outperforms inductive baselines without retraining, indicating that vocabulary-agnostic structural learning is a viable foundation for inference over the heterogeneous knowledge graphs of the Semantic Web.

Jiaxin Pan, Mojtaba Nayyeri, Osama Mohammed +4

University of Stuttgart, Stuttgart, Germany · SAP SE, Germany · University of Southampton, Southampton, United Kingdom

KG Embedding Temporal Link Prediction Cross-Domain Transfer Learning KG Completion Temporal KGs

Jul 28, 2026cs.CL

IRIS: Reusable Identity Representations from Frozen LLMs for Entity Alignment

Entity alignment (EA) identifies entities across knowledge graphs (KGs) that refer to the same real-world object. Conventional EA methods mainly exploit explicit graph structures and textual fields, which often provide insufficient semantic understanding to recognize the same entity under heterogeneous descriptions and distinguish it from semantically similar entities. Although large language models (LLMs) offer deeper entity understanding, existing LLM-based EA methods largely use this capability for auxiliary generation or candidate-conditioned decisions. Consequently, such understanding is not distilled into a stable and directly comparable identity space, leaving alignment tied to specific KG pairs or candidate sets and requiring repeated processing as the matching context changes. To address these limitations, we propose IRIS (Identity Representations from Internal States), a training-free framework that constructs for each entity an iris-like signature encoding its distinctive and stable identity characteristics. IRIS derives these signatures by eliciting identity-oriented contextual representations from a frozen LLM, thereby forming a shared space in which each entity is encoded once and can be aligned across different KGs through direct similarity comparison, without pair-dependent representation construction or candidate-wise LLM inference. Across four established EA benchmarks and two frozen LLM backbones, the best IRIS variants achieve Hits@1 scores of 100.00, 99.38, 98.31, and 97.99 on D-Y-15K V2, DBP-WIKI, ICEWS-WIKI, and ICEWS-YAGO, respectively.

Xinran Liu, Shengtao Li, Shouqian Shi +2

KG Embedding Knowledge Graphs

Jul 8, 2026cs.AI

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/.

Mayank Kharbanda, Michael Cochez, Rajiv Ratn Shah +1

IIIT-Delhi, India · Vrije Universiteit, Amsterdam, The Netherlands · Ellis Institute Finland +2

KG Embedding Knowledge Graph Question Answering Graph Reasoning Multi-Hop Reasoning

Jul 3, 2026cs.CL

Conditional Diffusion Guided Knowledge Transfer for Multi-Domain Knowledge Graph Completion

Multi-domain knowledge graph completion (MKGC) aims to improve missing triple prediction in a target KG by transferring knowledge from other support KGs. Existing methods typically enforce consistency constraints on equivalent entities across KGs to transfer knowledge, which risks suppressing domain-specific contextual information of entities. This design can also compromise entity representation information from all KG domains, impeding performance improvements, especially in low-resource data scenarios. To address this, we pioneer a generation-based paradigm for MKGC and propose DMKGC, a conditional diffusion-guided knowledge transfer framework. Our key insight is to treat each KG as a partial view of the entity entire information, and generate informative domain-general entity embeddings through diffusion models conditioned on support KGs. Particularly, we first initialize domain-agnostic entity embeddings as prior entity embeddings, and then encode them within individual KGs. Afterward, we fuse equivalent entities from support KGs as the conditional diffusion generation guidance. We leverage the prior entity embeddings as the proxy generation objective, which ensures this conditional generation to be unbiased towards any conditioned KGs. Simultaneously, we also train the generated embeddings to be predictive across KGs, thus preserving domain-specific information. Extensive experiments on 14 KGs in 3 benchmarks demonstrate a 4.3% average MRR improvement in tail entity prediction over state-of-the-art methods, with sustained gains in low-resource data settings.

Jiawei Sheng, Taoyu Su, Xixun Lin +2

Institute of Information Engineering, Chinese Academy of Sciences Beijing, China · Institute of Information Engineering, Chinese Academy of Sciences School of Cyber Security, UCAS Beijing, China

Diffusion Model Guidance KG Embedding Cross-Domain Transfer Learning KG Completion

Jul 2, 2026cs.LG

MKGR: Multimodal Knowledge-Graph Representation Learning for Cold-Start Protein-Protein Interaction Prediction

Accurate protein-protein interaction (PPI) prediction is central to functional genomics, disease mechanism discovery, and drug development. A difficult setting arises when candidate interactions include proteins that have no observed PPI edges during training, where models relying on network topology alone often lose useful context. This paper presents \method, a multimodal representation framework for cold-start PPI prediction. \method\ combines region-aware protein sequence encoding with four protein-centered biomedical knowledge graphs, including protein-drug, protein-disease, protein-miRNA, and protein-lncRNA associations. The sequence branch extracts contextual representations from structurally informed sequence regions, while graph attention encoders learn modality-specific protein embeddings from sparse biomedical associations. A bridge reconstruction objective regularizes graph learning by recovering shared protein-entity associations, and a pair-level gating module adaptively integrates sequence and graph evidence for each candidate protein pair. Experiments on two benchmark datasets under novel-old and novel-novel cold-start settings show that \method\ consistently outperforms competitive sequence, network, and knowledge-graph baselines across ACC, F1, AUC, AUPR, and MCC.

Wenbo Zhang

College of Computer and Information Science, Southwest University, Chongqing, Chongqing, China

KG Embedding Protein-Protein Interaction Prediction Multimodal Graph Learning Protein Representation Learning Biomedical KGs

Jun 29, 2026cs.AI

Beyond Triplet Plausibility: Relation Set Completion in Knowledge Graphs

Knowledge graphs (KGs) organize real-world knowledge as triplets and underpin many downstream applications. Due to their inherent incompleteness, knowledge graph completion (KGC) is widely studied and is typically formulated as triplet prediction, with link prediction as the dominant paradigm. However, this formulation focuses on the incompleteness of triplet-wise information and overlooks the incompleteness of entity-relation compatibility information. To address this limitation, we introduce a relation set completion task (RSC), which complements the link prediction task and aims to reason about missing relations that are semantically compatible with a given entity. We further propose a Relation Set Embedding model (RelSetE), which models latent patterns among the observed relations of entities to infer missing ones. To evaluate RelSetE, we derive three benchmark datasets from standard KG benchmarks. Extensive experiments demonstrate that RelSetE effectively captures entity-relation compatibility patterns and performs favorably in inferring missing relations of entities. Code and data are publicly available.

Zihao Zheng, Borui Cai, Yao Zhao +2

School of Information Technology, Deakin University, VIC 3125, Australia · Hangzhou International Innovation Institute, Beihang University, Hangzhou 311115, China · School of Information Technology, Victoria University, VIC 3011, Australia +1

KG Embedding KG Completion

Jun 28, 2026cs.AI

Measuring Graph-to-Graph Semantic Similarity in Knowledge Graphs: An Empirical Evaluation of Knowledge Graph Embeddings

A Knowledge Graph (KG) represents facts as structured triples and is widely used to organize relational knowledge across diverse domains. Just as textual information ranges from words and sentences to complete documents, KG information can be interpreted at multiple levels, from entities, relations, and triples to subgraphs and entire KGs. However, existing KG embedding methods mainly focus on entities, relations, and triples, leaving graph-level semantics largely unaddressed. Conventional graph-level methods, which typically compare graphs based on structural patterns, are also insufficient because structural similarity alone cannot guarantee semantic similarity between KGs. To evaluate how well different methods capture such graph-level semantic information, we study graph-to-graph semantic similarity, which determines whether a pair of KGs represents semantically corresponding underlying information. To obtain reliable ground-truth correspondences, we construct a semantic matching dataset by modifying text documents, extracting KGs from both original and modified documents, and transferring their known correspondences to KG pairs. We compare text-based, structure-based, and KG embedding-based approaches on each dataset. For the KG embedding-based approach, we introduce two scoring functions: \textit{EmbPairSim}, which uses maximal pairwise entity similarity, and \textit{AvgEmbSim}, which uses a frequency-weighted centroid. Experiments on WikiText-2 and CC-News show that \textit{EmbPairSim} achieves up to 5.3 pp higher MRR than Sentence-BERT while using substantially fewer parameters. These results suggest that KGE representations can serve as compact and effective signals for graph-to-graph semantic similarity in KGs. Our code is available at https://github.com/SeungRyeolBaek/KG-to-KG-Semantic-Similarity.

Seungryeol Baek, Wooseok Sim, Hogun Park

Department of Artificial Intelligence, Sungkyunkwan University Suwon, Republic of Korea

KG Embedding Knowledge Graphs

Jun 26, 2026cs.AI

RelBall: Relation Ball with Quaternion Rotation for Knowledge Graph Completion

Real-world knowledge graphs are often incomplete, lacking many valid facts. Knowledge Graph Completion (KGC) aims to predict missing links using known triples, thereby enhancing graph coverage. A key challenge is modeling diverse relational patterns such as symmetry, antisymmetry, inversion, composition and semantic hierarchy. Existing models such as RotatE can capture symmetric, antisymmetric, inverse, and commutative composition patterns, yet struggle with non-commutative composition. Rotate3D addresses this by introducing non-commutativity via three-dimensional rotations, but still fails to capture the semantic hierarchies prevalent in knowledge graphs. Moreover, both models cannot effectively model one-to-many relations. To overcome these limitations, we propose RelBall, which extends Rotate3D with two innovations. First, our model introduces modulus transformation to model hierarchies, driving abstract concepts toward smaller moduli and concrete instances toward larger ones. Second, it introduces a tail-centric relation ball to model one-to-one, one-to-many, many-to-one, and many-to-many relations. RelBall offers the following advantages: (1) coverage of all relational patterns, including the ones mentioned above; (2) an interpretable hierarchical representation where the modulus directly reflect semantic levels; (3) support for one-to-one, one-to-many, many-to-one, and many-to-many relations. Experiments on multiple datasets demonstrate RelBall's competitive link prediction performance against various baselines.

Yike Liu, Peijia Xie, Chao He +1

South China Normal University, Guangzhou, China

KG Embedding KG Completion

Jun 26, 2026cs.LG

TeRoR: Decoupled Temporal Rotation with Relational Circular Region for Temporal Knowledge Graph Embedding

In recent years, with the emergence of Temporal Knowledge Graphs (TKGs), research on learning entity and relation representations in TKGs has attracted increasing attention, giving rise to a large number of TKG embedding methods. TeRo is a simple and efficient temporal knowledge graph embedding approach. However, TeRo does not do well in modeling the mapping properties of various relations, such as one-to-many, many-to-one, and many-to-many. Meanwhile, it also has limitations in the expression of temporal information. To address these issues, we propose a novel TKG embedding method named TeRoR. This method divides the temporal evolution of entity embeddings, and conducts independent rotation transformations on head and tail entities in the complex vector space to strengthen temporal information modeling capacity. In terms of relational characteristics, we train a radius to constrain the rotated and translated head entities within a circular region centered on the tail entity, which effectively captures the diverse mapping properties of relations. Experimental results demonstrate that TeRoR achieves competitive performance against state-of-the-art models on four distinct TKG datasets.

Peijia Xie, Yike Liu, Chao He +1

South China Normal University, Guangzhou, China

KG Embedding Temporal Link Prediction Temporal KGs

Jun 23, 2026cs.LG

Holographic Memory for Zero-Shot Compositional Reasoning in Knowledge Graphs: A Mechanistic Study of Where and Why It Fails

Knowledge graph embedding (KGE) models predict single-hop links well but have no mechanism for zero-shot compositional queries: multi-hop questions whose relation chains never appeared during training. Holographic Reduced Representations (HRR), which bind and unbind symbols via circular convolution, are a theoretically attractive candidate, since binding is approximately invertible and associative. We test whether this promise holds. We study two holographic memory variants, real-valued HRR and phase-only Fourier HRR (FHRR), each with a modern Hopfield cleanup, on FB15k-237 over five seeds. Four findings follow. First, both are competitive single-hop retrievers (filtered MRR 0.358 +/- 0.002 for HRR, 0.350 +/- 0.021 for FHRR). Second, neither composes zero-shot: accuracy stays at chance across all cleanup temperatures. Third, the main contribution, we localise the failure mechanistically. A hop-1 probe shows the memory recovers the correct intermediate entity with high fidelity (MRR 0.896 +/- 0.002 for HRR), yet composition still fails even with a verified-correct intermediate. A second probe shows why: posing the ground-truth second-hop fact as a standalone atomic query, bypassing composition entirely, already recovers it at only 0.26 to 0.48x average atomic accuracy, uniformly across relation fan-out. The bottleneck is not the bind-unbind algebra or the cleanup; it is that facts compositional chains pass through are intrinsically harder for the superposed memory to retrieve, a capacity and interference effect present already at a single hop. Fourth, we prove (Lemma 4.1) that FHRR's softmax cleanup is not phase-equivariant, compounding the primary failure on the minority of chains where hop-1 itself errs. Fixing zero-shot composition requires improving retrieval capacity under superposition, not just redesigning the cleanup.

Randhir Kumar

Independent Researcher

Compositional Reasoning KG Embedding Knowledge Representation Hyperdimensional Computing Multi-Hop Reasoning KG Completion

Jun 22, 2026cs.CL

Predicate Importance Estimation and Decoupled Rationale-Score Distillation for Entity Alignment

Knowledge graphs (KGs) are increasingly used as structured context for Large Language Models (LLMs), but industrial KG-RAG systems often need to integrate public and domain-specific KGs constructed from heterogeneous databases. This integration relies on Entity Alignment (EA), where lexical matching alone is insufficient under predicate-name variation and incomplete local neighborhoods. We address EA for KG integration by constructing a pairwise EA dataset and proposing two complementary modules: Predicate Importance Estimation (PIE) and Decoupled Rationale-Score Distillation (DRSD). PIE is a compact embedding-based approach that removes the subject information from each 1-hop triple, encodes the resulting subjectless triples, and aggregates them with learnable predicate-importance weights to build predicate-aware entity embeddings. DRSD trains a distilled small language model (SLM) with pseudo-answers produced by a teacher LLM through distinct prompts. By converting binary EA labels into text-based supervision and decoupling confidence-score estimation from label-consistent rationales, DRSD enables the SLM to learn task-specific reasoning while retaining a less label-biased confidence signal. Experiments show that PIE and DRSD improve EA classification. Moreover, because DRSD decouples confidence-score estimation from the decision, a discrepancy between the two flags an uncertain prediction for human review, thereby enabling a practical discrepancy between automatic acceptance and human-in-the-loop verification.

Keunha Kim, Yoonjin Jang, Hyeon-gu Lee +2

SungKyunKwan University · NAVER

KG Embedding Knowledge Graphs Knowledge Distillation

Jun 15, 2026cs.AI

Model Graph Inductive Learning for Knowledge Graph Completion

Link prediction in knowledge graphs fundamentally depends on the quality of learned embeddings for entities and relations. However, most existing methods derive these embeddings by aggregating only the local neighborhood of each entity, neglecting the global structure of the knowledge graph. This limited view prevents models from capturing higher-level structural patterns that are essential for accurate and generalizable link prediction. To address these limitations, we introduce Model Graph Inductive Learning (\textbf{MGIL}), a framework that constructs a model graph by clustering entities based on the similarity of their incoming and outgoing relational structures or their entity types. A GNN is then applied to this model graph to produce embeddings that capture the global view of the knowledge graph. These embeddings subsequently serve as high-quality initial features %embeddings for the original knowledge graph, replacing random initialization and leading to more stable and expressive representations. Extensive experiments on standard and recently proposed inductive benchmarks demonstrate that MGIL achieves state-of-the-art or highly competitive performance in inductive link prediction, highlighting its effectiveness across diverse graph settings.

Mohommad Esmaei Khani, Mahdieh Hasheminejad, Ali Taherkhani +1

Faculty of Mathematical Science Department of Computer Science, Yazd Unversity,, 100190, Iran. · Department of Mathematics, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731, Iran. · Diagnostic and Research Institute of Human Genetics, Medizinische Universität Graz, Graz, 8010, Austria.

Graph Neural Networks Link Prediction KG Embedding KG Completion

Jun 12, 2026cs.LG

Recipe-Controlled Decoder Audit for Structural Knowledge-Graph Completion

We present a recipe-controlled decoder audit (RCDA) for structural transductive knowledge-graph completion (KGC). The audit asks a simple reporting question: before attributing gains to an encoder or training recipe, what changes when the decoder is swapped under the same recipe? Using ComplEx and DistMult as the primary controlled pair, with targeted RotatE/TransE spot-checks, we evaluate seven benchmarks. On five standard KGs, ComplEx-vs-DistMult differences are modest but consistent under our recipe (+0.005 to +0.012 MRR), whereas CompGCN-style encoder effects vary more by dataset. On small KGs, decoder effects become the main diagnostic: Kinship shows a stable ComplEx advantage of +0.143 MRR (6 seeds), while UMLS favours ComplEx by +0.022 MRR in a clean 6-seed server rerun but reverses in an earlier provenance variant. We therefore treat small-KG decoder choice as recipe- and provenance-sensitive rather than as a fixed dataset winner. We further show that decoder choice interacts with encoder depth on WN18RR, and that under our recipe L=0 ComplEx on YAGO3-10 reaches 0.6971 +/- 0.0048 MRR at d=128. The result is a compact audit protocol: report matched decoder rows, log small-KG provenance, and sweep decoder x depth before making encoder-level claims.

Xihang Shan, Ye Luo

School of Mathematical Sciences Xiamen University Fujian, China · School of Informatics Xiamen University Fujian, China

KG Embedding KG Completion

Jun 7, 2026cs.AI

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).

Angjelin Hila

KG Embedding Knowledge Representation Neuro-Symbolic Reasoning

Jun 4, 2026cs.CL

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.

Xingyu Chen, Yuanning Cui, Zequn Sun +1

State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing, China · Nanjing University of Information Science and Technology, Nanjing, China · National Institute of Healthcare Data Science, Nanjing University, Nanjing, China

KG Embedding Cross-Domain Transfer Learning Graph Foundation Models

Jun 2, 2026cs.LG

Link Prediction or Perdition: the Seeds of Instability in Knowledge Graph Embeddings

Embedding models (KGEMs) constitute the main link prediction approach to complete knowledge graphs. Standard evaluation protocols emphasize rank-based metrics such as MRR or Hits@

K

, but usually overlook the influence of random seeds on result stability. Moreover, these metrics conceal potential instabilities in individual predictions and in the organization of embedding spaces. In this work, we conduct a systematic stability analysis of multiple KGEMs across several datasets. We find that high-performance models actually produce divergent predictions at the triple level and highly variable embedding spaces. By isolating stochastic factors (i.e., initialization, triple ordering, negative sampling, dropout, hardware), we show that each independently induces instability of comparable magnitude. Furthermore, for a given model, hyperparameter configurations with better MRR are not guaranteed to be more stable. Moreover, voting, albeit a known remediation mechanism, only provides a limited enhancement of stability. These findings highlight critical limitations of current benchmarking protocols, and raise concerns about the reliability of KGEMs for knowledge graph completion.

Guillaume Méroué, Fabien Gandon, Pierre Monnin

Université Côte d’Azur, Inria, CNRS, I3S, France

Link Prediction KG Embedding KG Completion

May 26, 2026cs.AI

Boosting Knowledge Graph Foundation Models via Enhanced Negative Sampling

Knowledge graphs (KGs) have become the core backbone of numerous downstream tasks such as question answering and recommender systems. However, despite all this, KGs are often very incomplete. To perform zero-shot knowledge graph completion in unseen KGs, which have different relational vocabularies from those used for pre-training, KG foundation models (KGFMs) receive a wide range of attention. Existing KGFMs often perform training using random negative triples, which are constructed by replacing the head or tail entity of a positive triple with a random entity. However, these negative triples are often constructed with limited quality, providing weak supervision for KGFM training. In this paper, we propose a simple yet effective adaptive negative sampling approach, KMAS, to enhance existing KGFMs. KMAS constructs hard negative triples through the updated relation embeddings generated from the existing KGFM's relation encoder. To further adaptively align with the evolving capability of the KGFM during the training process, KMAS adjusts the ratio of hard negative triples dynamically throughout the whole training process: after a warmup phrase, it increases the ratio linearly and then decreases linearly. Extensive experiments are conducted over 44 data sets. Experimental results demonstrate that our proposed negative sampling method can enhance many SOTA KGFMs without requiring excessive additional time or memory consumption.

Yinan Liu, Wenjin Xu, Zhiyuan Zha +2

Northeastern University Shenyang, China

KG Embedding Graph Foundation Models KG Completion

May 19, 2026cs.CR

Inferring Sensitive Attributes from Knowledge Graph Embeddings: Attack and Defense Strategies

Knowledge Graphs (KGs) are a powerful representation of linked data, offering flexibility, semantic richness, and support for knowledge enrichment and reasoning. They help data owners organize and exploit heterogeneous data to provide insightful services (e.g., recommendations), yet real-world KGs are often incomplete, hiding true facts or missing valuable insights. Knowledge graph embedding techniques are commonly used to infer valuable missing information. However, reasoning over KGs can inadvertently expose sensitive user information, even when such data is not explicitly stored. In this work, we investigate the privacy risks associated with KGE-based reasoning, focusing on attribute inference attacks where adversaries attempt to deduce sensitive user attributes from seemingly non-sensitive outputs. We propose and evaluate a framework that mitigates these privacy risks by applying post processing sanitization techniques to KGE outputs. Preliminary results demonstrate the effectiveness of these attacks on the outputs of KGE models, and explore the trade-off between recommendation quality and privacy protection when applying randomization based approaches, highlighting the need to experiment with more advanced techniques in future work to address this issue.

Yasmine Hayder

PETSCRAFT · LIFO, INSA CVL, Univ. Orléans, Inria, France

Graph Representation Learning Adversarial Attacks KG Embedding Privacy-Preserving ML

May 12, 2026cs.LG

Automated Big Data Quality Assessment using Knowledge Graph Embeddings

Automated data quality assessment is crucial for managing big data, but existing solutions face challenges in achieving accurate context-aware assessment. This paper presents a novel knowledge-based approach to enhance automated data quality assessment. Our approach utilizes knowledge graph embeddings to predict missing edges between the input dataset's context representation and the relevant quality rules and dimensions within a knowledge graph representing contextual data characteristics and the required quality assessment operations. We surpass conventional practices by integrating diverse representations within the knowledge graph, drawing insights from contextual information from a thorough literature investigation. This integration allows us to develop a comprehensive and context-specific data quality assessment plan tailored to each context. Leveraging the knowledge graph improves our understanding of the input dataset's context, overcoming the limitations of traditional methods that rely solely on strict matching and overlook contextual characteristics. By injecting numerical edge attributes, we assign corresponding weights to each predicted quality measurement, providing a comprehensive data quality assessment plan for the input dataset. To evaluate our approach, we leverage AmpliGraph, a framework developed and benchmarked by AccentureLabs. The evaluation involves employing a real-world radiation sensors dataset provided by the Lebanese Atomic Energy Commission (LAEC-CNRS). The results obtained from this evaluation demonstrate the capability of our solution to generate a comprehensive data quality assessment plan for the given input dataset.

Hadi Fadlallah, Rima Kilany, Mitri Haber +1

Saint-Joseph University, Beirut, Lebanon · Lebanese University, Beirut, Lebanon

KG Embedding Knowledge Graphs

May 12, 2026cs.LG

Knowledge Graphs Meet Graph Neural Networks: A Comprehensive Survey

Graph Neural Networks (GNNs) have emerged as a powerful paradigm in Knowledge Graphs (KGs) due to their intrinsic ability to model graph-structured data. However, there remains a lack of a systematic review about GNN-based methodologies across the entire knowledge graph technologies pipeline. To address this gap, we first propose a novel two-level taxonomy framework for GNN-based knowledge graph technologies: the KG technologies pipeline and GNN-based perspective. Specifically, the knowledge graph technologies pipeline covers knowledge graph construction, knowledge graph embedding, knowledge reasoning and knowledge graph applications. Meanwhile, the GNN-based perspective provides a new categorization of knowledge graph technologies with GNN models, such as GCN, GAT, and HGNN. Then, we analyze the advantages of GNN technology based on the characteristics of different tasks in the knowledge graph lifecycle. Furthermore, we detailed review various GNN-based models for knowledge graph following the proposed taxonomy, and summarize strengths and limitations. Finally, we discuss unresolved challenges and outline promising directions for future research.

Chengcheng Sun, Jiayun Tian, Cheng Zhai +5

School of Safety Engineering, China University of Mining and Technology, China · School of Computer Science and Technology, China University of Mining and Technology, China · State Key Laboratory of Coal Mine Disaster Prevention and Control, China University of Mining and Technology, China +1

KG Construction Graph Neural Networks Graph Representation Learning KG Embedding Knowledge Graphs

May 11, 2026cs.LG

CORE: Cyclic Orthotope Relation Embedding for Knowledge Graph Completion

Knowledge graph completion (KGC) aims to automatically infer missing facts in multi-relational data by mapping entities and relations into continuous representation spaces. Recent region-based embedding models have shown great promise in capturing complex logical patterns by representing relations as geometric regions. However, these models inevitably suffer from absolute boundary constraints during optimization. Conversely, without such constraints, relation regions expand indefinitely. To address the limitation, we propose \textbf{CORE} (Cyclic Orthotope Relation Embedding), a novel KGC model that embeds entities and relations onto a boundary-less torus manifold.CORE represents relations as cyclic orthotopes on the torus manifold, allowing regions to seamlessly wrap around spatial boundaries to ensure smooth gradient conduction. Furthermore, an adaptive width regularization is introduced to prevent unconditional region expansion. Theoretical analysis proves that CORE can capture various complex relation patterns such as subsumption and intersection. Extensive experiments on four benchmark datasets demonstrate that CORE achieves highly competitive performance, significantly improving link prediction accuracy in dense semantic environments.

Yingqi Zeng, Luying Wang, Huiling Zhu

Graph Representation Learning KG Embedding Graph Embedding KG Completion

May 11, 2026cs.AI

PrimeKG-CL: A Continual Graph Learning Benchmark on Evolving Biomedical Knowledge Graphs

Biomedical knowledge graphs underwrite drug repurposing and clinical decision support, yet the upstream ontologies they depend on update on independent cycles that add millions of edges and deprecate hundreds of thousands more between releases. Yet existing continual graph learning has been studied almost exclusively on synthetic random splits of static, generic KGs, a regime that cannot reproduce the asynchronous, structured evolution real biomedical KGs undergo. To this end, we introduce PrimeKG-CL, a CGL benchmark built from nine authoritative biomedical databases (129K+ nodes, 8.1M+ edges, 10 node types, 30 relation types) with two genuine temporal snapshots (June 2021, July 2023; 5.83M edges added, 889K removed, 7.21M persistent), 10 entity-type-grouped tasks, multimodal node features, and a per-task persistent/added/removed test stratification. On three tasks (biomedical relationship prediction, entity classification, KGQA), we evaluate six CL strategies across four KGE decoders, plus LKGE, an LLM-RAG agent, and CMKL. We find that decoder choice and continual learning strategy interact strongly: no single strategy performs best across all decoders, and mismatched combinations can significantly degrade performance. Moreover, only DistMult exhibits a clear separation between persistent and deprecated knowledge, indicating that standard metrics conflate retention of still-valid facts with failure to forget outdated ones; this effect is absent under RotatE. In addition, multimodal features improve entity-level tasks by up to 60%, and a recent CKGE framework (IncDE) failed to scale to our 5.67M-triple base task across five attempts up to 350GB RAM. Data, pipeline, baselines, and the stratified split are released openly. Dataset:huggingface.co/datasets/yradwan147/PrimeKGCL|Code:github.com/yradwan147/primekg-cl-neurips2026

Yousef A. Radwan, Yao Li, Qing Qing +5

Technology, Innovation, Entrepreneurship Department King Abdullah University of Science and Technology · School of Computing and Information Systems The University of Melbourne · College of Computer Science and Technology Jilin University +3

KG Embedding Knowledge Graph Question Answering Knowledge Graphs KG Completion Temporal KGs Biomedical KGs

May 11, 2026cs.LG

CMKL: Modality-Aware Continual Learning for Evolving Biomedical Knowledge Graphs

Biomedical knowledge graphs are increasingly large, dynamic, and multimodal, driven by rapid advances in biotechnology such as high-throughput sequencing. Machine learning models can infer previously unobserved biomedical relationships and characterize biomedical entities in these graphs, but existing knowledge graph embedding methods and their continual learning extensions either assume static graph structure or fail to exploit multimodal information under evolving data distributions. They also apply uniform regularization across all model parameters, ignoring that different modalities may exhibit distinct forgetting dynamics as the graph evolves. We propose the Continual Multimodal Knowledge Graph Learner (CMKL), a CL framework for biomedical KGs that natively encodes structure, text, and molecules, fuses them through a Mixture-of-Experts (MoE) router, and protects previously learned knowledge with standard EWC regularization and a K-means-diverse multimodal replay buffer. We evaluate CMKL on a 129K-entity biomedical continual benchmark with 10 tasks. On continual biomedical entity classification, CMKL reaches AP 0.591 versus 0.370 for the strongest structural baseline, a 60% gain that is driven by access to multimodal features and preserved across the sequence with near-zero forgetting (AF 0.008). On continual relationship prediction, CMKL reaches AP

0.062

, matching Naive Sequential and EWC (0.058) within seed noise and outperforming Joint Training (0.047, p=0.045) and LKGE (0.039). A frozen-text ablation reaches AP 0.136, more than double any jointly trained model, yet that signal is unreachable by margin-ranking gradients: the greedy-modality asymmetry lives at the representation level, not the fusion level, and MoE routing manages it by suppressing the unreachable modality without forcing it through a learned bottleneck. Code: github.com/yradwan147/cmkl-neurips2026

Yousef A. Radwan, Yao Li, Qing Qing +5

Technology, Innovation, Entrepreneurship Department King Abdullah University of Science and Technology · School of Computing and Information Systems The University of Melbourne · College of Computer Science and Technology Jilin University +2

Continual Learning KG Embedding Multimodal Graph Learning Multimodal KGs Knowledge Graphs KG Completion+1