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
Continual Knowledge Graph Embedding (CKGE) seeks to integrate new knowledge while preserving past information. However, existing methods struggle with efficiency and scalability due to two key limitations: (1) suboptimal knowledge preservation between snapshots caused by manually designed node/relation importance scores that ignore graph dependencies relevant to the downstream task, and (2) computationally expensive graph traversal for node/relation importance calculation, leading to slow training and high memory overhead. To address these limitations, we introduce ETT-CKGE (Efficient, Task-driven, Tokens for Continual Knowledge Graph Embedding), a novel task-guided CKGE method that leverages efficient task-driven tokens for efficient and effective knowledge transfer between snapshots. Our method introduces a set of learnable tokens that directly capture task-relevant signals, eliminating the need for explicit node scoring or traversal. These tokens serve as consistent and reusable guidance across snapshots, enabling efficient token-masked embedding alignment between snapshots. Importantly, knowledge transfer is achieved through simple matrix operations, significantly reducing training time and memory usage. Extensive experiments across six benchmark datasets demonstrate that ETT-CKGE consistently achieves superior or competitive predictive performance, while substantially improving training efficiency and scalability compared to state-of-the-art CKGE methods. The code is available at: https://github.com/lijingzhu1/ETT-CKGE/tree/main
Knowledge graph embedding (KGE) models are extensively studied for knowledge graph completion, yet their evaluation remains constrained by unrealistic benchmarks. Standard evaluation metrics rely on the closed-world assumption, which penalizes models for correctly predicting missing triples, contradicting the fundamental goals of link prediction. These metrics often compress accuracy assessment into a single value, obscuring models' specific strengths and weaknesses. The prevailing evaluation protocol, link prediction, operates under the unrealistic assumption that an entity's properties, for which values are to be predicted, are known in advance. While alternative protocols such as property prediction, entity-pair ranking, and triple classification address some of these limitations, they remain underutilized. Moreover, commonly used datasets are either faulty or too small to reflect real-world data. Few studies examine the role of mediator nodes, which are essential for modeling n-ary relationships, or investigate model performance variation across domains. This paper conducts a comprehensive evaluation of four representative KGE models on large-scale datasets FB-CVT-REV and FB+CVT-REV. Our analysis reveals critical insights, including substantial performance variations between small and large datasets, both in relative rankings and absolute metrics, systematic overestimation of model capabilities when n-ary relations are binarized, and fundamental limitations in current evaluation protocols and metrics.
We focus on obtaining robust knowledge graph embedding under perturbation in the embedding space. To address these challenges, we introduce a novel framework, Robust Knowledge Graph Embedding via Denoising, which enhances the robustness of KGE models on noisy triples. By treating KGE methods as energy-based models, we leverage the established connection between denoising and score matching, enabling the training of a robust denoising KGE model. Furthermore, we propose certified robustness evaluation metrics for KGE methods based on the concept of randomized smoothing. Through comprehensive experiments on benchmark datasets, our framework consistently shows superior performance compared to existing state-of-the-art KGE methods when faced with perturbed entity embedding.
Uncertainty quantification in Knowledge Graph Embedding (KGE) methods is crucial for ensuring the reliability of downstream applications. A recent work applies conformal prediction to KGE methods, providing uncertainty estimates by generating a set of answers that is guaranteed to include the true answer with a predefined confidence level. However, existing methods provide probabilistic guarantees averaged over a reference set of queries and answers (marginal coverage guarantee). In high-stakes applications such as medical diagnosis, a stronger guarantee is often required: the predicted sets must provide consistent coverage per query (conditional coverage guarantee). We propose CondKGCP, a novel method that approximates predicate-conditional coverage guarantees while maintaining compact prediction sets. CondKGCP merges predicates with similar vector representations and augments calibration with rank information. We prove the theoretical guarantees and demonstrate empirical effectiveness of CondKGCP by comprehensive evaluations.
Integrating structured knowledge from Knowledge Graphs (KGs) into Large Language Models (LLMs) remains a key challenge for symbolic reasoning. Existing methods mainly rely on prompt engineering or fine-tuning, which lose structural fidelity or incur high computational costs. Building on recent encoding techniques which integrate graph embeddings within the LLM input as tokens, we extend this paradigm to the KG domain by leveraging Knowledge Graph Embedding (KGE) models, thus enabling graph-aware reasoning. Our approach is model-agnostic, resource-efficient, and compatible with any LLMs. Extensive experimentation on synthetic and real-world datasets shows that our method improves reasoning performance over established baselines, further achieving the best trade-off in terms of accuracy and efficiency against state-of-the-art LLMs.
Knowledge graph embedding (KGE) methods aim to represent entities and relations in a continuous space while preserving their structural and semantic properties. Quaternion-based KGEs have demonstrated strong potential in capturing complex relational patterns. In this work, we propose QuatE-D, a novel quaternion-based model that employs a distance-based scoring function instead of traditional inner-product approaches. By leveraging Euclidean distance, QuatE-D enhances interpretability and provides a more flexible representation of relational structures. Experimental results demonstrate that QuatE-D achieves competitive performance while maintaining an efficient parameterization, particularly excelling in Mean Rank reduction. These findings highlight the effectiveness of distance-based scoring in quaternion embeddings, offering a promising direction for knowledge graph completion.
Knowledge graph embedding (KGE) models encode the structural information of knowledge graphs to predicting new links. Effective training of these models requires distinguishing between positive and negative samples with high precision. Although prior research has shown that improving the quality of negative samples can significantly enhance model accuracy, identifying high-quality negative samples remains a challenging problem. This paper theoretically investigates the condition under which negative samples lead to optimal KG embedding and identifies a sufficient condition for an effective negative sample distribution. Based on this theoretical foundation, we propose \textbf{E}mbedding \textbf{MU}tation (\textsc{EMU}), a novel framework that \emph{generates} negative samples satisfying this condition, in contrast to conventional methods that focus on \emph{identifying} challenging negative samples within the training data. Importantly, the simplicity of \textsc{EMU} ensures seamless integration with existing KGE models and negative sampling methods. To evaluate its efficacy, we conducted comprehensive experiments across multiple datasets. The results consistently demonstrate significant improvements in link prediction performance across various KGE models and negative sampling methods. Notably, \textsc{EMU} enables performance improvements comparable to those achieved by models with embedding dimension five times larger. An implementation of the method and experiments are available at https://github.com/nec-research/EMU-KG.
Knowledge graph embedding (KGE) is a technique that enhances knowledge graphs by addressing incompleteness and improving knowledge retrieval. A limitation of the existing KGE models is their underutilization of ontologies, specifically the relationships between properties. This study proposes a KGE model, TransU, designed for knowledge graphs with well-defined ontologies that incorporate relationships between properties. The model treats properties as a subset of entities, enabling a unified representation. We present experimental results using a standard dataset and a practical dataset.
Current Continual Knowledge Graph Embedding (CKGE) methods primarily rely on translation-based embedding methods, leveraging previously acquired knowledge to initialize new facts. To enhance learning efficiency, these methods often integrate fine-tuning or continual learning strategies. However, this compromises the model's prediction accuracy and the translation-based methods lack support for complex relational structures (multi-hop relations). To tackle this challenge, we propose a novel CKGE framework SoTCKGE grounded in Spatial Offset Transformation. Within this framework, entity positions are defined as being jointly determined by base position vectors and offset vectors. This not only enhances the model's ability to represent complex relational structures but also allows for the embedding update of both new and old knowledge through simple spatial offset transformations, without the need for continuous learning methods. Furthermore, we introduce a hierarchical update strategy and a balanced embedding method to refine the parameter update process, effectively minimizing training costs and augmenting model accuracy. To comprehensively assess the performance of our model, we have conducted extensive experimlents on four publicly accessible datasets and a new dataset constructed by us. Experimental results demonstrate the advantage of our model in enhancing multi-hop relationship learning and further improving prediction accuracy.
Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of disease pathology. Therefore, machine learning has been used to process gene expression data, with patient diagnosis emerging as one of the most popular applications. Although gene expression data can provide valuable insights, challenges arise because the number of patients in expression datasets is usually limited, and the data from different datasets with different gene expressions cannot be easily combined. This work proposes a novel methodology to address these challenges by integrating multiple gene expression datasets and domain-specific knowledge using knowledge graphs, a unique tool for biomedical data integration. Then, vector representations are produced using knowledge graph embedding techniques, which are used as inputs for a graph neural network and a multi-layer perceptron. We evaluate the efficacy of our methodology in three settings: single-dataset learning, multi-dataset learning, and transfer learning. The experimental results show that combining gene expression datasets and domain-specific knowledge improves patient diagnosis in all three settings.
Zero-shot learning (ZL) is crucial for tasks involving unseen categories, such as natural language processing, image classification, and cross-lingual transfer. Current applications often fail to accurately infer and handle new relations or entities involving unseen categories, severely limiting their scalability and practicality in open-domain scenarios. ZL learning faces the challenge of effectively transferring semantic information of unseen categories in multi-modal knowledge graph (MMKG) embedding representation learning. In this paper, we propose ZSLLM, a framework for zero-shot embedding learning of MMKGs using large language models (LLMs). We leverage textual modality information of unseen categories as prompts to fully utilize the reasoning capabilities of LLMs, enabling semantic information transfer across different modalities for unseen categories. Through model-based learning, the embedding representation of unseen categories in MMKG is enhanced. Extensive experiments conducted on multiple real-world datasets demonstrate the superiority of our approach compared to state-of-the-art methods.
Multimodal knowledge graph completion (MMKGC) aims to predict missing links in multimodal knowledge graphs (MMKGs) by leveraging information from various modalities alongside structural data. Existing MMKGC approaches primarily extend traditional knowledge graph embedding (KGE) models, which often require creating an embedding for every entity. This results in large model sizes and inefficiencies in integrating multimodal information, particularly for real-world graphs. Meanwhile, Transformer-based models have demonstrated competitive performance in knowledge graph completion (KGC). However, their focus on single-modal knowledge limits their capacity to utilize cross-modal information. Recently, Large vision-language models (VLMs) have shown potential in cross-modal tasks but are constrained by the high cost of training. In this work, we propose a novel approach that integrates Transformer-based KGE models with cross-modal context generated by pre-trained VLMs, thereby extending their applicability to MMKGC. Specifically, we employ a pre-trained VLM to transform relevant visual information from entities and their neighbors into textual sequences. We then frame KGC as a sequence-to-sequence task, fine-tuning the model with the generated cross-modal context. This simple yet effective method significantly reduces model size compared to traditional KGE approaches while achieving competitive performance across multiple large-scale datasets with minimal hyperparameter tuning.
Large Language Models (LLMs) have attracted a lot of attention in various fields due to their superior performance, aiming to train hundreds of millions or more parameters on large amounts of text data to understand and generate natural language. As the superior performance of LLMs becomes apparent, they are increasingly being applied to knowledge graph embedding (KGE) related tasks to improve the processing results. As a deep learning model in the field of Natural Language Processing (NLP), it learns a large amount of textual data to predict the next word or generate content related to a given text. However, LLMs have recently been invoked to varying degrees in different types of KGE related scenarios such as multi-modal KGE and open KGE according to their task characteristics. In this paper, we investigate a wide range of approaches for performing LLMs-related tasks in different types of KGE scenarios. To better compare the various approaches, we summarize each KGE scenario in a classification. In addition to the categorization methods, we provide a tabular overview of the methods and their source code links for a more direct comparison. In the article we also discuss the applications in which the methods are mainly used and suggest several forward-looking directions for the development of this new research area.
Biomedical Knowledge Graphs (BKGs) integrate diverse datasets to elucidate complex relationships within the biomedical field. Effective link prediction on these graphs can uncover valuable connections, such as potential novel drug-disease relations. We introduce a novel multimodal approach that unifies embeddings from specialized Language Models (LMs) with Graph Contrastive Learning (GCL) to enhance intra-entity relationships while employing a Knowledge Graph Embedding (KGE) model to capture inter-entity relationships for effective link prediction. To address limitations in existing BKGs, we present PrimeKG++, an enriched knowledge graph incorporating multimodal data, including biological sequences and textual descriptions for each entity type. By combining semantic and relational information in a unified representation, our approach demonstrates strong generalizability, enabling accurate link predictions even for unseen nodes. Experimental results on PrimeKG++ and the DrugBank drug-target interaction dataset demonstrate the effectiveness and robustness of our method across diverse biomedical datasets. Our source code, pre-trained models, and data are publicly available at https://github.com/HySonLab/BioMedKG
Knowledge Graphs (KGs) provide a structured representation of knowledge but often suffer from challenges of incompleteness. To address this, link prediction or knowledge graph completion (KGC) aims to infer missing new facts based on existing facts in KGs. Previous knowledge graph embedding models are limited in their ability to capture expressive features, especially when compared to deeper, multi-layer models. These approaches also assign a single static embedding to each entity and relation, disregarding the fact that entities and relations can exhibit different behaviors in varying graph contexts. Due to complex context over a fact triple of a KG, existing methods have to leverage complex non-linear context encoder, like transformer, to project entity and relation into low dimensional representations, resulting in high computation cost. To overcome these limitations, we propose Triple Receptance Perception (TRP) architecture to model sequential information, enabling the learning of dynamic context of entities and relations. Then we use tensor decomposition to calculate triple scores, providing robust relational decoding capabilities. This integration allows for more expressive representations. Experiments on benchmark datasets such as YAGO3-10, UMLS, FB15k, and FB13 in link prediction and triple classification tasks demonstrate that our method performs better than several state-of-the-art models, proving the effectiveness of the integration.
Knowledge Graphs (KGs) and their machine learning counterpart, Knowledge Graph Embedding Models (KGEMs), have seen ever-increasing use in a wide variety of academic and applied settings. In particular, KGEMs are typically applied to KGs to solve the link prediction task; i.e. to predict new facts in the domain of a KG based on existing, observed facts. While this approach has been shown substantial power in many end-use cases, it remains incompletely characterised in terms of how KGEMs react differently to KG structure. This is of particular concern in light of recent studies showing that KG structure can be a significant source of bias as well as partially determinant of overall KGEM performance. This paper seeks to address this gap in the state-of-the-art. This paper provides, to the authors' knowledge, the first comprehensive survey exploring established relationships of Knowledge Graph Embedding Models and Graph structure in the literature. It is the hope of the authors that this work will inspire further studies in this area, and contribute to a more holistic understanding of KGs, KGEMs, and the link prediction task.
In this essay we discuss the recent trends in visual analysis and exploration of Knowledge Graphs, particularly in conjunction with Knowledge Graph Embedding techniques. We present an overview of the current state of visualization techniques and frameworks for KGs, in relation to four identified challenges. The challenges in visualizing Knowledge Graphs include the need for intuitive and modular interfaces, performance in handling big data, and difficulties for users in understanding and using query languages. We find frameworks that generally satisfy the intuitive UI, performance, and query support requirements, but few satisfying the modularity requirement. In the context of Knowledge Graph Embeddings, we divide the approaches that use embeddings to facilitate exploration of Knowledge Graphs from those that aim at the explanation of the embeddings themselves. We find significant differences between the two perspectives. Finally, we highlight some possible directions for future work, including diffusion of the unmet requirements, implementation of new visual features, and experimentation with relation visualization as a peculiar element of Knowledge Graphs.
Pedestrian detection is a critical task in autonomous driving, aimed at enhancing safety and reducing risks on the road. Over recent years, significant advancements have been made in improving detection performance. However, these achievements still fall short of human perception, particularly in cases involving occluded pedestrians, especially entirely invisible ones. In this work, we present the Occlusion-Rich Road Scenes with Pedestrians (OccluRoads) dataset, which features a diverse collection of road scenes with partially and fully occluded pedestrians in both real and virtual environments. All scenes are meticulously labeled and enriched with contextual information that encapsulates human perception in such scenarios. Using this dataset, we developed a pipeline to predict the presence of occluded pedestrians, leveraging Knowledge Graph (KG), Knowledge Graph Embedding (KGE), and a Bayesian inference process. Our approach achieves a F1 score of 0.91, representing an improvement of up to 42% compared to traditional machine learning models.
Quaternion contains one real part and three imaginary parts, which provided a more expressive hypercomplex space for learning knowledge graph. Existing quaternion embedding models measure the plausibility of a triplet either through semantic matching or geometric distance scoring functions. However, it appears that semantic matching diminishes the separability of entities, while the distance scoring function weakens the semantics of entities. To address this issue, we propose a novel quaternion knowledge graph embedding model. Our model combines semantic matching with entity's geometric distance to better measure the plausibility of triplets. Specifically, in the quaternion space, we perform a right rotation on head entity and a reverse rotation on tail entity to learn rich semantic features. Then, we utilize distance adaptive translations to learn geometric distance between entities. Furthermore, we provide mathematical proofs to demonstrate our model can handle complex logical relationships. Extensive experimental results and analyses show our model significantly outperforms previous models on well-known knowledge graph completion benchmark datasets. Our code is available at https://github.com/llqy123/DaBR.