Knowledge graphs offer a structured representation of real-world entities and their relationships, enabling a wide range of applications from information retrieval to automated reasoning. In this paper, we conduct a systematic comparison between traditional rule-based approaches and modern deep learning methods for link prediction. We focus on KBGAT, a graph neural network model that leverages multi-head attention to jointly encode both entity and relation features within local neighborhood structures. To advance this line of research, we introduce \textbf{GCAT} (Graph Collaborative Attention Network), a refined model that enhances context aggregation and interaction between heterogeneous nodes. Experimental results on four widely-used benchmark datasets demonstrate that GCAT not only consistently outperforms rule-based methods but also achieves competitive or superior performance compared to existing neural embedding models. Our findings highlight the advantages of attention-based architectures in capturing complex relational patterns for knowledge graph completion tasks.
Semantic context surrounding a triplet $(h, r, t)$ is crucial for Knowledge Graph Completion (KGC), providing vital cues for prediction. However, traditional node-based message passing mechanisms, when applied to knowledge graphs, often introduce noise and suffer from information dilution or over-smoothing by indiscriminately aggregating information from all neighboring edges. To address this challenge, we propose a semantic-aware relational message passing. A core innovation of this framework is the introduction of a \textbf{semantic-aware Top-K neighbor selection strategy}. Specifically, this strategy first evaluates the semantic relevance between a central node and its incident edges within a shared latent space, selecting only the Top-K most pertinent ones. Subsequently, information from these selected edges is effectively fused with the central node's own representation using a \textbf{multi-head attention aggregator} to generate a semantically focused node message. In this manner, our model not only leverages the structure and features of edges within the knowledge graph but also more accurately captures and propagates the contextual information most relevant to the specific link prediction task, thereby effectively mitigating interference from irrelevant information. Extensive experiments demonstrate that our method achieves superior performance compared to existing approaches on several established benchmarks.
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.
Knowledge graph completion aims to address the gaps of knowledge bases by adding new triples that represent facts. The complexity of this task depends on how many parts of a triple are already known. Instance completion involves predicting the relation-tail pair when only the head is given (h, ?, ?). Notably, modern knowledge bases often contain entity descriptions and types, which can provide valuable context for inferring missing facts. By leveraging these textual descriptions and the ability of large language models to extract facts from them and recognize patterns within the knowledge graph schema, we propose an LLM-powered, end-to-end instance completion approach. Specifically, we introduce GenIC: a two-step Generative Instance Completion framework. The first step focuses on property prediction, treated as a multi-label classification task. The second step is link prediction, framed as a generative sequence-to-sequence task. Experimental results on three datasets show that our method outperforms existing baselines. Our code is available at https://github.com/amal-gader/genic.
Knowledge graph completion (KGC) has attracted considerable attention in recent years because it is critical to improving the quality of knowledge graphs. Researchers have continuously explored various models. However, most previous efforts have neglected to take advantage of regularization from a deeper perspective and therefore have not been used to their full potential. This paper rethinks the application of regularization methods in KGC. Through extensive empirical studies on various KGC models, we find that carefully designed regularization not only alleviates overfitting and reduces variance but also enables these models to break through the upper bounds of their original performance. Furthermore, we introduce a novel sparse-regularization method that embeds the concept of rank-based selective sparsity into the KGC regularizer. The core idea is to selectively penalize those components with significant features in the embedding vector, thus effectively ignoring many components that contribute little and may only represent noise. Various comparative experiments on multiple datasets and multiple models show that the SPR regularization method is better than other regularization methods and can enable the KGC model to further break through the performance margin.
We revisit the efficacy of simple, real-valued embedding models for knowledge graph completion and introduce RelatE, an interpretable and modular method that efficiently integrates dual representations for entities and relations. RelatE employs a real-valued phase-modulus decomposition, leveraging sinusoidal phase alignments to encode relational patterns such as symmetry, inversion, and composition. In contrast to recent approaches based on complex-valued embeddings or deep neural architectures, RelatE preserves architectural simplicity while achieving competitive or superior performance on standard benchmarks. Empirically, RelatE outperforms prior methods across several datasets: on YAGO3-10, it achieves an MRR of 0.521 and Hit@10 of 0.680, surpassing all baselines. Additionally, RelatE offers significant efficiency gains, reducing training time by 24%, inference latency by 31%, and peak GPU memory usage by 22% compared to RotatE. Perturbation studies demonstrate improved robustness, with MRR degradation reduced by up to 61% relative to TransE and by up to 19% compared to RotatE under structural edits such as edge removals and relation swaps. Formal analysis further establishes the model's full expressiveness and its capacity to represent essential first-order logical inference patterns. These results position RelatE as a scalable and interpretable alternative to more complex architectures for knowledge graph completion.
Knowledge graphs (KGs) serve as fundamental structures for organizing interconnected data across diverse domains. However, most KGs remain incomplete, limiting their effectiveness in downstream applications. Knowledge graph completion (KGC) aims to address this issue by inferring missing links, but existing methods face critical challenges: deep graph neural networks (GNNs) suffer from over-smoothing, while embedding-based models fail to capture abstract relational features. This study aims to overcome these limitations by proposing a unified framework that integrates GNN distillation and abstract probabilistic interaction modeling (APIM). GNN distillation approach introduces an iterative message-feature filtering process to mitigate over-smoothing, preserving the discriminative power of node representations. APIM module complements this by learning structured, abstract interaction patterns through probabilistic signatures and transition matrices, allowing for a richer, more flexible representation of entity and relation interactions. We apply these methods to GNN-based models and the APIM to embedding-based KGC models, conducting extensive evaluations on the widely used WN18RR and FB15K-237 datasets. Our results demonstrate significant performance gains over baseline models, showcasing the effectiveness of the proposed techniques. The findings highlight the importance of both controlling information propagation and leveraging structured probabilistic modeling, offering new avenues for advancing knowledge graph completion. And our codes are available at https://anonymous.4open.science/r/APIM_and_GNN-Distillation-461C.
Knowledge Graphs (KGs), composed of triples in the form of (head, relation, tail) and consisting of entities and relations, play a key role in information retrieval systems such as question answering, entity search, and recommendation. In real-world KGs, although many entities exist, the relations exhibit a long-tail distribution, which can hinder information retrieval performance. Previous few-shot knowledge graph completion studies focused exclusively on the positive triple information that exists in the graph or, when negative triples were incorporated, used them merely as a signal to indicate incorrect triples. To overcome this limitation, we propose Relation-Based Conditional Diffusion with Attention Pooling (ReCDAP). First, negative triples are generated by randomly replacing the tail entity in the support set. By conditionally incorporating positive information in the KG and non-existent negative information into the diffusion process, the model separately estimates the latent distributions for positive and negative relations. Moreover, including an attention pooler enables the model to leverage the differences between positive and negative cases explicitly. Experiments on two widely used datasets demonstrate that our method outperforms existing approaches, achieving state-of-the-art performance. The code is available at https://github.com/hou27/ReCDAP-FKGC.
Few-shot knowledge graph completion (KGC) has obtained significant attention due to its practical applications in real-world scenarios, where new knowledge often emerges with limited available data. While most existing methods for few-shot KGC have predominantly focused on leveraging relational information, rich semantics inherent in KGs have been largely overlooked. To address this gap, we propose a novel prompted meta-learning (PromptMeta) framework that seamlessly integrates meta-semantics with relational information for few-shot KGC. PrompMeta has two key innovations: (1) a meta-semantic prompt pool that captures and consolidates high-level meta-semantics, enabling effective knowledge transfer and adaptation to rare and newly emerging relations. (2) a learnable fusion prompt that dynamically combines meta-semantic information with task-specific relational information tailored to different few-shot tasks. Both components are optimized together with model parameters within a meta-learning framework. Extensive experiments on two benchmark datasets demonstrate the effectiveness of our approach.
Large Language Models (LLMs) are transforming scientific hypothesis generation and validation by enabling information synthesis, latent relationship discovery, and reasoning augmentation. This survey provides a structured overview of LLM-driven approaches, including symbolic frameworks, generative models, hybrid systems, and multi-agent architectures. We examine techniques such as retrieval-augmented generation, knowledge-graph completion, simulation, causal inference, and tool-assisted reasoning, highlighting trade-offs in interpretability, novelty, and domain alignment. We contrast early symbolic discovery systems (e.g., BACON, KEKADA) with modern LLM pipelines that leverage in-context learning and domain adaptation via fine-tuning, retrieval, and symbolic grounding. For validation, we review simulation, human-AI collaboration, causal modeling, and uncertainty quantification, emphasizing iterative assessment in open-world contexts. The survey maps datasets across biomedicine, materials science, environmental science, and social science, introducing new resources like AHTech and CSKG-600. Finally, we outline a roadmap emphasizing novelty-aware generation, multimodal-symbolic integration, human-in-the-loop systems, and ethical safeguards, positioning LLMs as agents for principled, scalable scientific discovery.
Reasoning paths are reliable information in knowledge graph completion (KGC) in which algorithms can find strong clues of the actual relation between entities. However, in real-world applications, it is difficult to guarantee that computationally affordable paths exist toward all candidate entities. According to our observation, the prediction accuracy drops significantly when paths are absent. To make the proposed algorithm more stable against the missing path circumstances, we introduce soft reasoning paths. Concretely, a specific learnable latent path embedding is concatenated to each relation to help better model the characteristics of the corresponding paths. The combination of the relation and the corresponding learnable embedding is termed a soft path in our paper. By aligning the soft paths with the reasoning paths, a learnable embedding is guided to learn a generalized path representation of the corresponding relation. In addition, we introduce a hierarchical ranking strategy to make full use of information about the entity, relation, path, and soft path to help improve both the efficiency and accuracy of the model. Extensive experimental results illustrate that our algorithm outperforms the compared state-of-the-art algorithms by a notable margin. The code will be made publicly available after the paper is officially accepted.
Learning on large graphs presents significant challenges, with traditional Message Passing Neural Networks suffering from computational and memory costs scaling linearly with the number of edges. We introduce the Intersecting Block Graph (IBG), a low-rank factorization of large directed graphs based on combinations of intersecting bipartite components, each consisting of a pair of communities, for source and target nodes. By giving less weight to non-edges, we show how to efficiently approximate any graph, sparse or dense, by a dense IBG. Specifically, we prove a constructive version of the weak regularity lemma, showing that for any chosen accuracy, every graph, regardless of its size or sparsity, can be approximated by a dense IBG whose rank depends only on the accuracy. This dependence of the rank solely on the accuracy, and not on the sparsity level, is in contrast to previous forms of the weak regularity lemma. We present a graph neural network architecture operating on the IBG representation of the graph and demonstrating competitive performance on node classification, spatio-temporal graph analysis, and knowledge graph completion, while having memory and computational complexity linear in the number of nodes rather than edges.
Most current MKGC approaches are predominantly based on discriminative models that maximize conditional likelihood. These approaches struggle to efficiently capture the complex connections in real-world knowledge graphs, thereby limiting their overall performance. To address this issue, we propose a structure-aware multimodal Diffusion model for multimodal knowledge graph Completion (DiffusionCom). DiffusionCom innovatively approaches the problem from the perspective of generative models, modeling the association between the $(head, relation)$ pair and candidate tail entities as their joint probability distribution $p((head, relation), (tail))$, and framing the MKGC task as a process of gradually generating the joint probability distribution from noise. Furthermore, to fully leverage the structural information in MKGs, we propose Structure-MKGformer, an adaptive and structure-aware multimodal knowledge representation learning method, as the encoder for DiffusionCom. Structure-MKGformer captures rich structural information through a multimodal graph attention network (MGAT) and adaptively fuses it with entity representations, thereby enhancing the structural awareness of these representations. This design effectively addresses the limitations of existing MKGC methods, particularly those based on multimodal pre-trained models, in utilizing structural information. DiffusionCom is trained using both generative and discriminative losses for the generator, while the feature extractor is optimized exclusively with discriminative loss. This dual approach allows DiffusionCom to harness the strengths of both generative and discriminative models. Extensive experiments on the FB15k-237-IMG and WN18-IMG datasets demonstrate that DiffusionCom outperforms state-of-the-art models.
Text-based knowledge graph completion methods take advantage of pre-trained language models (PLM) to enhance intrinsic semantic connections of raw triplets with detailed text descriptions. Typical methods in this branch map an input query (textual descriptions associated with an entity and a relation) and its candidate entities into feature vectors, respectively, and then maximize the probability of valid triples. These methods are gaining promising performance and increasing attention for the rapid development of large language models. According to the property of the language models, the more related and specific context information the input query provides, the more discriminative the resultant embedding will be. In this paper, through observation and validation, we find a neglected fact that the relation-aware neighbors of the head entities in queries could act as effective contexts for more precise link prediction. Driven by this finding, we propose a relation-aware anchor enhanced knowledge graph completion method (RAA-KGC). Specifically, in our method, to provide a reference of what might the target entity be like, we first generate anchor entities within the relation-aware neighborhood of the head entity. Then, by pulling the query embedding towards the neighborhoods of the anchors, it is tuned to be more discriminative for target entity matching. The results of our extensive experiments not only validate the efficacy of RAA-KGC but also reveal that by integrating our relation-aware anchor enhancement strategy, the performance of current leading methods can be notably enhanced without substantial modifications.
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.
In this paper, we propose a new geometric approach for knowledge graph completion via low rank tensor approximation. We augment a pretrained and well-established Euclidean model based on a Tucker tensor decomposition with a novel hyperbolic interaction term. This correction enables more nuanced capturing of distributional properties in data better aligned with real-world knowledge graphs. By combining two geometries together, our approach improves expressivity of the resulting model achieving new state-of-the-art link prediction accuracy with a significantly lower number of parameters compared to the previous Euclidean and hyperbolic models.
Knowledge Graph Completion (KGC) aims to infer missing information in Knowledge Graphs (KGs) to address their inherent incompleteness. Traditional structure-based KGC methods, while effective, face significant computational demands and scalability challenges due to the need for dense embedding learning and scoring all entities in the KG for each prediction. Recent text-based approaches using language models like T5 and BERT have mitigated these issues by converting KG triples into text for reasoning. However, they often fail to fully utilize contextual information, focusing mainly on the neighborhood of the entity and neglecting the context of the relation. To address this issue, we propose KGC-ERC, a framework that integrates both types of context to enrich the input of generative language models and enhance their reasoning capabilities. Additionally, we introduce a sampling strategy to effectively select relevant context within input token constraints, which optimizes the utilization of contextual information and potentially improves model performance. Experiments on the Wikidata5M, Wiki27K, and FB15K-237-N datasets show that KGC-ERC outperforms or matches state-of-the-art baselines in predictive performance and scalability.
Knowledge graph completion (KGC) seeks to predict missing entities (e.g., heads or tails) or relationships in knowledge graphs (KGs), which often contain incomplete data. Traditional embedding-based methods, such as TransE and ComplEx, have improved tail entity prediction but struggle to generalize to unseen entities during testing. Textual-based models mitigate this issue by leveraging additional semantic context; however, their reliance on negative triplet sampling introduces high computational overhead, semantic inconsistencies, and data imbalance. Recent approaches, like KG-BERT, show promise but depend heavily on entity descriptions, which are often unavailable in KGs. Critically, existing methods overlook valuable structural information in the KG related to the entities and relationships. To address these challenges, we propose Multi-Context-Aware Knowledge Graph Completion (MuCo-KGC), a novel model that utilizes contextual information from linked entities and relations within the graph to predict tail entities. MuCo-KGC eliminates the need for entity descriptions and negative triplet sampling, significantly reducing computational complexity while enhancing performance. Our experiments on standard datasets, including FB15k-237, WN18RR, CoDEx-S, and CoDEx-M, demonstrate that MuCo-KGC outperforms state-of-the-art methods on three datasets. Notably, MuCo-KGC improves MRR on WN18RR, and CoDEx-S and CoDEx-M datasets by $1.63\%$, and $3.77\%$ and $20.15\%$ respectively, demonstrating its effectiveness for KGC tasks.
Fully inductive knowledge graph models can be trained on multiple domains and subsequently perform zero-shot knowledge graph completion (KGC) in new unseen domains. This is an important capability towards the goal of having foundation models for knowledge graphs. In this work, we introduce a more expressive and capable fully inductive model, dubbed TRIX, which not only yields strictly more expressive triplet embeddings (head entity, relation, tail entity) compared to state-of-the-art methods, but also introduces a new capability: directly handling both entity and relation prediction tasks in inductive settings. Empirically, we show that TRIX outperforms the state-of-the-art fully inductive models in zero-shot entity and relation predictions in new domains, and outperforms large-context LLMs in out-of-domain predictions. The source code is available at https://github.com/yuchengz99/TRIX.
Knowledge Graph Completion (KGC), which aims to infer missing or incomplete facts, is a crucial task for KGs. However, integrating the vital structural information of KGs into Large Language Models (LLMs) and outputting predictions deterministically remains challenging. To address this, we propose a new method called GLTW, which encodes the structural information of KGs and merges it with LLMs to enhance KGC performance. Specifically, we introduce an improved Graph Transformer (iGT) that effectively encodes subgraphs with both local and global structural information and inherits the characteristics of language model, bypassing training from scratch. Also, we develop a subgraph-based multi-classification training objective, using all entities within KG as classification objects, to boost learning efficiency.Importantly, we combine iGT with an LLM that takes KG language prompts as input.Our extensive experiments on various KG datasets show that GLTW achieves significant performance gains compared to SOTA baselines.