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.
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 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.
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.
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.
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.
Multimodal Knowledge Graph Completion (MMKGC) aims to address the critical issue of missing knowledge in multimodal knowledge graphs (MMKGs) for their better applications. However, both the previous MMGKC and negative sampling (NS) approaches ignore the employment of multimodal information to generate diverse and high-quality negative triples from various semantic levels and hardness levels, thereby limiting the effectiveness of training MMKGC models. Thus, we propose a novel Diffusion-based Hierarchical Negative Sampling (DHNS) scheme tailored for MMKGC tasks, which tackles the challenge of generating high-quality negative triples by leveraging a Diffusion-based Hierarchical Embedding Generation (DiffHEG) that progressively conditions on entities and relations as well as multimodal semantics. Furthermore, we develop a Negative Triple-Adaptive Training (NTAT) strategy that dynamically adjusts training margins associated with the hardness level of the synthesized negative triples, facilitating a more robust and effective learning procedure to distinguish between positive and negative triples. Extensive experiments on three MMKGC benchmark datasets demonstrate that our framework outperforms several state-of-the-art MMKGC models and negative sampling techniques, illustrating the effectiveness of our DHNS for training MMKGC models. The source codes and datasets of this paper are available at https://github.com/ngl567/DHNS.
The growing demand for halal cosmetic products has exposed significant challenges, especially in Muslim-majority countries. Recently, various machine learning-based strategies, e.g., image-based methods, have shown remarkable success in predicting the halal status of cosmetics. However, these methods mainly focus on analyzing the discrete and specific ingredients within separate cosmetics, which ignore the high-order and complex relations between cosmetics and ingredients. To address this problem, we propose a halal cosmetic recommendation framework, namely HaCKG, that leverages a knowledge graph of cosmetics and their ingredients to explicitly model and capture the relationships between cosmetics and their components. By representing cosmetics and ingredients as entities within the knowledge graph, HaCKG effectively learns the high-order and complex relations between entities, offering a robust method for predicting halal status. Specifically, we first construct a cosmetic knowledge graph representing the relations between various cosmetics, ingredients, and their properties. We then propose a pre-trained relational graph attention network model with residual connections to learn the structural relation between entities in the knowledge graph. The pre-trained model is then fine-tuned on downstream cosmetic data to predict halal status. Extensive experiments on the cosmetic dataset over halal prediction tasks demonstrate the superiority of our model over state-of-the-art baselines.
Inductive Knowledge Graph Completion (KGC) aims to infer missing facts between newly emerged entities within knowledge graphs (KGs), posing a significant challenge. While recent studies have shown promising results in inferring such entities through knowledge subgraph reasoning, they suffer from (i) the semantic inconsistencies of similar relations, and (ii) noisy interactions inherent in KGs due to the presence of unconvincing knowledge for emerging entities. To address these challenges, we propose a Semantic Structure-aware Denoising Network (S$^2$DN) for inductive KGC. Our goal is to learn adaptable general semantics and reliable structures to distill consistent semantic knowledge while preserving reliable interactions within KGs. Specifically, we introduce a semantic smoothing module over the enclosing subgraphs to retain the universal semantic knowledge of relations. We incorporate a structure refining module to filter out unreliable interactions and offer additional knowledge, retaining robust structure surrounding target links. Extensive experiments conducted on three benchmark KGs demonstrate that S$^2$DN surpasses the performance of state-of-the-art models. These results demonstrate the effectiveness of S$^2$DN in preserving semantic consistency and enhancing the robustness of filtering out unreliable interactions in contaminated KGs.
Link Prediction is a foundational task in Graph Representation Learning, supporting applications like link recommendation, knowledge graph completion and graph generation. Graph Neural Networks have shown the most promising results in this domain and are currently the de facto standard approach to learning from graph data. However, a key distinction exists between Undirected and Directed Link Prediction: the former just predicts the existence of an edge, while the latter must also account for edge directionality and bidirectionality. This translates to Directed Link Prediction (DLP) having three sub-tasks, each defined by how training, validation and test sets are structured. Most research on DLP overlooks this trichotomy, focusing solely on the "existence" sub-task, where training and test sets are random, uncorrelated samples of positive and negative directed edges. Even in the works that recognize the aforementioned trichotomy, models fail to perform well across all three sub-tasks. In this study, we experimentally demonstrate that training Neural DLP (NDLP) models only on the existence sub-task, using methods adapted from Neural Undirected Link Prediction, results in parameter configurations that fail to capture directionality and bidirectionality, even after rebalancing edge classes. To address this, we propose three strategies that handle the three tasks simultaneously. Our first strategy, the Multi-Class Framework for Neural Directed Link Prediction (MC-NDLP) maps NDLP to a Multi-Class training objective. The second and third approaches adopt a Multi-Task perspective, either with a Multi-Objective (MO-DLP) or a Scalarized (S-DLP) strategy. Our results show that these methods outperform traditional approaches across multiple datasets and models, achieving equivalent or superior performance in addressing the three DLP sub-tasks.
Large Language Models (LLMs) present massive inherent knowledge and superior semantic comprehension capability, which have revolutionized various tasks in natural language processing. Despite their success, a critical gap remains in enabling LLMs to perform knowledge graph completion (KGC). Empirical evidence suggests that LLMs consistently perform worse than conventional KGC approaches, even through sophisticated prompt design or tailored instruction-tuning. Fundamentally, applying LLMs on KGC introduces several critical challenges, including a vast set of entity candidates, hallucination issue of LLMs, and under-exploitation of the graph structure. To address these challenges, we propose a novel instruction-tuning-based method, namely FtG. Specifically, we present a \textit{filter-then-generate} paradigm and formulate the KGC task into a multiple-choice question format. In this way, we can harness the capability of LLMs while mitigating the issue casused by hallucinations. Moreover, we devise a flexible ego-graph serialization prompt and employ a structure-text adapter to couple structure and text information in a contextualized manner. Experimental results demonstrate that FtG achieves substantial performance gain compared to existing state-of-the-art methods. The instruction dataset and code are available at \url{https://github.com/LB0828/FtG}.
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.
Link prediction is a critical problem in graph learning with broad applications such as recommender systems and knowledge graph completion. Numerous research efforts have been directed at solving this problem, including approaches based on similarity metrics and Graph Neural Networks (GNN). However, most existing solutions are still rooted in conventional supervised learning, which makes it challenging to adapt over time to changing customer interests and to address the inherent dilemma of exploitation versus exploration in link prediction. To tackle these challenges, this paper reformulates link prediction as a sequential decision-making process, where each link prediction interaction occurs sequentially. We propose a novel fusion algorithm, PRB (PageRank Bandits), which is the first to combine contextual bandits with PageRank for collaborative exploitation and exploration. We also introduce a new reward formulation and provide a theoretical performance guarantee for PRB. Finally, we extensively evaluate PRB in both online and offline settings, comparing it with bandit-based and graph-based methods. The empirical success of PRB demonstrates the value of the proposed fusion approach. Our code is released at https://github.com/jiaruzouu/PRB.
Inductive knowledge graph completion (KGC) aims to predict missing triples with unseen entities. Recent works focus on modeling reasoning paths between the head and tail entity as direct supporting evidence. However, these methods depend heavily on the existence and quality of reasoning paths, which limits their general applicability in different scenarios. In addition, we observe that latent type constraints and neighboring facts inherent in KGs are also vital in inferring missing triples. To effectively utilize all useful information in KGs, we introduce CATS, a novel context-aware inductive KGC solution. With sufficient guidance from proper prompts and supervised fine-tuning, CATS activates the strong semantic understanding and reasoning capabilities of large language models to assess the existence of query triples, which consist of two modules. First, the type-aware reasoning module evaluates whether the candidate entity matches the latent entity type as required by the query relation. Then, the subgraph reasoning module selects relevant reasoning paths and neighboring facts, and evaluates their correlation to the query triple. Experiment results on three widely used datasets demonstrate that CATS significantly outperforms state-of-the-art methods in 16 out of 18 transductive, inductive, and few-shot settings with an average absolute MRR improvement of 7.2%.
Complex logical query answering (CLQA) is a challenging task that involves finding answer entities for complex logical queries over incomplete knowledge graphs (KGs). Previous research has explored the use of pre-trained knowledge graph completion (KGC) models, which can predict the missing facts in KGs, to answer complex logical queries. However, KGC models are typically evaluated using ranking evaluation metrics, which may result in values of predictions of KGC models that are not well-calibrated. In this paper, we propose a method for calibrating KGC models, namely CKGC, which enables KGC models to adapt to answering complex logical queries. Notably, CKGC is lightweight and effective. The adaptation function is simple, allowing the model to quickly converge during the adaptation process. The core concept of CKGC is to map the values of predictions of KGC models to the range [0, 1], ensuring that values associated with true facts are close to 1, while values linked to false facts are close to 0. Through experiments on three benchmark datasets, we demonstrate that our proposed calibration method can significantly boost model performance in the CLQA task. Moreover, our approach can enhance the performance of CLQA while preserving the ranking evaluation metrics of KGC models. The code is available at https://github.com/changyi7231/CKGC.
Knowledge graph (KG) completion aims to identify additional facts that can be inferred from the existing facts in the KG. Recent developments in this field have explored this task in the inductive setting, where at test time one sees entities that were not present during training; the most performant models in the inductive setting have employed path encoding modules in addition to standard subgraph encoding modules. This work similarly focuses on KG completion in the inductive setting, without the explicit use of path encodings, which can be time-consuming and introduces several hyperparameters that require costly hyperparameter optimization. Our approach uses a Transformer-based subgraph encoding module only; we introduce connection-biased attention and entity role embeddings into the subgraph encoding module to eliminate the need for an expensive and time-consuming path encoding module. Evaluations on standard inductive KG completion benchmark datasets demonstrate that our \textbf{C}onnection-\textbf{B}iased \textbf{Li}nk \textbf{P}rediction (CBLiP) model has superior performance to models that do not use path information. Compared to models that utilize path information, CBLiP shows competitive or superior performance while being faster. Additionally, to show that the effectiveness of connection-biased attention and entity role embeddings also holds in the transductive setting, we compare CBLiP's performance on the relation prediction task in the transductive setting.
Knowledge Graph Completion has been increasingly adopted as a useful method for several tasks in biomedical research, like drug repurposing or drug-target identification. To that end, a variety of datasets and Knowledge Graph Embedding models has been proposed over the years. However, little is known about the properties that render a dataset useful for a given task and, even though theoretical properties of Knowledge Graph Embedding models are well understood, their practical utility in this field remains controversial. We conduct a comprehensive investigation into the topological properties of publicly available biomedical Knowledge Graphs and establish links to the accuracy observed in real-world applications. By releasing all model predictions and a new suite of analysis tools we invite the community to build upon our work and continue improving the understanding of these crucial applications.
Temporal Knowledge Graphs (TKGs) incorporate temporal information to reflect the dynamic structural knowledge and evolutionary patterns of real-world facts. Nevertheless, TKGs are still limited in downstream applications due to the problem of incompleteness. Consequently, TKG completion (also known as link prediction) has been widely studied, with recent research focusing on incorporating independent embeddings of time or combining them with entities and relations to form temporal representations. However, most existing methods overlook the impact of history from a multi-granularity aspect. The inherent semantics of human-defined temporal granularities, such as ordinal dates, reveal general patterns to which facts typically adhere. To counter this limitation, this paper proposes \textbf{L}earning \textbf{G}ranularity \textbf{Re}presentation (termed $\mathsf{LGRe}$) for TKG completion. It comprises two main components: Granularity Representation Learning (GRL) and Adaptive Granularity Balancing (AGB). Specifically, GRL employs time-specific multi-layer convolutional neural networks to capture interactions between entities and relations at different granularities. After that, AGB generates adaptive weights for these embeddings according to temporal semantics, resulting in expressive representations of predictions. Moreover, to reflect similar semantics of adjacent timestamps, a temporal loss function is introduced. Extensive experimental results on four event benchmarks demonstrate the effectiveness of $\mathsf{LGRe}$ in learning time-related representations. To ensure reproducibility, our code is available at https://github.com/KcAcoZhang/LGRe.
Temporal knowledge graph completion aims to infer the missing facts in temporal knowledge graphs. Current approaches usually embed factual knowledge into continuous vector space and apply geometric operations to learn potential patterns in temporal knowledge graphs. However, these methods only adopt a single operation, which may have limitations in capturing the complex temporal dynamics present in temporal knowledge graphs. Therefore, we propose a simple but effective method, i.e. TCompoundE, which is specially designed with two geometric operations, including time-specific and relation-specific operations. We provide mathematical proofs to demonstrate the ability of TCompoundE to encode various relation patterns. Experimental results show that our proposed model significantly outperforms existing temporal knowledge graph embedding models. Our code is available at https://github.com/nk-ruiying/TCompoundE.
Traditional knowledge graph (KG) completion models learn embeddings to predict missing facts. Recent works attempt to complete KGs in a text-generation manner with large language models (LLMs). However, they need to ground the output of LLMs to KG entities, which inevitably brings errors. In this paper, we present a finetuning framework, DIFT, aiming to unleash the KG completion ability of LLMs and avoid grounding errors. Given an incomplete fact, DIFT employs a lightweight model to obtain candidate entities and finetunes an LLM with discrimination instructions to select the correct one from the given candidates. To improve performance while reducing instruction data, DIFT uses a truncated sampling method to select useful facts for finetuning and injects KG embeddings into the LLM. Extensive experiments on benchmark datasets demonstrate the effectiveness of our proposed framework.