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.
Graph Neural Networks (GNNs) have been widely used for various learning tasks, ranging from node classification to link prediction. They have demonstrated excellent performance in multiple domains involving graph-structured data. However, an important category of learning tasks, namely link weight prediction, has received less emphasis due to its increased complexity compared to binary link classification. Link weight prediction becomes even more challenging when considering multilayer networks, where nodes can be interconnected across multiple layers. To address these challenges, we propose a new method named Multiplex Spatial Graph Convolution Network (MSGCN), which spatially embeds information across multiple layers to predict interlayer link weights. The MSGCN model generalizes spatial graph convolution to multiplex networks and captures the geometric structure of nodes across multiple layers. Extensive experiments using data with known interlayer link information show that the MSGCN model has robust, accurate, and generalizable link weight prediction performance across a wide variety of multiplex network structures.
Graph neural networks (GNNs) are powerful tools for solving graph-related problems. Distributed GNN frameworks and systems enhance the scalability of GNNs and accelerate model training, yet most are optimized for node classification. Their performance on link prediction remains underexplored. This paper demystifies distributed training of GNNs for link prediction by investigating the issue of performance degradation when each worker trains a GNN on its assigned partitioned subgraph without having access to the entire graph. We discover that the main sources of the issue come from not only the information loss caused by graph partitioning but also the ways of drawing negative samples during model training. While sharing the complete graph information with each worker resolves the issue and preserves link prediction accuracy, it incurs a high communication cost. We propose SpLPG, which effectively leverages graph sparsification to mitigate the issue of performance degradation at a reduced communication cost. Experiment results on several public real-world datasets demonstrate the effectiveness of SpLPG, which reduces the communication overhead by up to about 80% while mostly preserving link prediction accuracy.
Accurate predictions rely on the expressiveness power of graph deep learning frameworks like graph neural networks and graph transformers, where a positional encoding mechanism has become much more indispensable in recent state-of-the-art works to record the canonical position information. However, the current positional encoding is limited in three aspects: (1) most positional encoding methods use pre-defined, and fixed functions, which are inadequate to adapt to the complex attributed graphs; (2) a few pioneering works proposed the learnable positional encoding but are still limited to the structural information, not considering the real-world time-evolving topological and feature information; (3) most positional encoding methods are equipped with transformers' attention mechanism to fully leverage their capabilities, where the dense or relational attention is often unaffordable on large-scale structured data. Hence, we aim to develop Learnable Spatial-Temporal Positional Encoding in an effective and efficient manner and propose a simple temporal link prediction model named L-STEP. Briefly, for L-STEP, we (1) prove the proposed positional learning scheme can preserve the graph property from the spatial-temporal spectral viewpoint, (2) verify that MLPs can fully exploit the expressiveness and reach transformers' performance on that encoding, (3) change different initial positional encoding inputs to show robustness, (4) analyze the theoretical complexity and obtain less empirical running time than SOTA, and (5) demonstrate its temporal link prediction out-performance on 13 classic datasets and with 10 algorithms in both transductive and inductive settings using 3 different sampling strategies. Also, L-STEP obtains the leading performance in the newest large-scale TGB benchmark. Our code is available at https://github.com/kthrn22/L-STEP.
N-ary Knowledge Graphs (NKGs) are a specialized type of knowledge graph designed to efficiently represent complex real-world facts. Unlike traditional knowledge graphs, where a fact typically involves two entities, NKGs can capture n-ary facts containing more than two entities. Link prediction in NKGs aims to predict missing elements within these n-ary facts, which is essential for completing NKGs and improving the performance of downstream applications. This task has recently gained significant attention. In this paper, we present the first comprehensive survey of link prediction in NKGs, providing an overview of the field, systematically categorizing existing methods, and analyzing their performance and application scenarios. We also outline promising directions for future research.
In the era of foundation models, Out-of- Distribution (OOD) problems, i.e., the data discrepancy between the training environments and testing environments, hinder AI generalization. Further, relational data like graphs disobeying the Independent and Identically Distributed (IID) condition makes the problem more challenging, especially much harder when it is associated with time. Motivated by this, to realize the robust invariant learning over temporal graphs, we want to investigate what components in temporal graphs are most invariant and representative with respect to labels. With the Information Bottleneck (IB) method, we propose an error-bounded Invariant Link Selector that can distinguish invariant components and variant components during the training process to make the deep learning model generalizable for different testing scenarios. Besides deriving a series of rigorous generalizable optimization functions, we also equip the training with task-specific loss functions, e.g., temporal link prediction, to make pretrained models solve real-world application tasks like citation recommendation and merchandise recommendation, as demonstrated in our experiments with state-of-the-art (SOTA) methods. Our code is available at https://github.com/kthrn22/OOD-Linker.
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.
Complex systems are often driven by higher-order interactions among multiple units, naturally represented as hypergraphs. Understanding dependency structures within these hypergraphs is crucial for understanding and predicting the behavior of complex systems but is made challenging by their combinatorial complexity and computational demands. In this paper, we introduce a class of probabilistic models that efficiently represents and discovers a broad spectrum of mesoscale structure in large-scale hypergraphs. The key insight enabling this approach is to treat classes of similar units as themselves nodes in a latent hypergraph. By modeling observed node interactions through latent interactions among classes using low-rank representations, our approach tractably captures rich structural patterns while ensuring model identifiability. This allows for direct interpretation of distinct node- and class-level structures. Empirically, our model improves link prediction over state-of-the-art methods and discovers interpretable structures in diverse real-world systems, including pharmacological and social networks, advancing the ability to incorporate large-scale higher-order data into the scientific process.
Future link prediction on temporal graphs is a fundamental task with wide applicability in real-world dynamic systems. These scenarios often involve both recurring (seen) and novel (unseen) interactions, requiring models to generalize effectively across both types of edges. However, existing methods typically rely on complex memory and aggregation modules, yet struggle to handle unseen edges. In this paper, we revisit the architecture of existing temporal graph models and identify two essential but overlooked modeling requirements for future link prediction: representing nodes with unique identifiers and performing target-aware matching between source and destination nodes. To this end, we propose Cross-Attention based Future Link Predictor on Temporal Graphs (CRAFT), a simple yet effective architecture that discards memory and aggregation modules and instead builds on two components: learnable node embeddings and cross-attention between the destination and the source's recent interactions. This design provides strong expressive power and enables target-aware modeling of the compatibility between candidate destinations and the source's interaction patterns. Extensive experiments on diverse datasets demonstrate that CRAFT consistently achieves superior performance with high efficiency, making it well-suited for large-scale real-world applications.
Link prediction for directed graphs is a crucial task with diverse real-world applications. Recent advances in embedding methods and Graph Neural Networks (GNNs) have shown promising improvements. However, these methods often lack a thorough analysis of their expressiveness and suffer from effective benchmarks for a fair evaluation. In this paper, we propose a unified framework to assess the expressiveness of existing methods, highlighting the impact of dual embeddings and decoder design on directed link prediction performance. To address limitations in current benchmark setups, we introduce DirLinkBench, a robust new benchmark with comprehensive coverage, standardized evaluation, and modular extensibility. The results on DirLinkBench show that current methods struggle to achieve strong performance, while DiGAE outperforms other baselines overall. We further revisit DiGAE theoretically, showing its graph convolution aligns with GCN on an undirected bipartite graph. Inspired by these insights, we propose a novel Spectral Directed Graph Auto-Encoder SDGAE that achieves state-of-the-art average performance on DirLinkBench. Finally, we analyze key factors influencing directed link prediction and highlight open challenges in this field.
The intrinsic complexity of human biology presents ongoing challenges to scientific understanding. Researchers collaborate across disciplines to expand our knowledge of the biological interactions that define human life. AI methodologies have emerged as powerful tools across scientific domains, particularly in computational biology, where graph data structures effectively model biological entities such as protein-protein interaction (PPI) networks and gene functional networks. Those networks are used as datasets for paramount network medicine tasks, such as gene-disease association prediction, drug repurposing, and polypharmacy side effect studies. Reliable predictions from machine learning models require high-quality foundational data. In this work, we present a comprehensive multi-purpose biological knowledge graph constructed by integrating and refining multiple publicly available datasets. Building upon the Drug Repurposing Knowledge Graph (DRKG), we define a pipeline tasked with a) cleaning inconsistencies and redundancies present in DRKG, b) coalescing information from the main available public data sources, and c) enriching the graph nodes with expressive feature vectors such as molecular fingerprints and gene ontologies. Biologically and chemically relevant features improve the capacity of machine learning models to generate accurate and well-structured embedding spaces. The resulting resource represents a coherent and reliable biological knowledge graph that serves as a state-of-the-art platform to advance research in computational biology and precision medicine. Moreover, it offers the opportunity to benchmark graph-based machine learning and network medicine models on relevant tasks. We demonstrate the effectiveness of the proposed dataset by benchmarking it against the task of drug repurposing, PPI prediction, and side-effect prediction, modeled as link prediction problems.
Link prediction in unmanned aerial vehicle (UAV) ad hoc networks (UANETs) aims to predict the potential formation of future links between UAVs. In adversarial environments where the route information of UAVs is unavailable, predicting future links must rely solely on the observed historical topological information of UANETs. However, the highly dynamic and sparse nature of UANET topologies presents substantial challenges in effectively capturing meaningful structural and temporal patterns for accurate link prediction. Most existing link prediction methods focus on temporal dynamics at a single structural scale while neglecting the effects of sparsity, resulting in insufficient information capture and limited applicability to UANETs. In this paper, we propose a multi-scale structural-temporal link prediction model (MUST) for UANETs. Specifically, we first employ graph attention networks (GATs) to capture structural features at multiple levels, including the individual UAV level, the UAV community level, and the overall network level. Then, we use long short-term memory (LSTM) networks to learn the temporal dynamics of these multi-scale structural features. Additionally, we address the impact of sparsity by introducing a sophisticated loss function during model optimization. We validate the performance of MUST using several UANET datasets generated through simulations. Extensive experimental results demonstrate that MUST achieves state-of-the-art link prediction performance in highly dynamic and sparse UANETs.
While Knowledge Graphs (KGs) have become increasingly popular across various scientific disciplines for their ability to model and interlink huge quantities of data, essentially all real-world KGs are known to be incomplete. As such, with the growth of KG use has been a concurrent development of machine learning tools designed to predict missing information in KGs, which is referred to as the Link Prediction Task. The majority of state-of-the-art link predictors to date have followed an embedding-based paradigm. In this paradigm, it is assumed that the information content of a KG is best represented by the (individual) vector representations of its nodes and edges, and that therefore node and edge embeddings are particularly well-suited to performing link prediction. This thesis proposes an alternative perspective on the field's approach to link prediction and KG data modelling. Specifically, this work re-analyses KGs and state-of-the-art link predictors from a graph-structure-first perspective that models the information content of a KG in terms of whole triples, rather than individual nodes and edges. Following a literature review and two core sets of experiments, this thesis concludes that a structure-first perspective on KGs and link prediction is both viable and useful for understanding KG learning and for enabling cross-KG transfer learning for the link prediction task. This observation is used to create and propose the Structural Alignment Hypothesis, which postulates that link prediction can be understood and modelled as a structural task. All code and data used for this thesis are open-sourced. This thesis was written bilingually, with the main document in English and an informal extended summary in Irish. An Irish-language translation dictionary of machine learning terms (the Focl\'oir Tr\'achtais) created for this work is open-sourced as well.
Effective and efficient graph representation learning is essential for enabling critical downstream tasks, such as node classification, link prediction, and subgraph search. However, existing graph neural network (GNN) architectures often struggle to adapt to diverse and complex graph structures, limiting their ability to produce structure-aware and task-discriminative representations. To address this challenge, we propose ABG-NAS, a novel framework for automated graph neural network architecture search tailored for efficient graph representation learning. ABG-NAS encompasses three key components: a Comprehensive Architecture Search Space (CASS), an Adaptive Genetic Optimization Strategy (AGOS), and a Bayesian-Guided Tuning Module (BGTM). CASS systematically explores diverse propagation (P) and transformation (T) operations, enabling the discovery of GNN architectures capable of capturing intricate graph characteristics. AGOS dynamically balances exploration and exploitation, ensuring search efficiency and preserving solution diversity. BGTM further optimizes hyperparameters periodically, enhancing the scalability and robustness of the resulting architectures. Empirical evaluations on benchmark datasets (Cora, PubMed, Citeseer, and CoraFull) demonstrate that ABG-NAS consistently outperforms both manually designed GNNs and state-of-the-art neural architecture search (NAS) methods. These results highlight the potential of ABG-NAS to advance graph representation learning by providing scalable and adaptive solutions for diverse graph structures. Our code is publicly available at https://github.com/sserranw/ABG-NAS.
Knowledge Graphs have become increasingly popular due to their wide usage in various downstream applications, including information retrieval, chatbot development, language model construction, and many others. Link prediction (LP) is a crucial downstream task for knowledge graphs, as it helps to address the problem of the incompleteness of the knowledge graphs. However, previous research has shown that knowledge graphs, often created in a (semi) automatic manner, are not free from social biases. These biases can have harmful effects on downstream applications, especially by leading to unfair behavior toward minority groups. To understand this issue in detail, we develop a framework -- AuditLP -- deploying fairness metrics to identify biased outcomes in LP, specifically how occupations are classified as either male or female-dominated based on gender as a sensitive attribute. We have experimented with the sensitive attribute of age and observed that occupations are categorized as young-biased, old-biased, and age-neutral. We conduct our experiments on a large number of knowledge triples that belong to 21 different geographies extracted from the open-sourced knowledge graph, Wikidata. Our study shows that the variance in the biased outcomes across geographies neatly mirrors the socio-economic and cultural division of the world, resulting in a transparent partition of the Global North from the Global South.
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.
Self-supervised learning (SSL) in graphs has garnered significant attention, particularly in employing Graph Neural Networks (GNNs) with pretext tasks initially designed for other domains, such as contrastive learning and feature reconstruction. However, it remains uncertain whether these methods effectively reflect essential graph properties, precisely representation similarity with its neighbors. We observe that existing methods position opposite ends of a spectrum driven by the graph embedding smoothness, with each end corresponding to outperformance on specific downstream tasks. Decomposing the SSL objective into three terms via an information-theoretic framework with a neighbor representation variable reveals that this polarization stems from an imbalance among the terms, which existing methods may not effectively maintain. Further insights suggest that balancing between the extremes can lead to improved performance across a wider range of downstream tasks. A framework, BSG (Balancing Smoothness in Graph SSL), introduces novel loss functions designed to supplement the representation quality in graph-based SSL by balancing the derived three terms: neighbor loss, minimal loss, and divergence loss. We present a theoretical analysis of the effects of these loss functions, highlighting their significance from both the SSL and graph smoothness perspectives. Extensive experiments on multiple real-world datasets across node classification and link prediction consistently demonstrate that BSG achieves state-of-the-art performance, outperforming existing methods. Our implementation code is available at https://github.com/steve30572/BSG.
Graph self-supervised learning has gained significant attention recently. However, many existing approaches heavily depend on perturbations, and inappropriate perturbations may corrupt the graph's inherent information. The Vector Quantized Variational Autoencoder (VQ-VAE) is a powerful autoencoder extensively used in fields such as computer vision; however, its application to graph data remains underexplored. In this paper, we provide an empirical analysis of vector quantization in the context of graph autoencoders, demonstrating its significant enhancement of the model's capacity to capture graph topology. Furthermore, we identify two key challenges associated with vector quantization when applying in graph data: codebook underutilization and codebook space sparsity. For the first challenge, we propose an annealing-based encoding strategy that promotes broad code utilization in the early stages of training, gradually shifting focus toward the most effective codes as training progresses. For the second challenge, we introduce a hierarchical two-layer codebook that captures relationships between embeddings through clustering. The second layer codebook links similar codes, encouraging the model to learn closer embeddings for nodes with similar features and structural topology in the graph. Our proposed model outperforms 16 representative baseline methods in self-supervised link prediction and node classification tasks across multiple datasets.
Text-attributed graphs (TAGs) present unique challenges in representation learning by requiring models to capture both the semantic richness of node-associated texts and the structural dependencies of the graph. While graph neural networks (GNNs) excel at modeling topological information, they lack the capacity to process unstructured text. Conversely, large language models (LLMs) are proficient in text understanding but are typically unaware of graph structure. In this work, we propose BiGTex (Bidirectional Graph Text), a novel architecture that tightly integrates GNNs and LLMs through stacked Graph-Text Fusion Units. Each unit allows for mutual attention between textual and structural representations, enabling information to flow in both directions, text influencing structure and structure guiding textual interpretation. The proposed architecture is trained using parameter-efficient fine-tuning (LoRA), keeping the LLM frozen while adapting to task-specific signals. Extensive experiments on five benchmark datasets demonstrate that BiGTex achieves state-of-the-art performance in node classification and generalizes effectively to link prediction. An ablation study further highlights the importance of soft prompting and bi-directional attention in the model's success.
Temporal Graph Networks (TGNs) have demonstrated significant success in dynamic graph tasks such as link prediction and node classification. Both tasks comprise transductive settings, where the model predicts links among known nodes, and in inductive settings, where it generalises learned patterns to previously unseen nodes. Existing TGN designs face a dilemma under these dual scenarios. Anonymous TGNs, which rely solely on temporal and structural information, offer strong inductive generalisation but struggle to distinguish known nodes. In contrast, non-anonymous TGNs leverage node features to excel in transductive tasks yet fail to adapt to new nodes. To address this challenge, we propose Trajectory Encoding TGN (TETGN). Our approach introduces automatically expandable node identifiers (IDs) as learnable temporal positional features and performs message passing over these IDs to capture each node's historical context. By integrating this trajectory-aware module with a standard TGN using multi-head attention, TETGN effectively balances transductive accuracy with inductive generalisation. Experimental results on three real-world datasets show that TETGN significantly outperforms strong baselines on both link prediction and node classification tasks, demonstrating its ability to unify the advantages of anonymous and non-anonymous models for dynamic graph learning.