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Link prediction is a fundamental problem in many graph based applications, such as protein-protein interaction prediction. Graph neural network (GNN) has recently been widely used for link prediction. However, existing GNN based link…

Machine Learning · Computer Science 2023-03-02 Kai-Lang Yao , Wu-Jun Li

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across…

Machine Learning · Computer Science 2023-10-10 Yu Wang , Tong Zhao , Yuying Zhao , Yunchao Liu , Xueqi Cheng , Neil Shah , Tyler Derr

Existing Graph Neural Networks (GNNs) usually assume a balanced situation where both the class distribution and the node degree distribution are balanced. However, in real-world situations, we often encounter cases where a few classes…

Machine Learning · Computer Science 2022-09-09 Sukwon Yun , Kibum Kim , Kanghoon Yoon , Chanyoung Park

Link Prediction (LP) is a crucial problem in graph-structured data. Graph Neural Networks (GNNs) have gained prominence in LP, with Graph AutoEncoders (GAEs) being a notable representation. However, our empirical findings reveal that GAEs'…

Machine Learning · Computer Science 2025-02-11 Yunhui Liu , Huaisong Zhang , Xinyi Gao , Liuye Guo , Zhen Tao , Tieke He

Inferring missing links or detecting spurious ones based on observed graphs, known as link prediction, is a long-standing challenge in graph data analysis. With the recent advances in deep learning, graph neural networks have been used for…

Social and Information Networks · Computer Science 2023-01-03 Xingping Xian , Tao Wu , Xiaoke Ma , Shaojie Qiao , Yabin Shao , Chao Wang , Lin Yuan , Yu Wu

Link prediction is a fundamental task in dynamic graph learning (DGL), inherently shaped by the topology of the DG. Recent advancements in dynamic graph neural networks (DGNN), primarily by modeling the relationships among nodes via a…

Machine Learning · Computer Science 2025-04-29 Ling Wang , Minglian Han

The message-passing mechanism underlying Graph Neural Networks (GNNs) is not naturally suited for heterophilic datasets, where adjacent nodes often have different labels. Most solutions to this problem remain confined to the task of node…

Machine Learning · Computer Science 2025-06-30 Andrea Giuseppe Di Francesco , Francesco Caso , Maria Sofia Bucarelli , Fabrizio Silvestri

Graph Neural Networks (GNNs) have shown exceptional performance in the task of link prediction. Despite their effectiveness, the high latency brought by non-trivial neighborhood data dependency limits GNNs in practical deployments.…

Machine Learning · Computer Science 2023-06-06 Zhichun Guo , William Shiao , Shichang Zhang , Yozen Liu , Nitesh V. Chawla , Neil Shah , Tong Zhao

Graph Neural Networks (GNNs) have achieved state-of-the-art performance in representation learning for graphs recently. However, the effectiveness of GNNs, which capitalize on the key operation of message propagation, highly depends on the…

Machine Learning · Computer Science 2023-08-16 Jie Liao , Jintang Li , Liang Chen , Bingzhe Wu , Yatao Bian , Zibin Zheng

Graph Convolutional Networks (GCNs) has demonstrated promising results for recommender systems, as they can effectively leverage high-order relationship. However, these methods usually encounter data sparsity issue in real-world scenarios.…

Information Retrieval · Computer Science 2023-09-21 Qian Zhao , Zhengwei Wu , Zhiqiang Zhang , Jun Zhou

User identity linkage (UIL), matching accounts of a person on different social networks, is a fundamental task in cross-network data mining. Recent works have achieved promising results by exploiting graph neural networks (GNNs) to capture…

Social and Information Networks · Computer Science 2023-08-11 Meixiu Long , Siyuan Chen , Xin Du , Jiahai Wang

Graph neural networks (GNNs) can learn effective node representations that significantly improve link prediction accuracy. However, most GNN-based link prediction algorithms are incompetent to predict weak ties connecting different…

Social and Information Networks · Computer Science 2024-10-22 Weiwei Gu , Linbi Lv , Gang Lu , Ruiqi Li

While Graph Neural Networks (GNNs) are remarkably successful in a variety of high-impact applications, we demonstrate that, in link prediction, the common practices of including the edges being predicted in the graph at training and/or test…

Machine Learning · Computer Science 2023-12-19 Jing Zhu , Yuhang Zhou , Vassilis N. Ioannidis , Shengyi Qian , Wei Ai , Xiang Song , Danai Koutra

Link prediction (LP), inferring the connectivity between nodes, is a significant research area in graph data, where a link represents essential information on relationships between nodes. Although graph neural network (GNN)-based models…

Machine Learning · Computer Science 2025-12-12 Junwon You , Eunwoo Heo , Jae-Hun Jung

Networks are ubiquitous in the real world. Link prediction, as one of the key problems for network-structured data, aims to predict whether there exists a link between two nodes. The traditional approaches are based on the explicit…

Machine Learning · Computer Science 2021-06-01 Wei Wu , Bin Li , Chuan Luo , Wolfgang Nejdl

Although Graph Neural Networks (GNNs) have become the dominant approach for graph representation learning, their performance on link prediction tasks does not always surpass that of traditional heuristic methods such as Common Neighbors and…

Social and Information Networks · Computer Science 2025-12-25 Lei Wang , Darong Lai

Protein function prediction may be framed as predicting subgraphs (with certain closure properties) of a directed acyclic graph describing the hierarchy of protein functions. Graph neural networks (GNNs), with their built-in inductive bias…

Machine Learning · Computer Science 2020-08-07 Stefan Spalević , Petar Veličković , Jovana Kovačević , Mladen Nikolić

Graph Neural Networks (GNNs) have attracted much attention due to their ability in learning representations from graph-structured data. Despite the successful applications of GNNs in many domains, the optimization of GNNs is less well…

Machine Learning · Computer Science 2023-09-06 Langzhang Liang , Zenglin Xu , Zixing Song , Irwin King , Yuan Qi , Jieping Ye

In this survey, we dive into Tabular Data Learning (TDL) using Graph Neural Networks (GNNs), a domain where deep learning-based approaches have increasingly shown superior performance in both classification and regression tasks compared to…

Machine Learning · Computer Science 2024-01-05 Cheng-Te Li , Yu-Che Tsai , Chih-Yao Chen , Jay Chiehen Liao

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…

Machine Learning · Computer Science 2025-06-27 Xin Huang , Chul-Ho Lee
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