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The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…

机器学习 · 计算机科学 2025-04-25 Binon Teji , Swarup Roy

Recently, graph neural networks (GNNs) have been widely used for document classification. However, most existing methods are based on static word co-occurrence graphs without sentence-level information, which poses three challenges:(1) word…

计算与语言 · 计算机科学 2022-03-22 Yinhua Piao , Sangseon Lee , Dohoon Lee , Sun Kim

Understanding the behavior of a trained network and finding explanations for its outputs is important for improving the network's performance and generalization ability, and for ensuring trust in automated systems. Several approaches have…

计算与语言 · 计算机科学 2018-08-30 Madhumita Sushil , Simon Šuster , Walter Daelemans

Graph representation learning based on graph neural networks (GNNs) can greatly improve the performance of downstream tasks, such as node and graph classification. However, the general GNN models do not aggregate node information in a…

机器学习 · 计算机科学 2020-07-30 Fei Ding , Xiaohong Zhang , Justin Sybrandt , Ilya Safro

We study the problem of embedding edgeless nodes such as users who newly enter the underlying network, while using graph neural networks (GNNs) widely studied for effective representation learning of graphs. Our study is motivated by the…

社会与信息网络 · 计算机科学 2022-11-01 Yong-Min Shin , Cong Tran , Won-Yong Shin , Xin Cao

Link prediction for knowledge graphs aims to predict missing connections between entities. Prevailing methods are limited to a transductive setting and hard to process unseen entities. The recent proposed subgraph-based models provided…

机器学习 · 计算机科学 2021-08-03 Shuangjia Zheng , Sijie Mai , Ya Sun , Haifeng Hu , Yuedong Yang

Relation prediction for knowledge graphs aims at predicting missing relationships between entities. Despite the importance of inductive relation prediction, most previous works are limited to a transductive setting and cannot process…

人工智能 · 计算机科学 2021-07-27 Sijie Mai , Shuangjia Zheng , Yuedong Yang , Haifeng Hu

The advent of the "pre-train, prompt" paradigm has recently extended its generalization ability and data efficiency to graph representation learning, following its achievements in Natural Language Processing (NLP). Initial graph prompt…

机器学习 · 计算机科学 2025-01-20 Jiapeng Zhu , Zichen Ding , Jianxiang Yu , Jiaqi Tan , Xiang Li , Weining Qian

Graphs have become an important modeling tool for web applications, and Graph Neural Networks (GNNs) have achieved great success in graph representation learning. However, the performance of traditional GNNs heavily relies on a large amount…

机器学习 · 计算机科学 2024-06-05 Chenghua Gong , Xiang Li , Jianxiang Yu , Cheng Yao , Jiaqi Tan , Chengcheng Yu

Signed Graph Neural Networks (SGNNs) are widely adopted to analyze complex patterns in signed graphs with both positive and negative links. Given the noisy nature of real-world connections, the robustness of SGNN has also emerged as a…

机器学习 · 计算机科学 2025-10-28 Junran Wu , Beng Chin Ooi , Ke Xu

Link prediction on graphs is a fundamental problem. Subgraph representation learning approaches (SGRLs), by transforming link prediction to graph classification on the subgraphs around the links, have achieved state-of-the-art performance…

机器学习 · 计算机科学 2024-10-21 Paul Louis , Shweta Ann Jacob , Amirali Salehi-Abari

Graph Neural Networks (GNNs) have garnered widespread attention for their potential to address the challenges posed by graph representation learning, which face complex graph-structured data across various domains. However, due to the…

机器学习 · 计算机科学 2024-08-23 Hang Gao , Jiaguo Yuan , Jiangmeng Li , Peng Qiao , Fengge Wu , Changwen Zheng , Huaping Liu

We propose a novel model-level GNN explanation framework that shifts the explanation target from class-wise rule extraction to rule-based logit reconstruction. Our method recasts the graph-level readout of a pretrained GNN as a weighted…

机器学习 · 计算机科学 2026-05-13 Shengyao Lu , Jiuding Yang , Aedan J. DeFrates , Keith G. Mills , Baochun Li , Di Niu

Encoding facts as representations of entities and binary relationships between them, as learned by knowledge graph representation models, is useful for various tasks, including predicting new facts, question answering, fact checking and…

机器学习 · 计算机科学 2022-02-01 Ivana Balažević

Inductive link prediction -- where entities during training and inference stages can be different -- has been shown to be promising for completing continuously evolving knowledge graphs. Existing models of inductive reasoning mainly focus…

机器学习 · 计算机科学 2021-03-08 Jiajun Chen , Huarui He , Feng Wu , Jie Wang

Knowledge Graph(KG) has gained traction as a machine-readable organization of real-world knowledge for analytics using artificial intelligence systems. Graph Neural Network(GNN), is proven to be an effective KG embedding technique that…

机器学习 · 计算机科学 2026-02-24 Rajesh Rajagopalamenon , Unnikrishnan Cheramangalath

Reasoning on the knowledge graph (KG) aims to infer new facts from existing ones. Methods based on the relational path have shown strong, interpretable, and transferable reasoning ability. However, paths are naturally limited in capturing…

人工智能 · 计算机科学 2022-01-24 Yongqi Zhang , Quanming Yao

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…

机器学习 · 计算机科学 2023-12-19 Jing Zhu , Yuhang Zhou , Vassilis N. Ioannidis , Shengyi Qian , Wei Ai , Xiang Song , Danai Koutra

Graph Neural Networks (GNNs) have demonstrated remarkable proficiency in modeling data with graph structures, yet recent research reveals their susceptibility to adversarial attacks. Traditional attack methodologies, which rely on…

机器学习 · 计算机科学 2025-06-23 Wenlun Zhang , Enyan Dai , Kentaro Yoshioka

Despite the enormous success of graph neural networks (GNNs), most existing GNNs can only be applicable to undirected graphs where relationships among connected nodes are two-way symmetric (i.e., information can be passed back and forth).…

机器学习 · 计算机科学 2021-10-15 Zhuo Tan , Bin Liu , Guosheng Yin