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Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the…

机器学习 · 计算机科学 2024-04-19 Mingda Xu , Peisheng Qian , Ziyuan Zhao , Zeng Zeng , Jianguo Chen , Weide Liu , Xulei Yang

Graph neural networks (GNNs) are a class of effective deep learning models for node classification tasks; yet their predictive capability may be severely compromised under adversarially designed unnoticeable perturbations to the graph…

机器学习 · 计算机科学 2023-01-05 Xiao Zang , Jie Chen , Bo Yuan

Graph neural networks (GNN) have been ubiquitous in graph node classification tasks. Most of GNN methods update the node embedding iteratively by aggregating its neighbors' information. However, they often suffer from negative disturbance,…

机器学习 · 计算机科学 2022-02-02 Jie Chen , Shouzhen Chen , Mingyuan Bai , Jian Pu , Junping Zhang , Junbin Gao

Graph neural network (GNN) and label propagation algorithm (LPA) are both message passing algorithms, which have achieved superior performance in semi-supervised classification. GNN performs feature propagation by a neural network to make…

机器学习 · 计算机科学 2021-05-12 Yunsheng Shi , Zhengjie Huang , Shikun Feng , Hui Zhong , Wenjin Wang , Yu Sun

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model…

机器学习 · 计算机科学 2021-10-07 Jie Zhou , Ganqu Cui , Shengding Hu , Zhengyan Zhang , Cheng Yang , Zhiyuan Liu , Lifeng Wang , Changcheng Li , Maosong Sun

Graph Neural Networks (GNNs) have shown advantages in various graph-based applications. Most existing GNNs assume strong homophily of graph structure and apply permutation-invariant local aggregation of neighbors to learn a representation…

机器学习 · 计算机科学 2022-01-04 Tianmeng Yang , Yujing Wang , Zhihan Yue , Yaming Yang , Yunhai Tong , Jing Bai

Graph neural networks are emerging as continuation of deep learning success w.r.t. graph data. Tens of different graph neural network variants have been proposed, most following a neighborhood aggregation scheme, where the node features are…

机器学习 · 计算机科学 2021-02-09 Dawei Leng , Jinjiang Guo , Lurong Pan , Jie Li , Xinyu Wang

Scalable graph neural networks (GNNs) have emerged as a promising technique, which exhibits superior predictive performance and high running efficiency across numerous large-scale graph-based web applications. However, (i) Most scalable…

机器学习 · 计算机科学 2024-02-12 Xunkai Li , Jingyuan Ma , Zhengyu Wu , Daohan Su , Wentao Zhang , Rong-Hua Li , Guoren Wang

Graph Neural Networks have emerged as a useful tool to learn on the data by applying additional constraints based on the graph structure. These graphs are often created with assumed intrinsic relations between the entities. In recent years,…

机器学习 · 统计学 2021-05-18 Sunil Kumar Maurya , Xin Liu , Tsuyoshi Murata

Graph Neural Networks have become one of the indispensable tools to learn from graph-structured data, and their usefulness has been shown in wide variety of tasks. In recent years, there have been tremendous improvements in architecture…

机器学习 · 统计学 2021-11-15 Sunil Kumar Maurya , Xin Liu , Tsuyoshi Murata

Graph Neural Networks (GNNs) have received considerable attention on graph-structured data learning for a wide variety of tasks. The well-designed propagation mechanism which has been demonstrated effective is the most fundamental part of…

机器学习 · 计算机科学 2021-01-29 Meiqi Zhu , Xiao Wang , Chuan Shi , Houye Ji , Peng Cui

In representation learning on graph-structured data, many popular graph neural networks (GNNs) fail to capture long-range dependencies, leading to performance degradation. Furthermore, this weakness is magnified when the concerned graph is…

机器学习 · 计算机科学 2024-03-07 Mengying Jiang , Guizhong Liu , Yuanchao Su , Xinliang Wu

Graph neural networks (GNNs) have shown significant success in learning graph representations. However, recent studies reveal that GNNs often fail to outperform simple MLPs on heterophilous graph tasks, where connected nodes may differ in…

机器学习 · 计算机科学 2025-04-10 Songwei Zhao , Yuan Jiang , Zijing Zhang , Yang Yu , Hechang Chen

Graph neural networks (GNNs) are typically applied to static graphs that are assumed to be known upfront. This static input structure is often informed purely by insight of the machine learning practitioner, and might not be optimal for the…

Graph Convolutional Networks (GCNs) have been widely studied for compact data representation and semi-supervised learning tasks. However, existing GCNs usually use a fixed neighborhood graph which is not guaranteed to be optimal for…

计算机视觉与模式识别 · 计算机科学 2019-11-22 Bo Jiang , Leiling Wang , Jin Tang , Bin Luo

Graph Neural Network (GNN) has achieved remarkable success in various graph learning tasks, such as node classification, link prediction and graph classification. The key to the success of GNN lies in its effective structure information…

密码学与安全 · 计算机科学 2024-05-30 Peican Zhu , Zechen Pan , Keke Tang , Xiaodong Cui , Jinhuan Wang , Qi Xuan

While graph neural networks (GNNs) have gained popularity for learning circuit representations in various electronic design automation (EDA) tasks, they face challenges in scalability when applied to large graphs and exhibit limited…

机器学习 · 计算机科学 2024-04-12 Chenhui Deng , Zichao Yue , Cunxi Yu , Gokce Sarar , Ryan Carey , Rajeev Jain , Zhiru Zhang

Self-attention mechanism in graph neural networks (GNNs) led to state-of-the-art performance on many graph representation learning tasks. Currently, at every layer, attention is computed between connected pairs of nodes and depends solely…

机器学习 · 计算机科学 2021-08-27 Guangtao Wang , Rex Ying , Jing Huang , Jure Leskovec

The dominant paradigm for machine learning on graphs uses Message Passing Graph Neural Networks (MP-GNNs), in which node representations are updated by aggregating information in their local neighborhood. Recently, there have been…

机器学习 · 计算机科学 2023-03-02 Daniel Glickman , Eran Yahav

Graph neural networks (GNNs) have exhibited exceptional efficacy in a diverse array of applications. However, the sheer size of large-scale graphs presents a significant challenge to real-time inference with GNNs. Although existing Scalable…

机器学习 · 计算机科学 2023-12-13 Xinyi Gao , Wentao Zhang , Junliang Yu , Yingxia Shao , Quoc Viet Hung Nguyen , Bin Cui , Hongzhi Yin