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Graph neural networks (GNNs) are prominent for their effectiveness in processing graph data for semi-supervised node classification tasks. Most works of GNNs assume that the observed structure accurately represents the underlying node…

Machine Learning · Computer Science 2024-11-08 Shuangjie Li , Jiangqing Song , Baoming Zhang , Gaoli Ruan , Junyuan Xie , Chongjun Wang

Recently, graph neural networks (GNNs) have been shown powerful capacity at modeling structural data. However, when adapted to downstream tasks, it usually requires abundant task-specific labeled data, which can be extremely scarce in…

Machine Learning · Computer Science 2022-03-04 Yupeng Hou , Binbin Hu , Wayne Xin Zhao , Zhiqiang Zhang , Jun Zhou , Ji-Rong Wen

While Graph Neural Network (GNN) has shown superiority in learning node representations of homogeneous graphs, leveraging GNN on heterogeneous graphs remains a challenging problem. The dominating reason is that GNN learns node…

Social and Information Networks · Computer Science 2020-09-22 Ziyue Qiao , Pengyang Wang , Yanjie Fu , Yi Du , Pengfei Wang , Yuanchun Zhou

Graphs neural networks (GNNs) learn node features by aggregating and combining neighbor information, which have achieved promising performance on many graph tasks. However, GNNs are mostly treated as black-boxes and lack human intelligible…

Machine Learning · Computer Science 2020-06-05 Hao Yuan , Jiliang Tang , Xia Hu , Shuiwang Ji

Machine learning (ML) has been increasingly applied in concrete research to optimize performance and mixture design. However, one major challenge in applying ML to cementitious materials is the limited size and diversity of available…

Computational Engineering, Finance, and Science · Computer Science 2025-12-18 Mahmuda Sharmin , Taihao Han , Jie Huang , Narayanan Neithalath , Gaurav Sant , Aditya Kumar

Graph neural networks (GNNs) have attracted much attention due to their ability to leverage the intrinsic geometries of the underlying data. Although many different types of GNN models have been developed, with many benchmarking procedures…

Despite the recent success of graph neural networks (GNN), common architectures often exhibit significant limitations, including sensitivity to oversmoothing, long-range dependencies, and spurious edges, e.g., as can occur as a result of…

Machine Learning · Computer Science 2021-12-06 Yongyi Yang , Tang Liu , Yangkun Wang , Jinjing Zhou , Quan Gan , Zhewei Wei , Zheng Zhang , Zengfeng Huang , David Wipf

Graphs are a powerful data structure to represent relational data and are widely used to describe complex real-world data structures. Probabilistic Graphical Models (PGMs) have been well-developed in the past years to mathematically model…

Artificial Intelligence · Computer Science 2023-01-31 Chenqing Hua , Sitao Luan , Qian Zhang , Jie Fu

Graph neural networks (GNNs) have emerged as a powerful tool for graph classification and representation learning. However, GNNs tend to suffer from over-smoothing problems and are vulnerable to graph perturbations. To address these…

Machine Learning · Computer Science 2021-11-01 Yuzhou Chen , Baris Coskunuzer , Yulia R. Gel

Unraveling the complexities of Gene Regulatory Networks (GRNs) is crucial for understanding cellular processes and disease mechanisms. Traditional computational methods often struggle with the dynamic nature of these networks. This study…

Machine Learning · Computer Science 2025-03-04 Hakan T. Otal , Abdulhamit Subasi , Furkan Kurt , M. Abdullah Canbaz , Yasin Uzun

This paper presents a novel graph-based deep learning model for tasks involving relations between two nodes (edge-centric tasks), where the focus lies on predicting relationships and interactions between pairs of nodes rather than node…

Machine Learning · Computer Science 2025-07-08 Eugenio Borzone , Leandro Di Persia , Matias Gerard

Graph Neural Networks (GNN) have emerged as a popular and standard approach for learning from graph-structured data. The literature on GNN highlights the potential of this evolving research area and its widespread adoption in real-life…

Machine Learning · Computer Science 2024-03-25 Sukhdeep Singh , Anuj Sharma , Vinod Kumar Chauhan

Graph Neural Networks (GNNs) have excelled in predicting graph properties in various applications ranging from identifying trends in social networks to drug discovery and malware detection. With the abundance of new architectures and…

Machine Learning · Computer Science 2024-06-06 Roya Aliakbarisani , Robert Jankowski , M. Ángeles Serrano , Marián Boguñá

Graph representation of structured data can facilitate the extraction of stereoscopic features, and it has demonstrated excellent ability when working with deep learning systems, the so-called Graph Neural Networks (GNNs). Choosing a…

Machine Learning · Computer Science 2021-01-27 Yingfang Yuan , Wenjun Wang , George M. Coghill , Wei Pang

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive…

Biomolecules · Quantitative Biology 2025-06-10 Odin Zhang , Haitao Lin , Xujun Zhang , Xiaorui Wang , Zhenxing Wu , Qing Ye , Weibo Zhao , Jike Wang , Kejun Ying , Yu Kang , Chang-yu Hsieh , Tingjun Hou

We study a recent class of models which uses graph neural networks (GNNs) to improve forecasting in multivariate time series. The core assumption behind these models is that there is a latent graph between the time series (nodes) that…

Data selection methods, such as active learning and core-set selection, are useful tools for improving the data efficiency of deep learning models on large-scale datasets. However, recent deep learning models have moved forward from…

Machine Learning · Computer Science 2021-08-03 Wentao Zhang , Zhi Yang , Yexin Wang , Yu Shen , Yang Li , Liang Wang , Bin Cui

We propose an end-to-end framework based on a Graph Neural Network (GNN) to balance the power flows in energy grids. The balancing is framed as a supervised vertex regression task, where the GNN is trained to predict the current and power…

Machine Learning · Computer Science 2022-08-15 Jonas Berg Hansen , Stian Normann Anfinsen , Filippo Maria Bianchi

Graph neural network (GNN)'s success in graph classification is closely related to the Weisfeiler-Lehman (1-WL) algorithm. By iteratively aggregating neighboring node features to a center node, both 1-WL and GNN obtain a node representation…

Machine Learning · Computer Science 2021-10-27 Muhan Zhang , Pan Li

Graph Neural Networks (GNNs) have emerged as powerful tools for predicting outcomes in graph-structured data. However, a notable limitation of GNNs is their inability to provide robust uncertainty estimates, which undermines their…

Machine Learning · Computer Science 2024-10-10 S. Akansha