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How to obtain informative representations of molecules is a crucial prerequisite in AI-driven drug design and discovery. Recent researches abstract molecules as graphs and employ Graph Neural Networks (GNNs) for molecular representation…

Biomolecules · Quantitative Biology 2020-10-30 Yu Rong , Yatao Bian , Tingyang Xu , Weiyang Xie , Ying Wei , Wenbing Huang , Junzhou Huang

Graph Neural Networks (GNN) are indispensable in learning from graph-structured data, yet their rising computational costs, especially on massively connected graphs, pose significant challenges in terms of execution performance. To tackle…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-11-05 Aishwarya Sarkar , Sayan Ghosh , Nathan R. Tallent , Ali Jannesari

Graph neural networks (GNNs) have been widely used in representation learning on graphs and achieved state-of-the-art performance in tasks such as node classification and link prediction. However, most existing GNNs are designed to learn…

Machine Learning · Computer Science 2020-02-06 Seongjun Yun , Minbyul Jeong , Raehyun Kim , Jaewoo Kang , Hyunwoo J. Kim

Modern microelectronic devices are composed of interfaces between a large number of materials, many of which are in amorphous or polycrystalline phases. Modeling such non-crystalline materials using first-principles methods such as density…

Materials Science · Physics 2023-10-12 Pratik Brahma , Krishnakumar Bhattaram , Sayeef Salahuddin

Due to a huge volume of information in many domains, the need for classification methods is imperious. In spite of many advances, most of the approaches require a large amount of labeled data, which is often not available, due to costs and…

Computer Vision and Pattern Recognition · Computer Science 2023-04-26 Lucas Pascotti Valem , Daniel Carlos Guimarães Pedronette , Longin Jan Latecki

Graph neural networks (GNNs) have been applied to a large variety of applications in materials science and chemistry. Here, we recapitulate the graph construction for crystalline (periodic) materials and investigate its impact on the GNNs…

Machine Learning · Computer Science 2023-08-10 Robin Ruff , Patrick Reiser , Jan Stühmer , Pascal Friederich

A long-standing goal in deep learning has been to characterize the learning behavior of black-box models in a more interpretable manner. For graph neural networks (GNNs), considerable advances have been made in formalizing what functions…

Machine Learning · Computer Science 2024-06-19 Chenxiao Yang , Qitian Wu , David Wipf , Ruoyu Sun , Junchi Yan

Semi-supervised node classification on graphs is an important research problem, with many real-world applications in information retrieval such as content classification on a social network and query intent classification on an e-commerce…

Machine Learning · Computer Science 2022-03-29 Zhihao Wen , Yuan Fang , Zemin Liu

Exploring the complex structure of the human brain is crucial for understanding its functionality and diagnosing brain disorders. Thanks to advancements in neuroimaging technology, a novel approach has emerged that involves modeling the…

Machine Learning · Computer Science 2024-06-06 Xuexiong Luo , Jia Wu , Jian Yang , Shan Xue , Amin Beheshti , Quan Z. Sheng , David McAlpine , Paul Sowman , Alexis Giral , Philip S. Yu

Graph neural networks have emerged as a powerful tool for learning spatiotemporal interactions. However, conventional approaches often rely on predefined graphs, which may obscure the precise relationships being modeled. Additionally,…

Machine Learning · Computer Science 2025-02-21 Jeehong Kim , Minchan Kim , Jaeseong Ju , Youngseok Hwang , Wonhee Lee , Hyunwoo Park

With the increasing demands of training graph neural networks (GNNs) on large-scale graphs, graph data condensation has emerged as a critical technique to relieve the storage and time costs during the training phase. It aims to condense the…

Machine Learning · Computer Science 2024-06-10 Zhanyu Liu , Chaolv Zeng , Guanjie Zheng

Graph Convolutional Networks(GCNs) play a crucial role in graph learning tasks, however, learning graph embedding with few supervised signals is still a difficult problem. In this paper, we propose a novel training algorithm for Graph…

Machine Learning · Computer Science 2020-02-21 Ke Sun , Zhouchen Lin , Zhanxing Zhu

Graph-structured data consisting of objects (i.e., nodes) and relationships among objects (i.e., edges) are ubiquitous. Graph-level learning is a matter of studying a collection of graphs instead of a single graph. Traditional graph-level…

Machine Learning · Computer Science 2022-06-01 Ge Zhang , Jia Wu , Jian Yang , Shan Xue , Wenbin Hu , Chuan Zhou , Hao Peng , Quan Z. Sheng , Charu Aggarwal

Graph Neural Networks (GNNs) have enjoyed wide spread applications in graph-structured data. However, existing graph based applications commonly lack annotated data. GNNs are required to learn latent patterns from a limited amount of…

Machine Learning · Computer Science 2023-03-22 Wenqi Wei , Mu Qiao , Divyesh Jadav

Nonlinear finite element crash simulations are accurate but computationally expensive, limiting their use in iterative design optimisation. Machine-learning surrogate models based on graph neural networks (GNNs) offer a faster alternative.…

Machine Learning · Computer Science 2026-05-18 Haoran Li , Tobias Lehrer , Yingxue Zhao , Haosu Zhou , Philipp Stocker , Tobias Pfaff , Nan Li

Many interesting problems in machine learning are being revisited with new deep learning tools. For graph-based semisupervised learning, a recent important development is graph convolutional networks (GCNs), which nicely integrate local…

Machine Learning · Computer Science 2018-01-24 Qimai Li , Zhichao Han , Xiao-Ming Wu

Graph Neural Networks (GNNs) combine node attributes over a fixed granularity of the local graph structure around a node to predict its label. However, different nodes may relate to a node-level property with a different granularity of its…

Machine Learning · Computer Science 2025-06-19 Kartik Sharma , Vineeth Rakesh , Yingtong Dou , Srijan Kumar , Mahashweta Das

Machine Learning surrogates for Computational Fluid Dynamics (CFD), particularly Graph Neural Networks (GNNs) and Transformers, have become a new important approach for accelerating physics simulations. However, we identify a critical…

Machine Learning · Computer Science 2026-05-05 Paul Garnier , Vincent Lannelongue , Elie Hachem

Graph neural networks have pushed state-of-the-arts in graph classifications recently. Typically, these methods are studied within the context of supervised end-to-end training, which necessities copious task-specific labels. However, in…

Machine Learning · Computer Science 2023-06-01 Xiao Luo , Yusheng Zhao , Yifang Qin , Wei Ju , Ming Zhang

Graph Neural Networks (GNNs) are widely adopted in advanced AI systems due to their capability of representation learning on graph data. Even though GNN explanation is crucial to increase user trust in the systems, it is challenging due to…

Machine Learning · Computer Science 2022-08-08 Tien-Cuong Bui , Wen-syan Li , Sang-Kyun Cha
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