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Graph Neural Networks (GNNs) are the dominant architecture for molecular machine learning, particularly for molecular property prediction and machine learning interatomic potentials (MLIPs). GNNs perform message passing on predefined graphs…

Machine Learning · Computer Science 2025-10-03 Tobias Kreiman , Yutong Bai , Fadi Atieh , Elizabeth Weaver , Eric Qu , Aditi S. Krishnapriyan

Graph Neural Networks (GNNs) are an effective framework for representation learning of graphs. GNNs follow a neighborhood aggregation scheme, where the representation vector of a node is computed by recursively aggregating and transforming…

Machine Learning · Computer Science 2019-02-26 Keyulu Xu , Weihua Hu , Jure Leskovec , Stefanie Jegelka

Machine learning on graphs is an important and ubiquitous task with applications ranging from drug design to friendship recommendation in social networks. The primary challenge in this domain is finding a way to represent, or encode, graph…

Social and Information Networks · Computer Science 2018-04-11 William L. Hamilton , Rex Ying , Jure Leskovec

As powerful tools for representation learning on graphs, graph neural networks (GNNs) have facilitated various applications from drug discovery to recommender systems. Nevertheless, the effectiveness of GNNs is immensely challenged by…

Machine Learning · Computer Science 2023-02-28 Wei Jin , Tong Zhao , Jiayuan Ding , Yozen Liu , Jiliang Tang , Neil Shah

In the realm of Graph Neural Networks (GNNs), two exciting research directions have recently emerged: Subgraph GNNs and Graph Transformers. In this paper, we propose an architecture that integrates both approaches, dubbed Subgraphormer,…

Machine Learning · Computer Science 2024-05-29 Guy Bar-Shalom , Beatrice Bevilacqua , Haggai Maron

Graph Transformers (GTs) have demonstrated remarkable performance in graph representation learning over popular graph neural networks (GNNs). However, self--attention, the core module of GTs, preserves only low-frequency signals in graph…

Machine Learning · Computer Science 2025-05-30 Guoguo Ai , Guansong Pang , Hezhe Qiao , Yuan Gao , Hui Yan

Spectral graph neural networks (GNNs) learn graph representations via spectral-domain graph convolutions. However, most existing spectral graph filters are scalar-to-scalar functions, i.e., mapping a single eigenvalue to a single filtered…

Machine Learning · Computer Science 2023-03-03 Deyu Bo , Chuan Shi , Lele Wang , Renjie Liao

Transformers have been designed for channel acquisition tasks such as channel prediction and other tasks such as precoding, while graph neural networks (GNNs) have been demonstrated to be efficient for learning a multitude of communication…

Signal Processing · Electrical Eng. & Systems 2025-03-06 Yuxuan Duan , Jia Guo , Chenyang Yang

Transformers, adapted from natural language processing, are emerging as a leading approach for graph representation learning. Contemporary graph transformers often treat nodes or edges as separate tokens. This approach leads to…

Machine Learning · Computer Science 2023-10-04 Zihan Pengmei , Zimu Li , Chih-chan Tien , Risi Kondor , Aaron R. Dinner

Graph Neural Networks (GNNs) are widely used in graph data mining tasks. Traditional GNNs follow a message passing scheme that can effectively utilize local and structural information. However, the phenomena of over-smoothing and…

Machine Learning · Computer Science 2025-04-14 Zijie Zhou , Zhaoqi Lu , Xuekai Wei , Rongqin Chen , Shenghui Zhang , Pak Lon Ip , Leong Hou U

Transformers have attained outstanding performance across various modalities, owing to their simple but powerful scaled-dot-product (SDP) attention mechanisms. Researchers have attempted to migrate Transformers to graph learning, but most…

Machine Learning · Computer Science 2026-01-30 Liheng Ma , Soumyasundar Pal , Yingxue Zhang , Philip H. S. Torr , Mark Coates

Transformers serve as the backbone architectures of Foundational Models, where domain-specific tokenizers allow them to adapt to various domains. Graph Transformers (GTs) have recently emerged as leading models in geometric deep learning,…

Neural and Evolutionary Computing · Computer Science 2025-04-03 Limei Wang , Kaveh Hassani , Si Zhang , Dongqi Fu , Baichuan Yuan , Weilin Cong , Zhigang Hua , Hao Wu , Ning Yao , Bo Long

The success of a specific neural network architecture is closely tied to the dataset and task it tackles; there is no one-size-fits-all solution. Thus, considerable efforts have been made to quickly and accurately estimate the performances…

Machine Learning · Computer Science 2024-03-22 Dongyeong Hwang , Hyunju Kim , Sunwoo Kim , Kijung Shin

Graph Transformer (GT), as a special type of Graph Neural Networks (GNNs), utilizes multi-head attention to facilitate high-order message passing. However, this also imposes several limitations in node classification applications: 1) nodes…

Machine Learning · Computer Science 2024-10-16 Jiajun Zhou , Xuanze Chen , Chenxuan Xie , Yu Shanqing , Qi Xuan , Xiaoniu Yang

Recent advances in Graph Convolutional Neural Networks (GCNNs) have shown their efficiency for non-Euclidean data on graphs, which often require a large amount of labeled data with high cost. It it thus critical to learn graph feature…

Computer Vision and Pattern Recognition · Computer Science 2020-03-20 Xiang Gao , Wei Hu , Guo-Jun Qi

Graph Neural Networks (GNNs) have emerged as powerful tools for learning on graph-structured data, but often struggle to balance local and global information. While graph Transformers aim to address this by enabling long-range interactions,…

Machine Learning · Computer Science 2025-11-18 Jeongwhan Choi , Seungjun Park , Sumin Park , Sung-Bae Cho , Noseong Park

Graph Neural Networks (GNNs) have emerged as powerful tools for learning representations of graph-structured data, demonstrating remarkable performance across various tasks. Recognising their importance, there has been extensive research…

Machine Learning · Computer Science 2025-01-06 Akshit Sinha , Sreeram Vennam , Charu Sharma , Ponnurangam Kumaraguru

Proposing an effective and flexible matrix to represent a graph is a fundamental challenge that has been explored from multiple perspectives, e.g., filtering in Graph Fourier Transforms. In this work, we develop a novel and general…

Machine Learning · Computer Science 2023-05-11 Mingqi Yang , Wenjie Feng , Yanming Shen , Bryan Hooi

Graph Neural Networks (GNNs) have gained momentum in graph representation learning and boosted the state of the art in a variety of areas, such as data mining (\emph{e.g.,} social network analysis and recommender systems), computer vision…

Computer Vision and Pattern Recognition · Computer Science 2024-08-15 Chaoqi Chen , Yushuang Wu , Qiyuan Dai , Hong-Yu Zhou , Mutian Xu , Sibei Yang , Xiaoguang Han , Yizhou Yu

Graph Neural Networks (GNNs) have paved the way for being a cornerstone in graph-related learning tasks. Yet, the ability of GNNs to capture structural interactions within graphs remains under-explored. In this work, we address this gap by…

Machine Learning · Computer Science 2025-03-04 Asela Hevapathige , Qing Wang