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To alleviate the local receptive issue of GCN, Transformers have been exploited to capture the long range dependences of nodes for graph data representation and learning. However, existing graph Transformers generally employ regular…

Machine Learning · Computer Science 2023-05-15 Bo Jiang , Fei Xu , Ziyan Zhang , Jin Tang , Feiping Nie

The dominant graph-to-sequence transduction models employ graph neural networks for graph representation learning, where the structural information is reflected by the receptive field of neurons. Unlike graph neural networks that restrict…

Computation and Language · Computer Science 2019-12-03 Deng Cai , Wai Lam

Graph Transformers have recently attracted attention for molecular property prediction by combining the inductive biases of graph neural networks (GNNs) with the global receptive field of Transformers. However, many existing hybrid…

Machine Learning · Computer Science 2026-04-09 Yi Yang , Ovidiu Daescu

We propose the Graph2Graph Transformer architecture for conditioning on and predicting arbitrary graphs, and apply it to the challenging task of transition-based dependency parsing. After proposing two novel Transformer models of…

Computation and Language · Computer Science 2021-03-22 Alireza Mohammadshahi , James Henderson

Scene graph representations, which form a graph of visual object nodes together with their attributes and relations, have proved useful across a variety of vision and language applications. Recent work in the area has used Natural Language…

Computation and Language · Computer Science 2019-09-16 Martin Andrews , Yew Ken Chia , Sam Witteveen

For automotive applications, the Graph Attention Network (GAT) is a prominently used architecture to include relational information of a traffic scenario during feature embedding. As shown in this work, however, one of the most popular GAT…

Machine Learning · Computer Science 2023-05-26 Marion Neumeier , Andreas Tollkühn , Sebastian Dorn , Michael Botsch , Wolfgang Utschick

Graph representation learning (GRL) methods, such as graph neural networks and graph transformer models, have been successfully used to analyze graph-structured data, mainly focusing on node classification and link prediction tasks.…

Machine Learning · Computer Science 2023-08-21 Van Thuy Hoang , O-Joun Lee

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 foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared…

Machine Learning · Computer Science 2025-12-23 Heng Zhang , Tianyi Zhang , Yuling Shi , Xiaodong Gu , Yaomin Shen , Haochen You , Zijian Zhang , Yilei Yuan , Jin Huang

Graph Transformer shows remarkable potential in brain network analysis due to its ability to model graph structures and complex node relationships. Most existing methods typically model the brain as a flat network, ignoring its modular…

Machine Learning · Computer Science 2025-11-25 Jiajun Ma , Yongchao Zhang , Chao Zhang , Zhao Lv , Shengbing Pei

Incorporating prior knowledge can improve existing pre-training models in cloze-style machine reading and has become a new trend in recent studies. Notably, most of the existing models have integrated external knowledge graphs (KG) and…

Computation and Language · Computer Science 2023-09-25 Shima Foolad , Kourosh Kiani

Graph Neural Networks (GNNs) have been widely studied for graph data representation and learning. However, existing GNNs generally conduct context-aware learning on node feature representation only which usually ignores the learning of edge…

Machine Learning · Computer Science 2019-10-07 Bo Jiang , Leiling Wang , Jin Tang , Bin Luo

Learning to compute, the ability to model the functional behavior of a circuit graph, is a fundamental challenge for graph representation learning. Yet, the dominant paradigm is architecturally mismatched for this task. This flawed…

Artificial Intelligence · Computer Science 2026-02-10 Ziyang Zheng , Jiaying Zhu , Jingyi Zhou , Qiang Xu

By incorporating the graph structural information into Transformers, graph Transformers have exhibited promising performance for graph representation learning in recent years. Existing graph Transformers leverage specific strategies, such…

Machine Learning · Computer Science 2022-11-16 Gaichao Li , Jinsong Chen , Kun He

Knowledge graph reasoning plays a vital role in various applications and has garnered considerable attention. Recently, path-based methods have achieved impressive performance. However, they may face limitations stemming from constraints in…

Artificial Intelligence · Computer Science 2024-12-18 Junnan Liu , Qianren Mao , Weifeng Jiang , Jianxin Li

Graphs are widely used as a popular representation of the network structure of connected data. Graph data can be found in a broad spectrum of application domains such as social systems, ecosystems, biological networks, knowledge graphs, and…

Machine Learning · Computer Science 2021-05-04 Feng Xia , Ke Sun , Shuo Yu , Abdul Aziz , Liangtian Wan , Shirui Pan , Huan Liu

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

We propose the Quantum Graph Attention Network (QGAT), a hybrid graph neural network that integrates variational quantum circuits into the attention mechanism. At its core, QGAT employs strongly entangling quantum circuits with…

Machine Learning · Computer Science 2025-08-29 An Ning , Tai Yue Li , Nan Yow Chen

Graph Neural Networks (GNNs) have been successfully used in many problems involving graph-structured data, achieving state-of-the-art performance. GNNs typically employ a message-passing scheme, in which every node aggregates information…

Machine Learning · Computer Science 2022-11-22 Michail Chatzianastasis , Johannes F. Lutzeyer , George Dasoulas , Michalis Vazirgiannis

As the field of Graph Neural Networks (GNN) continues to grow, it experiences a corresponding increase in the need for large, real-world datasets to train and test new GNN models on challenging, realistic problems. Unfortunately, such graph…

Machine Learning · Computer Science 2023-06-12 Minji Yoon , Yue Wu , John Palowitch , Bryan Perozzi , Ruslan Salakhutdinov