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While tokenized graph Transformers have demonstrated strong performance in node classification tasks, their reliance on a limited subset of nodes with high similarity scores for constructing token sequences overlooks valuable information…

Machine Learning · Computer Science 2025-02-18 Jinsong Chen , Hanpeng Liu , John E. Hopcroft , Kun He

Graph Transformers have garnered significant attention for learning graph-structured data, thanks to their superb ability to capture long-range dependencies among nodes. However, the quadratic space and time complexity hinders the…

Information Retrieval · Computer Science 2024-05-08 Huiyuan Chen , Zhe Xu , Chin-Chia Michael Yeh , Vivian Lai , Yan Zheng , Minghua Xu , Hanghang Tong

Single-cell RNA sequencing (scRNA-seq) reveals cell heterogeneity, with cell clustering playing a key role in identifying cell types and marker genes. Recent advances, especially graph neural networks (GNNs)-based methods, have…

Genomics · Quantitative Biology 2025-10-03 Ping Xu , Zhiyuan Ning , Pengjiang Li , Wenhao Liu , Pengyang Wang , Jiaxu Cui , Yuanchun Zhou , Pengfei Wang

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

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

Clustering is a fundamental task in data analysis. Recently, deep clustering, which derives inspiration primarily from deep learning approaches, achieves state-of-the-art performance and has attracted considerable attention. Current deep…

Machine Learning · Computer Science 2020-02-13 Deyu Bo , Xiao Wang , Chuan Shi , Meiqi Zhu , Emiao Lu , Peng Cui

As the core building block of vision transformers, attention is a powerful tool to capture long-range dependency. However, such power comes at a cost: it incurs a huge computation burden and heavy memory footprint as pairwise token…

Computer Vision and Pattern Recognition · Computer Science 2023-03-16 Lei Zhu , Xinjiang Wang , Zhanghan Ke , Wayne Zhang , Rynson Lau

Transformers have shown dominant performance across a range of domains including language and vision. However, their computational cost grows quadratically with the sequence length, making their usage prohibitive for resource-constrained…

Computation and Language · Computer Science 2023-10-24 Yinghan Long , Sayeed Shafayet Chowdhury , Kaushik Roy

Recently, Graph Transformers have emerged as a promising solution to alleviate the inherent limitations of Graph Neural Networks (GNNs) and enhance graph representation performance. Unfortunately, Graph Transformers are computationally…

Neural and Evolutionary Computing · Computer Science 2024-03-26 Yundong Sun , Dongjie Zhu , Yansong Wang , Zhaoshuo Tian , Ning Cao , Gregory O'Hared

Transformer has been popular in recent crowd counting work since it breaks the limited receptive field of traditional CNNs. However, since crowd images always contain a large number of similar patches, the self-attention mechanism in…

Computer Vision and Pattern Recognition · Computer Science 2024-01-09 Hui Lin , Zhiheng Ma , Xiaopeng Hong , Qinnan Shangguan , Deyu Meng

Recent advances in deep learning have established Transformer architectures as the predominant modeling paradigm. Central to the success of Transformers is the self-attention mechanism, which scores the similarity between query and key…

Machine Learning · Computer Science 2025-03-05 Jie Zhang , Mao-Hsuan Mao , Bo-Wei Chiu , Min-Te Sun

Graph convolutional networks (GCNs) have been widely used and achieved remarkable results in skeleton-based action recognition. We think the key to skeleton-based action recognition is a skeleton hanging in frames, so we focus on how the…

Computer Vision and Pattern Recognition · Computer Science 2023-12-07 Nguyen Huu Bao Long

Graph transformer has been proven as an effective graph learning method for its adoption of attention mechanism that is capable of capturing expressive representations from complex topological and feature information of graphs. Graph…

Machine Learning · Computer Science 2024-03-26 Dongqi Fu , Zhigang Hua , Yan Xie , Jin Fang , Si Zhang , Kaan Sancak , Hao Wu , Andrey Malevich , Jingrui He , Bo Long

Transformers have achieved remarkable performance in a myriad of fields including natural language processing and computer vision. However, when it comes to the graph mining area, where graph neural network (GNN) has been the dominant…

Machine Learning · Computer Science 2021-10-26 Jianan Zhao , Chaozhuo Li , Qianlong Wen , Yiqi Wang , Yuming Liu , Hao Sun , Xing Xie , Yanfang Ye

Accurate cell type annotation is a crucial step in analyzing single-cell RNA sequencing (scRNA-seq) data, which provides valuable insights into cellular heterogeneity. However, due to the high dimensionality and prevalence of zero elements…

Machine Learning · Computer Science 2025-08-14 Huifa Li , Jie Fu , Xinlin Zhuang , Haolin Yang , Xinpeng Ling , Tong Cheng , Haochen xue , Imran Razzak , Zhili Chen

Clustering high-dimensional multivariate spatiotemporal climate data is challenging due to complex temporal dependencies, evolving spatial interactions, and non-stationary dynamics. Conventional clustering methods, including recurrent and…

Machine Learning · Computer Science 2025-09-17 Francis Ndikum Nji , Vandana Janaja , Jianwu Wang

Graph neural networks have been extensively studied for learning with inter-connected data. Despite this, recent evidence has revealed GNNs' deficiencies related to over-squashing, heterophily, handling long-range dependencies, edge…

Machine Learning · Computer Science 2023-06-16 Qitian Wu , Wentao Zhao , Zenan Li , David Wipf , Junchi Yan

Transformers have become widely used in various tasks, such as natural language processing and machine vision. This paper proposes Gransformer, an algorithm based on Transformer for generating graphs. We modify the Transformer encoder to…

Machine Learning · Computer Science 2024-06-03 Ahmad Khajenezhad , Seyed Ali Osia , Mahmood Karimian , Hamid Beigy

Single-cell RNA sequencing (scRNA-seq) enables dissecting cellular heterogeneity in tissues, resulting in numerous biological discoveries. Various computational methods have been devised to delineate cell types by clustering scRNA-seq data…

Quantitative Methods · Quantitative Biology 2023-09-18 Tram Huynh , Zixuan Cang

Spectral Graph Neural Networks have demonstrated superior performance in graph representation learning. However, many current methods focus on employing shared polynomial coefficients for all nodes, i.e., learning node-unified filters,…

Machine Learning · Computer Science 2024-07-22 Jiahong Ma , Mingguo He , Zhewei Wei