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We propose a symmetric graph convolutional autoencoder which produces a low-dimensional latent representation from a graph. In contrast to the existing graph autoencoders with asymmetric decoder parts, the proposed autoencoder has a newly…

Machine Learning · Computer Science 2019-08-08 Jiwoong Park , Minsik Lee , Hyung Jin Chang , Kyuewang Lee , Jin Young Choi

Several graph data mining, signal processing, and machine learning downstream tasks rely on information related to the eigenvectors of the associated adjacency or Laplacian matrix. Classical eigendecomposition methods are powerful when the…

Machine Learning · Statistics 2026-03-23 Mohammad Eini , Abdullah Karaaslanli , Vassilis Kalantzis , Panagiotis A. Traganitis

Point forecasting for graph-structured multivariate time series is a fundamental problem, but rigorous uncertainty quantification for such predictions is still underexplored. Conformal prediction (CP) offers uncertainty estimation with a…

Machine Learning · Computer Science 2026-05-07 Ruichao Guo , Xingyao Han , Luo Wenshui , Zhe Liu , Chen Gong , Hesheng Wang

The adoption of Transformer-based architectures in the medical domain is growing rapidly. In medical imaging, the analysis of complex shapes - such as organs, tissues, or other anatomical structures - combined with the often anisotropic…

Computer Vision and Pattern Recognition · Computer Science 2025-09-03 Nabil Jabareen , Dongsheng Yuan , Dingming Liu , Foo-Wei Ten , Sören Lukassen

Positional Encodings (PEs) are used to inject word-order information into transformer-based language models. While they can significantly enhance the quality of sentence representations, their specific contribution to language models is not…

Computation and Language · Computer Science 2023-10-20 Lihu Chen , Gaël Varoquaux , Fabian M. Suchanek

Recent advancements in large-scale pre-training have shown the potential to learn generalizable representations for downstream tasks. In the graph domain, however, capturing and transferring structural information across different graph…

Machine Learning · Computer Science 2026-02-24 Jialin Chen , Haolan Zuo , Haoyu Peter Wang , Siqi Miao , Pan Li , Rex Ying

Graph diffusion problems such as the propagation of rumors, computer viruses, or smart grid failures are ubiquitous and societal. Hence it is usually crucial to identify diffusion sources according to the current graph diffusion…

Machine Learning · Computer Science 2022-06-27 Chen Ling , Junji Jiang , Junxiang Wang , Liang Zhao

Graph representation learning is a fundamental research theme and can be generalized to benefit multiple downstream tasks from the node and link levels to the higher graph level. In practice, it is desirable to develop task-agnostic general…

Machine Learning · Computer Science 2023-12-12 Hanxuan Yang , Qingchao Kong , Wenji Mao

Cycles are fundamental elements in graph-structured data and have demonstrated their effectiveness in enhancing graph learning models. To encode such information into a graph learning framework, prior works often extract a summary quantity,…

Machine Learning · Computer Science 2023-12-01 Zuoyu Yan , Tengfei Ma , Liangcai Gao , Zhi Tang , Chao Chen , Yusu Wang

Implicit neural representations (INRs) are increasingly being used as tools to map coordinates to signals, encompassing applications from neural fields to texture compression, shape representations, and beyond. Most INR methods are based on…

Computer Vision and Pattern Recognition · Computer Science 2026-04-28 Guillaume Perez , Janarbek Matai , Takahiro Harada

Positional encoding has become a standard component in graph learning, especially for graph Transformers and other models that must distinguish structurally similar nodes, yet its fundamental identifiability remains poorly understood. In…

Information Theory · Computer Science 2026-03-27 Zimo Yan , Zheng Xie , Chang Liu , Yiqin Lv , Runfan Duan

Transformers rely on both content-based and position-based addressing mechanisms to make predictions, but existing positional encoding techniques often diminish the effectiveness of position-based addressing. Many current methods enforce…

Computation and Language · Computer Science 2025-08-22 Jiajun Zhu , Peihao Wang , Ruisi Cai , Jason D. Lee , Pan Li , Zhangyang Wang

Positional encoding (PE) is a core architectural component of Transformers, yet its impact on the Transformer's generalization and robustness remains unclear. In this work, we provide the first generalization analysis for a single-layer…

Machine Learning · Statistics 2026-03-25 Weiyi He , Yue Xing

Generating learning-friendly representations for points in a 2D space is a fundamental and long-standing problem in machine learning. Recently, multi-scale encoding schemes (such as Space2Vec) were proposed to directly encode any point in…

Computer Vision and Pattern Recognition · Computer Science 2022-01-26 Gengchen Mai , Yao Xuan , Wenyun Zuo , Krzysztof Janowicz , Ni Lao

We introduce a novel positional encoding strategy for Transformer-style models, addressing the shortcomings of existing, often ad hoc, approaches. Our framework provides a flexible mapping from the algebraic specification of a domain to an…

Machine Learning · Computer Science 2024-11-01 Konstantinos Kogkalidis , Jean-Philippe Bernardy , Vikas Garg

Fourier features based positional encoding (PE) is commonly used in machine learning tasks that involve learning high-frequency features from low-dimensional inputs, such as 3D view synthesis and time series regression with neural tangent…

Machine Learning · Computer Science 2024-07-18 Chuanhao Sun , Zhihang Yuan , Kai Xu , Luo Mai , N. Siddharth , Shuo Chen , Mahesh K. Marina

Since self-attention layers in Transformers are permutation invariant by design, positional encodings must be explicitly incorporated to enable spatial understanding. However, fixed-size lookup tables used in traditional learnable position…

Machine Learning · Computer Science 2025-06-18 Huayang Li , Yahui Liu , Hongyu Sun , Deng Cai , Leyang Cui , Wei Bi , Peilin Zhao , Taro Watanabe

Masked graph autoencoder (MGAE) has emerged as a promising self-supervised graph pre-training (SGP) paradigm due to its simplicity and effectiveness. However, existing efforts perform the mask-then-reconstruct operation in the raw data…

Machine Learning · Computer Science 2023-04-07 Wenxuan Tu , Qing Liao , Sihang Zhou , Xin Peng , Chuan Ma , Zhe Liu , Xinwang Liu , Zhiping Cai

Characterizing the long term behavior of dynamical systems given limited measurements is a common challenge throughout the physical and biological sciences. This is a challenging task due to the sparsity and noise inherent to empirical…

Machine Learning · Computer Science 2026-03-10 Roy Friedman , Noa Moriel , Matthew Ricci , Guy Pelc , Yair Weiss , Mor Nitzan

Attributed graph embedding, which learns vector representations from graph topology and node features, is a challenging task for graph analysis. Recently, methods based on graph convolutional networks (GCNs) have made great progress on this…

Machine Learning · Computer Science 2020-07-06 Ganqu Cui , Jie Zhou , Cheng Yang , Zhiyuan Liu