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Positional encodings (PEs) are essential for building powerful and expressive graph neural networks and graph transformers, as they effectively capture the relative spatial relationships between nodes. Although extensive research has been…

Machine Learning · Computer Science 2026-03-16 Yinan Huang , Haoyu Wang , Pan Li

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

We study the extent to which rotary position encodings (RoPE), a recent transformer position encoding algorithm broadly adopted in large language models (LLMs) and vision transformers (ViTs), can be applied to graph-structured data. We find…

Graph neural networks (GNNs) largely rely on the message-passing paradigm, where nodes iteratively aggregate information from their neighbors. Yet, standard message passing neural networks (MPNNs) face well-documented theoretical and…

Machine Learning · Computer Science 2026-05-15 Juan Amboage , Ernst Röell , Patrick Schnider , Bastian Rieck

Length generalization, the ability to generalize from small training context sizes to larger ones, is a critical challenge in the development of Transformer-based language models. Positional encoding (PE) has been identified as a major…

Computation and Language · Computer Science 2023-11-08 Amirhossein Kazemnejad , Inkit Padhi , Karthikeyan Natesan Ramamurthy , Payel Das , Siva Reddy

Transformers rely on positional encoding to compensate for the inherent permutation invariance of self-attention. Traditional approaches use absolute sinusoidal embeddings or learned positional vectors, while more recent methods emphasize…

Machine Learning · Computer Science 2025-11-18 Chase van de Geijn , Ayush Paliwal , Timo Lüddecke , Alexander S. Ecker

Relative position encoding (RPE) is important for transformer to capture sequence ordering of input tokens. General efficacy has been proven in natural language processing. However, in computer vision, its efficacy is not well studied and…

Computer Vision and Pattern Recognition · Computer Science 2021-07-30 Kan Wu , Houwen Peng , Minghao Chen , Jianlong Fu , Hongyang Chao

Position encoding is the primary mechanism which induces notion of sequential order for input tokens in transformer architectures. Even though this formulation in the original transformer paper has yielded plausible performance for general…

Computation and Language · Computer Science 2023-10-10 Eren Unlu

There are several improvements proposed over the baseline Absolute Positional Encoding (APE) method used in original transformer. In this study, we aim to investigate the implications of inadequately representing positional encoding in…

Computation and Language · Computer Science 2024-05-09 Arpit Aggarwal

The development of effective explainability tools for Transformers is a crucial pursuit in deep learning research. One of the most promising approaches in this domain is Layer-wise Relevance Propagation (LRP), which propagates relevance…

Machine Learning · Computer Science 2025-06-04 Yarden Bakish , Itamar Zimerman , Hila Chefer , Lior Wolf

A current goal in the graph neural network literature is to enable transformers to operate on graph-structured data, given their success on language and vision tasks. Since the transformer's original sinusoidal positional encodings (PEs)…

Machine Learning · Computer Science 2023-04-11 Patrick Soga , David Chiang

Rotary Positional Encodings (RoPE) have emerged as a highly effective technique for one-dimensional sequences in Natural Language Processing spurring recent progress towards generalizing RoPE to higher-dimensional data such as images and…

Computer Vision and Pattern Recognition · Computer Science 2025-11-12 Chase van de Geijn , Timo Lüddecke , Polina Turishcheva , Alexander S. Ecker

The attention mechanism in a Transformer architecture matches key to query based on both content -- the what -- and position in a sequence -- the where. We present an analysis indicating that what and where are entangled in the popular RoPE…

Machine Learning · Computer Science 2025-12-24 Anand Gopalakrishnan , Robert Csordás , Jürgen Schmidhuber , Michael C. Mozer

Rotary Positional Embedding (RoPE) is a common choice in transformer architectures for encoding relative positional information. Although earlier work has examined omitting RoPE in specific layers, the effect of varying the fraction of…

Machine Learning · Computer Science 2026-03-13 Mohammad Aflah Khan , Krishna P. Gummadi , Manish Gupta , Abhilasha Ravichander

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

Recent neural heuristics for the Vehicle Routing Problem (VRP) primarily rely on node coordinates as input, which may be less effective in practical scenarios where real cost metrics-such as edge-based distances-are more relevant. To…

Machine Learning · Computer Science 2025-06-23 Dian Meng , Zhiguang Cao , Yaoxin Wu , Yaqing Hou , Hongwei Ge , Qiang Zhang

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

In transformers, the positional encoding (PE) provides essential information that distinguishes the position and order amongst tokens in a sequence. Most prior investigations of PE effects on generalization were tailored to 1D input…

Machine Learning · Computer Science 2025-06-24 Takuya Ito , Luca Cocchi , Tim Klinger , Parikshit Ram , Murray Campbell , Luke Hearne

Understanding spatial location and relationships is a fundamental capability for modern artificial intelligence systems. Insights from human spatial cognition provide valuable guidance in this domain. Neuroscientific discoveries have…

Neural and Evolutionary Computing · Computer Science 2024-09-17 Boyang Li , Yulin Wu , Nuoxian Huang , Wenjia Zhang

Finding a feasible and prompt solution to the Vehicle Routing Problem (VRP) is a prerequisite for efficient freight transportation, seamless logistics, and sustainable mobility. Traditional optimization methods reach their limits when…

Machine Learning · Computer Science 2024-11-08 Elija Deineko , Carina Kehrt