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We propose a novel positional encoding for learning graph on Transformer architecture. Existing approaches either linearize a graph to encode absolute position in the sequence of nodes, or encode relative position with another node using…

Machine Learning · Computer Science 2022-10-17 Wonpyo Park , Woonggi Chang , Donggeon Lee , Juntae Kim , Seung-won Hwang

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

Graph Transformers (GTs) facilitate the comprehension of graph-structured data by calculating the self-attention of node pairs without considering node position information. To address this limitation, we introduce an innovative and…

Machine Learning · Computer Science 2023-12-12 Kushal Bose , Swagatam Das

Positional Encodings (PEs) are essential for injecting structural information into Graph Neural Networks (GNNs), particularly Graph Transformers, yet their empirical impact remains insufficiently understood. We introduce a unified…

Machine Learning · Computer Science 2026-01-15 Florian Grötschla , Jiaqing Xie , Roger Wattenhofer

Positional and structural encodings (PSE) enable better identifiability of nodes within a graph, rendering them essential tools for empowering modern GNNs, and in particular graph Transformers. However, designing PSEs that work optimally…

Positional encodings (PEs) are essential for effective graph representation learning because they provide position awareness in inherently position-agnostic transformer architectures and increase the expressive capacity of Graph Neural…

Machine Learning · Computer Science 2025-02-04 Charilaos I. Kanatsoulis , Evelyn Choi , Stephanie Jegelka , Jure Leskovec , Alejandro Ribeiro

Positional encoding plays a crucial role in transformers, significantly impacting model performance and length generalization. Prior research has introduced absolute positional encoding (APE) and relative positional encoding (RPE) to…

Computation and Language · Computer Science 2024-11-06 Chuanyang Zheng , Yihang Gao , Han Shi , Minbin Huang , Jingyao Li , Jing Xiong , Xiaozhe Ren , Michael Ng , Xin Jiang , Zhenguo Li , Yu Li

Relative Positional Encoding (RPE), which encodes the relative distance between any pair of tokens, is one of the most successful modifications to the original Transformer. As far as we know, theoretical understanding of the RPE-based…

Machine Learning · Computer Science 2022-10-31 Shengjie Luo , Shanda Li , Shuxin Zheng , Tie-Yan Liu , Liwei Wang , Di He

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

Without positional information, attention-based Transformer neural networks are permutation-invariant. Absolute or relative positional embeddings are the most popular ways to feed Transformer models with positional information. Absolute…

Machine Learning · Computer Science 2021-11-10 Tatiana Likhomanenko , Qiantong Xu , Gabriel Synnaeve , Ronan Collobert , Alex Rogozhnikov

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

Recent studies have demonstrated the effectiveness of position encoding in transformer architectures. By incorporating positional information, this approach provides essential guidance for modeling dependencies between elements across…

Machine Learning · Computer Science 2025-08-27 Avinash Amballa

Recent advances in Transformer models allow for unprecedented sequence lengths, due to linear space and time complexity. In the meantime, relative positional encoding (RPE) was proposed as beneficial for classical Transformers and consists…

Machine Learning · Computer Science 2021-06-11 Antoine Liutkus , Ondřej Cífka , Shih-Lun Wu , Umut Şimşekli , Yi-Hsuan Yang , Gaël Richard

Positional encoding (PE) underpins how permutation-invariant Transformers represent sequence order, yet how positional information is processed and stored remains poorly understood. Modern PE methods such as RoPE still struggle on tasks…

Computation and Language · Computer Science 2026-05-29 Pierre-Antoine Lequeu , Camille Barboule , Benjamin Piwowarski

We conducted empirical experiments to assess the transferability of a light curve transformer to datasets with different cadences and magnitude distributions using various positional encodings (PEs). We proposed a new approach to…

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

Transformer-based models have become the dominant paradigm for neural combinatorial optimization (NCO) of vehicle routing problems (VRPs), yet the role of positional encoding (PE) in these architectures remains largely unexplored. Unlike…

Recent advances in integrating positional and structural encodings (PSEs) into graph neural networks (GNNs) have significantly enhanced their performance across various graph learning tasks. However, the general applicability of these…

Machine Learning · Computer Science 2025-03-04 Billy Joe Franks , Moshe Eliasof , Semih Cantürk , Guy Wolf , Carola-Bibiane Schönlieb , Sophie Fellenz , Marius Kloft

An important aspect subtending language understanding and production is the ability to independently encode positional and symbolic information of the words within a sentence. In Transformers, positional information is typically encoded…

Machine Learning · Computer Science 2025-11-18 Felipe Urrutia , Jorge Salas , Alexander Kozachinskiy , Cristian Buc Calderon , Hector Pasten , Cristobal Rojas

Graph neural networks (GNNs) have become the standard learning architectures for graphs. GNNs have been applied to numerous domains ranging from quantum chemistry, recommender systems to knowledge graphs and natural language processing. A…

Machine Learning · Computer Science 2022-02-11 Vijay Prakash Dwivedi , Anh Tuan Luu , Thomas Laurent , Yoshua Bengio , Xavier Bresson
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