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Positional Encoder Graph Neural Networks (PE-GNNs) are among the most effective models for learning from continuous spatial data. However, their predictive distributions are often poorly calibrated, limiting their utility in applications…

Most existing graph neural networks (GNNs) learn node embeddings using the framework of message passing and aggregation. Such GNNs are incapable of learning relative positions between graph nodes within a graph. To empower GNNs with the…

Machine Learning · Computer Science 2024-11-05 Zhenyue Qin , Yiqun Zhang Saeed Anwar , Dongwoo Kim , Yang Liu , Pan Ji , Tom Gedeon

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

Graph neural networks (GNNs) have emerged as a powerful framework for a wide range of node-level graph learning tasks. However, their performance typically depends on random or minimally informed initial feature representations, where poor…

Machine Learning · Computer Science 2026-02-24 Shiyu Chen , Cencheng Shen , Youngser Park , Carey E. Priebe

Learning representations of sets of nodes in a graph is crucial for applications ranging from node-role discovery to link prediction and molecule classification. Graph Neural Networks (GNNs) have achieved great success in graph…

Machine Learning · Computer Science 2020-10-30 Pan Li , Yanbang Wang , Hongwei Wang , Jure Leskovec

Supervised learning with tabular data presents unique challenges, including low data sizes, the absence of structural cues, and heterogeneous features spanning both categorical and continuous domains. Unlike vision and language tasks, where…

Machine Learning · Computer Science 2025-12-18 Yunze Leng , Rohan Ghosh , Mehul Motani

Graph Neural Networks (GNNs) have emerged as the de facto standard for modeling graph data, with attention mechanisms and transformers significantly enhancing their performance on graph-based tasks. Despite these advancements, the…

Machine Learning · Computer Science 2025-04-07 Nikhil Shivakumar Nayak

Incorporating spectral information to enhance Graph Neural Networks (GNNs) has shown promising results but raises a fundamental challenge due to the inherent ambiguity of eigenvectors. Various architectures have been proposed to address…

Machine Learning · Computer Science 2024-06-07 Bohang Zhang , Lingxiao Zhao , Haggai Maron

Graph representation learning (GRL) is to encode graph elements into informative vector representations, which can be used in downstream tasks for analyzing graph-structured data and has seen extensive applications in various domains.…

Machine Learning · Computer Science 2024-06-21 Hewen Wang , Renchi Yang , Xiaokui Xiao

Learning node representations that incorporate information from graph structure benefits wide range of tasks on graph. The majority of existing graph neural networks (GNNs) have limited power in capturing position information for a given…

Machine Learning · Computer Science 2021-06-15 Yuheng Lu , Jinpeng Chen , ChuXiong Sun , Jie Hu

Equivariant Graph Neural Networks (EGNNs) have emerged as a promising approach in Multi-Agent Reinforcement Learning (MARL), leveraging symmetry guarantees to greatly improve sample efficiency and generalization. However, real-world…

Machine Learning · Computer Science 2025-03-21 Joshua McClellan , Greyson Brothers , Furong Huang , Pratap Tokekar

Natural reading orders of words are crucial for information extraction from form-like documents. Despite recent advances in Graph Convolutional Networks (GCNs) on modeling spatial layout patterns of documents, they have limited ability to…

Computation and Language · Computer Science 2021-06-22 Chen-Yu Lee , Chun-Liang Li , Chu Wang , Renshen Wang , Yasuhisa Fujii , Siyang Qin , Ashok Popat , Tomas Pfister

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

In many deployed systems, new text inputs are handled by retrieving similar past cases, for example when routing and responding to citizen messages in digital governance platforms. When these systems fail, the problem is often not the…

Machine Learning · Computer Science 2026-01-27 Ruiyu Zhang , Lin Nie , Wai-Fung Lam , Qihao Wang , Xin Zhao

The message-passing scheme is the core of graph representation learning. While most existing message-passing graph neural networks (MPNNs) are permutation-invariant in graph-level representation learning and permutation-equivariant in node-…

Machine Learning · Computer Science 2022-11-22 Chang Liu , Yuwen Yang , Yue Ding , Hongtao Lu

Do autoregressive Transformer language models require explicit positional encodings (PEs)? The answer is 'no' provided they have more than one layer -- they can distinguish sequences with permuted tokens without the need for explicit PEs.…

Machine Learning · Computer Science 2025-06-03 Kazuki Irie

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

Link prediction is a core challenge in graph machine learning, demanding models that capture rich and complex topological dependencies. While Graph Neural Networks (GNNs) are the standard solution, state-of-the-art pipelines often rely on…

Machine Learning · Computer Science 2026-02-03 Quang Truong , Yu Song , Donald Loveland , Mingxuan Ju , Tong Zhao , Neil Shah , Jiliang Tang

This paper introduces a new model to learn graph neural networks equivariant to rotations, translations, reflections and permutations called E(n)-Equivariant Graph Neural Networks (EGNNs). In contrast with existing methods, our work does…

Machine Learning · Computer Science 2022-02-17 Victor Garcia Satorras , Emiel Hoogeboom , Max Welling

Equivariant Graph neural Networks (EGNs) are powerful in characterizing the dynamics of multi-body physical systems. Existing EGNs conduct flat message passing, which, yet, is unable to capture the spatial/dynamical hierarchy for complex…

Machine Learning · Computer Science 2022-10-18 Jiaqi Han , Wenbing Huang , Tingyang Xu , Yu Rong