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The self-attention mechanism, a cornerstone of Transformer-based state-of-the-art deep learning architectures, is largely heuristic-driven and fundamentally challenging to interpret. Establishing a robust theoretical foundation to explain…

Computer Vision and Pattern Recognition · Computer Science 2026-02-10 Laziz U. Abdullaev , Maksim Tkachenko , Tan M. Nguyen

Recent advances in Graph Convolutional Neural Networks (GCNNs) have shown their efficiency for non-Euclidean data on graphs, which often require a large amount of labeled data with high cost. It it thus critical to learn graph feature…

Computer Vision and Pattern Recognition · Computer Science 2020-03-20 Xiang Gao , Wei Hu , Guo-Jun Qi

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of…

Machine Learning · Computer Science 2020-07-21 Meng Liu , Hongyang Gao , Shuiwang Ji

Transformers flexibly operate over sets of real-valued vectors representing task-specific entities and their attributes, where each vector might encode one word-piece token and its position in a sequence, or some piece of information that…

Machine Learning · Computer Science 2023-03-14 Cameron Diao , Ricky Loynd

The incredible success of transformers on sequence modeling tasks can be largely attributed to the self-attention mechanism, which allows information to be transferred between different parts of a sequence. Self-attention allows…

Machine Learning · Computer Science 2024-08-14 Eshaan Nichani , Alex Damian , Jason D. Lee

We propose an extension to the transformer neural network architecture for general-purpose graph learning by adding a dedicated pathway for pairwise structural information, called edge channels. The resultant framework - which we call…

Machine Learning · Computer Science 2022-06-06 Md Shamim Hussain , Mohammed J. Zaki , Dharmashankar Subramanian

Transformers have demonstrated remarkable performance across diverse domains. The key component of Transformers is self-attention, which learns the relationship between any two tokens in the input sequence. Recent studies have revealed that…

Machine Learning · Computer Science 2025-05-14 Hyowon Wi , Jeongwhan Choi , Noseong Park

Transformer models have recently gained popularity in graph representation learning as they have the potential to learn complex relationships beyond the ones captured by regular graph neural networks. The main research question is how to…

Machine Learning · Computer Science 2023-10-31 Yuankai Luo , Veronika Thost , Lei Shi

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

There has been a recent surge in transformer-based architectures for learning on graphs, mainly motivated by attention as an effective learning mechanism and the desire to supersede handcrafted operators characteristic of message passing…

Machine Learning · Computer Science 2025-06-10 David Buterez , Jon Paul Janet , Dino Oglic , Pietro Lio

Transformers are increasingly employed for graph data, demonstrating competitive performance in diverse tasks. To incorporate graph information into these models, it is essential to enhance node and edge features with positional encodings.…

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

Graph Transformers (GTs) have shown strong empirical performance, yet current architectures vary widely in their use of attention mechanisms, positional embeddings (PEs), and expressivity. Existing expressivity results are often tied to…

Machine Learning · Computer Science 2025-11-12 Timo Stoll , Luis Müller , Christopher Morris

Transformers have achieved remarkable success across domains, motivating the rise of Graph Transformers (GTs) as attention-based architectures for graph-structured data. A key design choice in GTs is the use of Graph Neural Network…

Machine Learning · Computer Science 2026-05-29 Javier Porras-Valenzuela , Zhiyang Wang , Xiaotao Shang , Yusu Wang , Alejandro Ribeiro

Pretraining plays a pivotal role in acquiring generalized knowledge from large-scale data, achieving remarkable successes as evidenced by large models in CV and NLP. However, progress in the graph domain remains limited due to fundamental…

Artificial Intelligence · Computer Science 2024-06-21 Yu Song , Haitao Mao , Jiachen Xiao , Jingzhe Liu , Zhikai Chen , Wei Jin , Carl Yang , Jiliang Tang , Hui Liu

We argue that Transformers are essentially graph-to-graph models, with sequences just being a special case. Attention weights are functionally equivalent to graph edges. Our Graph-to-Graph Transformer architecture makes this ability…

Computation and Language · Computer Science 2023-10-30 James Henderson , Alireza Mohammadshahi , Andrei C. Coman , Lesly Miculicich

Transformers, adapted from natural language processing, are emerging as a leading approach for graph representation learning. Contemporary graph transformers often treat nodes or edges as separate tokens. This approach leads to…

Machine Learning · Computer Science 2023-10-04 Zihan Pengmei , Zimu Li , Chih-chan Tien , Risi Kondor , Aaron R. Dinner

Graph Transformer is gaining increasing attention in the field of machine learning and has demonstrated state-of-the-art performance on benchmarks for graph representation learning. However, as current implementations of Graph Transformer…

Machine Learning · Computer Science 2023-05-08 Wenhao Zhu , Tianyu Wen , Guojie Song , Xiaojun Ma , Liang Wang

In the realm of Graph Neural Networks (GNNs), two exciting research directions have recently emerged: Subgraph GNNs and Graph Transformers. In this paper, we propose an architecture that integrates both approaches, dubbed Subgraphormer,…

Machine Learning · Computer Science 2024-05-29 Guy Bar-Shalom , Beatrice Bevilacqua , Haggai Maron

Many real-world problems can be represented as graph-based learning problems. In this paper, we propose a novel framework for learning spatial and attentional convolution neural networks on arbitrary graphs. Different from previous…

Machine Learning · Computer Science 2019-02-26 Hao Peng , Jianxin Li , Qiran Gong , Senzhang Wang , Yuanxing Ning , Philip S. Yu