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We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections…

Machine Learning · Computer Science 2021-01-26 Vijay Prakash Dwivedi , Xavier Bresson

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

Transformer networks have seen great success in natural language processing and machine vision, where task objectives such as next word prediction and image classification benefit from nuanced context sensitivity across high-dimensional…

Machine Learning · Computer Science 2022-12-13 Yuxuan Li , James L. McClelland

We establish connections between the Transformer architecture, originally introduced for natural language processing, and Graph Neural Networks (GNNs) for representation learning on graphs. We show how Transformers can be viewed as message…

Machine Learning · Computer Science 2025-06-30 Chaitanya K. Joshi

Graphs have become a central representation in machine learning for capturing relational and structured data across various domains. Traditional graph neural networks often struggle to capture long-range dependencies between nodes due to…

Machine Learning · Computer Science 2025-08-26 Leon Dimitrov

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

We propose a graph-oriented attention-based explainability method for tabular data. Tasks involving tabular data have been solved mostly using traditional tree-based machine learning models which have the challenges of feature selection and…

Machine Learning · Computer Science 2024-06-05 Andrea Treviño Gavito , Diego Klabjan , Jean Utke

Graph learning architectures based on the k-dimensional Weisfeiler-Leman (k-WL) hierarchy offer a theoretically well-understood expressive power. However, such architectures often fail to deliver solid predictive performance on real-world…

Machine Learning · Computer Science 2024-11-11 Luis Müller , Daniel Kusuma , Blai Bonet , Christopher Morris

Real-world graphs naturally exhibit hierarchical or cyclical structures that are unfit for the typical Euclidean space. While there exist graph neural networks that leverage hyperbolic or spherical spaces to learn representations that embed…

Machine Learning · Computer Science 2023-09-11 Sungjun Cho , Seunghyuk Cho , Sungwoo Park , Hankook Lee , Honglak Lee , Moontae Lee

Graph Transformers, which incorporate self-attention and positional encoding, have recently emerged as a powerful architecture for various graph learning tasks. Despite their impressive performance, the complex non-convex interactions…

Machine Learning · Computer Science 2024-06-05 Hongkang Li , Meng Wang , Tengfei Ma , Sijia Liu , Zaixi Zhang , Pin-Yu Chen

The transformer is the most popular neural architecture for language modeling. The cornerstone of the transformer is its global attention mechanism, which lets the model aggregate information from all preceding tokens before generating the…

Computation and Language · Computer Science 2026-05-20 Jiaoda Li , Ryan Cotterell

We present a generalization of Transformers to any-order permutation invariant data (sets, graphs, and hypergraphs). We begin by observing that Transformers generalize DeepSets, or first-order (set-input) permutation invariant MLPs. Then,…

Machine Learning · Computer Science 2022-01-25 Jinwoo Kim , Saeyoon Oh , Seunghoon Hong

We introduce Attention Graphs, a new tool for mechanistic interpretability of Graph Neural Networks (GNNs) and Graph Transformers based on the mathematical equivalence between message passing in GNNs and the self-attention mechanism in…

Machine Learning · Computer Science 2025-02-26 Batu El , Deepro Choudhury , Pietro Liò , Chaitanya K. Joshi

We investigate the capabilities of transformer models on relational reasoning tasks. In these tasks, models are trained on a set of strings encoding abstract relations, and are then tested out-of-distribution on data that contains symbols…

Computation and Language · Computer Science 2024-04-17 Enric Boix-Adsera , Omid Saremi , Emmanuel Abbe , Samy Bengio , Etai Littwin , Joshua Susskind

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

Learning representations on large-sized graphs is a long-standing challenge due to the inter-dependence nature involved in massive data points. Transformers, as an emerging class of foundation encoders for graph-structured data, have shown…

Machine Learning · Computer Science 2024-08-19 Qitian Wu , Wentao Zhao , Chenxiao Yang , Hengrui Zhang , Fan Nie , Haitian Jiang , Yatao Bian , Junchi Yan

Graph Neural Networks (GNNs) and Transformers share significant similarities in their encoding strategies for interacting with features from nodes of interest, where Transformers use query-key scores and GNNs use edges. Compared to GNNs,…

Machine Learning · Computer Science 2025-07-08 Jiaxin Qi , Yan Cui , Jinli Ou , Jianqiang Huang , Gaogang Xie

There is a growing interest in the ability of neural networks to execute algorithmic tasks (e.g., arithmetic, summary statistics, and sorting). The goal of this work is to better understand the role of attention in Transformers for…

Machine Learning · Computer Science 2025-06-11 Artur Back de Luca , George Giapitzakis , Shenghao Yang , Petar Veličković , Kimon Fountoulakis

Transformer architecture has become ubiquitous in the natural language processing field. To interpret the Transformer-based models, their attention patterns have been extensively analyzed. However, the Transformer architecture is not only…

Computation and Language · Computer Science 2021-09-16 Goro Kobayashi , Tatsuki Kuribayashi , Sho Yokoi , Kentaro Inui

Graph neural networks are powerful architectures for structured datasets. However, current methods struggle to represent long-range dependencies. Scaling the depth or width of GNNs is insufficient to broaden receptive fields as larger GNNs…

Machine Learning · Computer Science 2022-01-24 Zhanghao Wu , Paras Jain , Matthew A. Wright , Azalia Mirhoseini , Joseph E. Gonzalez , Ion Stoica
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