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Recently a variety of methods have been developed to encode graphs into low-dimensional vectors that can be easily exploited by machine learning algorithms. The majority of these methods start by embedding the graph nodes into a…

Machine Learning · Computer Science 2018-09-13 Yu Jin , Joseph F. JaJa

We study an issue commonly seen with graph data analysis: many real-world complex systems involving high-order interactions are best encoded by hypergraphs; however, their datasets often end up being published or studied only in the form of…

Social and Information Networks · Computer Science 2022-11-28 Yanbang Wang , Jon Kleinberg

Despite that going deep has proven successful in many neural architectures, the existing graph transformers are relatively shallow. In this work, we explore whether more layers are beneficial to graph transformers, and find that current…

Machine Learning · Computer Science 2023-03-02 Haiteng Zhao , Shuming Ma , Dongdong Zhang , Zhi-Hong Deng , Furu Wei

Deep representation learning on non-Euclidean data types, such as graphs, has gained significant attention in recent years. Invent of graph neural networks has improved the state-of-the-art for both node and the entire graph representation…

Machine Learning · Computer Science 2020-06-09 Sambaran Bandyopadhyay , Manasvi Aggarwal , M. Narasimha Murty

Computing latent representations for graph-structured data is an ubiquitous learning task in many industrial and academic applications ranging from molecule synthetization to social network analysis and recommender systems. Knowledge graphs…

Neural and Evolutionary Computing · Computer Science 2023-08-25 Victor Caceres Chian , Marcel Hildebrandt , Thomas Runkler , Dominik Dold

Graph transformers are a recent advancement in machine learning, offering a new class of neural network models for graph-structured data. The synergy between transformers and graph learning demonstrates strong performance and versatility…

Machine Learning · Computer Science 2025-12-23 Ahsan Shehzad , Feng Xia , Shagufta Abid , Ciyuan Peng , Shuo Yu , Dongyu Zhang , Karin Verspoor

Learning expressive representations for high-dimensional yet sparse features has been a longstanding problem in information retrieval. Though recent deep learning methods can partially solve the problem, they often fail to handle the…

Information Retrieval · Computer Science 2023-05-30 Kaize Ding , Albert Jiongqian Liang , Bryan Perrozi , Ting Chen , Ruoxi Wang , Lichan Hong , Ed H. Chi , Huan Liu , Derek Zhiyuan Cheng

Downsampling produces coarsened, multi-resolution representations of data and it is used, for example, to produce lossy compression and visualization of large images, reduce computational costs, and boost deep neural representation…

Machine Learning · Computer Science 2023-07-04 Davide Bacciu , Alessio Conte , Francesco Landolfi

We demonstrate that graph-based models are fully capable of representing higher-order interactions, and have a long history of being used for precisely this purpose. This stands in contrast to a common claim in the recent literature on…

Physics and Society · Physics 2026-02-20 Tiago P. Peixoto , Leto Peel , Thilo Gross , Manlio De Domenico

Graph Transformers (GTs) have made remarkable achievements in graph-level tasks. However, most existing works regard graph structures as a form of guidance or bias for enhancing node representations, which focuses on node-central…

Machine Learning · Computer Science 2024-12-10 Xiaorui Qi , Qijie Bai , Yanlong Wen , Haiwei Zhang , Xiaojie Yuan

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically…

Machine Learning · Computer Science 2024-01-17 Yanbang Wang , Jon Kleinberg

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

Hyperbolic geometry has emerged as an effective latent space for representing complex networks, owing to its ability to capture hierarchical organization and heterogeneous connectivity patterns using low-dimensional embeddings. As a result,…

Machine Learning · Computer Science 2026-05-01 Sofía Pérez Casulo , Marcelo Fiori , Bernardo Marenco , Federico Larroca

Graph Neural Networks (GNNs) are a powerful representational tool for solving problems on graph-structured inputs. In almost all cases so far, however, they have been applied to directly recovering a final solution from raw inputs, without…

Machine Learning · Statistics 2020-01-16 Petar Veličković , Rex Ying , Matilde Padovano , Raia Hadsell , Charles Blundell

Transformers often fail to learn generalizable algorithms, instead relying on brittle heuristics. Using graph connectivity as a testbed, we explain this phenomenon both theoretically and empirically. We consider a simplified Transformer…

Machine Learning · Computer Science 2026-02-19 Qilin Ye , Deqing Fu , Robin Jia , Vatsal Sharan

Hypergraphs, as a generalization of traditional graphs, naturally capture high-order relationships. In recent years, hypergraph neural networks (HNNs) have been widely used to capture complex high-order relationships. However, most existing…

Machine Learning · Computer Science 2025-11-25 Renchu Guan , Xuyang Li , Yachao Zhang , Wei Pang , Fausto Giunchiglia , Ximing Li , Yonghao Liu , Xiaoyue Feng

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

Networks with higher-order interactions, prevalent in biological, social, and information systems, are naturally represented as hypergraphs, yet their structural complexity poses fundamental challenges for geometric characterization. While…

Machine Learning · Computer Science 2025-06-05 Shiyi Yang , Can Chen , Didong Li

Algorithmic reasoning requires capabilities which are most naturally understood through recurrent models of computation, like the Turing machine. However, Transformer models, while lacking recurrence, are able to perform such reasoning…

Machine Learning · Computer Science 2023-05-03 Bingbin Liu , Jordan T. Ash , Surbhi Goel , Akshay Krishnamurthy , Cyril Zhang

We show theoretically and empirically that the linear Transformer, when applied to graph data, can implement algorithms that solve canonical problems such as electric flow and eigenvector decomposition. The Transformer has access to…

Machine Learning · Computer Science 2025-03-04 Xiang Cheng , Lawrence Carin , Suvrit Sra