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We propose the Graph2Graph Transformer architecture for conditioning on and predicting arbitrary graphs, and apply it to the challenging task of transition-based dependency parsing. After proposing two novel Transformer models of…

Computation and Language · Computer Science 2021-03-22 Alireza Mohammadshahi , James Henderson

The Transformer based neural networks have been showing significant advantages on most evaluations of various natural language processing and other sequence-to-sequence tasks due to its inherent architecture based superiorities. Although…

Computation and Language · Computer Science 2019-10-31 Hailiang Li , Adele Y. C. Wang , Yang Liu , Du Tang , Zhibin Lei , Wenye Li

Graph pre-training has been concentrated on graph-level tasks involving small graphs (e.g., molecular graphs) or learning node representations on a fixed graph. Extending graph pre-trained models to web-scale graphs with billions of nodes…

Machine Learning · Computer Science 2025-11-07 Yufei He , Zhenyu Hou , Yukuo Cen , Jun Hu , Feng He , Xu Cheng , Jie Tang , Bryan Hooi

Positional encoding (PE) is a core architectural component of Transformers, yet its impact on the Transformer's generalization and robustness remains unclear. In this work, we provide the first generalization analysis for a single-layer…

Machine Learning · Statistics 2026-03-25 Weiyi He , Yue Xing

Signed Graph Neural Networks (SGNNs) have been shown to be effective in analyzing complex patterns in real-world situations where positive and negative links coexist. However, SGNN models suffer from poor explainability, which limit their…

Machine Learning · Computer Science 2024-12-13 Lu Li , Jiale Liu , Xingyu Ji , Maojun Wang , Zeyu Zhang

Graph structured data are abundant in the real world. Among different graph types, directed acyclic graphs (DAGs) are of particular interest to machine learning researchers, as many machine learning models are realized as computations on…

Machine Learning · Computer Science 2019-10-30 Muhan Zhang , Shali Jiang , Zhicheng Cui , Roman Garnett , Yixin Chen

Graph Auto-Encoders (GAEs) are powerful tools for graph representation learning. In this paper, we develop a novel Hierarchical Cluster-based GAE (HC-GAE), that can learn effective structural characteristics for graph data analysis. To this…

Machine Learning · Computer Science 2024-05-24 Zhuo Xu , Lu Bai , Lixin Cui , Ming Li , Yue Wang , Edwin R. Hancock

We explore the use of graph neural networks (GNNs) to model spatial processes in which there is no a priori graphical structure. Similar to finite element analysis, we assign nodes of a GNN to spatial locations and use a computational…

Machine Learning · Computer Science 2019-11-19 Ferran Alet , Adarsh K. Jeewajee , Maria Bauza , Alberto Rodriguez , Tomas Lozano-Perez , Leslie Pack Kaelbling

Graph autoencoders (AE) and variational autoencoders (VAE) are powerful node embedding methods, but suffer from scalability issues. In this paper, we introduce FastGAE, a general framework to scale graph AE and VAE to large graphs with…

Machine Learning · Computer Science 2021-04-14 Guillaume Salha , Romain Hennequin , Jean-Baptiste Remy , Manuel Moussallam , Michalis Vazirgiannis

New algorithms for embedding graphs have reduced the asymptotic complexity of finding low-dimensional representations. One-Hot Graph Encoder Embedding (GEE) uses a single, linear pass over edges and produces an embedding that converges…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-02-08 Ariel Lubonja , Cencheng Shen , Carey Priebe , Randal Burns

Invertible transformation of large graphs into fixed dimensional vectors (embeddings) remains a challenge. Its overcoming would reduce any operation on graphs to an operation in a vector space. However, most existing methods are limited to…

Machine Learning · Computer Science 2022-07-12 Adam Małkowski , Jakub Grzechociński , Paweł Wawrzyński

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these…

Computation and Language · Computer Science 2020-10-07 Xuanli He , Quan Hung Tran , Gholamreza Haffari , Walter Chang , Trung Bui , Zhe Lin , Franck Dernoncourt , Nhan Dam

Accurate predictions rely on the expressiveness power of graph deep learning frameworks like graph neural networks and graph transformers, where a positional encoding mechanism has become much more indispensable in recent state-of-the-art…

Machine Learning · Computer Science 2025-06-12 Katherine Tieu , Dongqi Fu , Zihao Li , Ross Maciejewski , Jingrui He

Fourier features based positional encoding (PE) is commonly used in machine learning tasks that involve learning high-frequency features from low-dimensional inputs, such as 3D view synthesis and time series regression with neural tangent…

Machine Learning · Computer Science 2024-07-18 Chuanhao Sun , Zhihang Yuan , Kai Xu , Luo Mai , N. Siddharth , Shuo Chen , Mahesh K. Marina

Positional encoding is a vital component of Transformer architectures, enabling models to incorporate sequence order into self-attention mechanisms. Rotary Positional Embeddings (RoPE) have become a widely adopted solution due to their…

Computation and Language · Computer Science 2025-08-01 Ali Veisi , Delaram Fartoot , Hamidreza Amirzadeh

Learning-based methods have become increasingly popular for solving vehicle routing problems due to their near-optimal performance and fast inference speed. Among them, the combination of deep reinforcement learning and graph representation…

Machine Learning · Computer Science 2024-05-22 Zhenwei Wang , Ruibin Bai , Fazlullah Khan , Ender Ozcan , Tiehua Zhang

Graph Neural Networks (GNNs) have shown impressive performance in graph representation learning, but they face challenges in capturing long-range dependencies due to their limited expressive power. To address this, Graph Transformers (GTs)…

Machine Learning · Computer Science 2024-06-19 Kaan Sancak , Zhigang Hua , Jin Fang , Yan Xie , Andrey Malevich , Bo Long , Muhammed Fatih Balin , Ümit V. Çatalyürek

Graph-based methods are known to be successful in many machine learning and pattern classification tasks. These methods consider semi-structured data as graphs where nodes correspond to primitives (parts, interest points, segments, etc.)…

Computer Vision and Pattern Recognition · Computer Science 2018-03-02 Anjan Dutta , Hichem Sahbi

Power electronic converter control is typically tuned per topology, limiting transfer across heterogeneous designs. This letter proposes a topology-agnostic meta-control framework that encodes converter netlists as typed bipartite graphs…

Systems and Control · Electrical Eng. & Systems 2026-01-13 Darius Jakobeit , Oliver Wallscheid

We propose the Graph Context Encoder (GCE), a simple but efficient approach for graph representation learning based on graph feature masking and reconstruction. GCE models are trained to efficiently reconstruct input graphs similarly to a…

Machine Learning · Computer Science 2021-06-21 Oriel Frigo , Rémy Brossard , David Dehaene