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Graph Neural Networks (GNNs) have been proposed as a tool for learning sparse matrix preconditioners, which are key components in accelerating linear solvers. We present theoretical and empirical evidence that message-passing GNNs are…

Machine Learning · Computer Science 2026-05-26 Vladislav Trifonov , Ekaterina Muravleva , Ivan Oseledets

Strategies to improve the predicting performance of Message-Passing Neural-Networks for molecular property predictions can be achieved by simplifying how the message is passed and by using descriptors that capture multiple aspects of…

Machine Learning · Computer Science 2025-10-22 Alma C. Castaneda-Leautaud , Rommie E. Amaro

Graph convolutional networks (GCNs) have achieved remarkable learning ability for dealing with various graph structural data recently. In general, deep GCNs do not work well since graph convolution in conventional GCNs is a special form of…

Machine Learning · Computer Science 2021-12-08 Zhilong Xiong , Jia Cai

Accurate prediction of blood-brain barrier permeability (BBBP) is essential for central nervous system (CNS) drug development. While graph neural networks (GNNs) have advanced molecular property prediction, they often rely on molecular…

Machine Learning · Computer Science 2025-12-09 Trung Nguyen , Md Masud Rana , Farjana Tasnim Mukta , Chang-Guo Zhan , Duc Duy Nguyen

Graph representation learning has become a crucial task in machine learning and data mining due to its potential for modeling complex structures such as social networks, chemical compounds, and biological systems. Spiking neural networks…

Artificial Intelligence · Computer Science 2024-03-27 Huifeng Yin , Mingkun Xu , Jing Pei , Lei Deng

Time, cost, and energy efficiency are critical considerations in Deep-Learning (DL), particularly when processing long texts. Transformers, which represent the current state of the art, exhibit quadratic computational complexity relative to…

Computation and Language · Computer Science 2025-07-11 Fardin Rastakhiz

Graph Neural Networks (GNNs) have received much attention in the graph deep learning domain. However, recent research empirically and theoretically shows that deep GNNs suffer from over-fitting and over-smoothing problems. The usual…

Machine Learning · Computer Science 2022-09-05 Chuxiong Sun , Jie Hu , Hongming Gu , Jinpeng Chen , Mingchuan Yang

Graph Neural Networks (GNNs) have become a dominant approach to learning graph representations, primarily because of their message-passing mechanisms. However, GNNs typically adopt a fixed aggregator function such as Mean, Max, or Sum…

Machine Learning · Computer Science 2025-07-29 Xuanting Xie , Bingheng Li , Erlin Pan , Zhao Kang , Wenyu Chen

Graph neural networks (GNNs) have achieved champion in wide applications. Neural message passing is a typical key module for feature propagation by aggregating neighboring features. In this work, we propose a new message passing based on…

Machine Learning · Computer Science 2023-03-01 Xinliang Liu , Bingxin Zhou , Chutian Zhang , Yu Guang Wang

The graph neural network (GNN) models have presented impressive achievements in numerous machine learning tasks. However, many existing GNN models are shown to be vulnerable to adversarial attacks, which creates a stringent need to build…

Machine Learning · Computer Science 2022-10-04 Zepeng Zhang , Songtao Lu , Zengfeng Huang , Ziping Zhao

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect…

Machine Learning · Computer Science 2020-11-10 Emily Alsentzer , Samuel G. Finlayson , Michelle M. Li , Marinka Zitnik

In this work we propose Pathfinder Discovery Networks (PDNs), a method for jointly learning a message passing graph over a multiplex network with a downstream semi-supervised model. PDNs inductively learn an aggregated weight for each edge,…

Machine Learning · Computer Science 2021-02-18 Benedek Rozemberczki , Peter Englert , Amol Kapoor , Martin Blais , Bryan Perozzi

Message Passing Neural Networks (MPNNs) are widely used for learning on graphs, but their ability to process long-range information is limited by the phenomenon of oversquashing. This limitation has led some researchers to advocate Graph…

Machine Learning · Computer Science 2025-11-26 Yaaqov Mishayev , Yonatan Sverdlov , Tal Amir , Nadav Dym

We propose Graph Tree Networks (GTNets), a deep graph learning architecture with a new general message passing scheme that originates from the tree representation of graphs. In the tree representation, messages propagate upward from the…

Machine Learning · Computer Science 2022-04-28 Nan Wu , Chaofan Wang

We propose a framework that automatically transforms non-scalable GNNs into precomputation-based GNNs which are efficient and scalable for large-scale graphs. The advantages of our framework are two-fold; 1) it transforms various…

Machine Learning · Computer Science 2022-07-26 Seiji Maekawa , Yuya Sasaki , George Fletcher , Makoto Onizuka

Graph Convolutional Networks (GCNs) have been drawing significant attention with the power of representation learning on graphs. Unlike Convolutional Neural Networks (CNNs), which are able to take advantage of stacking very deep layers,…

Machine Learning · Computer Science 2020-06-16 Guohao Li , Chenxin Xiong , Ali Thabet , Bernard Ghanem

Graph representation learning has recently been applied to a broad spectrum of problems ranging from computer graphics and chemistry to high energy physics and social media. The popularity of graph neural networks has sparked interest, both…

Machine Learning · Computer Science 2020-11-05 Fabrizio Frasca , Emanuele Rossi , Davide Eynard , Ben Chamberlain , Michael Bronstein , Federico Monti

Graph Neural Networks (GNNs) have emerged as powerful tools for supervised machine learning over graph-structured data, while sampling-based node representation learning is widely utilized in unsupervised learning. However, scalability…

Machine Learning · Computer Science 2024-07-23 Vipul Gupta , Xin Chen , Ruoyun Huang , Fanlong Meng , Jianjun Chen , Yujun Yan

Graph Neural Networks (GNNs) are routinely used in molecular physics, social sciences, and economics to model many-body interactions in graph-like systems. However, GNNs are inherently local and can suffer from information flow bottlenecks.…

Computational Physics · Physics 2025-02-21 Alessandro Caruso , Jacopo Venturin , Lorenzo Giambagli , Edoardo Rolando , Frank Noé , Cecilia Clementi

Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work (Kim et al., 2022) shows that with…

Machine Learning · Computer Science 2023-06-22 Chen Cai , Truong Son Hy , Rose Yu , Yusu Wang