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Graph neural networks (GNNs) excel on homophilic graphs where connected nodes share labels, but struggle with heterophilic graphs where edges do not imply similarity. Moreover, iterative message passing limits scalability due to…

Machine Learning · Computer Science 2026-02-16 Turja Kundu , Sanjukta Bhowmick

Graph neural networks (GNNs) face significant challenges with class imbalance, leading to biased inference results. To address this issue in heterogeneous graphs, we propose a novel framework that combines Graph Neural Network (GNN) and…

Machine Learning · Computer Science 2024-11-26 Hung-Chun Hsu , Bo-Jun Wu , Ming-Yi Hong , Che Lin , Chih-Yu Wang

While Graph Neural Network (GNN) has shown superiority in learning node representations of homogeneous graphs, leveraging GNN on heterogeneous graphs remains a challenging problem. The dominating reason is that GNN learns node…

Social and Information Networks · Computer Science 2020-09-22 Ziyue Qiao , Pengyang Wang , Yanjie Fu , Yi Du , Pengfei Wang , Yuanchun Zhou

Developing scalable solutions for training Graph Neural Networks (GNNs) for link prediction tasks is challenging due to the high data dependencies which entail high computational cost and huge memory footprint. We propose a new method for…

Machine Learning · Computer Science 2022-01-11 Nasrullah Sheikh , Xiao Qin , Berthold Reinwald , Chuan Lei

Graph Convolutional Networks (GCNs) have received significant attention from various research fields due to the excellent performance in learning graph representations. Although GCN performs well compared with other methods, it still faces…

Machine Learning · Computer Science 2021-09-06 Xin Liu , Mingyu Yan , Lei Deng , Guoqi Li , Xiaochun Ye , Dongrui Fan

This paper studies graph-based active learning, where the goal is to reconstruct a binary signal defined on the nodes of a weighted graph, by sampling it on a small subset of the nodes. A new sampling algorithm is proposed, which…

Machine Learning · Computer Science 2016-05-19 Eyal En Gad , Akshay Gadde , A. Salman Avestimehr , Antonio Ortega

The success of graph embeddings or node representation learning in a variety of downstream tasks, such as node classification, link prediction, and recommendation systems, has led to their popularity in recent years. Representation learning…

Machine Learning · Computer Science 2018-09-07 Saba A. Al-Sayouri , Danai Koutra , Evangelos E. Papalexakis , Sarah S. Lam

Graph Neural Networks (GNNs) and their message passing framework that leverages both structural and feature information, have become a standard method for solving graph-based machine learning problems. However, these approaches still…

Machine Learning · Computer Science 2024-11-20 Simon Delarue , Thomas Bonald , Tiphaine Viard

Graph-based models require aggregating information in the graph from neighbourhoods of different sizes. In particular, when the data exhibit varying levels of smoothness on the graph, a multi-scale approach is required to capture the…

Machine Learning · Computer Science 2022-02-22 Felix L. Opolka , Yin-Cong Zhi , Pietro Liò , Xiaowen Dong

Node embedding is the task of extracting informative and descriptive features over the nodes of a graph. The importance of node embeddings for graph analytics, as well as learning tasks such as node classification, link prediction and…

Machine Learning · Computer Science 2019-06-17 Dimitris Berberidis , Georgios B. Giannakis

Graph Neural Networks (GNNs) are powerful tools for learning from graph-structured data, but their application to large graphs is hindered by computational costs. The need to process every neighbor for each node creates memory and…

Machine Learning · Computer Science 2025-12-30 Omar Alsaqa , Linh Thi Hoang , Muhammed Fatih Balin

Graph Neural Networks (GNNs) have emerged as powerful tools for learning over structured data, including text-attributed graphs (TAGs), which are common in domains such as citation networks, social platforms, and knowledge graphs. GNNs are…

Machine Learning · Computer Science 2026-04-23 Peyman Baghershahi , Gregoire Fournier , Pranav Nyati , Sourav Medya

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…

Quantitative Methods · Quantitative Biology 2025-05-09 Changxi Chi , Jun Xia , Jingbo Zhou , Jiabei Cheng , Chang Yu , Stan Z. Li

State-of-the-art Graph Neural Networks (GNNs) have limited scalability with respect to the graph and model sizes. On large graphs, increasing the model depth often means exponential expansion of the scope (i.e., receptive field). Beyond…

Graph Neural Networks (GNNs) is an architecture for structural data, and has been adopted in a mass of tasks and achieved fabulous results, such as link prediction, node classification, graph classification and so on. Generally, for a…

Machine Learning · Computer Science 2022-05-12 Ye Tang , Xuesong Yang , Xinrui Liu , Xiwei Zhao , Zhangang Lin , Changping Peng

Graph Neural Networks (GNNs) have shown advantages in various graph-based applications. Most existing GNNs assume strong homophily of graph structure and apply permutation-invariant local aggregation of neighbors to learn a representation…

Machine Learning · Computer Science 2022-01-04 Tianmeng Yang , Yujing Wang , Zhihan Yue , Yaming Yang , Yunhai Tong , Jing Bai

Learning meaningful graphs from data plays important roles in many data mining and machine learning tasks, such as data representation and analysis, dimension reduction, data clustering, and visualization, etc. In this work, for the first…

Machine Learning · Computer Science 2020-07-30 Yongyu Wang , Zhiqiang Zhao , Zhuo Feng

Graph neural network (GNN) based methods have saturated the field of recommender systems. The gains of these systems have been significant, showing the advantages of interpreting data through a network structure. However, despite the…

Machine Learning · Computer Science 2022-09-12 Rebecca Salganik , Fernando Diaz , Golnoosh Farnadi

Graph neural networks (GNNs) build on the success of deep learning models by extending them for use in graph spaces. Transfer learning has proven extremely successful for traditional deep learning problems: resulting in faster training and…

Machine Learning · Computer Science 2022-02-03 Nishai Kooverjee , Steven James , Terence van Zyl

Graph neural networks (GNNs) have been increasingly deployed in various applications that involve learning on non-Euclidean data. However, recent studies show that GNNs are vulnerable to graph adversarial attacks. Although there are several…

Machine Learning · Computer Science 2023-01-10 Chenhui Deng , Xiuyu Li , Zhuo Feng , Zhiru Zhang
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