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Graphs are a central representation in biomedical research, capturing molecular interaction networks, gene regulatory circuits, cell--cell communication maps, and knowledge graphs. Despite their importance, currently there is not a broadly…

Machine Learning · Computer Science 2026-04-09 Sakib Mostafa , Lei Xing , Md. Tauhidul Islam

Graph Neural Networks (GNNs) have emerged as powerful tools for learning over graph-structured data, yet recent studies have shown that their performance gains are beginning to plateau. In many cases, well-established models such as GCN and…

Machine Learning · Computer Science 2026-02-13 Mohit Meena , Yash Punjabi , Abhishek A , Vishal Sharma , Mahesh Chandran

Existing methods for graph out-of-distribution (OOD) detection typically depend on training graph neural network (GNN) classifiers using a substantial amount of labeled in-distribution (ID) data. However, acquiring high-quality labeled…

Machine Learning · Computer Science 2025-03-31 Haoyan Xu , Zhengtao Yao , Yushun Dong , Ziyi Wang , Ryan A. Rossi , Mengyuan Li , Yue Zhao

Graph Neural Networks (GNNs) have become a central tool for learning on graph-structured data, yet their applicability to real-world systems remains limited by key challenges such as scalability, temporality, directionality, data…

Machine Learning · Computer Science 2025-10-28 Emanuele Rossi

Graph classification aims to extract accurate information from graph-structured data for classification and is becoming more and more important in graph learning community. Although Graph Neural Networks (GNNs) have been successfully…

Machine Learning · Computer Science 2020-06-24 Ning Ma , Jiajun Bu , Jieyu Yang , Zhen Zhang , Chengwei Yao , Zhi Yu , Sheng Zhou , Xifeng Yan

Zero-shot learning relies on semantic class representations such as hand-engineered attributes or learned embeddings to predict classes without any labeled examples. We propose to learn class representations by embedding nodes from common…

Machine Learning · Computer Science 2022-08-29 Nihal V. Nayak , Stephen H. Bach

Prior to the introduction of Graph Neural Networks (GNNs), modeling and analyzing irregular data, particularly graphs, was thought to be the Achilles' heel of deep learning. The core concept of GNNs is to find a representation by…

Machine Learning · Computer Science 2021-09-22 Jieming Zhou , Tong Zhang , Pengfei Fang , Lars Petersson , Mehrtash Harandi

Graph neural networks (GNN) are powerful models for many graph-structured tasks. Existing models often assume that the complete structure of the graph is available during training. In practice, however, graph-structured data is usually…

Machine Learning · Computer Science 2022-03-29 Chen Wang , Yuheng Qiu , Dasong Gao , Sebastian Scherer

Graph Neural Networks (GNNs) have received a lot of interest in the recent times. From the early spectral architectures that could only operate on undirected graphs per a transductive learning paradigm to the current state of the art…

Machine Learning · Computer Science 2021-05-18 Pushkar Mishra , Aleksandra Piktus , Gerard Goossen , Fabrizio Silvestri

Graph Neural Networks (GNNs) with numerical node features and graph structure as inputs have demonstrated superior performance on various supervised learning tasks with graph data. However the numerical node features utilized by GNNs are…

Machine Learning · Computer Science 2022-06-20 Jiuhai Chen , Jonas Mueller , Vassilis N. Ioannidis , Tom Goldstein , David Wipf

We investigate input normalization methods for Time-Series Foundation Models (TSFMs). While normalization is well-studied in dataset-specific time-series models, it remains overlooked in TSFMs where generalization is critical. Time-series…

Machine Learning · Computer Science 2026-01-30 Ihab Ahmed , Denis Krompaß , Cheng Feng , Volker Tresp

Graph neural networks (GNNs) are the dominant paradigm for classifying nodes in a graph, but they have several undesirable attributes stemming from their message passing architecture. Recently, distillation methods succeeded in eliminating…

Machine Learning · Computer Science 2024-02-09 Daniel Winter , Niv Cohen , Yedid Hoshen

Graphs are essential for modeling complex interactions across domains such as social networks, biology, and recommendation systems. Traditional Graph Neural Networks, particularly Message Passing Neural Networks (MPNNs), rely heavily on…

Machine Learning · Computer Science 2025-06-13 Wei Li , Mengcheng Lan , Jiaxing Xu , Yiping Ke

Graph Neural Networks (GNNs) extend basic Neural Networks (NNs) by additionally making use of graph structure based on the relational inductive bias (edge bias), rather than treating the nodes as collections of independent and identically…

Machine Learning · Computer Science 2023-11-07 Sitao Luan , Chenqing Hua , Qincheng Lu , Jiaqi Zhu , Xiao-Wen Chang , Doina Precup

In the realm of Text-attributed Graphs (TAGs), traditional graph neural networks (GNNs) often fall short due to the complex textual information associated with each node. Recent methods have improved node representations by leveraging large…

Machine Learning · Computer Science 2025-06-10 Huanyi Xie , Lijie Hu , Lu Yu , Tianhao Huang , Longfei Li , Meng Li , Jun Zhou , Huan Wang , Di Wang

Federated Graph Learning (FGL) enables privacy-preserving, distributed training of graph neural networks without sharing raw data. Among its approaches, subgraph-FL has become the dominant paradigm, with most work focused on improving…

Machine Learning · Computer Science 2025-04-15 Zhengyu Wu , Boyang Pang , Xunkai Li , Yinlin Zhu , Daohan Su , Bowen Fan , Rong-Hua Li , Guoren Wang , Chenghu Zhou

Graph neural networks (GNNs) are powerful deep learning models for graph-structured data, demonstrating remarkable success across diverse domains. Recently, the database (DB) community has increasingly recognized the potentiality of GNNs,…

Databases · Computer Science 2025-02-20 Ziming Li , Youhuan Li , Yuyu Luo , Guoliang Li , Chuxu Zhang

Graph anomaly detection (GAD) has attracted increasing attention in recent years for identifying malicious samples in a wide range of graph-based applications, such as social media and e-commerce. However, most GAD methods assume identical…

Machine Learning · Computer Science 2025-09-09 Junjun Pan , Yu Zheng , Yue Tan , Yixin Liu

While Graph Neural Networks (GNNs) and Large Language Models (LLMs) are powerful approaches for learning on Text-Attributed Graphs (TAGs), a comprehensive understanding of their robustness remains elusive. Current evaluations are…

Machine Learning · Computer Science 2025-10-21 Runlin Lei , Lu Yi , Mingguo He , Pengyu Qiu , Zhewei Wei , Yongchao Liu , Chuntao Hong

Identifying meaningful feature interactions is a central challenge in building accurate and interpretable models for tabular data. Generalized additive models (GAMs) have shown great success at modeling tabular data, but often rely on…

Machine Learning · Computer Science 2026-04-16 Jingyun Jia , Chandan Singh , Rich Caruana , Ben Lengerich