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Graph Neural Networks (GNNs) have become the state-of-the-art method for many applications on graph structured data. GNNs are a model for graph representation learning, which aims at learning to generate low dimensional node embeddings that…

Machine Learning · Computer Science 2022-05-23 Davide Buffelli , Fabio Vandin

Textual graphs are ubiquitous in real-world applications, featuring rich text information with complex relationships, which enables advanced research across various fields. Textual graph representation learning aims to generate…

Machine Learning · Computer Science 2024-08-22 Wenbin Hu , Huihao Jing , Qi Hu , Haoran Li , Yangqiu Song

Unsupervised graph representation learning aims to distill various graph information into a downstream task-agnostic dense vector embedding. However, existing graph representation learning approaches are designed mainly under the node…

Machine Learning · Computer Science 2022-03-04 You Li , Bei Lin , Binli Luo , Ning Gui

We propose WS-DINO as a novel framework to use weak label information in learning phenotypic representations from high-content fluorescent images of cells. Our model is based on a knowledge distillation approach with a vision transformer…

Computer Vision and Pattern Recognition · Computer Science 2022-11-18 Jan Oscar Cross-Zamirski , Guy Williams , Elizabeth Mouchet , Carola-Bibiane Schönlieb , Riku Turkki , Yinhai Wang

Modern data analysis pipelines are becoming increasingly complex due to the presence of multi-view information sources. While graphs are effective in modeling complex relationships, in many scenarios a single graph is rarely sufficient to…

Machine Learning · Statistics 2019-04-02 Uday Shankar Shanthamallu , Jayaraman J. Thiagarajan , Huan Song , Andreas Spanias

Self-supervised vision models have achieved notable success in digital pathology. However, their domain-agnostic transformer architectures are not originally designed to account for fundamental biological elements of histopathology images,…

Computer Vision and Pattern Recognition · Computer Science 2026-03-03 Sevda Öğüt , Cédric Vincent-Cuaz , Natalia Dubljevic , Carlos Hurtado , Vaishnavi Subramanian , Pascal Frossard , Dorina Thanou

Detecting intrusions in network traffic is a challenging task, particularly under limited supervision and constantly evolving attack patterns. While recent works have leveraged graph neural networks for network intrusion detection, they…

Machine Learning · Computer Science 2025-12-23 Lorenzo Guerra , Thomas Chapuis , Guillaume Duc , Pavlo Mozharovskyi , Van-Tam Nguyen

Graph neural networks~(GNNs) apply deep learning techniques to graph-structured data and have achieved promising performance in graph representation learning. However, existing GNNs rely heavily on enough labels or well-designed negative…

Machine Learning · Computer Science 2020-11-13 Feihu Che , Guohua Yang , Dawei Zhang , Jianhua Tao , Pengpeng Shao , Tong Liu

Self-supervised graph representation learning (SSGRL) is a representation learning paradigm used to reduce or avoid manual labeling. An essential part of SSGRL is graph data augmentation. Existing methods usually rely on heuristics commonly…

Machine Learning · Computer Science 2024-12-25 Ahmed E. Samy , Zekarias T. Kefatoa , Sarunas Girdzijauskasa

Graph Transformers, which incorporate self-attention and positional encoding, have recently emerged as a powerful architecture for various graph learning tasks. Despite their impressive performance, the complex non-convex interactions…

Machine Learning · Computer Science 2024-06-05 Hongkang Li , Meng Wang , Tengfei Ma , Sijia Liu , Zaixi Zhang , Pin-Yu Chen

Understanding how neuronal networks reorganize in response to external stimuli and give rise to behavior is a central challenge in neuroscience and artificial intelligence. However, existing methods often fail to capture the evolving…

Neurons and Cognition · Quantitative Biology 2025-06-02 Moein Khajehnejad , Forough Habibollahi , Ahmad Khajehnejad , Chris French , Brett J. Kagan , Adeel Razi

Despite their black-box nature, deep learning models are extensively used in image-based drug discovery to extract feature vectors from single cells in microscopy images. To better understand how these networks perform representation…

Image and Video Processing · Electrical Eng. & Systems 2024-03-27 Vivek Gopalakrishnan , Jingzhe Ma , Zhiyong Xie

The visual attributes of cells, such as the nuclear morphology and chromatin openness, are critical for histopathology image analysis. By learning cell-level visual representation, we can obtain a rich mix of features that are highly…

Computer Vision and Pattern Recognition · Computer Science 2018-07-10 Bo Hu , Ye Tang , Eric I-Chao Chang , Yubo Fan , Maode Lai , Yan Xu

Graph Neural Networks (GNNs) are a framework for graph representation learning, where a model learns to generate low dimensional node embeddings that encapsulate structural and feature-related information. GNNs are usually trained in an…

Machine Learning · Computer Science 2020-12-15 Davide Buffelli , Fabio Vandin

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

Graph neural network, as a powerful graph representation technique based on deep learning, has shown superior performance and attracted considerable research interest. However, it has not been fully considered in graph neural network for…

Social and Information Networks · Computer Science 2021-01-21 Xiao Wang , Houye Ji , Chuan Shi , Bai Wang , Peng Cui , P. Yu , Yanfang Ye

Graph representation learning has attracted lots of attention recently. Existing graph neural networks fed with the complete graph data are not scalable due to limited computation and memory costs. Thus, it remains a great challenge to…

Machine Learning · Computer Science 2020-11-24 Yizhu Jiao , Yun Xiong , Jiawei Zhang , Yao Zhang , Tianqi Zhang , Yangyong Zhu

Dynamic graph neural networks have been widely used in modeling and representation learning of graph structure data. Current dynamic representation learning focuses on either discrete learning which results in temporal information loss or…

Machine Learning · Computer Science 2022-02-11 Yan Pang , Chao Liu

Studying influential nodes (I-nodes) in brain networks is of great significance in the field of brain imaging. Most existing studies consider brain connectivity hubs as I-nodes. However, this approach relies heavily on prior knowledge from…

Neurons and Cognition · Quantitative Biology 2024-09-18 Yanqing Kang , Di Zhu , Haiyang Zhang , Enze Shi , Sigang Yu , Jinru Wu , Xuhui Wang , Xuan Liu , Geng Chen , Xi Jiang , Tuo Zhang , Shu Zhang

Most existing semi-supervised graph-based clustering methods exploit the supervisory information by either refining the affinity matrix or directly constraining the low-dimensional representations of data points. The affinity matrix…

Machine Learning · Computer Science 2022-09-07 Huaming Ling , Chenglong Bao , Xin Liang , Zuoqiang Shi