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Live-cell imaging of multiple subcellular structures is essential for understanding subcellular dynamics. However, the conventional multi-color sequential fluorescence microscopy suffers from significant imaging delays and limited number of…

Subcellular Processes · Quantitative Biology 2025-01-13 Mingyang Chen , Luhong Jin , Xuwei Xuan , Defu Yang , Yun Cheng , Ju Zhang

Graph neural networks (GNNs) learn to represent nodes by aggregating information from their neighbors. As GNNs increase in depth, their receptive field grows exponentially, leading to high memory costs. Several existing methods address this…

Machine Learning · Computer Science 2025-07-16 Taraneh Younesian , Daniel Daza , Emile van Krieken , Thiviyan Thanapalasingam , Peter Bloem

Graph embedding is the task of representing nodes of a graph in a low-dimensional space and its applications for graph tasks have gained significant traction in academia and industry. The primary difference among the many recently proposed…

Social and Information Networks · Computer Science 2019-08-28 Palash Goyal , Di Huang , Ankita Goswami , Sujit Rokka Chhetri , Arquimedes Canedo , Emilio Ferrara

Neural architecture search (NAS) has recently been addressed from various directions, including discrete, sampling-based methods and efficient differentiable approaches. While the former are notoriously expensive, the latter suffer from…

Machine Learning · Computer Science 2021-05-13 Jovita Lukasik , David Friede , Arber Zela , Frank Hutter , Margret Keuper

Attributed graph embedding, which learns vector representations from graph topology and node features, is a challenging task for graph analysis. Recently, methods based on graph convolutional networks (GCNs) have made great progress on this…

Machine Learning · Computer Science 2020-07-06 Ganqu Cui , Jie Zhou , Cheng Yang , Zhiyuan Liu

Hyperbolic geometry has emerged as an effective latent space for representing complex networks, owing to its ability to capture hierarchical organization and heterogeneous connectivity patterns using low-dimensional embeddings. As a result,…

Machine Learning · Computer Science 2026-05-01 Sofía Pérez Casulo , Marcelo Fiori , Bernardo Marenco , Federico Larroca

Graphs are ubiquitous real-world data structures, and generative models that approximate distributions over graphs and derive new samples from them have significant importance. Among the known challenges in graph generation tasks,…

Machine Learning · Computer Science 2019-10-04 Wataru Kawai , Yusuke Mukuta , Tatsuya Harada

Representation learning on graphs has been gaining attention due to its wide applicability in predicting missing links, and classifying and recommending nodes. Most embedding methods aim to preserve certain properties of the original graph…

Social and Information Networks · Computer Science 2019-09-13 Palash Goyal , Di Huang , Sujit Rokka Chhetri , Arquimedes Canedo , Jaya Shree , Evan Patterson

Neural Architecture Search (NAS) automates and prospers the design of neural networks. Estimator-based NAS has been proposed recently to model the relationship between architectures and their performance to enable scalable and flexible…

Artificial Intelligence · Computer Science 2020-09-29 Hsin-Pai Cheng , Tunhou Zhang , Yixing Zhang , Shiyu Li , Feng Liang , Feng Yan , Meng Li , Vikas Chandra , Hai Li , Yiran Chen

Graph alignment, the problem of identifying corresponding nodes across multiple graphs, is fundamental to numerous applications. Most existing unsupervised methods embed node features into latent representations to enable cross-graph…

Machine Learning · Computer Science 2025-09-30 Maysam Behmanesh , Erkan Turan , Maks Ovsjanikov

Embedding methods transform the knowledge graph into a continuous, low-dimensional space, facilitating inference and completion tasks. Existing methods are mainly divided into two types: translational distance models and semantic matching…

Information Retrieval · Computer Science 2025-03-11 Deepak Banerjee , Anjali Ishaan

Knowledge graph embedding methods learn embeddings of entities and relations in a low dimensional space which can be used for various downstream machine learning tasks such as link prediction and entity matching. Various graph convolutional…

Machine Learning · Computer Science 2021-02-16 Nasrullah Sheikh , Xiao Qin , Berthold Reinwald , Christoph Miksovic , Thomas Gschwind , Paolo Scotton

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an…

Machine Learning · Computer Science 2022-02-28 Federico Errica

Graphs are ubiquitous due to their flexibility in representing social and technological systems as networks of interacting elements. Graph representation learning methods, such as node embeddings, are powerful approaches to map nodes into a…

Machine Learning · Computer Science 2023-10-03 Simone Piaggesi , Megha Khosla , André Panisson , Avishek Anand

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

Recently, Graph Neural Networks (GNNs) have proven their effectiveness for recommender systems. Existing studies have applied GNNs to capture collaborative relations in the data. However, in real-world scenarios, the relations in a…

Information Retrieval · Computer Science 2021-11-30 Xiaohan Li , Zhiwei Liu , Stephen Guo , Zheng Liu , Hao Peng , Philip S. Yu , Kannan Achan

Graph neural networks (GNNs) have exhibited exceptional efficacy in a diverse array of applications. However, the sheer size of large-scale graphs presents a significant challenge to real-time inference with GNNs. Although existing Scalable…

Machine Learning · Computer Science 2023-12-13 Xinyi Gao , Wentao Zhang , Junliang Yu , Yingxia Shao , Quoc Viet Hung Nguyen , Bin Cui , Hongzhi Yin

Knowledge bases, and their representations in the form of knowledge graphs (KGs), are naturally incomplete. Since scientific and industrial applications have extensively adopted them, there is a high demand for solutions that complete their…

Artificial Intelligence · Computer Science 2025-07-30 Vítor Lourenço , Aline Paes

Recently popularized graph neural networks achieve the state-of-the-art accuracy on a number of standard benchmark datasets for graph-based semi-supervised learning, improving significantly over existing approaches. These architectures…

Machine Learning · Statistics 2018-03-13 Kiran K. Thekumparampil , Chong Wang , Sewoong Oh , Li-Jia Li

Graph representation learning is a fundamental problem for modeling relational data and benefits a number of downstream applications. Traditional Bayesian-based graph models and recent deep learning based GNN either suffer from…

Machine Learning · Computer Science 2024-03-27 Hanxuan Yang , Qingchao Kong , Wenji Mao