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Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context.…

Molecular Networks · Quantitative Biology 2022-12-13 Chris S. Magnano , Anthony Gitter

Graph Neural Networks (GNNs) rely on graph convolutions to exploit meaningful patterns in networked data. Based on matrix multiplications, convolutions incur in high computational costs leading to scalability limitations in practice. To…

Machine Learning · Computer Science 2022-10-28 Juan Cervino , Luana Ruiz , Alejandro Ribeiro

Marginal MAP problems are notoriously difficult tasks for graphical models. We derive a general variational framework for solving marginal MAP problems, in which we apply analogues of the Bethe, tree-reweighted, and mean field…

Machine Learning · Computer Science 2013-02-28 Qiang Liu , Alexander T. Ihler

We present a novel approach for graph classification based on tabularizing graph data via new variants of the Weisfeiler-Leman algorithm and then applying methods for tabular data. The variants are obtained by modifying the underlying…

Machine Learning · Computer Science 2026-05-25 Reijo Jaakkola , Tomi Janhunen , Antti Kuusisto , Magdalena Ortiz , Matias Selin , Mantas Šimkus

Most instruments - formalisms, concepts, and metrics - for social networks analysis fail to capture their dynamics. Typical systems exhibit different scales of dynamics, ranging from the fine-grain dynamics of interactions (which recently…

Social and Information Networks · Computer Science 2011-02-04 Nicola Santoro , Walter Quattrociocchi , Paola Flocchini , Arnaud Casteigts , Frederic Amblard

We adapt multilevel, force-directed graph layout techniques to visualizing dynamic graphs in which vertices and edges are added and removed in an online fashion (i.e., unpredictably). We maintain multiple levels of coarseness using a…

Graphics · Computer Science 2007-12-11 Todd L. Veldhuizen

The Exponential-family Random Graph Model (ERGM) is a powerful model to fit networks with complex structures. However, for dynamic valued networks whose observations are matrices of counts that evolve over time, the development of the ERGM…

Methodology · Statistics 2023-06-21 Yik Lun Kei , Yanzhen Chen , Oscar Hernan Madrid Padilla

The purpose of this article is to introduce a new L\'evy process, termed Variance Gamma++ process, to model the dynamic of assets in illiquid markets. Such a process has the mathematical tractability of the Variance Gamma process and is…

Mathematical Finance · Quantitative Finance 2022-07-03 M. Gardini , P. Sabino , E. Sasso

Expressivity and generalization are two critical aspects of graph neural networks (GNNs). While significant progress has been made in studying the expressivity of GNNs, much less is known about their generalization capabilities,…

Machine Learning · Computer Science 2024-10-15 Shouheng Li , Floris Geerts , Dongwoo Kim , Qing Wang

Graph neural networks (GNNs) are the most widely adopted model in graph-structured data oriented learning and representation. Despite their extraordinary success in real-world applications, understanding their working mechanism by theory is…

Machine Learning · Computer Science 2023-05-16 Huayi Tang , Yong Liu

Estimation of model uncertainty can help improve the explainability of Graph Convolutional Networks and the accuracy of the models at the same time. Uncertainty can also be used in critical applications to verify the results of the model by…

Machine Learning · Computer Science 2025-07-03 Illia Oleksiienko , Juho Kanniainen , Alexandros Iosifidis

Despite the celebrated popularity of Graph Neural Networks (GNNs) across numerous applications, the ability of GNNs to generalize remains less explored. In this work, we propose to study the generalization of GNNs through a novel…

Machine Learning · Computer Science 2024-04-17 Shouheng Li , Dongwoo Kim , Qing Wang

Some probabilistic aspects of the number variance statistic are investigated. Infinite systems of independent Brownian motions and symmetric alpha-stable processes are used to construct new examples of processes which exhibit both divergent…

Probability · Mathematics 2007-05-23 Ben Hambly , Liza Jones

In this paper, we consider a one-dimensional random geometric graph process with the inter-nodal gaps evolving according to an exponential AR(1) process, which may serve as a mobile wireless network model. The transition probability matrix…

Information Theory · Computer Science 2009-12-09 Yilun Shang

We propose generalizations of a number of standard network models, including the classic random graph, the configuration model, and the stochastic block model, to the case of time-varying networks. We assume that the presence and absence of…

Social and Information Networks · Computer Science 2018-05-02 Xiao Zhang , Cristopher Moore , M. E. J. Newman

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine…

Machine Learning · Computer Science 2025-03-11 Jiawei Liu , Cheng Yang , Zhiyuan Lu , Junze Chen , Yibo Li , Mengmei Zhang , Ting Bai , Yuan Fang , Lichao Sun , Philip S. Yu , Chuan Shi

In this paper, we present two localized graph filtering based methods for interpolating graph signals defined on the vertices of arbitrary graphs from only a partial set of samples. The first method is an extension of previous work on…

Machine Learning · Computer Science 2013-10-11 Sunil K. Narang , Akshay Gadde , Eduard Sanou , Antonio Ortega

The natural habitat of most Bayesian methods is data represented by exchangeable sequences of observations, for which de Finetti's theorem provides the theoretical foundation. Dirichlet process clustering, Gaussian process regression, and…

Statistics Theory · Mathematics 2015-02-16 Peter Orbanz , Daniel M. Roy

This work provides a theoretical framework for assessing the generalization error of graph neural networks in the over-parameterized regime, where the number of parameters surpasses the quantity of data points. We explore two widely…

Machine Learning · Statistics 2024-07-02 Gholamali Aminian , Yixuan He , Gesine Reinert , Łukasz Szpruch , Samuel N. Cohen

A sequence of graphs with diverging number of nodes is a dense graph sequence if the number of edges grows approximately as for complete graphs. To each such sequence a function, called graphon, can be associated, which contains information…

Analysis of PDEs · Mathematics 2018-06-12 Andrea Braides , Paolo Cermelli , Simone Dovetta