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We discuss probabilistic methods for predicting protein functions from protein-protein interaction networks. Previous work based on Markov Randon Fields is extended and compared to a general machine-learning theoretic approach. Using actual…

Molecular Networks · Quantitative Biology 2007-05-23 Christoph Best , Ralf Zimmer , Joannis Apostolakis

In graph signal processing, data samples are associated to vertices on a graph, while edge weights represent similarities between those samples. We propose a convex optimization problem to learn sparse well connected graphs from data. We…

Signal Processing · Electrical Eng. & Systems 2020-04-21 Eduardo Pavez , Antonio Ortega

Predicting the occurrence of links is a fundamental problem in networks. In the link prediction problem we are given a snapshot of a network and would like to infer which interactions among existing members are likely to occur in the near…

Social and Information Networks · Computer Science 2010-11-19 L. Backstrom , J. Leskovec

Graph neural networks use relational information as an inductive bias to enhance prediction performance. Not rarely, task-relevant relations are unknown and graph structure learning approaches have been proposed to learn them from data.…

Machine Learning · Computer Science 2025-05-29 Alessandro Manenti , Daniele Zambon , Cesare Alippi

In network data analysis, it is becoming common to work with a collection of graphs that exhibit \emph{heterogeneity}. For example, neuroimaging data from patient cohorts are increasingly available. A critical analytical task is to identify…

Methodology · Statistics 2020-03-11 Leo L Duan , George Michailidis , Mingzhou Ding

We develop graph-based methods for semi-supervised learning based on label propagation on a data similarity graph. When data is abundant or arrive in a stream, the problems of computation and data storage arise for any graph-based method.…

Machine Learning · Computer Science 2026-05-06 Michal Valko

Active learning in semi-supervised classification involves introducing additional labels for unlabelled data to improve the accuracy of the underlying classifier. A challenge is to identify which points to label to best improve performance…

Machine Learning · Statistics 2024-11-18 Kevin Miller , Andrea L. Bertozzi

Two approaches for graph based semi-supervised learning are proposed. The firstapproach is based on iteration of an affine map. A key element of the affine map iteration is sparsematrix-vector multiplication, which has several very…

Machine Learning · Computer Science 2015-09-07 Konstantin Avrachenkov , Vivek Borkar , Krishnakant Saboo

Image matting is an important vision problem. The main stream methods for it combine sampling-based methods and propagation-based methods. In this paper, we deal with the combination with a normalized weighting parameter, which could well…

Computer Vision and Pattern Recognition · Computer Science 2017-10-30 Ping Li , Tingyan Duan , Yongfeng Cao

Semi-supervised learning provides an effective paradigm for leveraging unlabeled data to improve a model's performance. Among the many strategies proposed, graph-based methods have shown excellent properties, in particular since they allow…

Machine Learning · Statistics 2021-03-29 Mourad El Hamri , Younès Bennani

Simplicial complexes are generalizations of graphs that describe higher-order network interactions among nodes in the graph. Network dynamics described by graph Laplacian flows have been widely studied in network science and control theory,…

Optimization and Control · Mathematics 2026-02-04 Mathias Hudoba de Badyn , Tyler Summers

Designing networks to optimize robustness and other performance metrics is a well-established problem with applications ranging from electrical engineering to communication networks. Many such performance measures rely on the Laplacian…

Social and Information Networks · Computer Science 2025-12-23 Samuel Rosa , Radoslav Harman

Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein…

Quantitative Methods · Quantitative Biology 2019-04-11 Carlos Fernandez-Lozano , Ruben F. Cuinas , Jose A. Seoane , Enrique Fernandez-Blanco , Julian Dorado , Cristian R. Munteanu

In the graph-based semi-supervised learning, the Green-function method is a classical method that works by computing the Green's function in the graph space. However, when applied to large graphs, especially those sparse ones, this method…

Machine Learning · Computer Science 2024-11-05 Feiping Nie , Yitao Song , Wei Chang , Rong Wang , Xuelong Li

Subgraph representation learning based on Graph Neural Network (GNN) has exhibited broad applications in scientific advancements, such as predictions of molecular structure-property relationships and collective cellular function. In…

Machine Learning · Computer Science 2022-10-17 Yili Shen , Xiao Liu , Cheng-Wei Ju , Jiaxu Yan , Jun Yi , Zhou Lin , Hui Guan

We consider the problem of estimating the topology of multiple networks from nodal observations, where these networks are assumed to be drawn from the same (unknown) random graph model. We adopt a graphon as our random graph model, which is…

Machine Learning · Statistics 2022-12-21 Madeline Navarro , Santiago Segarra

Meta-reinforcement learning trains a single reinforcement learning agent on a distribution of tasks to quickly generalize to new tasks outside of the training set at test time. From a Bayesian perspective, one can interpret this as…

Machine Learning · Computer Science 2025-11-20 Joery A. de Vries , Jinke He , Mathijs M. de Weerdt , Matthijs T. J. Spaan

Steerable convolutional neural networks (SCNNs) enhance task performance by modelling geometric symmetries through equivariance constraints on weights. Yet, unknown or varying symmetries can lead to overconstrained weights and decreased…

Machine Learning · Computer Science 2025-05-09 Lars Veefkind , Gabriele Cesa

We analyze performance of a class of time-delay first-order consensus networks from a graph topological perspective and present methods to improve it. The performance is measured by network's square of H-2 norm and it is shown that it is a…

Systems and Control · Computer Science 2018-10-22 Yaser Ghaedsharaf , Milad Siami , Christoforos Somarakis , Nader Motee

This paper proposes a parameter collaborative optimization algorithm for large language models, enhanced with graph spectral analysis. The goal is to improve both fine-tuning efficiency and structural awareness during training. In the…

Machine Learning · Computer Science 2025-06-03 Hanlu Zhang , Yumeng Ma , Shuo Wang , Guiran Liu , Binrong Zhu
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