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Biological network alignment identifies topologically and functionally conserved regions between networks of different species. It encompasses two algorithmic steps: node cost function (NCF), which measures similarities between nodes in…

Molecular Networks · Quantitative Biology 2014-07-21 Joseph Crawford , Yihan Sun , Tijana Milenković

Low-dimensional representations, or embeddings, of a graph's nodes facilitate several practical data science and data engineering tasks. As such embeddings rely, explicitly or implicitly, on a similarity measure among nodes, they require…

Machine Learning · Computer Science 2023-01-06 Anton Tsitsulin , Marina Munkhoeva , Davide Mottin , Panagiotis Karras , Ivan Oseledets , Emmanuel Müller

In this paper, a class of Decentralized Approximate Newton (DEAN) methods for addressing convex optimization on a networked system are developed, where nodes in the networked system seek for a consensus that minimizes the sum of their…

Optimization and Control · Mathematics 2020-12-01 Hejie Wei , Zhihai Qu , Xuyang Wu , Hao Wang , Jie Lu

Inferencing with network data necessitates the mapping of its nodes into a vector space, where the relationships are preserved. However, with multi-layered networks, where multiple types of relationships exist for the same set of nodes, it…

Social and Information Networks · Computer Science 2019-03-05 Huan Song , Jayaraman J. Thiagarajan

Aligning users across networks using graph representation learning has been found effective where the alignment is accomplished in a low-dimensional embedding space. Yet, achieving highly precise alignment is still challenging, especially…

Social and Information Networks · Computer Science 2023-01-02 Li Liu , Penggang Chen , Xin Li , William K. Cheung , Youmin Zhang , Qun Liu , Guoyin Wang

In process mining, alignments quantify the degree of deviation between an observed event trace and a business process model and constitute the most important conformance checking technique. We study the algorithmic complexity of computing…

Formal Languages and Automata Theory · Computer Science 2026-03-06 Christopher T. Schwanen , Wied Pakusa , Wil M. P. van der Aalst

Graph Neural Networks (GNNs) have proven to be powerful in many graph-based applications. However, they fail to generalize well under heterophilic setups, where neighbor nodes have different labels. To address this challenge, we employ a…

Machine Learning · Computer Science 2023-04-13 Yoonhyuk Choi , Jiho Choi , Taewook Ko , Chong-Kwon Kim

Deep learning models suffer from opaqueness. For Convolutional Neural Networks (CNNs), current research strategies for explaining models focus on the target classes within the associated training dataset. As a result, the understanding of…

Computer Vision and Pattern Recognition · Computer Science 2021-02-23 Xuehao Liu , Sarah Jane Delany , Susan McKeever

Deep neural networks are notoriously miscalibrated, i.e., their outputs do not reflect the true probability of the event we aim to predict. While networks for tabular or image data are usually overconfident, recent works have shown that…

Machine Learning · Computer Science 2024-03-11 Erik Nascimento , Diego Mesquita , Samuel Kaski , Amauri H Souza

This paper presents a novel graph-based deep learning model for tasks involving relations between two nodes (edge-centric tasks), where the focus lies on predicting relationships and interactions between pairs of nodes rather than node…

Machine Learning · Computer Science 2025-07-08 Eugenio Borzone , Leandro Di Persia , Matias Gerard

We address the problem of finding reliable dense correspondences between a pair of images. This is a challenging task due to strong appearance differences between the corresponding scene elements and ambiguities generated by repetitive…

Computer Vision and Pattern Recognition · Computer Science 2018-11-30 Ignacio Rocco , Mircea Cimpoi , Relja Arandjelović , Akihiko Torii , Tomas Pajdla , Josef Sivic

Graph neural networks have been shown to be very effective in utilizing pairwise relationships across samples. Recently, there have been several successful proposals to generalize graph neural networks to hypergraph neural networks to…

Machine Learning · Computer Science 2024-02-21 Michael Ng , Hanrui Wu , Andy Yip

Neural node embeddings have recently emerged as a powerful representation for supervised learning tasks involving graph-structured data. We leverage this recent advance to develop a novel algorithm for unsupervised community discovery in…

Social and Information Networks · Computer Science 2017-06-30 Weicong Ding , Christy Lin , Prakash Ishwar

We propose a new method for embedding graphs while preserving directed edge information. Learning such continuous-space vector representations (or embeddings) of nodes in a graph is an important first step for using network information…

Machine Learning · Computer Science 2017-09-15 Sami Abu-El-Haija , Bryan Perozzi , Rami Al-Rfou

This paper addresses the challenging problem of retrieval and matching of graph structured objects, and makes two key contributions. First, we demonstrate how Graph Neural Networks (GNN), which have emerged as an effective model for various…

Machine Learning · Computer Science 2019-05-14 Yujia Li , Chenjie Gu , Thomas Dullien , Oriol Vinyals , Pushmeet Kohli

Studies continually find that message-passing graph convolutional networks suffer from the over-smoothing issue. Basically, the issue of over-smoothing refers to the phenomenon that the learned embeddings for all nodes can become very…

Machine Learning · Computer Science 2024-04-16 Haimin Zhang , Min Xu

Network representation learning (NRL) plays a vital role in a variety of tasks such as node classification and link prediction. It aims to learn low-dimensional vector representations for nodes based on network structures or node…

Social and Information Networks · Computer Science 2020-08-17 Ke Hou , Jiaying Liu , Yin Peng , Bo Xu , Ivan Lee , Feng Xia

This paper proposes a new deep convolutional neural network (DCNN) architecture that learns pixel embeddings, such that pairwise distances between the embeddings can be used to infer whether or not the pixels lie on the same region. That…

Computer Vision and Pattern Recognition · Computer Science 2016-01-11 Adam W. Harley , Konstantinos G. Derpanis , Iasonas Kokkinos

Compound graphs are networks in which vertices can be grouped into larger subsets, with these subsets capable of further grouping, resulting in a nesting that can be many levels deep. In several applications, including biological workflows,…

Human-Computer Interaction · Computer Science 2024-08-09 Chang Han , Justin Lieffers , Clayton Morrison , Katherine E. Isaacs

Finding optimal matchings in dense graphs is of general interest and of particular importance in social, transportation and biological networks. While developing optimal solutions for various matching problems is important, the running…

Data Structures and Algorithms · Computer Science 2020-11-16 Nitish K. Panigrahy , Prithwish Basu , Don Towsley