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This work presents the use of graph learning for the prediction of multi-step experimental outcomes for applications across experimental research, including material science, chemistry, and biology. The viability of geometric learning for…

Machine Learning · Computer Science 2024-08-13 Amanda A. Volk , Robert W. Epps , Jeffrey G. Ethier , Luke A. Baldwin

Predicting the emergence of links in large evolving networks is a difficult task with many practical applications. Recently, the Science4cast competition has illustrated this challenge presenting a network of 64.000 AI concepts and asking…

Social and Information Networks · Computer Science 2022-01-26 Francisco Andrades , Ricardo Ñanculef

Electron charge density distribution of materials is one of the key quantities in computational materials science as theoretically it determines the ground state energy and practically it is used in many materials analyses. However, the…

Computational Physics · Physics 2019-11-13 Sheng Gong , Tian Xie , Taishan Zhu , Shuo Wang , Eric R. Fadel , Yawei Li , Jeffrey C. Grossman

Differential equations are a ubiquitous tool to study dynamics, ranging from physical systems to complex systems, where a large number of agents interact through a graph with non-trivial topological features. Data-driven approximations of…

Statistical Mechanics · Physics 2024-04-26 Vaiva Vasiliauskaite , Nino Antulov-Fantulin

Flexible network design deals with building a network that guarantees some connectivity requirements between its vertices, even when some of its elements (like vertices or edges) fail. In particular, the set of edges (resp. vertices) of a…

Data Structures and Algorithms · Computer Science 2024-04-16 Dylan Hyatt-Denesik , Afrouz Jabal Ameli , Laura Sanita

Graph neural networks (GNNs) have recently gained much attention for node and graph classification tasks on graph-structured data. However, multiple recent works showed that an attacker can easily make GNNs predict incorrectly via…

Cryptography and Security · Computer Science 2021-07-19 Binghui Wang , Jinyuan Jia , Xiaoyu Cao , Neil Zhenqiang Gong

Graph neural networks (GNNs) have achieved great success in many scenarios with graph-structured data. However, in many real applications, there are three issues when applying GNNs: graphs are unknown, nodes have noisy features, and graphs…

Machine Learning · Computer Science 2022-10-11 Yixiang Shan , Jielong Yang , Xing Liu , Yixing Gao , Hechang Chen , Shuzhi Sam Ge

The success of deep learning has revolutionized many fields of research including areas of computer vision, text and speech processing. Enormous research efforts have led to numerous methods that are capable of efficiently analyzing data,…

Machine Learning · Computer Science 2020-07-20 Christoph Heindl

Graph neural networks are prominent models for representation learning over graph-structured data. While the capabilities and limitations of these models are well-understood for simple graphs, our understanding remains incomplete in the…

Machine Learning · Computer Science 2023-10-27 Xingyue Huang , Miguel Romero Orth , İsmail İlkan Ceylan , Pablo Barceló

Graph Neural Networks (GNNs) have made significant advances on several fundamental inference tasks. As a result, there is a surge of interest in using these models for making potentially important decisions in high-regret applications.…

Machine Learning · Computer Science 2020-02-26 Kaidi Xu , Sijia Liu , Pin-Yu Chen , Mengshu Sun , Caiwen Ding , Bhavya Kailkhura , Xue Lin

Many real-world networks exhibit correlations between the node degrees. For instance, in social networks nodes tend to connect to nodes of similar degree. Conversely, in biological and technological networks, high-degree nodes tend to be…

Discrete Mathematics · Computer Science 2015-09-30 Kevin E. Bassler , Charo I. Del Genio , Péter L. Erdős , István Miklós , Zoltán Toroczkai

While statistical analysis of a single network has received a lot of attention in recent years, with a focus on social networks, analysis of a sample of networks presents its own challenges which require a different set of analytic tools.…

Methodology · Statistics 2019-10-23 Jesús D. Arroyo-Relión , Daniel Kessler , Elizaveta Levina , Stephan F. Taylor

Attractive colloidal gels exhibit solid-like behavior at vanishingly small fractions of solids, owing to ramified space-spanning networks that form due to particle-particle interactions. These networks give the gel its rigidity, and as the…

The Recommender system is a vital information service on today's Internet. Recently, graph neural networks have emerged as the leading approach for recommender systems. We try to review recent literature on graph neural network-based…

Information Retrieval · Computer Science 2023-11-14 Haojun Zhu , Vikram Kapoor , Priya Sharma

Graph neural networks trained to predict observable dynamics can be used to decompose the temporal activity of complex heterogeneous systems into simple, interpretable representations. Here we apply this framework to simulated neural…

Neurons and Cognition · Quantitative Biology 2026-02-17 Cédric Allier , Larissa Heinrich , Magdalena Schneider , Stephan Saalfeld

This paper explores the ability of Graph Neural Networks (GNNs) in learning various forms of information for link prediction, alongside a brief review of existing link prediction methods. Our analysis reveals that GNNs cannot effectively…

Social and Information Networks · Computer Science 2025-12-09 Shuming Liang , Yu Ding , Zhidong Li , Bin Liang , Siqi Zhang , Yang Wang , Fang Chen

For joint inference over multiple variables, a variety of structured prediction techniques have been developed to model correlations among variables and thereby improve predictions. However, many classical approaches suffer from one of two…

Machine Learning · Computer Science 2020-01-07 Colin Graber , Alexander Schwing

Deep networks have recently been shown to be vulnerable to universal perturbations: there exist very small image-agnostic perturbations that cause most natural images to be misclassified by such classifiers. In this paper, we propose the…

Computer Vision and Pattern Recognition · Computer Science 2021-03-03 Seyed-Mohsen Moosavi-Dezfooli , Alhussein Fawzi , Omar Fawzi , Pascal Frossard , Stefano Soatto

Heterogeneous molecular entities and their interactions, commonly depicted as a network, are crucial for advancing our systems-level understanding of biology. With recent advancements in high-throughput data generation and a significant…

Quantitative Methods · Quantitative Biology 2026-03-18 Kishan KC , Rui Li , Paribesh Regmi , Anne R. Haake

We present exact solutions for the size of the giant connected component (GCC) of graphs composed of higher-order homogeneous cycles, including weak cycles and cliques, following bond percolation. We use our theoretical result to find the…

Physics and Society · Physics 2021-08-11 Peter Mann , V Anne Smith , John Mitchell , Christopher Jefferson , Simon Dobson