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In this paper we show how to express RNA tertiary interactions via the concepts of tangled diagrams. Tangled diagrams allow to formulate RNA base triples and pseudoknot-interactions and to control the maximum number of mutually crossing…

Combinatorics · Mathematics 2007-12-10 Jing Qin , Christian M. Reidys

Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…

Statistical Mechanics · Physics 2025-07-15 Shesha Gopal Marehalli Srinivas , Massimiliano Esposito , Nahuel Freitas

Recurrent Neural Network models have elucidated the interplay between structure and dynamics in biological neural networks, particularly the emergence of irregular and rhythmic activities in cortex. However, most studies have focused on…

Neurons and Cognition · Quantitative Biology 2025-09-04 Nimrod Sherf , Xaq Pitkow , Krešimir Josić , Kevin E. Bassler

Coupled oscillator networks provide mathematical models for interacting periodic processes. If the coupling is weak, phase reduction -- the reduction of the dynamics onto an invariant torus -- captures the emergence of collective dynamical…

Dynamical Systems · Mathematics 2024-08-06 Christian Bick , Tobias Böhle , Christian Kuehn

Hypergraphs effectively model higher-order relationships in natural phenomena, capturing complex interactions beyond pairwise connections. We introduce a novel hypergraph message passing framework inspired by interacting particle systems,…

Machine Learning · Computer Science 2025-05-27 Yixuan Ma , Kai Yi , Pietro Lio , Shi Jin , Yu Guang Wang

In network science, collective dynamics of complex systems are typically modelled as (nonlinear, often including many-body) vertex-level update rules evolving over a graph interaction structure. In recent years, frameworks that explicitly…

Physics and Society · Physics 2026-03-03 Lucas Lacasa

In many complex systems, elements interact via time-varying network topologies. Recent research shows that temporal correlations in the chronological ordering of interactions crucially influence network properties and dynamical processes.…

Physics and Society · Physics 2020-12-01 Yan Zhang , Antonios Garas , Ingo Scholtes

We define a higher order Deffuant model by generalizing the original pairwise interaction model for bounded-confidence opinion-dynamics to interactions involving a group of agents of size k. The generalized model is naturally encoded in a…

Physics and Society · Physics 2021-11-25 Hendrik Schawe , Laura Hernández

Although higher-order interactions are known to affect the typical state of dynamical processes giving rise to new collective behavior, how they drive the emergence of rare events and fluctuations is still an open problem. We investigate…

Disordered Systems and Neural Networks · Physics 2024-09-09 Leonardo Di Gaetano , Giorgio Carugno , Federico Battiston , Francesco Coghi

All intelligence is collective intelligence, in the sense that it is made of parts which must align with respect to system-level goals. Understanding the dynamics which facilitate or limit navigation of problem spaces by aligned parts thus…

Statistical Mechanics · Physics 2026-05-18 Francesco Sacco , Dalton A R Sakthivadivel , Michael Levin

Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…

Molecular Networks · Quantitative Biology 2018-09-21 Thomas Gaudelet , Noel Malod-Dognin , Natasa Przulj

We consider percolation on high-dimensional product graphs, where the base graphs are regular and of bounded order. In the subcritical regime, we show that typically the largest component is of order logarithmic in the number of vertices.…

Combinatorics · Mathematics 2024-04-11 Sahar Diskin , Joshua Erde , Mihyun Kang , Michael Krivelevich

In functionally complex systems, higher-order connectivity is often revealed in the underlying geometry of networked units. Furthermore, such systems often show signatures of self-organized criticality, a specific type of non-equilibrium…

Statistical Mechanics · Physics 2026-03-11 Bosiljka Tadic , Roderick Melnik

Going beyond networks, to include higher-order interactions of arbitrary sizes, is a major step to better describe complex systems. In the resulting hypergraph representation, tools to identify structures and central nodes are scarce. We…

Physics and Society · Physics 2023-10-11 Marco Mancastroppa , Iacopo Iacopini , Giovanni Petri , Alain Barrat

Hypergraphs are a generalization of graphs in which edges can connect any number of vertices. They allow the modeling of complex networks with higher-order interactions, and their spectral theory studies the qualitative properties that can…

Combinatorics · Mathematics 2021-12-01 Raffaella Mulas

The function of a real network depends not only on the reliability of its own components, but is affected also by the simultaneous operation of other real networks coupled with it. Robustness of systems composed of interdependent network…

Physics and Society · Physics 2015-07-10 Filippo Radicchi

Several biological and social contagion phenomena, such as superspreading events or social reinforcement, are the results of multi-body interactions, for which hypergraphs offer a natural mathematical description. In this paper, we develop…

Contagion processes relying on the exposure to multiple sources are prevalent in social systems, and are effectively represented by hypergraphs. In this Letter, we derive a mean-field model that goes beyond node- and pair-based…

Physics and Society · Physics 2024-12-06 Giulio Burgio , Sergio Gómez , Alex Arenas

The irreducible complexity of natural phenomena has led Graph Neural Networks to be employed as a standard model to perform representation learning tasks on graph-structured data. While their capacity to capture local and global patterns is…

Machine Learning · Computer Science 2024-02-13 Lorenzo Giusti

Majority bootstrap percolation is a model of infection spreading in networks. Starting with a set of initially infected vertices, new vertices become infected once half of their neighbours are infected. Balogh, Bollob\'{a}s and Morris…

Combinatorics · Mathematics 2025-07-10 Maurício Collares , Joshua Erde , Anna Geisler , Mihyun Kang
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