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Brain can be represented as a network, where regions are the nodes and relations between the regions are edges. Within a network, co-existence of cooperative and competitive relationships between different nodes is called coopetition.…

Neurons and Cognition · Quantitative Biology 2018-02-13 Subhadip Paul , Satyam Mukherjee , Sagnik Bhattacharyya

The structure of the supply chain network has important implications for modelling economic systems, from growth trajectories to responses to shocks or natural disasters. However, reconstructing firm-to-firm networks from available…

Physics and Society · Physics 2024-12-23 Leonardo Niccolò Ialongo , Sylvain Bangma , Fabian Jansen , Diego Garlaschelli

The past few years has witnessed the great success of recommender systems, which can significantly help users find relevant and interesting items for them in the information era. However, a vast class of researches in this area mainly focus…

Information Retrieval · Computer Science 2012-04-10 Xiao Hu , Chuibo Chen , Xiaolong Chen , Zi-Ke Zhang

A widely recognized organizing principle of networks is structural homophily, which suggests that people with more common neighbors are more likely to connect with each other. However, what influence the diverse structures embedded in…

Social and Information Networks · Computer Science 2017-10-06 Yuxiao Dong , Reid A. Johnson , Jian Xu , Nitesh V. Chawla

The ability to reroute and control flow is vital to the function of venation networks across a wide range of organisms. By modifying individual edges in these networks, either by adjusting edge conductances or creating and destroying edges,…

Soft Condensed Matter · Physics 2021-01-14 Jason W. Rocks , Andrea J. Liu , Eleni Katifori

Understanding the structural complexity and predictability of complex networks is a central challenge in network science. Although recent studies have revealed a relationship between compression-based entropy and link prediction…

Social and Information Networks · Computer Science 2025-10-14 Sebastián Brzovic , Cristóbal Rojas , Andrés Abeliuk

Networks are useful for describing systems of interacting objects, where the nodes represent the objects and the edges represent the interactions between them. The applications include chemical and metabolic systems, food webs as well as…

Computational Physics · Physics 2009-10-20 Baruch Barzel , Ofer Biham

Semi-structured networks (SSNs) merge the structures familiar from additive models with deep neural networks, allowing the modeling of interpretable partial feature effects while capturing higher-order non-linearities at the same time. A…

Machine Learning · Computer Science 2024-10-15 David Rügamer , Bernard X. W. Liew , Zainab Altai , Almond Stöcker

Network science plays an increasingly important role to model complex data in many scientific disciplines. One notable feature of network organization is community structure, which refers to clusters of tightly interconnected nodes. A…

Social and Information Networks · Computer Science 2016-03-18 Dimitri Van De Ville

There is increasing evidence to suggest functional connectivity networks are non-stationary. This has lead to the development of novel methodologies with which to accurately estimate time-varying functional connectivity networks. Many of…

We study the structure of inter-industry relationships using networks of money flows between industries in 20 national economies. We find these networks vary around a typical structure characterized by a Weibull link weight distribution,…

Physics and Society · Physics 2014-07-25 James McNerney , Brian D. Fath , Gerald Silverberg

In many applications, such as those arising from the field of cellular networks, it is often desired to determine the interaction (graph) structure of a set of differential equations, using as data measured sensitivities. This note proposes…

Biological Physics · Physics 2007-05-23 Boris N. Kholodenko , Eduardo D. Sontag

Bipartite networks are widely used to encode the ecological interactions. Being able to compare the organization of bipartite networks is a first step toward a better understanding of how environmental factors shape community structure and…

Machine Learning · Statistics 2025-12-02 Louis Lacoste , Pierre Barbillon , Sophie Donnet

Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…

Biological Physics · Physics 2015-02-03 Olga Kononova , Lee Jones , Valeri Barsegov

Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…

Quantitative Methods · Quantitative Biology 2020-01-01 Ryan E. Langendorf , Debra S. Goldberg

The lack of studying the complex organization of directed network usually limits to the understanding of underlying relationship between network structures and functions. Structural controllability and structural predictability, two…

Physics and Society · Physics 2022-03-31 Fei Jing , Chuang Liu , Jian-Liang Wu , Zi-Ke Zhang

In this work we focus on examination and comparison of whole-brain functional connectivity patterns measured with fMRI across experimental conditions. Direct examination and comparison of condition-specific matrices is challenging due to…

Applications · Statistics 2013-01-02 Svetlana V. Shinkareva , Vladimir Gudkov , Jing Wang

It is well-known that intrinsically disordered proteins (IDP) are highly dynamic, which is related to their functionality in various biological processes. However, the characterization of the intricate structures of IDP has been a…

Biological Physics · Physics 2025-03-18 Danqi Lang , Le Chen , Jingyuan Li

Many fMRI analyses examine functional connectivity, or statistical dependencies among remote brain regions. Yet popular methods for studying whole-brain functional connectivity often yield results that are difficult to interpret. Factor…

Methodology · Statistics 2024-09-24 Kyle Stanley , Nicole Lazar , Matthew Reimherr

Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier…

Quantitative Methods · Quantitative Biology 2026-05-22 Kingsley Yeon , Xuefeng Liu , Promit Ghosal