Journal of Physics Complexity最新文献_第3页

Comparing discriminating abilities of evaluation metrics in link prediction 比较链接预测中评价指标的判别能力

IF 2.7

Journal of Physics Complexity Pub Date : 2024-05-15 DOI: 10.1088/2632-072x/ad46be

Xinshan Jiao, Shuyan Wan, Qian Liu, Yilin Bi, Yan-Li Lee, En Xu, Dong Hao and Tao Zhou

{"title":"Comparing discriminating abilities of evaluation metrics in link prediction","authors":"Xinshan Jiao, Shuyan Wan, Qian Liu, Yilin Bi, Yan-Li Lee, En Xu, Dong Hao and Tao Zhou","doi":"10.1088/2632-072x/ad46be","DOIUrl":"https://doi.org/10.1088/2632-072x/ad46be","url":null,"abstract":"Link prediction aims to predict the potential existence of links between two unconnected nodes within a network based on the known topological characteristics. Evaluation metrics are used to assess the effectiveness of algorithms in link prediction. The discriminating ability of these evaluation metrics is vitally important for accurately evaluating link prediction algorithms. In this study, we propose an artificial network model, based on which one can adjust a single parameter to monotonically and continuously turn the prediction accuracy of the specifically designed link prediction algorithm. Building upon this foundation, we show a framework to depict the effectiveness of evaluating metrics by focusing on their discriminating ability. Specifically, a quantitative comparison in the abilities of correctly discerning varying prediction accuracies was conducted encompassing nine evaluation metrics: Precision, Recall, F1-Measure, Matthews correlation coefficient, balanced precision, the area under the receiver operating characteristic curve (AUC), the area under the precision-recall curve (AUPR), normalized discounted cumulative gain (NDCG), and the area under the magnified receiver operating characteristic. The results indicate that the discriminating abilities of the three metrics, AUC, AUPR, and NDCG, are significantly higher than those of other metrics.","PeriodicalId":53211,"journal":{"name":"Journal of Physics Complexity","volume":"240 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141060233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Beyond the aggregated paradigm: phenology and structure in mutualistic networks 超越聚合范式：互惠网络中的物候和结构

IF 2.7

Journal of Physics Complexity Pub Date : 2024-05-13 DOI: 10.1088/2632-072x/ad459e

Clàudia Payrató-Borràs, Carlos Gracia-Lázaro, Laura Hernández and Yamir Moreno

{"title":"Beyond the aggregated paradigm: phenology and structure in mutualistic networks","authors":"Clàudia Payrató-Borràs, Carlos Gracia-Lázaro, Laura Hernández and Yamir Moreno","doi":"10.1088/2632-072x/ad459e","DOIUrl":"https://doi.org/10.1088/2632-072x/ad459e","url":null,"abstract":"Mutualistic relationships, where species interact to obtain mutual benefits, constitute an essential component of natural ecosystems. The use of ecological networks to represent the species and their ecological interactions allows the study of structural and dynamic patterns common to different ecosystems. However, by neglecting the temporal dimension of mutualistic communities, relevant insights into the organization and functioning of natural ecosystems can be lost. Therefore, it is crucial to incorporate empirical phenology -the cycles of species’ activity within a season- to fully understand the impact of temporal variability on network architecture. In this paper, by using empirical datasets together with a set of synthetic models, we propose a framework to characterize the phenology of plant-pollinator communities and assess how it reshapes their portrayal as a network. Analyses of three empirical cases reveal that non-trivial information is missed when representing the network of interactions as static, which leads to overestimating the value of fundamental structural features. We discuss the implications of our findings for mutualistic relationships and intra-guild competition for common resources. We show that recorded interactions and species’ activity duration are pivotal factors in accurately replicating observed patterns within mutualistic communities. Furthermore, our exploration of synthetic models underscores the system-specific character of the mechanisms driving phenology, increasing our understanding of the complexities of natural ecosystems.","PeriodicalId":53211,"journal":{"name":"Journal of Physics Complexity","volume":"46 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140932613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The effect of heterogeneous distributions of social norms on the spread of infectious diseases 社会规范的异质分布对传染病传播的影响

IF 2.7

Journal of Physics Complexity Pub Date : 2024-05-12 DOI: 10.1088/2632-072x/ad459f

Daniele Vilone, Eva Vriens and Giulia Andrighetto

引用次数: 0

Amplitude chimeras and bump states with and without frequency entanglement: a toy model 有频率纠缠和无频率纠缠的振幅嵌合体和凹凸态：一个玩具模型

IF 2.7

Journal of Physics Complexity Pub Date : 2024-05-09 DOI: 10.1088/2632-072x/ad4228

A Provata

{"title":"Amplitude chimeras and bump states with and without frequency entanglement: a toy model","authors":"A Provata","doi":"10.1088/2632-072x/ad4228","DOIUrl":"https://doi.org/10.1088/2632-072x/ad4228","url":null,"abstract":"When chaotic oscillators are coupled in complex networks a number of interesting synchronization phenomena emerge. Notable examples are the frequency and amplitude chimeras, chimera death states, solitary states as well as combinations of these. In a previous study (Provata 2020 <italic toggle=\"yes\">J. Phys. Complex.</italic>\u0000<bold>1</bold> 025006), a toy model was introduced addressing possible mechanisms behind the formation of frequency chimera states. In the present study a variation of the toy model is proposed to address the formation of amplitude chimeras. The proposed oscillatory model is now equipped with an additional 3rd order equation modulating the amplitude of the network oscillators. This way, the single oscillators are constructed as bistable in amplitude and depending on the initial conditions their amplitude may result in one of the two stable fixed points. Numerical simulations demonstrate that when these oscillators are nonlocally coupled in networks, they organize in domains with alternating amplitudes (related to the two fixed points), naturally forming amplitude chimeras. A second extension of this model incorporates nonlinear terms merging amplitude together with frequency, and this extension allows for the spontaneous production of composite amplitude-and-frequency chimeras occurring simultaneously in the network. Moreover the extended model allows to understand the emergence of bump states via the continuous passage from chimera states, when both fixed point amplitudes are positive, to bump states when one of the two fixed points vanishes. The synchronization properties of the network are studied as a function of the system parameters for the case of amplitude chimeras, bump states and composite amplitude-and-frequency chimeras. The proposed mechanisms of creating domains with variable amplitudes and/or frequencies provide a generic scenario for understanding the formation of the complex synchronization phenomena observed in networks of coupled nonlinear and chaotic oscillators.","PeriodicalId":53211,"journal":{"name":"Journal of Physics Complexity","volume":"28 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140932441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Spiral wave dynamics in a neuronal network model 神经元网络模型中的螺旋波动动力学

IF 2.7

Journal of Physics Complexity Pub Date : 2024-05-06 DOI: 10.1088/2632-072x/ad42f6

Diogo L M Souza, Fernando S Borges, Enrique C Gabrick, Lucas E Bentivoglio, Paulo R Protachevicz, Vagner dos Santos, Ricardo L Viana, Ibere L Caldas, Kelly C Iarosz, Antonio M Batista and Jürgen Kurths

{"title":"Spiral wave dynamics in a neuronal network model","authors":"Diogo L M Souza, Fernando S Borges, Enrique C Gabrick, Lucas E Bentivoglio, Paulo R Protachevicz, Vagner dos Santos, Ricardo L Viana, Ibere L Caldas, Kelly C Iarosz, Antonio M Batista and Jürgen Kurths","doi":"10.1088/2632-072x/ad42f6","DOIUrl":"https://doi.org/10.1088/2632-072x/ad42f6","url":null,"abstract":"Spiral waves are spatial-temporal patterns that can emerge in different systems as heart tissues, chemical oscillators, ecological networks and the brain. These waves have been identified in the neocortex of turtles, rats, and humans, particularly during sleep-like states. Although their functions in cognitive activities remain until now poorly understood, these patterns are related to cortical activity modulation and contribute to cortical processing. In this work, ,we construct a neuronal network layer based on the spatial distribution of pyramidal neurons. Our main goal is to investigate how local connectivity and coupling strength are associated with the emergence of spiral waves. Therefore, we propose a trustworthy method capable of detecting different wave patterns, based on local and global phase order parameters. As a result, we find that the range of connection radius (R) plays a crucial role in the appearance of spiral waves. For R < 20 µm, only asynchronous activity is observed due to small number of connections. The coupling strength ( ) greatly influences the pattern transitions for higher R, where spikes and bursts firing patterns can be observed in spiral and non-spiral waves. Finally, we show that for some values of R and bistable states of wave patterns are obtained.","PeriodicalId":53211,"journal":{"name":"Journal of Physics Complexity","volume":"19 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140889414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The high-frequency and rare events barriers to neural closures of atmospheric dynamics 大气动力学神经闭合的高频和罕见事件障碍

IF 2.7

Journal of Physics Complexity Pub Date : 2024-04-21 DOI: 10.1088/2632-072x/ad3e59

Mickaël D Chekroun, Honghu Liu, Kaushik Srinivasan and James C McWilliams

引用次数: 0

Taming travel time fluctuations through adaptive stop pooling 通过自适应停靠站集合控制旅行时间波动

IF 2.7

Journal of Physics Complexity Pub Date : 2024-04-10 DOI: 10.1088/2632-072x/ad370a

Charlotte Lotze, Philip Marszal, Malte Schröder, Marc Timme

引用次数: 0

Higher-order connection Laplacians for directed simplicial complexes 有向简并复数的高阶连接拉普拉斯

IF 2.7

Journal of Physics Complexity Pub Date : 2024-03-28 DOI: 10.1088/2632-072x/ad353b

Xue Gong, Desmond J Higham, Konstantinos Zygalakis, Ginestra Bianconi

{"title":"Higher-order connection Laplacians for directed simplicial complexes","authors":"Xue Gong, Desmond J Higham, Konstantinos Zygalakis, Ginestra Bianconi","doi":"10.1088/2632-072x/ad353b","DOIUrl":"https://doi.org/10.1088/2632-072x/ad353b","url":null,"abstract":"Higher-order networks encode the many-body interactions existing in complex systems, such as the brain, protein complexes, and social interactions. Simplicial complexes are higher-order networks that allow a comprehensive investigation of the interplay between topology and dynamics. However, simplicial complexes have the limitation that they only capture undirected higher-order interactions while in real-world scenarios, often there is a need to introduce the direction of simplices, extending the popular notion of direction of edges. On graphs and networks the Magnetic Laplacian, a special case of connection Laplacian, is becoming a popular operator to address edge directionality. Here we tackle the challenge of handling directionality in simplicial complexes by formulating higher-order connection Laplacians taking into account the configurations induced by the simplices’ directions. Specifically, we define all the connection Laplacians of directed simplicial complexes of dimension two and we discuss the induced higher-order diffusion dynamics by considering instructive synthetic examples of simplicial complexes. The proposed higher-order diffusion processes can be adopted in real scenarios when we want to consider higher-order diffusion displaying non-trivial frustration effects due to conflicting directionalities of the incident simplices.","PeriodicalId":53211,"journal":{"name":"Journal of Physics Complexity","volume":"35 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140572522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On the information-theoretic formulation of network participation 关于网络参与的信息论表述

IF 2.7

Journal of Physics Complexity Pub Date : 2024-03-27 DOI: 10.1088/2632-072x/ad32da

Pavle Cajic, Dominic Agius, Oliver M Cliff, James M Shine, Joseph T Lizier, Ben D Fulcher

引用次数: 0

Reconstructing supply networks 重建供应网络

IF 2.7

Journal of Physics Complexity Pub Date : 2024-03-25 DOI: 10.1088/2632-072x/ad30bf

Luca Mungo, Alexandra Brintrup, Diego Garlaschelli, François Lafond

引用次数: 0