Journal of Physics Complexity最新文献_第9页

A scientific portrait of Giorgio Parisi: complex systems and much more 乔治·帕里西的科学肖像：复杂的系统和更多

IF 2.7

Journal of Physics Complexity Pub Date : 2023-03-01 DOI: 10.1088/2632-072X/acb8a1

L. Cugliandolo

引用次数: 3

Exploring 3D community inconsistency in human chromosome contact networks 探索人类染色体接触网络中的三维群落不一致性

IF 2.7

Journal of Physics Complexity Pub Date : 2023-02-28 DOI: 10.1088/2632-072X/acef9d

Dolores Bernenko, Sang Hoon Lee, L. Lizana

{"title":"Exploring 3D community inconsistency in human chromosome contact networks","authors":"Dolores Bernenko, Sang Hoon Lee, L. Lizana","doi":"10.1088/2632-072X/acef9d","DOIUrl":"https://doi.org/10.1088/2632-072X/acef9d","url":null,"abstract":"Researchers have developed chromosome capture methods such as Hi-C to better understand DNA’s 3D folding in nuclei. The Hi-C method captures contact frequencies between DNA segment pairs across the genome. When analyzing Hi-C data sets, it is common to group these pairs using standard bioinformatics methods (e.g. PCA). Other approaches handle Hi-C data as weighted networks, where connected node pairs represent DNA segments in 3D proximity. In this representation, one can leverage community detection techniques developed in complex network theory to group nodes into mesoscale communities containing nodes with similar connection patterns. While there are several successful attempts to analyze Hi-C data in this way, it is common to report and study the most typical community structure. But in reality, there are often several valid candidates. Therefore, depending on algorithm design, different community detection methods focusing on slightly different connectivity features may have differing views on the ideal node groupings. In fact, even the same community detection method may yield different results if using a stochastic algorithm. This ambiguity is fundamental to community detection and shared by most complex networks whenever interactions span all scales in the network. This is known as community inconsistency. This paper explores this inconsistency of 3D communities in Hi-C data for all human chromosomes. We base our analysis on two inconsistency metrics, one local and one global, and quantify the network scales where the community separation is most variable. For example, we find that TADs are less reliable than A/B compartments and that nodes with highly variable node-community memberships are associated with open chromatin. Overall, our study provides a helpful framework for data-driven researchers and increases awareness of some inherent challenges when clustering Hi-C data into 3D communities.","PeriodicalId":53211,"journal":{"name":"Journal of Physics Complexity","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44751293","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

Production process networks: a trophic analysis 生产过程网络:营养分析

IF 2.7

Journal of Physics Complexity Pub Date : 2023-02-20 DOI: 10.1088/2632-072X/acbd7c

Aurélien Hazan

引用次数: 0

Measuring the pitch control of professional football players using spatiotemporal tracking data 利用时空跟踪数据测量职业足球运动员的球场控制能力

IF 2.7

Journal of Physics Complexity Pub Date : 2023-01-26 DOI: 10.1088/2632-072X/acb67d

Lewis Higgins, T. Galla, Brian Prestidge, T. Wyatt

{"title":"Measuring the pitch control of professional football players using spatiotemporal tracking data","authors":"Lewis Higgins, T. Galla, Brian Prestidge, T. Wyatt","doi":"10.1088/2632-072X/acb67d","DOIUrl":"https://doi.org/10.1088/2632-072X/acb67d","url":null,"abstract":"We study pitch control in football, using data from six complete seasons of the English Premier League. Our objective is to investigate features of pitch control in the data. We process the data to ensure consistency of the tracking and event datasets. This represents the largest coherent dataset analysed in the literature and allows the observation of consistent patterns across several seasons’ data. We demonstrate that teams playing in front of a crowd at home control on average 2.9±0.2% more of the pitch than teams playing away, which reduces to 1.5±0.6% in matches played behind closed doors. We observe that match by match the difference in pitch control between the teams has a weak, positive correlation with the difference in expected goals (Pearson correlation R = 0.38). As a further manifestation of home advantage we find that in games which the two teams have equal pitch control, on average the home team accumulates greater expected goals ( 0.16±0.03 ). The concept of weighted pitch control is introduced, by assigning a weight to regions of the pitch. We demonstrate that pitch control of the penalty box of the out-of-possession team is negatively correlated with expected goals in each of the six seasons, and interpret this apparently counter-intuitive result.","PeriodicalId":53211,"journal":{"name":"Journal of Physics Complexity","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45813186","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

Complex systems in the spotlight: next steps after the 2021 Nobel Prize in Physics 聚光灯下的复杂系统:2021年诺贝尔物理学奖后的下一步

IF 2.7

Journal of Physics Complexity Pub Date : 2023-01-16 DOI: 10.1088/2632-072X/ac7f75

G. Bianconi, A. Arenas, J. Biamonte, L. Carr, B. Kahng, J. Kertész, Jürgen Kurths, Linyuan Lü, C. Masoller, A. Motter, M. Perc, F. Radicchi, R. Ramaswamy, Francisco A Rodrigues, M. Sales-Pardo, M. San Miguel, S. Thurner, T. Yasseri

引用次数: 13

Meaningful local signalling in sinoatrial node identified by random matrix theory and PCA 应用随机矩阵理论和主成分分析识别窦房结有意义的局部信号

IF 2.7

Journal of Physics Complexity Pub Date : 2023-01-01 DOI: 10.1088/2632-072X/acadc8

Chloe F. Norris, A. Maltsev

{"title":"Meaningful local signalling in sinoatrial node identified by random matrix theory and PCA","authors":"Chloe F. Norris, A. Maltsev","doi":"10.1088/2632-072X/acadc8","DOIUrl":"https://doi.org/10.1088/2632-072X/acadc8","url":null,"abstract":"The sinoatrial node (SAN) is the pacemaker of the heart. Recently calcium signals, believed to be crucially important in rhythm generation, have been imaged in intact SAN and shown to be heterogeneous in various regions of the SAN with a lot of analysis relying on visual inspection rather than mathematical tools. Here we apply methods of random matrix theory (RMT) developed for financial data and various biological data sets including β-cell collectives and electroencephalograms (EEG) to analyse correlations in SAN calcium signals using eigenvalues and eigenvectors of the correlation matrix. We use principal component analysis to locate signalling modules corresponding to localization properties the eigenvectors corresponding to high eigenvalues. We find that the top eigenvector captures the global behaviour of the SAN i.e. action potential (AP) induced calcium transient. In some cases, the eigenvector corresponding to the second highest eigenvalue yields a pacemaker region whose calcium signals predict the AP. Furthermore, using new analytic methods, we study the relationship between covariance coefficients and distance, and find that even inside the central zone, there are non-trivial long range correlations, indicating intercellular interactions in most cases. Lastly, we perform an analysis of nearest-neighbour eigenvalue distances and find that it coincides with universal Wigner surmise under all available experimental conditions, while the number variance, which captures eigenvalue correlations, is sensitive to experimental conditions. Thus RMT application to SAN allows to remove noise and the global effects of the AP-induced calcium transient and thereby isolate the local and meaningful correlations in calcium signalling.","PeriodicalId":53211,"journal":{"name":"Journal of Physics Complexity","volume":"4 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61190590","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: 1

Inferring directional interactions in collective dynamics: a critique to intrinsic mutual information 推断集体动力中的定向相互作用:对内在相互信息的批判

IF 2.7

Journal of Physics Complexity Pub Date : 2022-12-19 DOI: 10.1088/2632-072X/acace0

Pietro De Lellis, Manuel Ruiz Marín, M. Porfiri

引用次数: 0

Ecological Analogy for Generative Adversarial Networks and Diversity Control 生成对抗性网络的生态类比与多样性控制

IF 2.7

Journal of Physics Complexity Pub Date : 2022-12-19 DOI: 10.1088/2632-072X/acacdf

K. Nakazato

引用次数: 1

Directed random geometric graphs: structural and spectral properties 有向随机几何图：结构和谱性质

IF 2.7

Journal of Physics Complexity Pub Date : 2022-12-19 DOI: 10.1088/2632-072X/acace1

K. Peralta-Martinez, J. A. Méndez-Bermúdez

{"title":"Directed random geometric graphs: structural and spectral properties","authors":"K. Peralta-Martinez, J. A. Méndez-Bermúdez","doi":"10.1088/2632-072X/acace1","DOIUrl":"https://doi.org/10.1088/2632-072X/acace1","url":null,"abstract":"In this work we analyze structural and spectral properties of a model of directed random geometric graphs: given n vertices uniformly and independently distributed on the unit square, a directed edge is set between two vertices if their distance is smaller than the connection radius ℓ , which is randomly drawn from a Pareto distribution. This Pareto distribution is characterized by the power-law decay α and the lower bound of its support ℓ0 ; thus the graphs depend on three parameters G(n,α,ℓ0) . By increasing ℓ0 , for fixed (n,α) , the model transits from isolated vertices ( ℓ0≈0 ) to complete graphs ( ℓ0=2 ). We first propose a phenomenological expression for the average degree ⟨k(G)⟩ which works well for α > 3, when k is a self-averaging quantity. Then we numerically demonstrate that 〈Vx(G)〉≈n[1−exp(−〈k〉] , for all α, where Vx(G) is the number of nonisolated vertices of G. Finally, we explore the spectral properties of G(n,α,ℓ0) by the use of adjacency matrices represented by diluted random matrix ensembles; a non-Hermitian and a Hermitian one. We find that ⟨k⟩ is a good scaling parameter of spectral and eigenvector properties of G mainly for large α.","PeriodicalId":53211,"journal":{"name":"Journal of Physics Complexity","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2022-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46182837","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: 1

Formation of trade networks by economies of scale and product differentiation 通过规模经济和产品差异化形成贸易网络

IF 2.7

Journal of Physics Complexity Pub Date : 2022-12-06 DOI: 10.1088/2632-072X/acc91f

Chengyuan Han, Malte Schröder, D. Witthaut, Philipp C. Böttcher

引用次数: 0