A generalised significance test for individual communities in networks

Many empirical networks have community structure, in which nodes are densely interconnected within each community (i.e., a group of nodes) and sparsely across different communities. Like other local and meso-scale structure of networks, communities are generally heterogeneous in various aspects such as the size, density of edges, connectivity to other communities and significance. In the present study, we propose a method to statistically test the significance of individual communities in a given network. Compared to the previous methods, the present algorithm is unique in that it accepts different community-detection algorithms and the corresponding quality function for single communities. The present method requires that a quality of each community can be quantified and that community detection is performed as optimisation of such a quality function summed over the communities. Various community detection algorithms including modularity maximisation and graph partitioning meet this criterion. Our method estimates a distribution of the quality function for randomised networks to calculate a likelihood of each community in the given network. We illustrate our algorithm by synthetic and empirical networks.Comment: 20 pages, 4 figures and 4 table

Finding multiple core-periphery pairs in networks

With a core-periphery structure of networks, core nodes are densely interconnected, peripheral nodes are connected to core nodes to different extents, and peripheral nodes are sparsely interconnected. Core-periphery structure composed of a single core and periphery has been identified for various networks. However, analogous to the observation that many empirical networks are composed of densely interconnected groups of nodes, i.e., communities, a network may be better regarded as a collection of multiple cores and peripheries. We propose a scalable algorithm to detect multiple non-overlapping groups of core-periphery structure in a network. We illustrate our algorithm using synthesised and empirical networks. For example, we find distinct core-periphery pairs with different political leanings in a network of political blogs and separation between international and domestic subnetworks of airports in some single countries in a world-wide airport network.Comment: 11 figures and 9 tables. MATLAB codes are available at www.naokimasuda.net/cp_codes.zi

Configuration model for correlation matrices preserving the node strength

Correlation matrices are a major type of multivariate data. To examine properties of a given correlation matrix, a common practice is to compare the same quantity between the original correlation matrix and reference correlation matrices, such as those derived from random matrix theory, that partially preserve properties of the original matrix. We propose a model to generate such reference correlation and covariance matrices for the given matrix. Correlation matrices are often analysed as networks, which are heterogeneous across nodes in terms of the total connectivity to other nodes for each node. Given this background, the present algorithm generates random networks that preserve the expectation of total connectivity of each node to other nodes, akin to configuration models for conventional networks. Our algorithm is derived from the maximum entropy principle. We will apply the proposed algorithm to measurement of clustering coefficients and community detection, both of which require a null model to assess the statistical significance of the obtained results.Comment: 8 figures, 4 table

Comparative Study of Lipid Composition of Candida albicans in the Yeast and Mycelial Forms

Candida albicans was grown in the yeast and mycelial forms in the same conditions except keeping the temperature of the medium at 25°C for the yeast form and 37°C for the mycelial form, respectively, and the lipid composition of the organism in the two forms was studied comparatively. The contents of fatty acids, phospholipids, sterols (except zymosterol) and squalene of the mycelial form of the fungus per DNA were found to be significantly higher than those in the yeast form. Furthermore, in the yeast form the relative composition of the fatty acids which are considered to be the further metabolites of the nascent palmitic acid, e.g. C18:0, C18:1, C18:2, and C18:3, were higher than those in the mycelial form, whereas that of fatty acids such as C16:0 and C16:1 were higher in the mycelial form. These results seem to suggest an immaturity in lipid composition of the mycelial form compared to that in the yeast form. Essentially a similar result was obtained with [2-^14C]acetate added in culture media. Such an immaturity might be due to the increased biosynthesis of lipids in the mycelial form of C. albicans

Structural changes in the interbank market across the financial crisis from multiple core-periphery analysis

Interbank markets are often characterised in terms of a core-periphery network structure, with a highly interconnected core of banks holding the market together, and a periphery of banks connected mostly to the core but not internally. This paradigm has recently been challenged for short time scales, where interbank markets seem better characterised by a bipartite structure with more core-periphery connections than inside the core. Using a novel core-periphery detection method on the eMID interbank market, we enrich this picture by showing that the network is actually characterised by multiple core-periphery pairs. Moreover, a transition from core-periphery to bipartite structures occurs by shortening the temporal scale of data aggregation. We further show how the global financial crisis transformed the market, in terms of composition, multiplicity and internal organisation of core-periphery pairs. By unveiling such a fine-grained organisation and transformation of the interbank market, our method can find important applications in the understanding of how distress can propagate over financial networks.Comment: 17 pages, 9 figures, 1 tabl

1. Cumhuriyet'in B. M. Meclisinde söylenen son nutuk:Osman Bölükbaşı

Taha Toros Arşivi, Dosya No: 256-Osman Bölükbaş

The effectiveness of backward contact tracing in networks

Discovering and isolating infected individuals is a cornerstone of epidemic control. Because many infectious diseases spread through close contacts, contact tracing is a key tool for case discovery and control. However, although contact tracing has been performed widely, the mathematical understanding of contact tracing has not been fully established and it has not been clearly understood what determines the efficacy of contact tracing. Here, we reveal that, compared with "forward" tracing---tracing to whom disease spreads, "backward" tracing---tracing from whom disease spreads---is profoundly more effective. The effectiveness of backward tracing is due to simple but overlooked biases arising from the heterogeneity in contacts. Using simulations on both synthetic and high-resolution empirical contact datasets, we show that even at a small probability of detecting infected individuals, strategically executed contact tracing can prevent a significant fraction of further transmissions. We also show that---in terms of the number of prevented transmissions per isolation---case isolation combined with a small amount of contact tracing is more efficient than case isolation alone. By demonstrating that backward contact tracing is highly effective at discovering super-spreading events, we argue that the potential effectiveness of contact tracing has been underestimated. Therefore, there is a critical need for revisiting current contact tracing strategies so that they leverage all forms of biases. Our results also have important consequences for digital contact tracing because it will be crucial to incorporate the capability for backward and deep tracing while adhering to the privacy-preserving requirements of these new platforms.Comment: 15 pages, 4 figure

The Sources of Wealth and Future of the Constitution in The Spirit of the Laws: The Implicit Contrast Between Eighteenth-Century England and the Late Roman Republic

The most famous chapter of Montesquieu’s The Spirit of the Laws (1748), Book XI, Chapter 6, 'On the constitution of England,' was an important inspiration to the creators of modern constitutions, to which they often referred. However, as a result of scholarly focus on the political institutions discussed in this book, Montesquieu’s economic analysis has been woefully neglected. In order to correct this scholarly imbalance, this paper will elucidate the essential significance of Montesquieu’s comparison between the constitution of modern England and that of ancient Rome in Book XI of The Spirit of the Laws; inextricable relationship between military and political institutions on the one hand, and the transfer and distribution of wealth on the other. To argue this point, this paper will focus on Montesquieu’s other writings in the same year and shortly after the publication of The Spirit of the Laws: the revised edition in 1748 of The Considerations on the Causes of the Greatness of the Romans and their Decline (1734), for example, included substantial additions to the first edition, much of which was centered on the sources and distribution of wealth in ancient Rome. Secondly, an important letter to William Domville, a friend of Montesquieu in England, drafted in 1749 but never sent, contrasts the military despotism of late republican Rome with the freedom of 18th century England, attributing much of the differences to the two nations’ sources of wealth. By referring to these two writings, we can understand that unlike the political system of republican Rome, which was finally transformed into a military despotism, Montesquieu believes that the main reason why the English had been able to maintain their liberty and the rule of law resides in the way they acquired wealth. The source of the Romans' wealth was the plunder and taxation of conquered nations, and the resulting extreme inequality of wealth caused the collapse of their republican regime. The English, on the other hand, sought their sources of wealth in their proper industry and commerce, without recourse to military force, and by accumulating small profits over a long term, created a 'middle class' which became the bearers of both political freedom and the rule of law in the country. From the above analysis, this paper reveals the broader context in which Montesquieu’s views of political economy in The Spirit of the Laws, must be seen: i.e., the distribution of political power and the distribution of wealth are discussed as inseparable.Le livre XI, chapitre 6, intitulé 'De la constitution d'Angleterre' est le chapitre le plus célèbre de L'Esprit des lois de Montesquieu (1748), et a été une source d'inspiration importante pour les constitutions modernes, auquel leurs auteurs se sont souvent référés. Cependant, en raison de l'attention portée par les chercheurs aux institutions politiques décrites dans cet ouvrage, l'analyse économique de Montesquieu a été malheurement négligée. Afin de corriger cet oubli, l'article élucidera la signification essentielle de la comparaison faite par Montesquieu entre la constitution de l'Angleterre moderne et celle de la Rome antique dans le livre XI de L'Esprit des lois, c'est-à-dire la relation inextricable entre les institutions militaires et politiques, d'une part, et le transfert et la distribution des richesses, d'autre part. Pour démontrer ce point, l'article se concentrera sur les autres textes de Montesquieu, écrits au moment de la publication de L'Esprit des lois : l'édition révisée en 1748 des Considérations sur les causes de la grandeur des Romains et de leur décadence (1734), par exemple, comportait des ajouts substantiels par rapport à la première édition, dont une grande partie était centrée sur les sources et la répartition des richesses dans la Rome antique. Deuxièmement, une lettre à William Domville, un ami de Montesquieu en Angleterre, rédigée en 1749, mais jamais envoyée, oppose le despotisme militaire de la Rome républicaine tardive à la liberté de l'Angleterre du XVIIIe siècle, attribuant une grande partie des différences aux sources de richesse des deux nations. En se référant à ces deux écrits, on peut comprendre que contrairement au système politique de la Rome républicaine, qui s'est finalement transformé en un despotisme militaire, Montesquieu estime que la principale raison pour laquelle les Anglais ont su maintenir leurs liberté et constitution réside dans la manière dont ils ont acquis des richesses. La richesse des Romains provenait du pillage et de l'imposition des nations conquises, et l'extrême inégalité des richesses qui en résultait a provoqué l'effondrement de leur régime républicain. Les Anglais, quant à eux, trouvaient leurs sources de richesse dans l'industrie et le commerce, sans s'appuyer sur la force militaire, et en accumulant profits sur le long terme, ils ont créé une 'classe moyenne' qui est devenue porteuse à la fois de la liberté politique et de respect de l'état de droit dans ce pays. Cet article révèle ainsi le contexte plus large dans lequel les vues de Montesquieu sur l'économie politique dans L'Esprit des lois doivent être considérées, à savoir que la distribution du pouvoir politique et la distribution des richesses sont indissociables

Detecting anomalous citation groups in journal networks

The ever-increasing competitiveness in the academic publishing market incentivizes journal editors to pursue higher impact factors. This translates into journals becoming more selective, and, ultimately, into higher publication standards. However, the fixation on higher impact factors leads some journals to artificially boost impact factors through the coordinated effort of a “citation cartel” of journals. “Citation cartel” behavior has become increasingly common in recent years, with several instances being reported. Here, we propose an algorithm—named CIDRE—to detect anomalous groups of journals that exchange citations at excessively high rates when compared against a null model that accounts for scientific communities and journal size. CIDRE detects more than half of the journals suspended from Journal Citation Reports due to anomalous citation behavior in the year of suspension or in advance. Furthermore, CIDRE detects many new anomalous groups, where the impact factors of the member journals are lifted substantially higher by the citations from other member journals. We describe a number of such examples in detail and discuss the implications of our findings with regard to the current academic climate