arXiv subjects

Jing Zhao

Publications and source records attributed to Jing Zhao.

118 records · Page 7Linked to original sources

arXiv2014

Predicting missing links and their weights via reliable-route-based method

Link prediction aims to uncover missing links or predict the emergence of future relationships according to the current networks structure. Plenty of algorithms have been developed for link prediction in unweighted networks, with only a very few of them having been extended to weighted networks. Thus far, how to predict weights of links is important but rarely studied. In this Letter, we present a reliable-route-based method to extend unweighted local similarity indices to weighted indices and propose a method to predict both the link existence and link weights accordingly. Experiments on different real networks suggest that the weighted resource allocation index has the best performance to predict the existence of links, while the reliable-route-based weighted resource allocation index performs noticeably better on weight prediction. Further analysis shows a strong correlation for both link prediction and weight prediction: the larger the clustering coefficient, the higher the prediction accuracy.

cs.SI↗

arXiv2013

Simulation study on origin of multi-core events in cosmic rays extensive air showers

Some experiments have found multi-core events in cosmic rays extensive air showers which should be interpreted by hadronic interaction theory. In this paper, the multi-core events are reproduced by Monte Carlo simulation with CORSIKA. The origin of each sub-cores is tracked back from the observation level. The interaction mechanism and original particles of sub-core are studied in this paper.

astro-ph.HE↗

arXiv2013

Enhanced Tumor Accumulation of Sub-2 nm Gold Nanoclusters for Cancer Radiation Therapy

A new type of metabolizable and efficient radiosensitizer for cancer radiotherapy is presented in this study by combining ultrasmall Au nanoclusters (NCs, <2 nm) with biocompatible coating ligands (glutathione, GSH). The new nano-construct (GSH-coated Au25 NCs) inherits attractive features of both the Au core (strong radiosensitizing effect) and GSH shell (good biocompatibility). It can preferentially accumulate in tumor via the improved EPR effect, which leads to strong enhancement for cancer radiotherapy. After the treatment, the small-sized GSH-Au25 NCs can be efficiently cleared by the kidney, minimizing any potential side effects due to the accumulation of Au25 NCs in the body.

physics.bio-ph↗

arXiv2013

Topological Structure of Urban Street Networks from the Perspective of Degree Correlations

Many complex networks demonstrate a phenomenon of striking degree correlations, i.e., a node tends to link to other nodes with similar (or dissimilar) degrees. From the perspective of degree correlations, this paper attempts to characterize topological structures of urban street networks. We adopted six urban street networks (three European and three North American), and converted them into network topologies in which nodes and edges respectively represent individual streets and street intersections, and compared the network topologies to three reference network topologies (biological, technological, and social). The urban street network topologies (with the exception of Manhattan) showed a consistent pattern that distinctly differs from the three reference networks. The topologies of urban street networks lack striking degree correlations in general. Through reshuffling the network topologies towards for example maximum or minimum degree correlations while retaining the initial degree distributions, we found that all the surrogate topologies of the urban street networks, as well as the reference ones, tended to deviate from small world properties. This implies that the initial degree correlations do not have any positive or negative effect on the networks' performance or functions. Keywords: Scale free, small world, rewiring, rich club effect, reshuffle, and complex networks

physics.soc-ph↗

arXiv2009

Three faces of metabolites: Pathways, localizations and network positions

To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed description of the organization of metabolism. In this study, we investigate the relative organization of three categorizations of metabolites -- pathways, subcellular localizations and network clusters, by block-model techniques borrowed from social-network studies and further characterize the categories from topological point of view. The picture of the metabolism we obtain is that of peripheral modules, characterized both by being dense network clusters and localized to organelles, connected by a central, highly connected core. Pathways typically run through several network clusters and localizations, connecting them laterally. The strong overlap between organelles and network clusters suggest that these are natural "modules" -- relatively independent sub-systems. The different categorizations divide the core metabolism differently suggesting that this, if possible, should be not be treated as a module on par with the organelles. Although overlapping more than chance, none of the pathways correspond very closely to a network cluster or localization. This, we believe, highlights the benefits of different orthogonal classifications and future experimental categorizations based on simple principles.

q-bio.MN↗

arXiv2007

Modular co-evolution of metabolic networks

The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular network affects the evolution of its member proteins remains unclear. In this work, the functional and evolutionary modularity of Homo sapiens (H. sapiens) metabolic network were investigated from a topological point of view. Network decomposition shows that the metabolic network is organized in a highly modular core-periphery way, in which the core modules are tightly linked together and perform basic metabolism functions, whereas the periphery modules only interact with few modules and accomplish relatively independent and specialized functions. Moreover, over half of the modules exhibit co-evolutionary feature and belong to specific evolutionary ages. Peripheral modules tend to evolve more cohesively and faster than core modules do. The correlation between functional, evolutionary and topological modularity suggests that the evolutionary history and functional requirements of metabolic systems have been imprinted in the architecture of metabolic networks. Such systems level analysis could demonstrate how the evolution of genes may be placed in a genome-scale network context, giving a novel perspective on molecular evolution.

q-bio.MN↗

arXiv2007

The effects of degree correlations on network topologies and robustness

Complex networks have been applied to model numerous interactive nonlinear systems in the real world. Knowledge about network topology is crucial for understanding the function, performance and evolution of complex systems. In the last few years, many network metrics and models have been proposed to illuminate the network topology, dynamics and evolution. Since these network metrics and models derive from a wide range of studies, a systematic study is required to investigate the correlations between them. The present paper explores the effect of degree correlation on the other network metrics through studying an ensemble of graphs where the degree sequence (set of degrees) is fixed. We show that to some extent, the characteristic path length, clustering coefficient, modular extent and robustness of networks are directly influenced by the degree correlation.

physics.soc-ph↗

arXiv2006

Exploring the assortativity-clustering space of a network's degree sequence

Nowadays there is a multitude of measures designed to capture different aspects of network structure. To be able to say if the structure of certain network is expected or not, one needs a reference model (null model). One frequently used null model is the ensemble of graphs with the same set of degrees as the original network. In this paper we argue that this ensemble can be more than just a null model -- it also carries information about the original network and factors that affect its evolution. By mapping out this ensemble in the space of some low-level network structure -- in our case those measured by the assortativity and clustering coefficients -- one can for example study how close to the valid region of the parameter space the observed networks are. Such analysis suggests which quantities are actively optimized during the evolution of the network. We use four very different biological networks to exemplify our method. Among other things, we find that high clustering might be a force in the evolution of protein interaction networks. We also find that all four networks are conspicuously robust to both random errors and targeted attacks.

q-bio.OT↗

arXiv2006

Hierarchical modularity of nested bow-ties in metabolic networks

The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural characteristics of complex metabolic networks.In this work, metabolic networks of 75 organisms were investigated from a topological point of view. Network decomposition of three microbes (Escherichia coli, Aeropyrum pernix and Saccharomyces cerevisiae) shows that almost all of the sub-networks exhibit a highly modularized bow-tie topological pattern similar to that of the global metabolic networks. Moreover, these small bow-ties are hierarchically nested into larger ones and collectively integrated into a large metabolic network, and important features of this modularity are not observed in the random shuffled network. In addition, such a bow-tie pattern appears to be present in certain chemically isolated functional modules and spatially separated modules including carbohydrate metabolism, cytosol and mitochondrion respectively. The highly modularized bow-tie pattern is present at different levels and scales, and in different chemical and spatial modules of metabolic networks, which is likely the result of the evolutionary process rather than a random accident. Identification and analysis of such a pattern is helpful for understanding the design principles and facilitate the modelling of metabolic networks.

q-bio.MN↗

arXiv2006

Complex networks theory for analyzing metabolic networks

One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing principles that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.

q-bio.MN↗