Spectral Learning Algorithm Reveals Propagation Capability of Complex Networks

Influential nodes identification method based on adaptive adjustment of voting ability

Influential nodes identification technology is one of the important topics which has been widely applied to logistics node location, social information dissemination, transportation network carrying, biological virus dissemination, power network anti-destruction, etc. At present, a large number of influential nodes identification methods have been studied, but the algorithms that are simple to execute, have high accuracy and can be better applied to real networks are still the focus of research. Therefore, due to the advantages of simple to execute in voting mechanism, a novel algorithm based on adaptive adjustment of voting ability (AAVA) to identify the influential nodes is presented by considering the local attributes of node and the voting contribution of its neighbor nodes, to solve the problem of low accuracy and discrimination of the existing algorithms. This proposed algorithm uses the similarity between the voting node and the voted node to dynamically adjust its voting ability without setting any parameters, so that a node can contribute different voting abilities to different neighbor nodes. To verify the performance of AAVA algorithm, the running results of 13 algorithms are analyzed and compared on 10 different networks with the SIR model as a reference. The experimental results show that the influential nodes identified by AAVA have high consistency with SIR model in Top-10 nodes and Kendall correlation, and have better infection effect of the network. Therefore, it is proved that AAV algorithm has high accuracy and effectiveness, and can be applied to real complex networks of different types and sizes.

Interlayer Link Prediction in Multiplex Social Networks Based on Multiple Types of Consistency Between Embedding Vectors

Online users are typically active on multiple social media networks (SMNs), which constitute a multiplex social network. With improvements in cybersecurity awareness, users increasingly choose different usernames and provide different profiles on different SMNs. Thus, it is becoming increasingly challenging to determine whether given accounts on different SMNs belong to the same user; this can be expressed as an interlayer link prediction problem in a multiplex network. To address the challenge of predicting interlayer links, feature or structure information is leveraged. Existing methods that use network embedding techniques to address this problem focus on learning a mapping function to unify all nodes into a common latent representation space for prediction; positional relationships between unmatched nodes and their common matched neighbors (CMNs) are not utilized. Furthermore, the layers are often modeled as unweighted graphs, ignoring the strengths of the relationships between nodes. To address these limitations, we propose a framework based on multiple types of consistency between embedding vectors (MulCEVs). In MulCEV, the traditional embedding-based method is applied to obtain the degree of consistency between the vectors representing the unmatched nodes, and a proposed distance consistency index based on the positions of nodes in each latent space provides additional clues for prediction. By associating these two types of consistency, the effective information in the latent spaces is fully utilized. In addition, MulCEV models the layers as weighted graphs to obtain representation. In this way, the higher the strength of the relationship between nodes, the more similar their embedding vectors in the latent representation space will be. The results of our experiments on several real-world and synthetic datasets demonstrate that the proposed MulCEV framework markedly outperforms current embedding-based methods, especially when the number of training iterations is small.

Identification of Network Topology Variations Based on Spectral Entropy

Based on the fact that the traditional probability distribution entropy describing a local feature of the system cannot effectively capture the global topology variations of the network, some indicators constructed by the network adjacency matrix and Laplacian matrix come into being. Specifically, these measures are based on the eigenvalues of the scaled Laplace matrix, the eigenvalues of the network communicability matrix, and the spectral entropy based on information diffusion that has been proposed recently, respectively. In this article, we systematically study the dependence of these measures on the topological structure of the network. We prove from various aspects that spectral entropy has a better ability to identify the global topology than the traditional distribution entropy. Furthermore, the indicator based on the eigenvalues of the network communicability matrix achieves good results in some aspects while, overall, the spectral entropy is able to identify network topology variations from a global perspective.

Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications

Gene co-expression network (GCN) becomes an increasingly important tool in omics data analysis. A great challenge for GCN construction is that the sample size is far lower than the number of genes. Traditional methods rely on considerable samples. Moreover, association signals are likely weak, nonlinear and stochastic, which are difficult to be identified among thousands of candidates. In this paper, the gray correlation coefficient (GCC) is introduced, and a novel method to construct gene differential co-expression networks (GDCNs) is proposed. Based on the GDCNs, three measures are proposed to explore informative genes. The proposed method can make full use of the information provided by a handful of samples and overcome the shortages of GCNs, which can evaluate the changes of co-expression relationships that are possibly triggered by treatments. Based on RNA-seq data of Brassica napus, GDCNs under multiple experimental conditions are constructed and investigated. It is found that the GCC-based method is very robust to data processing. The GDCNs facilitate the inference of gene functions and the identification of informative genes that are responsible for stress responsiveness. The GDCN-based approaches integrate the 'guilt by association' and the 'guilt by rewiring' rules, which provide alternative tools for omics data analysis.

Data analysis methods for defining biomarkers from omics data

Omics mainly includes genomics, epigenomics, transcriptomics, proteomics and metabolomics. The rapid development of omics technology has opened up new ways to study disease diagnosis and prognosis and to define prospective information of complex diseases. Since omics data are usually large and complex, the method used to analyze the data and to define important information is crucial in omics study. In this review, we focus on advances in biomarker discovery methods based on omics data in the last decade, and categorize them as individual feature analysis, combinatorial feature analysis and network analysis. We also discuss the challenges and perspectives in this field.

Statistical Identification of Important Nodes in Biological Systems

Biological systems can be modeled and described by biological networks. Biological networks are typical complex networks with widely real-world applications. Many problems arising in biological systems can be boiled down to the identification of important nodes. For example, biomedical researchers frequently need to identify important genes that potentially leaded to disease phenotypes in animal and explore crucial genes that were responsible for stress responsiveness in plants. To facilitate the identification of important nodes in biological systems, one needs to know network structures or behavioral data of nodes (such as gene expression data). If network topology was known, various centrality measures can be developed to solve the problem; while if only behavioral data of nodes were given, some sophisticated statistical methods can be employed. This paper reviewed some of the recent works on statistical identification of important nodes in biological systems from three aspects, that is, 1) in general complex networks based on complex networks theory and epidemic dynamic models; 2) in biological networks based on network motifs; and 3) in plants based on RNA-seq data. The identification of important nodes in a complex system can be seen as a mapping from the system to the ranking score vector of nodes, such mapping is not necessarily with explicit form. The three aspects reflected three typical approaches on ranking nodes in biological systems and can be integrated into one general framework. This paper also proposed some challenges and future works on the related topics. The associated investigations have potential real-world applications in the control of biological systems, network medicine and new variety cultivation of crops.

Evolutionary Divide-and-Conquer Algorithm for Virus Spreading Control Over Networks

The control of virus spreading over complex networks with a limited budget has attracted much attention but remains challenging. This article aims at addressing the combinatorial, discrete resource allocation problems (RAPs) in virus spreading control. To meet the challenges of increasing network scales and improve the solving efficiency, an evolutionary divide-and-conquer algorithm is proposed, namely, a coevolutionary algorithm with network-community-based decomposition (NCD-CEA). It is characterized by the community-based dividing technique and cooperative coevolution conquering thought. First, to reduce the time complexity, NCD-CEA divides a network into multiple communities by a modified community detection method such that the most relevant variables in the solution space are clustered together. The problem and the global swarm are subsequently decomposed into subproblems and subswarms with low-dimensional embeddings. Second, to obtain high-quality solutions, an alternative evolutionary approach is designed by promoting the evolution of subswarms and the global swarm, in turn, with subsolutions evaluated by local fitness functions and global solutions evaluated by a global fitness function. Extensive experiments on different networks show that NCD-CEA has a competitive performance in solving RAPs. This article advances toward controlling virus spreading over large-scale networks.

Epidemic Propagation With Positive and Negative Preventive Information in Multiplex Networks

We propose a novel epidemic model based on two-layered multiplex networks to explore the influence of positive and negative preventive information on epidemic propagation. In the model, one layer represents a social network with positive and negative preventive information spreading competitively, while the other one denotes the physical contact network with epidemic propagation. The individuals who are aware of positive prevention will take more effective measures to avoid being infected than those who are aware of negative prevention. Taking the microscopic Markov chain (MMC) approach, we analytically derive the expression of the epidemic threshold for the proposed epidemic model, which indicates that the diffusion of positive and negative prevention information, as well as the topology of the physical contact network have a significant impact on the epidemic threshold. By comparing the results obtained with MMC and those with the Monte Carlo (MC) simulations, it is found that they are in good agreement, but MMC can well describe the dynamics of the proposed model. Meanwhile, through extensive simulations, we demonstrate the impact of positive and negative preventive information on the epidemic threshold, as well as the prevalence of infectious diseases. We also find that the epidemic prevalence and the epidemic outbreaks can be suppressed by the diffusion of positive preventive information and be promoted by the diffusion of negative preventive information.

Statistical Identification of Important Nodes in Biological Systems

Biological systems can be modeled and described by biological networks. Biological networks are typical complex networks with widely real-world applications. Many problems arising in biological systems can be boiled down to the identification of important nodes. For example, biomedical researchers frequently need to identify important genes that potentially leaded to disease phenotypes in animal and explore crucial genes that were responsible for stress responsiveness in plants. To facilitate the identification of important nodes in biological systems, one needs to know network structures or behavioral data of nodes (such as gene expression data). If network topology was known, various centrality measures can be developed to solve the problem; while if only behavioral data of nodes were given, some sophisticated statistical methods can be employed. This paper reviewed some of the recent works on statistical identification of important nodes in biological systems from three aspects, that is, 1) in general complex networks based on complex networks theory and epidemic dynamic models; 2) in biological networks based on network motifs; and 3) in plants based on RNA-seq data. The identification of important nodes in a complex system can be seen as a mapping from the system to the ranking score vector of nodes, such mapping is not necessarily with explicit form. The three aspects reflected three typical approaches on ranking nodes in biological systems and can be integrated into one general framework. This paper also proposed some challenges and future works on the related topics. The associated investigations have potential real-world applications in the control of biological systems, network medicine and new variety cultivation of crops.

Statistical and network analysis of 1212 COVID-19 patients in Henan, China

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Almost all currently infected COVID-19 patients in Henan province were analyzed.

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COVID-19 patients in Henan province show gender and age preferences, migrant workers or college students are at high risk.

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The incubation period was statistically estimated.

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The state transition diagram can reveal the time-phased nature of the COVID-19 epidemic.

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Network analysis reveals the aggregate outbreak phenomena of COVID-19.

Background

COVID-19 is spreading quickly all over the world. Publicly released data for 1212 COVID-19 patients in Henan of China were analyzed in this paper.

Methods

Various statistical and network analysis methods were employed.

Results

We found that COVID-19 patients show gender (55% vs 45%) and age (81% aged between 21 and 60) preferences; possible causes were explored. The estimated average, mode and median incubation periods are 7.4, 4 and 7 days. Incubation periods of 92% of patients were no more than 14 days. The epidemic in Henan has undergone three stages and has shown high correlations with the numbers of patients recently returned from Wuhan. Network analysis revealed that 208 cases were clustering infected, and various People's Hospitals are the main force in treating COVID-19.

Conclusions

The incubation period was statistically estimated, and the proposed state transition diagram can explore the epidemic stages of emerging infectious disease. We suggest that although the quarantine measures are gradually working, strong measures still might be needed for a period of time, since ∼7.45% of patients may have very long incubation periods. Migrant workers or college students are at high risk. State transition diagrams can help us to recognize the time-phased nature of the epidemic. Our investigations have implications for the prevention and control of COVID-19 in other regions of the world.

A new SAIR model on complex networks for analysing the 2019 novel coronavirus (COVID-19)

Nowadays, the novel coronavirus (COVID-19) is spreading around the world and has attracted extremely wide public attention. From the beginning of the outbreak to now, there have been many mathematical models proposed to describe the spread of the pandemic, and most of them are established with the assumption that people contact with each other in a homogeneous pattern. However, owing to the difference of individuals in reality, social contact is usually heterogeneous, and the models on homogeneous networks cannot accurately describe the outbreak. Thus, we propose a susceptible-asymptomatic-infected-removed (SAIR) model on social networks to describe the spread of COVID-19 and analyse the outbreak based on the epidemic data of Wuhan from January 24 to March 2. Then, according to the results of the simulations, we discover that the measures that can curb the spread of COVID-19 include increasing the recovery rate and the removed rate, cutting off connections between symptomatically infected individuals and their neighbours, and cutting off connections between hub nodes and their neighbours. The feasible measures proposed in the paper are in fair agreement with the measures that the government took to suppress the outbreak. Furthermore, effective measures should be carried out immediately, otherwise the pandemic would spread more rapidly and last longer. In addition, we use the epidemic data of Wuhan from January 24 to March 2 to analyse the outbreak in the city and explain why the number of the infected rose in the early stage of the outbreak though a total lockdown was implemented. Moreover, besides the above measures, a feasible way to curb the spread of COVID-19 is to reduce the density of social networks, such as restricting mobility and decreasing in-person social contacts. This work provides a series of effective measures, which can facilitate the selection of appropriate approaches for controlling the spread of the COVID-19 pandemic to mitigate its adverse impact on people's livelihood, societies and economies.

Critical Components Identification for Service-Oriented Systems

Identifying critical components are of great significance to the overall reliability of service-oriented systems (SOSs). As the size of the SOS increases, identifying critical components in the process of predicting the SOS reliability can reduce the number of components that need to be predicted and shorten the prediction time. Moreover, predicting the reliability of critical components can also ensure the stability of the SOS. Therefore, we transform the relationships among service components of the SOS into a service dependency graph. Then, an improved weighted LeaderRank algorithm (IW-LeaderRank) is proposed to measure the importance of components and obtain the sequence of critical components. Through experimental analysis, the method can accurately and efficiently identify critical components in SOSs.

Exploring transcription factors reveals crucial members and regulatory networks involved in different abiotic stresses in Brassica napus L

BACKGROUND

Brassica napus (B. napus) encompasses diverse transcription factors (TFs), but thorough identification and characterization of TF families, as well as their transcriptional responsiveness to multifarious stresses are still not clear.

RESULTS

Totally 2167 TFs belonging to five families were genome-widely identified in B. napus, including 518 BnAP2/EREBPs, 252 BnbZIPs, 721 BnMYBs, 398 BnNACs and 278 BnWRKYs, which contained some novel members in comparison with existing results. Sub-genome distributions of BnAP2/EREBPs and BnMYBs indicated that the two families might have suffered from duplication and divergence during evolution. Synteny analysis revealed strong co-linearity between B. napus and its two ancestors, although chromosomal rearrangements have occurred and 85 TFs were lost. About 7.6% and 9.4% TFs of the five families in B. napus were novel genes and conserved genes, which both showed preference on the C sub-genome. RNA-Seq revealed that more than 80% TFs were abiotic stress inducible and 315 crucial differentially expressed genes (DEGs) were screened out. Network analysis revealed that the 315 DEGs are highly co-expressed. The homologous gene network in A. thaliana revealed that a considerable amount of TFs could trigger the differential expression of targeted genes, resulting in a complex clustered network with clusters of genes responsible for targeted stress responsiveness.

CONCLUSIONS

We identified and characterized five TF families in B. napus. Some crucial members and regulatory networks involved in different abiotic stresses have been explored. The investigations deepen our understanding of TFs for stress tolerance in B. napus.